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Sample records for affymetrix genechip 500k

  1. VIZARD: analysis of Affymetrix Arabidopsis GeneChip data

    NASA Technical Reports Server (NTRS)

    Moseyko, Nick; Feldman, Lewis J.

    2002-01-01

    SUMMARY: The Affymetrix GeneChip Arabidopsis genome array has proved to be a very powerful tool for the analysis of gene expression in Arabidopsis thaliana, the most commonly studied plant model organism. VIZARD is a Java program created at the University of California, Berkeley, to facilitate analysis of Arabidopsis GeneChip data. It includes several integrated tools for filtering, sorting, clustering and visualization of gene expression data as well as tools for the discovery of regulatory motifs in upstream sequences. VIZARD also includes annotation and upstream sequence databases for the majority of genes represented on the Affymetrix Arabidopsis GeneChip array. AVAILABILITY: VIZARD is available free of charge for educational, research, and not-for-profit purposes, and can be downloaded at http://www.anm.f2s.com/research/vizard/ CONTACT: moseyko@uclink4.berkeley.edu.

  2. Qualitative assessment of gene expression in affymetrix genechip arrays

    NASA Astrophysics Data System (ADS)

    Nagarajan, Radhakrishnan; Upreti, Meenakshi

    2007-01-01

    Affymetrix Genechip microarrays are used widely to determine the simultaneous expression of genes in a given biological paradigm. Probes on the Genechip array are atomic entities which by definition are randomly distributed across the array and in turn govern the gene expression. In the present study, we make several interesting observations. We show that there is considerable correlation between the probe intensities across the array which defy the independence assumption. While the mechanism behind such correlations is unclear, we show that scaling behavior and the profiles of perfect match (PM) as well as mismatch (MM) probes are similar and immune-to-background subtraction. We believe that the observed correlations are possibly an outcome of inherent non-stationarities or patchiness in the array devoid of biological significance. This is demonstrated by inspecting their scaling behavior and profiles of the PM and MM probe intensities obtained from publicly available Genechip arrays from three eukaryotic genomes, namely: Drosophila melanogaster (fruit fly), Homo sapiens (humans) and Mus musculus (house mouse) across distinct biological paradigms and across laboratories, with and without background subtraction. The fluctuation functions were estimated using detrended fluctuation analysis (DFA) with fourth-order polynomial detrending. The results presented in this study provide new insights into correlation signatures of PM and MM probe intensities and suggests the choice of DFA as a tool for qualitative assessment of Affymetrix Genechip microarrays prior to their analysis. A more detailed investigation is necessary in order to understand the source of these correlations.

  3. Motif effects in Affymetrix GeneChips seriously affect probe intensities

    PubMed Central

    Upton, Graham J. G.; Harrison, Andrew P.

    2012-01-01

    An Affymetrix GeneChip consists of an array of hundreds of thousands of probes (each a sequence of 25 bases) with the probe values being used to infer the extent to which genes are expressed in the biological material under investigation. In this article, we demonstrate that these probe values are also strongly influenced by their precise base sequence. We use data from >28 000 CEL files relating to 10 different Affymetrix GeneChip platforms and involving nearly 1000 experiments. Our results confirm known effects (those due to the T7-primer and the formation of G-quadruplexes) but reveal other effects. We show that there can be huge variations from one experiment to another, and that there may also be sizeable disparities between batches within an experiment and between CEL files within a batch. PMID:22904084

  4. Using probe secondary structure information to enhance Affymetrix GeneChip background estimates

    PubMed Central

    Gharaibeh, Raad Z.; Fodor, Anthony A.; Gibas, Cynthia J.

    2007-01-01

    High-density short oligonucleotide microarrays are a primary research tool for assessing global gene expression. Background noise on microarrays comprises a significant portion of the measured raw data. A number of statistical techniques have been developed to correct for this background noise. Here, we demonstrate that probe minimum folding energy and structure can be used to enhance a previously existing model for background noise correction. We estimate that probe secondary structure accounts for up to 3% of all variation on Affymetrix microarrays. PMID:17387043

  5. Global Expression Patterns of Three Festuca Species Exposed to Different Doses of Glyphosate Using the Affymetrix GeneChip Wheat Genome Array

    PubMed Central

    Cebeci, Ozge; Budak, Hikmet

    2009-01-01

    Glyphosate has been shown to act as an inhibitor of an aromatic amino acid biosynthetic pathway, while other pathways that may be affected by glyphosate are not known. Cross species hybridizations can provide a tool for elucidating biological pathways conserved among organisms. Comparative genome analyses have indicated a high level of colinearity among grass species and Festuca, on which we focus here, and showed rearrangements common to the Pooideae family. Based on sequence conservation among grass species, we selected the Affymetrix GeneChip Wheat Genome Array as a tool for the analysis of expression profiles of three Festuca (fescue) species with distinctly different tolerances to varying levels of glyphosate. Differences in transcript expression were recorded upon foliar glyphosate application at 1.58 mM and 6.32 mM, representing 5% and 20%, respectively, of the recommended rate. Differences highlighted categories of general metabolic processes, such as photosynthesis, protein synthesis, stress responses, and a larger number of transcripts responded to 20% glyphosate application. Differential expression of genes encoding proteins involved in the shikimic acid pathway could not be identified by cross hybridization. Microarray data were confirmed by RT-PCR and qRT-PCR analyses. This is the first report to analyze the potential of cross species hybridization in Fescue species and the data and analyses will help extend our knowledge on the cellular processes affected by glyphosate. PMID:20182642

  6. Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.)

    PubMed Central

    2012-01-01

    Background High-resolution genetic maps are needed in many crops to help characterize the genetic diversity that determines agriculturally important traits. Hybridization to microarrays to detect single feature polymorphisms is a powerful technique for marker discovery and genotyping because of its highly parallel nature. However, microarrays designed for gene expression analysis rarely provide sufficient gene coverage for optimal detection of nucleotide polymorphisms, which limits utility in species with low rates of polymorphism such as lettuce (Lactuca sativa). Results We developed a 6.5 million feature Affymetrix GeneChip® for efficient polymorphism discovery and genotyping, as well as for analysis of gene expression in lettuce. Probes on the microarray were designed from 26,809 unigenes from cultivated lettuce and an additional 8,819 unigenes from four related species (L. serriola, L. saligna, L. virosa and L. perennis). Where possible, probes were tiled with a 2 bp stagger, alternating on each DNA strand; providing an average of 187 probes covering approximately 600 bp for each of over 35,000 unigenes; resulting in up to 13 fold redundancy in coverage per nucleotide. We developed protocols for hybridization of genomic DNA to the GeneChip® and refined custom algorithms that utilized coverage from multiple, high quality probes to detect single position polymorphisms in 2 bp sliding windows across each unigene. This allowed us to detect greater than 18,000 polymorphisms between the parental lines of our core mapping population, as well as numerous polymorphisms between cultivated lettuce and wild species in the lettuce genepool. Using marker data from our diversity panel comprised of 52 accessions from the five species listed above, we were able to separate accessions by species using both phylogenetic and principal component analyses. Additionally, we estimated the diversity between different types of cultivated lettuce and distinguished morphological types

  7. Performance of the Affymetrix GeneChip HIV PRT 440 Platform for Antiretroviral Drug Resistance Genotyping of Human Immunodeficiency Virus Type 1 Clades and Viral Isolates with Length Polymorphisms

    PubMed Central

    Vahey, Maryanne; Nau, Martin E.; Barrick, Sandra; Cooley, John D.; Sawyer, Robert; Sleeker, Alex A.; Vickerman, Peter; Bloor, Stuart; Larder, Brendan; Michael, Nelson L.; Wegner, Scott A.

    1999-01-01

    The performance of a silica chip-based resequencing method, the Affymetrix HIV PRT 440 assay (hereafter referred to as the Affymetrix assay), was evaluated on a panel of well-characterized nonclade B viral isolates and on isolates exhibiting length polymorphisms. Sequencing of human immunodeficiency virus type 1 (HIV-1) pol cDNAs from clades A, C, D, E, and F resulted in clade-specific regions of base-calling ambiguities in regions not known to be associated with resistance polymorphisms, as well as a small number of spurious resistance polymorphisms. The Affymetrix assay failed to detect the presence of additional serine codons distal to reverse transcriptase (RT) codon 68 that are associated with multinucleoside RT inhibitor resistance. The increasing prevalence of non-clade B HIV-1 strains in the United States and Europe and the identification of clinically relevant pol gene length polymorphisms will impact the generalizability of the Affymetrix assay, emphasizing the need to accommodate this expanding pool of pol genotypes in future assay versions. PMID:10405396

  8. Thermodynamic scaling behavior in genechips

    PubMed Central

    Ferrantini, Alessandro; Allemeersch, Joke; Van Hummelen, Paul; Carlon, Enrico

    2009-01-01

    Background Affymetrix Genechips are characterized by probe pairs, a perfect match (PM) and a mismatch (MM) probe differing by a single nucleotide. Most of the data preprocessing algorithms neglect MM signals, as it was shown that MMs cannot be used as estimators of the non-specific hybridization as originally proposed by Affymetrix. The aim of this paper is to study in detail on a large number of experiments the behavior of the average PM/MM ratio. This is taken as an indicator of the quality of the hybridization and, when compared between different chip series, of the quality of the chip design. Results About 250 different GeneChip hybridizations performed at the VIB Microarray Facility for Homo sapiens, Drosophila melanogaster, and Arabidopsis thaliana were analyzed. The investigation of such a large set of data from the same source minimizes systematic experimental variations that may arise from differences in protocols or from different laboratories. The PM/MM ratios are derived theoretically from thermodynamic laws and a link is made with the sequence of PM and MM probe, more specifically with their central nucleotide triplets. Conclusion The PM/MM ratios subdivided according to the different central nucleotides triplets follow qualitatively those deduced from the hybridization free energies in solution. It is shown also that the PM and MM histograms are related by a simple scale transformation, in agreement with what is to be expected from hybridization thermodynamics. Different quantitative behavior is observed on the different chip organisms analyzed, suggesting that some organism chips have superior probe design compared to others. PMID:19123958

  9. Development and Evaluation of an Affymetrix array for Aspergillus flavus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A multi-species Affymetrix GeneChip array was developed to study development, metabolism and pathogenicity of A. flavus. This chip based on the whole genome sequence of A. flavus, contains 13,000 A. flavus genes, 8,000 maize genes and 25 human and mouse innate immune response genes, as well as the ...

  10. CEL_INTERROGATOR: A FREE AND OPEN SOURCE PACKAGE FOR AFFYMETRIX CEL FILE PARSING

    Technology Transfer Automated Retrieval System (TEKTRAN)

    CEL_Interrogator Package is a suite of programs designed to extract the average probe intensity and other information for each probe sequence from an Affymetrix GeneChip CEL file and unite them with their human-readable Affymetrix consensus sequence names. The resulting text file is suitable for di...

  11. Discovery and mapping of single feature polymorphisms in wheat using affymetrix arrays

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Single feature polymorphisms (SFPs) can be a rich source of markers for gene mapping and function studies. To explore the feasibility of using the Affymetrix GeneChip to discover and map SFPs in the large hexaploid wheat genome, six wheat varieties of diverse origins were analyzed for significant pr...

  12. Novel definition files for human GeneChips based on GeneAnnot

    PubMed Central

    Ferrari, Francesco; Bortoluzzi, Stefania; Coppe, Alessandro; Sirota, Alexandra; Safran, Marilyn; Shmoish, Michael; Ferrari, Sergio; Lancet, Doron; Danieli, Gian Antonio; Bicciato, Silvio

    2007-01-01

    Background Improvements in genome sequence annotation revealed discrepancies in the original probeset/gene assignment in Affymetrix microarray and the existence of differences between annotations and effective alignments of probes and transcription products. In the current generation of Affymetrix human GeneChips, most probesets include probes matching transcripts from more than one gene and probes which do not match any transcribed sequence. Results We developed a novel set of custom Chip Definition Files (CDF) and the corresponding Bioconductor libraries for Affymetrix human GeneChips, based on the information contained in the GeneAnnot database. GeneAnnot-based CDFs are composed of unique custom-probesets, including only probes matching a single gene. Conclusion GeneAnnot-based custom CDFs solve the problem of a reliable reconstruction of expression levels and eliminate the existence of more than one probeset per gene, which often leads to discordant expression signals for the same transcript when gene differential expression is the focus of the analysis. GeneAnnot CDFs are freely distributed and fully compliant with Affymetrix standards and all available software for gene expression analysis. The CDF libraries are available from , along with supplementary information (CDF libraries, installation guidelines and R code, CDF statistics, and analysis results). PMID:18005434

  13. COMPARISON OF GENE EXPRESSION IN TILLER AND RHIZOME MERISTEMS OF PERENNIAL LEYMUS WILDRYES USING AFFYMETRIX GENECHIPS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rhizomes and tillers grow from underground axillary meristems, which are important determinants of perennial growth habit and architecture in grasses. Leymus cinereus grows from intravaginal axillary meristems (tillers), forming a compact tussock year after year. Conversely, L. triticoides grow fr...

  14. IGG: A tool to integrate GeneChips for genetic studies.

    PubMed

    Li, M-X; Jiang, L; Ho, S-L; Song, Y-Q; Sham, P-C

    2007-11-15

    To facilitate genetic studies using high-throughput genotyping technologies, we have developed an open source tool to integrate genotype data across the Affymetrix and Illumina platforms. It can efficiently integrate a large amount of data from various GeneChips, add genotypes of the HapMap Project into a specific project, flexibly trim and export the integrated data with different formats of popular genetic analysis tools, and highly control the quality of genotype data. Furthermore, this tool has sufficiently simplified its usage through its user-friendly graphic interface and is independent of third-party databases. IGG has successfully been applied to a genome-wide linkage scan in a Charcot-Marie-Tooth disease pedigree by integrating three types of GeneChips and HapMap project genotypes. PMID:17872914

  15. 500 kV shield wires; Sectionalize or ground everywhere

    SciTech Connect

    Tuominen, M.W. )

    1992-01-01

    The primary purpose of shield wires on transmission lines in lightning protection. Development of fiber-optic shied wires added communications capabilities. Schemes for adapting fiber-optic shield wires to sectionalized shield wire designs remain untested. It is a present policy to segment and insulate 500 kV shield wires. Computer modeling and supportive field measurements have revealed a characteristic distribution of grounded tower voltage versus distance for long lines. The intent of this paper is to report these results plus predict the outcome of grounding shield wires on transmission lines already in place. Shield wires are often called overhead ground wires and abbreviated OHGW.

  16. 500-kW DCHX pilot-plant evaluation testing

    SciTech Connect

    Hlinak, A.; Lee, T.; Loback, J.; Nichols, K.; Olander, R.; Oshmyansky, S.; Roberts, G.; Werner, D.

    1981-10-01

    Field tests with the 500 kW Direct Contact Pilot Plant were conducted utilizing brine from well Mesa 6-2. The tests were intended to develop comprehensive performance data, design criteria, and economic factors for the direct contact power plant. The tests were conducted in two phases. The first test phase was to determine specific component performance of the DCHX, turbine, condensers and pumps, and to evaluate chemical mass balances of non-condensible gases in the IC/sub 4/ loop and IC/sub 4/ in the brine stream. The second test phase was to provide a longer term run at nearly fixed operating conditions in order to evaluate plant performance and identify operating cost data for the pilot plant. During these tests the total accumulated run time on major system components exceeded 1180 hours with 777 hours on the turbine prime mover. Direct contact heat exchanger performance exceeded the design prediction.

  17. A Robust Plant RNA Isolation Method for Affymetrix Genechip® Analysis and Quantitative Real-Time RT-PCR

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microarray analysis and quantitative real-time RT-PCR are the major high-throughput techniques that are used to study transcript profiles. One of the major limitations in these technologies is the isolation maximum yield of highly-pure RNA from plant tissues rich in complex polysaccharides, polyphen...

  18. Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Natural antisense transcripts (NATs) are transcripts of the opposite DNA strand to the sense-strand either at the same locus (cis-encoded) or a different locus (trans-encoded). They can affect gene expression at multiple stages including transcription, RNA processing and transport, and translation....

  19. Performance of 500kCi Tritium Storage Vessel for WTRF

    SciTech Connect

    Paek, S.; Ahn, D.H.; Kim, K.R.; Chung, H.; Yim, S.P.; Lee, M.

    2005-07-15

    A prototype TSV (Tritide Storage Vessel) has been manufactured for the long-term storage of tritium of the WTRF (Wolsong Tritium Removal Facility). A performance test was carried out to demonstrate that the TSV could hold a minimum of 500kCi of tritium. This experiment was conducted by a batch type hydriding reaction. Hydrogen gas equivalent to 50kCi of tritium was reacted with the titanium sponge in a batch reaction. Experimental results for 10 batches show that the TSV has enough capacity to store 500kCi of tritium.

  20. TVA's 500-kV electric and magnetic fields: measurements and analyses

    SciTech Connect

    Not Available

    1983-09-01

    This report summarizes the results of the 500-kV electric and magnetic fields data project, performed by the Electrical Systems Group of the Tennessee Valley Authority (TVA). The objectives of the project were to measure, record, and analyze electric and magnetic fields in the vicintiy of TVA's 500-kV transmission lines. Also the effects of transmission line fields on the growth and development of selected agricultural and forest plant species were to be investigated. This report contains only the categorization and the statistical analysis of the fields data.

  1. 26Al measurements below 500 kV in charge state 2+

    NASA Astrophysics Data System (ADS)

    Müller, Arnold Milenko; Christl, Marcus; Lachner, Johannes; Synal, Hans-Arno; Vockenhuber, Christof; Zanella, Claudia

    2015-10-01

    The use of helium as stripper gas improved the measurement efficiency of compact AMS systems for many radionuclides significantly because of a higher mean charge state and reduced scattering losses compared with other conventional gases. Recent tests at the ETH 500 kV AMS facility (Tandy) with aluminum have demonstrated that a transmission of more than 50% is achievable in the charge state 2+ at terminal voltages between 300 and 500 kV. On the other hand the m/q interference of 13C1+ entering the detector at very high intensity has to be suppressed. Based on first positive results with a very simple absorber cell a more elaborate absorber detector configuration was designed and built in order to eliminate the carbon interference. The suppression of carbon with the new detector-absorber design has been studied extensively at 300 kV (950 keV) and 500 kV (1550 keV) and the results are compared with simulated data. With the new configuration an overall transmission for 26Al of more than 42% at 500 kV and about 30% at 300 kV terminal voltage is achieved, while 26Al/27Al blank ratios of aluminum targets in the range of 5-14·10-15 are measured.

  2. Development of 500 kV DC PPLP-insulated oil-filled submarine cable

    SciTech Connect

    Fujimori, A.; Tanaka, T.; Takashima, H.; Imajo, T.; Hata, R.; Tanabe, T.; Yoshida, S.; Kakihana, T.

    1996-01-01

    This paper outlines the development of a 500 kV DC oil-filled submarine cable capable of transmitting 2,800 MW with {+-} 500 kV 2800A bipole system. Polypropylene Laminated Paper (PPL) was employed as the insulation material, which is the worlds first application to DC cables. The conductor size is 3,000 mm{sup 2}, which is the largest size for submarine cables ever put into practical use. Through various fundamental and prototype tests, the cable proved to have excellent electrical characteristics for DC voltage as well as transient overvoltage. The cable and accessories are currently undergoing a long-term accelerated aging test as the final confirmation of their reliability and stability.

  3. [Mortality of people residing near electric power supply line with voltage of 500 kV].

    PubMed

    Gurvich, E B; Novokhatskaia, E A; Rubtsova, N B

    1996-01-01

    The epidemiologic study covered causes and levels of mortality in the settlement situated near electric power supply line (voltage is 500 kV). The work used retrospective cohort method adjusted for evaluation of mortality in general population. The study revealed no higher mortality risk with all the causes totally and with leading causal groups under influence of high frequency electromagnetic fields. However, higher relative mortality risk with leukemia and suicide appeared statistically insignificant. PMID:9019327

  4. Stereoscopic Planar Laser-Induced Fluorescence Imaging at 500 kHz

    NASA Technical Reports Server (NTRS)

    Medford, Taylor L.; Danehy, Paul M.; Jones, Stephen B.; Jiang, N.; Webster, M.; Lempert, Walter; Miller, J.; Meyer, T.

    2011-01-01

    A new measurement technique for obtaining time- and spatially-resolved image sequences in hypersonic flows is developed. Nitric-oxide planar laser-induced fluorescence (NO PLIF) has previously been used to investigate transition from laminar to turbulent flow in hypersonic boundary layers using both planar and volumetric imaging capabilities. Low flow rates of NO were typically seeded into the flow, minimally perturbing the flow. The volumetric imaging was performed at a measurement rate of 10 Hz using a thick planar laser sheet that excited NO fluorescence. The fluorescence was captured by a pair of cameras having slightly different views of the flow. Subsequent stereoscopic reconstruction of these images allowed the three-dimensional flow structures to be viewed. In the current paper, this approach has been extended to 50,000 times higher repetition rates. A laser operating at 500 kHz excites the seeded NO molecules, and a camera, synchronized with the laser and fitted with a beam-splitting assembly, acquires two separate images of the flow. The resulting stereoscopic images provide three-dimensional flow visualizations at 500 kHz for the first time. The 200 ns exposure time in each frame is fast enough to freeze the flow while the 500 kHz repetition rate is fast enough to time-resolve changes in the flow being studied. This method is applied to visualize the evolving hypersonic flow structures that propagate downstream of a discrete protuberance attached to a flat plate. The technique was demonstrated in the NASA Langley Research Center s 31-Inch Mach 10 Air Tunnel facility. Different tunnel Reynolds number conditions, NO flow rates and two different cylindrical protuberance heights were investigated. The location of the onset of flow unsteadiness, an indicator of transition, was observed to move downstream during the tunnel runs, coinciding with an increase in the model temperature.

  5. LM2500 plant for PNEM rated 21,500 kW base load

    SciTech Connect

    Farmer, R.

    1982-09-01

    The first uprated version of BE's LM2500 generator set will produce an extra 1500 kW (2000 hp) for Provinciale Noordbrabantse Elektricitiets Maatschappij's (PNEM) Helmond power station in the Netherlands. Unlike conventional LM2500s, this natural-gas fueled unit carried a 21,500 kW baseload rating; moreover, it operates at a higher firing temperature, a hotter exhaust, an increased mass flow, and an improved system heat rate. Although the unit is currently slated for simple-cycle operation, PNEM plants to shift its role to combined service through retrofitting an exhaust-heat-recovery steam generator and turbine - perhaps as early as 1984.

  6. Development of flexible joint for 500kV Al-sheathed O. F. cable

    SciTech Connect

    Komaba, T.; Kanai, K. ); Yoshida, S.; Shigetoshi, I.; Amano, K. )

    1992-10-01

    This paper reports on a flexible dimensionaly flush joint for 500kV aluminum-sheathed oil-filled cables capable of being assembled, pulled an installed in a similar manner to cables at site which has been developed. This joint is intended for use at intermediate points on long bridges or tunnels where local assembly and installation of conventional joints would be difficult. In developing the joint various novel and original techniques have been employed, including the flexible flush jointing of segmental conductors, the flexible jointing of paper insulation by a combination of wrapping-back and stepping methods, plus on-site aluminum sheath corrugating and sealing methods.

  7. Transient voltages in a tranformer connected to a 500 kV transmission line

    SciTech Connect

    Indulkar, C.S.; Kothari, D.P.; Saha, S.N.

    1985-09-01

    The objective of the study described in this paper was to formulate a simple way of calculating the distribution of transient voltages at different points of a cascaded system consisting of a transformer winding connected to a transmission line. A method of calculating the steady-state voltage distribution based on a simple eigenvalue technique for the analysis of identical ladder networks representing the line and the transformer winding is described which is then used in conjunction with the numerical inversion of the Fourier integral to obtain the transient voltage waveforms at various points in a 500 kV line and in the transformer winding.

  8. Decay heat calculations for a 500 kW W-Ta spallation target

    NASA Astrophysics Data System (ADS)

    Yu, Quanzhi; Lu, Youlian; Hu, Zhiliang; Zhou, Bin; Yin, Wen; Liang, Tianjiao

    2015-05-01

    The China Spallation Neutron Source (CSNS) is a short-pulsed neutron scattering facility. The beam power is designed to be 100 kW in Phase I, with the capability of upgrading to 500 kW. Tantalum (Ta)-cladded tungsten (W) was chosen as the spallation target due to its high neutron yield. Ta claddings can solve the problem of the corrosiveness of W plates, although they produce high decay heat after intense irradiation. This paper presents the decay heat distributions and evolutions for the future upgraded 500 kW W-Ta spallation target. The calculations are performed using the MCNPX2.5 Monte Carlo code and the CINDER'90 activation code. The decay heat distributions show that for the W plates, decay heat is mainly produced via the spallation reaction process, whereas for the Ta claddings, it is mainly produced via the neutron capture process. An effective method of reducing the decay heat in the W-Ta target is also presented and discussed.

  9. Problems of operating the 500-kV outdoor electrical equipment of the Sayano-Shushenskoe hydroelectric station

    SciTech Connect

    Mitrofanov, A.N.

    1994-10-01

    The Sayano-Shushenskoe hydroelectric station is part of the Siberian interconnected power system. Power is transmitted to the grid by two 500 kV transmission lines. The site characteristics made nearby placement of conventional 500 kV switchyard equipment impossible. The original plans were to place the switchyard 35 km away, but the 500 kV lines to the yard would have passed through mountain regions with intense thunderstorm activity. Because of the unique design of the generators, the number of lightning-induced disconnects was substantial. For greater reliability, 500 kV equipment suitable for placement at the sight was designed, and the overall electrical layout of the yard was revised by reconstructing the middle network of the 4/3 scheme to three networks with two switches per connection. Sectioning of the collecting bus systems was necessary for a further increase in the reliability of the yard.

  10. Design of 84 GHz 500 kW Gyrotron for Technological Millimeter Wave Applications

    NASA Astrophysics Data System (ADS)

    Singh, Udaybir; Kumar, Nitin; Kumar, Anil; Purohit, L. P.; Sinha, A. K.

    2011-04-01

    In this paper, the design and the numerical simulation of the 84 GHz, 500 kW gyrotron at first harmonic operation for technological applications is described. The operating mode of the gyrotron is TE10, 4. Various in-house developed and commercially available computer codes are used for the design purpose. The triode-type magnetron injection gun with the accelerating voltage 70-kV, the beam current 10-A and the maximum transverse velocity spread less than 5% is designed. The preliminary design is obtained by using some trade-off equations. The mode selection, the cold cavity and the beam-wave interaction analysis are discussed for the design of weakly tapered open resonator type of the interaction cavity. The parametric analysis of the interaction cavity and the electron gun is also presented.

  11. 500 K and Below - Finding Ultracool Dwarfs with the UKIRT/WFCAM and VISTA surveys

    NASA Astrophysics Data System (ADS)

    Lucas, P. W.; Ukidss Consortium; Vista Consortium

    2003-10-01

    I describe the very large area infrared UKIRT surveys which will begin in 2003 and their impact on the field of brown dwarf searches. These surveys will reach K≈19 and survey on the order of 20% of the sky. Present plans are for ZJHK imaging, with repeats in J or K to detect proper motions. It is expected that brown dwarfs in the 400-500 K range will be detected, possibly reaching the threshold at which liquid water droplet clouds will form in the upper atmosphere. Some planetary mass 'sub-brown dwarfs' may also be detected if any exist within 10 parsecs. These surveys form natural successors to 2MASS, DENIS and SLOAN. The 4-m VISTA telescope will conduct similar surveys in the southern hemisphere beginning around 2005-6.

  12. Stirling engines for solar power generation in the 50 to 500 kW range

    NASA Astrophysics Data System (ADS)

    Wells, D.; Percival, W.; Bratt, C.; Rosenqvist, K.; Berntell, J.

    Qualitative analyses are presented of solar Stirling power modules in terms of the engines, the concentrators, and the interaction between the size and efficiency of the modules with the cost of the system. A test unit with a parabolic dish concentrator has furnished 31.6 kWe using an 1800 rpm, 93% efficient permanent magnet alternator. Operating temperatures were 750 C, and engine efficiencies reached 38%. Point focus parabolic dishes, tracking heliostats, and stationary concentrators with tracking receivers are being examined. The engine cost has been projected to be only a small part of the total unit cost in mass production, and parabolic dishes are the lowest-cost configuration for manufacturing. Enclosing the dishes in greenhouses can lessen erosion of the surfaces. Foamglass has been identified as the most cost-effective concentrator material. Design alternatives for a 50-500 kW power array are described.

  13. Absolute rate constants for the reaction of atomic hydrogen with ketene from 298 to 500 K

    NASA Technical Reports Server (NTRS)

    Michael, J. V.; Nava, D. F.; Payne, W. A.; Stief, L. J.

    1979-01-01

    Rate constants for the reaction of atomic hydrogen with ketene have been measured at room temperature by two techniques, flash photolysis-resonance fluorescence and discharge flow-resonance fluorescence. The measured values are (6.19 + or - 1.68) x 10 to the -14th and (7.3 + or - 1.3) x 10 to the -14th cu cm/molecule/s, respectively. In addition, rate constants as a function of temperature have been measured over the range 298-500 K using the FP-RF technique. The results are best represented by the Arrhenius expression k = (1.88 + or - 1.12) x 10 to the -11th exp(-1725 + or - 190/T) cu cm/molecule/s, where the indicated errors are at the two standard deviation level.

  14. Rate constant for the reaction of atomic chlorine with formaldehyde from 200 to 500 K

    NASA Technical Reports Server (NTRS)

    Michael, J. V.; Nava, D. F.; Payne, W. A.

    1979-01-01

    The absolute rate constant for the reaction of atomic chlorine with formaldehyde has been measured from 200 to 500 K using the flash photolysis-resonance fluorescence technique. The results were independent of substantial variations in (H2CO), total pressure (Ar), and flash intensity (i.e., initial (Cl)). The rate constant was shown to be invariant with temperature, the best representation for this temperature range being k-sub-1 = (7.48 + or - 0.50) times 10 to the -11 cu cm/molecule sec, where the error is one standard deviation. This result is compared with the only previous determination of k-sub-1, which was a relative value obtained at 298 K. The rate constant is theoretically discussed, and the potential importance of the reaction in stratospheric chemistry is considered.

  15. 486nm blue laser operating at 500 kHz pulse repetition frequency

    NASA Astrophysics Data System (ADS)

    Creeden, Daniel; Blanchard, Jon; Pretorius, Herman; Limongelli, Julia; Setzler, Scott D.

    2016-03-01

    Compact, high power blue light in the 470-490nm region is difficult to generate due to the lack of laser sources which are easily convertible (through parametric processes) to those wavelengths. By using a pulsed Tm-doped fiber laser as a pump source for a 2-stage second harmonic generation (SHG) scheme, we have generated ~2W of 486.5nm light at 500kHz pulse repetition frequency (PRF). To our knowledge, this is the highest PRF and output power achieved in the blue region based on a frequency converted, monolithic fiber laser. This pump laser is a pulsed Tm-doped fiber laser/amplifier which generates 12.8W of 1946nm power at 500kHz PRF with diffraction-limited output from a purely single-mode fiber. The output from this laser is converted to 973nm through second harmonic generation (SHG). The 973nm is then converted to 486.5nm via another SHG stage. This architecture operates with very low peak power, which can be challenging from a nonlinear conversion standpoint. However, the low peak power enables the use of a single-mode monolithic fiber amplifier without undergoing nonlinear effects in the fiber. This also eliminates the need for novel fiber designs, large-mode area fiber, or free-space coupling to rod-type amplifiers, improving reliability and robustness of the laser source. Higher power and conversion efficiency are possible through the addition of Tm-doped fiber amplification stages as well as optimization of the nonlinear conversion process and nonlinear materials. In this paper, we discuss the laser layout, results, and challenges with generating blue light using a low peak power approach.

  16. Multicenter Evaluation of Genechip for Detection of Multidrug-Resistant Mycobacterium tuberculosis

    PubMed Central

    Pang, Yu; Xia, Hui; Zhang, Zhiying; Li, Junchen; Dong, Yi; Li, Qiang; Ou, Xichao; Song, Yuanyuan; Wang, Yufeng; O'Brien, Richard; Kam, Kai Man; Chi, Junying; Huan, Shitong; Chin, Daniel P.

    2013-01-01

    Drug-resistant tuberculosis (TB), especially multidrug-resistant TB (MDR-TB), is still one of the most serious threats to TB control worldwide. Early diagnosis of MDR-TB is important for effectively blocking transmission and establishing an effective protocol for chemotherapy. Genechip is a rapid diagnostic method based on molecular biology that overcomes the poor biosafety, time consumption, and other drawbacks of traditional drug sensitivity testing (DST) that can detect MDR-TB. However, the Genechip approach has not been effectively evaluated, especially in limited-resource laboratories. In this study, we evaluated the performance of Genechip for MDR-TB in 1,814 patients in four prefectural or municipal laboratories and compared its performance with that of traditional DST. The results showed that the sensitivity and specificity of Genechip were 87.56% and 97.95% for rifampin resistance and 80.34% and 95.82% for isoniazid resistance, respectively. In addition, we found that the positive grade of the sputum smears influenced the judgment of results by Genechip. The test judged only 75% of the specimens of “scanty” positive grade. However, the positive grade of the specimens showed no influence on the accuracy of Genechip. Overall, the study suggests that, in limited-resource laboratories, Genechip showed high sensitivity and specificity for rifampin and isoniazid resistance, making it a more effective, rapid, safe, and cost-beneficial method worthy of broader use in limited-resource laboratories in China. PMID:23515537

  17. Grand Coulee - Bell 500-kV Transmission Line Project, Draft Environmental Impact Statement

    SciTech Connect

    N /A

    2002-08-09

    BPA is proposing to construct a 500-kilovolt (kV) transmission line that would extend approximately 84 miles between the Grand Coulee 500-kV Switchyard, near Grand Coulee Dam, and the Bell Substation, in Mead just north of Spokane. The new line would cross portions of Douglas, Grant, Lincoln, and Spokane counties. In addition to the transmission line, new equipment would be installed at the substations at each end of the new line and at other facilities. The proposed action would remove an existing 115-kV transmission line and replace it with the new 500-kV line on existing right-of-way for most of its length. Additional right-of-way would be needed in the first 3.5 miles out of the Grand Coulee Switchyard to connect to the existing 115-kV right-of-way. Since the mid-1990s, the transmission path west of Spokane, called the West of Hatwai transmission pathway, has grown increasingly constrained. To date, BPA has been able to manage operation of the path through available operating practices, and customer needed have been met while maintaining the reliability of the path. however, in early 2001, operations showed that the amount of electricity that needs to flow from east to west along this path creates severe transmission congestion. Under these conditions, the system is at risk of overloads and violation of industry safety and reliability standards. The problem is particularly acute in the spring and summer months because of the large amount of power generated by dams east of the path. Large amounts of water cannot be spilled during that time in order for BPA to fulfill its obligation to protect threatened and endangered fish. The amount of power that needs to move through this area during these months at times could exceed the carrying capacity of the existing transmission lines. In additional capacity is not added, BPA will run a significant risk that it will not be able to continue to meet its contractual obligations to deliver power and maintain reliability

  18. Status of the DOE/SANDIA 500 kW VAWT test bed

    SciTech Connect

    Dodd, H.M.

    1985-08-27

    The DOE/Sandia Vertical Axis Wind Turbine (VAWT) Test Bed represents an evolutionary step in the development of larger and more efficient VAWT's. It is an advanced research machine whose purposes include prototype scale evaluations of improved aerodynamic designs, aerodynamic/structural loads determination for fatigue life improvements, and investigation of new operational modes to increase energy capture while maintaining or improving turbine life. The significant physical features of the machine include a rated power of 500 kW at 37.5 rpm in a 13.4 m/s (30 mph) wind, a diameter of 33.5 m (110 ft), and a height to diameter ratio of 1.25. Significant technological features include blades with multiple laminar airfoil shapes and multiple chord lengths, tailored aerodynamic performance and loads, and variable speed operating capability. The Test Bed will be assembled and operated at the USDA's Agricultural Research Service facility in Bushland, Texas, by Sandia and USDA personnel. Initial operation is schedules for the fall of 1986.

  19. Optical Spectroscopy Experiments on the 500 kA XP Pulsed-Power Generator

    SciTech Connect

    Bell, K. S.; Shelkovenko, T. A.; Pikuz, S. A.; McBride, R. D.; Blesener, I. C.; Knapp, P. F.; Hammer, D. A.; Greenly, J. B.; Maron, Y.

    2009-01-21

    Recent experiments on the 500 kA XP pulsed-power generator at Cornell University have explored the properties of optical spectra in single wires and wire arrays. In the single wire experiments, {approx}1% of the current from XP has been directed through the single wire. Spectra have been recorded using a half-meter spectrometer and a CCD camera located adjacent to the XP pulser. We are studying the visible spectra emitted by the wires and the background light from the machine hardware in order to identify the levels of current per wire for which visible spectroscopy might provide a means to measure magnetic field strength. We have also investigated the dependence of single wire visible spectra on the current, which was measured using a calibrated non-integrating Rogowski coil. UV and XUV diodes were employed to gather information about the temporal structure of the background and wire radiation. The line radiation in the spectra was recorded with wire currents at the few kA level. This is comparable to the first 10 ns of a 32-wire array experiment on 1 Ma generator and a 600-wire array at 20 MA.

  20. Reclamation and revegetation along a 250-mile 500 kV power line corridor

    SciTech Connect

    Griffith, E.F.

    1990-12-31

    Reclamation and revegetation success along the Montana Power Company Colstrip to Deepdale 500 kV powerline was monitored from 1985 through 1989. Followup revegetation was hampered by inadequate road and tower site earth work as a result of premature release of the reclamation bond. Drought conditions in 1985 and 1988 seriously affected revegetation efforts, especially on difficult sites. Weed control improved markedly, and all ROW areas are weed free except those next to infested range and cropland where a major cooperative effort is needed to control weeds. Access roads in previously unroaded areas resulted in changes of access, management practices, and cattle grazing behavior, all of which adversely affected revegetation success. Erosion, exacerbated by undersized culverts, the presence of very erodible soils, the occasional untrained contractor, is now the major ROW maintenance concern. Observation of the revegetation efforts clearly shows the need for adequate and appropriate reclamation by qualified equipment operators up front, and a patient, measured effort of continued revegetation, weed control and erosion control over the long term. The bond period of 5 years may not be long enough to achieve the 90 percent revegetation success required by the permit. Future projects guidelines should consider look to a flexible timeframe and more realistic vegetation requirements to account for the effects of non-construction related impacts.

  1. Design, performance, and economics of 50-kW and 500-kW vertical axis wind turbines

    SciTech Connect

    Scheinbein, L.A.; Malcolm, D.J.

    1983-11-01

    A review of the development and performance of the DAF Indal 50-kW vertical axis Darrieus wind turbine shows that a high level of technical development and reliability has been achieved. Features of the drive train, braking and control systems are discussed and performance details are presented. Details are also presented of a 500-kW VAWT that is currently in production. A discussion of the economics of both the 50-kW and 500-kW VAWTs is included, showing the effects of charge rate, installed cost, operating cost, performance, and efficiency.

  2. Design, performance, and economics of 50-kW and 500-kW vertical axis wind turbines

    SciTech Connect

    Schienbein, L.A.; Malcolm, D.J.

    1983-11-01

    A review of the development and performance of the DAF Indal 50-kW vertical axis Darrieus wind turbine shows that a high level of technical development and reliability has been achieved. Features of the drive train, braking and control systems are discussed and performance details are presented. Details are also presented of a 500-kW VAWT that is currently in production. A discussion of the economics of both the 50-kW and 500-kW VAWTs is included, showing the effects of charge rate, installed cost, operating cost, performance, and efficiency. 6 references.

  3. Zinc Oxide Surge Arresters and HVDC 125kV-upgrade 500kV Converter Stations

    NASA Astrophysics Data System (ADS)

    Shirakawa, Shingo; Kobayashi, Takayuki; Matsushita, Yoshinao; Sakai, Takehisa; Suzuki, Hironori; Ozaki, Yuzo

    Gapless Metal (Zinc) Oxide Surge Arresters for a.c. systems contribute to the insulation co-ordination based on the suppression of lightning surges and switching surges. These gapless metal oxide surge arresters using ZnO elements are effective to HVDC systems. This paper describes basic characteristics of ZnO (zinc oxide) elements for d.c. systems and applications of gapless surge arresters to HVDC 125kV frequency converters, HVDC 250kV, upgrade HVDC 500kV converter stations, and HVDC 500kV cables of Japan through the experience of developments and applications of gapless metal oxide surge arresters.

  4. Power quality measurements on a 500 kW variable speed VAWT

    SciTech Connect

    Newton, S.C.; Clark, R.N.

    1992-11-01

    Power quality tests have been conducted with the DOE/Sandia 34-m VAWT Test Bed located at the USDA Agricultural Research Service in Bushland, Texas. These tests were conducted in conjunction with the local electric utility, Southwestern Public Service Company, to determine the effects of the turbine on the 13.2 kV utility line. The Test Bed consists of a 34-m diameter wind turbine coupled, via a mechanical transmission, to a 500 kW electric synchronous motor/generator. The motor/generator is controlled by a load-commutated inverter (LCI) variable-speed motor drive. This AC-DC-AC LCI system converts the variable output voltage and frequency of the motor/generator to dc and then converts the dc to the voltage and frequency of the utility line. The LCI is also used as a variable-speed motor drive to rotate the turbine up to operating speed. The turbine is connected to a feeder line that is 25 km from the first substation. The line is one branch of three feeders that are common to the same substation breaker. The total peak load on this feeder is approximately 1.4 MW. The minimum penetration of the turbine at rated power into the feeders is 35% with the possibility existing of penetration into the utility transmission grid. This ``soft line`` is an ideal configuration to test the effects that a wind generating system may have on a remote or isolated utility line. As a result of this testing, the harmonic distortion present before and after the LCI isolation transformer has been quantified and the damping effect the isolation transformer has on the distortion has been observed. Also, the operating conditions that produce the maximum distortion have been determined. The data taken comparing power factor with rotor torque and generator speed indicate that the LCI`s power factor increases with rotor torque but is limited by the speed of the generator.

  5. Power quality measurements on a 500 kW variable speed VAWT

    SciTech Connect

    Newton, S.C. ); Clark, R.N. , Bushland, TX )

    1992-01-01

    Power quality tests have been conducted with the DOE/Sandia 34-m VAWT Test Bed located at the USDA Agricultural Research Service in Bushland, Texas. These tests were conducted in conjunction with the local electric utility, Southwestern Public Service Company, to determine the effects of the turbine on the 13.2 kV utility line. The Test Bed consists of a 34-m diameter wind turbine coupled, via a mechanical transmission, to a 500 kW electric synchronous motor/generator. The motor/generator is controlled by a load-commutated inverter (LCI) variable-speed motor drive. This AC-DC-AC LCI system converts the variable output voltage and frequency of the motor/generator to dc and then converts the dc to the voltage and frequency of the utility line. The LCI is also used as a variable-speed motor drive to rotate the turbine up to operating speed. The turbine is connected to a feeder line that is 25 km from the first substation. The line is one branch of three feeders that are common to the same substation breaker. The total peak load on this feeder is approximately 1.4 MW. The minimum penetration of the turbine at rated power into the feeders is 35% with the possibility existing of penetration into the utility transmission grid. This soft line'' is an ideal configuration to test the effects that a wind generating system may have on a remote or isolated utility line. As a result of this testing, the harmonic distortion present before and after the LCI isolation transformer has been quantified and the damping effect the isolation transformer has on the distortion has been observed. Also, the operating conditions that produce the maximum distortion have been determined. The data taken comparing power factor with rotor torque and generator speed indicate that the LCI's power factor increases with rotor torque but is limited by the speed of the generator.

  6. Crystal structure of the 500 kD yeast acetyl-CoA carboxylase holoenzyme dimer

    PubMed Central

    Wei, Jia; Tong, Liang

    2015-01-01

    Acetyl-CoA carboxylase (ACC) has crucial roles in fatty acid metabolism and is an attractive target for drug discovery against diabetes, cancer and other diseases1–6. Saccharomyces cerevisiae ACC (ScACC) is crucial for the production of very-long-chain fatty acids and the maintenance of the nuclear envelope7,8. ACC contains biotin carboxylase (BC) and carboxyltransferase (CT) activities, and its biotin is linked covalently to the biotin carboxyl carrier protein (BCCP). Most eukaryotic ACCs are 250 kD, multi-domain enzymes and function as homo-dimers and higher oligomers. They contain a unique, 80 kD central region that shares no homology with other proteins. While the structures of the BC, CT and BCCP domains and other biotin-dependent carboxylase holoenzymes are known1,9–14, currently there is no structural information on the ACC holoenzyme. Here we report the crystal structure of the full-length, 500 kD holoenzyme dimer of ScACC. The structure is strikingly different from those of the other biotin-dependent carboxylases. The central region contains five domains and is important for positioning the BC and CT domains for catalysis. The structure unexpectedly reveals a dimer of the BC domain and extensive conformational differences compared to the structure of BC domain alone, which is a monomer. These structural changes explain why the BC domain alone is catalytically inactive and define the molecular mechanism for the inhibition of eukaryotic ACC by the natural product soraphen A15,16 and by phosphorylation of a Ser residue just prior to the BC domain core in mammalian ACC. The BC and CT active sites are separated by 80 Å, and the entire BCCP domain must translocate during catalysis. PMID:26458104

  7. Crystal structure of the 500-kDa yeast acetyl-CoA carboxylase holoenzyme dimer.

    PubMed

    Wei, Jia; Tong, Liang

    2015-10-29

    Acetyl-CoA carboxylase (ACC) has crucial roles in fatty acid metabolism and is an attractive target for drug discovery against diabetes, cancer and other diseases. Saccharomyces cerevisiae ACC (ScACC) is crucial for the production of very-long-chain fatty acids and the maintenance of the nuclear envelope. ACC contains biotin carboxylase (BC) and carboxyltransferase (CT) activities, and its biotin is linked covalently to the biotin carboxyl carrier protein (BCCP). Most eukaryotic ACCs are 250-kilodalton (kDa), multi-domain enzymes and function as homodimers and higher oligomers. They contain a unique, 80-kDa central region that shares no homology with other proteins. Although the structures of the BC, CT and BCCP domains and other biotin-dependent carboxylase holoenzymes are known, there is currently no structural information on the ACC holoenzyme. Here we report the crystal structure of the full-length, 500-kDa holoenzyme dimer of ScACC. The structure is remarkably different from that of the other biotin-dependent carboxylases. The central region contains five domains and is important for positioning the BC and CT domains for catalysis. The structure unexpectedly reveals a dimer of the BC domain and extensive conformational differences compared to the structure of the BC domain alone, which is a monomer. These structural changes reveal why the BC domain alone is catalytically inactive and define the molecular mechanism for the inhibition of eukaryotic ACC by the natural product soraphen A and by phosphorylation of a Ser residue just before the BC domain core in mammalian ACC. The BC and CT active sites are separated by 80 Å, and the entire BCCP domain must translocate during catalysis. PMID:26458104

  8. Washing scaling of GeneChip microarray expression

    PubMed Central

    2010-01-01

    Background Post-hybridization washing is an essential part of microarray experiments. Both the quality of the experimental washing protocol and adequate consideration of washing in intensity calibration ultimately affect the quality of the expression estimates extracted from the microarray intensities. Results We conducted experiments on GeneChip microarrays with altered protocols for washing, scanning and staining to study the probe-level intensity changes as a function of the number of washing cycles. For calibration and analysis of the intensity data we make use of the 'hook' method which allows intensity contributions due to non-specific and specific hybridization of perfect match (PM) and mismatch (MM) probes to be disentangled in a sequence specific manner. On average, washing according to the standard protocol removes about 90% of the non-specific background and about 30-50% and less than 10% of the specific targets from the MM and PM, respectively. Analysis of the washing kinetics shows that the signal-to-noise ratio doubles roughly every ten stringent washing cycles. Washing can be characterized by time-dependent rate constants which reflect the heterogeneous character of target binding to microarray probes. We propose an empirical washing function which estimates the survival of probe bound targets. It depends on the intensity contribution due to specific and non-specific hybridization per probe which can be estimated for each probe using existing methods. The washing function allows probe intensities to be calibrated for the effect of washing. On a relative scale, proper calibration for washing markedly increases expression measures, especially in the limit of small and large values. Conclusions Washing is among the factors which potentially distort expression measures. The proposed first-order correction method allows direct implementation in existing calibration algorithms for microarray data. We provide an experimental 'washing data set' which might

  9. The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface.

    PubMed

    Chen, Josephine; Zhao, Po; Massaro, Donald; Clerch, Linda B; Almon, Richard R; DuBois, Debra C; Jusko, William J; Hoffman, Eric P

    2004-01-01

    Publicly accessible DNA databases (genome browsers) are rapidly accelerating post-genomic research (see http://www.genome.ucsc.edu/), with integrated genomic DNA, gene structure, EST/ splicing and cross-species ortholog data. DNA databases have relatively low dimensionality; the genome is a linear code that anchors all associated data. In contrast, RNA expression and protein databases need to be able to handle very high dimensional data, with time, tissue, cell type and genes, as interrelated variables. The high dimensionality of microarray expression profile data, and the lack of a standard experimental platform have complicated the development of web-accessible databases and analytical tools. We have designed and implemented a public resource of expression profile data containing 1024 human, mouse and rat Affymetrix GeneChip expression profiles, generated in the same laboratory, and subject to the same quality and procedural controls (Public Expression Profiling Resource; PEPR). Our Oracle-based PEPR data warehouse includes a novel time series query analysis tool (SGQT), enabling dynamic generation of graphs and spreadsheets showing the action of any transcript of interest over time. In this report, we demonstrate the utility of this tool using a 27 time point, in vivo muscle regeneration series. This data warehouse and associated analysis tools provides access to multidimensional microarray data through web-based interfaces, both for download of all types of raw data for independent analysis, and also for straightforward gene-based queries. Planned implementations of PEPR will include web-based remote entry of projects adhering to quality control and standard operating procedure (QC/SOP) criteria, and automated output of alternative probe set algorithms for each project (see http://microarray.cnmcresearch.org/pgadatatable.asp). PMID:14681485

  10. Estimating RNA-quality using GeneChip microarrays

    PubMed Central

    2012-01-01

    Background Microarrays are a powerful tool for transcriptome analysis. Best results are obtained using high-quality RNA samples for preparation and hybridization. Issues with RNA integrity can lead to low data quality and failure of the microarray experiment. Results Microarray intensity data contains information to estimate the RNA quality of the sample. We here study the interplay of the characteristics of RNA surface hybridization with the effects of partly truncated transcripts on probe intensity. The 3′/5′ intensity gradient, the basis of microarray RNA quality measures, is shown to depend on the degree of competitive binding of specific and of non-specific targets to a particular probe, on the degree of saturation of the probes with bound transcripts and on the distance of the probe from the 3′-end of the transcript. Increasing degrees of non-specific hybridization or of saturation reduce the 3′/5′ intensity gradient and if not taken into account, this leads to biased results in common quality measures for GeneChip arrays such as affyslope or the control probe intensity ratio. We also found that short probe sets near the 3′-end of the transcripts are prone to non-specific hybridization presumable because of inaccurate positional assignment and the existence of transcript isoforms with variable 3′ UTRs. Poor RNA quality is associated with a decreased amount of RNA material hybridized on the array paralleled by a decreased total signal level. Additionally, it causes a gene-specific loss of signal due to the positional bias of transcript abundance which requires an individual, gene-specific correction. We propose a new RNA quality measure that considers the hybridization mode. Graphical characteristics are introduced allowing assessment of RNA quality of each single array (‘tongs plot’ and ‘degradation hook’). Furthermore, we suggest a method to correct for effects of RNA degradation on microarray intensities. Conclusions The presented RNA

  11. Design and RF measurements of a 5 GHz 500 kW window for the ITER LHCD system

    NASA Astrophysics Data System (ADS)

    Hillairet, J.; Achard, J.; Bae, Y. S.; Bernard, J. M.; Dechambre, N.; Delpech, L.; Ekedahl, A.; Faure, N.; Goniche, M.; Kim, J.; Larroque, S.; Magne, R.; Marfisi, L.; Namkung, W.; Park, H.; Park, S.; Poli, S.; Vulliez, K.

    2014-02-01

    CEA/IRFM is conducting R&D efforts in order to validate the critical RF components of the 5 GHz ITER LHCD system, which is expected to transmit 20 MW of RF power to the plasma. Two 5 GHz 500 kW BeO pill-box type window prototypes have been manufactured in 2012 by the PMB Company, in close collaboration with CEA/IRFM. Both windows have been validated at low power, showing good agreement between measured and modeling, with a return loss better than 32 dB and an insertion loss below 0.05 dB. This paper reports on the window RF design and the low power measurements. The high power tests up to 500kW have been carried out in March 2013 in collaboration with NFRI. Results of these tests are also reported.

  12. Recent progress in developing a 170 GHz, 500 kW gyrotron for testing ITER transmission line components

    NASA Astrophysics Data System (ADS)

    Felch, Kevin; Blank, Monica; Borchard, Philipp; Cahalan, Pat; Cauffman, Steve

    2011-10-01

    A 170 GHz, 500 kW CW gyrotron has been developed for testing ITER transmission line components. Although specified as a 500 kW source, the electrical design has been conceived with the goal of generating up to 1 MW of continuous output power. The design employs a double-anode electron gun, an interaction cavity operating in the TE31,8 cavity mode, a three-mirror internal converter to produce a fundamental Gaussian output beam, a CVD diamond output window and a depressed collector to safely dissipate the spent electron beam power. Fabrication of the gyrotron is nearly complete and initial high-power tests will soon be carried out. Details of the gyrotron design, results of low-power tests on the internal converter and initial high-power tests will be presented.

  13. Verifications on the Installed Number of Surge Arresters for 66-500kV Power Systems in Japan

    NASA Astrophysics Data System (ADS)

    Shirakawa, Shingo; Kobayashi, Takayuki; Tanae, Hiroshi; Takamatsu, Tadashi; Kumai, Toshiya; Imura, Hajime; Nishimura, Seisuke

    Surge arresters have contributed to supply of electric power by suppressing lightning surge on transmission lines in case of lightning phenomena. Surge arresters using zinc oxide (ZnO) elements are suitable for insulation coordination, and are enable to reduce LIWV (Lightning Impulse Withstand Voltage) and construction cost of power systems. This paper describes applications and results of surge arresters to verify effectiveness of surge protection for 66-500kV power systems in Japan.

  14. Absolute rate of the reaction of Cl(p-2) with molecular hydrogen from 200 - 500 K

    NASA Technical Reports Server (NTRS)

    Whytock, D. A.; Lee, J. H.; Michael, J. V.; Payne, W. A.; Stief, L. J.

    1976-01-01

    Rate constants for the reaction of atomic chlorine with hydrogen are measured from 200 - 500 K using the flash photolysis-resonance fluorescence technique. The results are compared with previous work and are discussed with particular reference to the equilibrium constant for the reaction and to relative rate data for chlorine atom reactions. Theoretical calculations, using the BEBO method with tunneling, give excellent agreement with experiment.

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

    PubMed

    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. The results of systems tests of the 500 kV busbar controllable shunting reactor in the Tavricheskaya substation

    SciTech Connect

    Gusev, S. I.; Karpov, V. N.; Kiselev, A. N.; Kochkin, V. I.

    2009-09-15

    The results of systems tests of the 500 kV busbar magnetization-controllable shunting reactor (CSR), set up in the Tavricheskaya substation, including measurements of the quality of the electric power, the harmonic composition of the network currents of the reactor for different values of the reactive power consumed, the determination of the regulating characteristics of the reactor, the speed of response of the shunting reactor in the current and voltage stabilization modes, and also the operation of the reactor under dynamic conditions for different perturbations, are presented. The results obtained are analyzed.

  17. The radiation tolerance of MTP and LC optical fibre connectors to 500 kGy(Si) of gamma radiation

    NASA Astrophysics Data System (ADS)

    Hall, D. C.; Hamilton, P.; Huffman, B. T.; Teng, P. K.; Weidberg, A. R.

    2012-04-01

    The LHC luminosity upgrade, known as the High Luminosity LHC (HL-LHC), will require high-speed optical links to read out data from the detectors. The optical fibre connectors contained within such a link must have a small form factor and be capable of operating in the harsh radiation environment at the HL-LHC. MTP ribbon fibre connectors and LC single fibre connectors were exposed to 500 kGy(Si) of gamma radiation and their radiation hardness was investigated. Neither type of connector exhibited evidence for any significant radiation damage and both connectors could be qualified for use at HL-LHC detectors.

  18. Rate Coefficient for the (4)Heμ + CH4 Reaction at 500 K: Comparison between Theory and Experiment.

    PubMed

    Arseneau, Donald J; Fleming, Donald G; Li, Yongle; Li, Jun; Suleimanov, Yury V; Guo, Hua

    2016-03-01

    The rate constant for the H atom abstraction reaction from methane by the muonic helium atom, Heμ + CH4 → HeμH + CH3, is reported at 500 K and compared with theory, providing an important test of both the potential energy surface (PES) and reaction rate theory for the prototypical polyatomic CH5 reaction system. The theory used to characterize this reaction includes both variational transition-state (CVT/μOMT) theory (VTST) and ring polymer molecular dynamics (RPMD) calculations on a recently developed PES, which are compared as well with earlier calculations on different PESs for the H, D, and Mu + CH4 reactions, the latter, in particular, providing for a variation in atomic mass by a factor of 36. Though rigorous quantum calculations have been carried out for the H + CH4 reaction, these have not yet been extended to the isotopologues of this reaction (in contrast to H3), so it is important to provide tests of less rigorous theories in comparison with kinetic isotope effects measured by experiment. In this regard, the agreement between the VTST and RPMD calculations and experiment for the rate constant of the Heμ + CH4 reaction at 500 K is excellent, within 10% in both cases, which overlaps with experimental error. PMID:26484648

  19. An experimental setup for the simultaneous measurement of thermoelectric power of two samples from 77 K to 500 K

    SciTech Connect

    Tripathi, T. S.; Bala, M.; Asokan, K.

    2014-08-01

    We report on an experimental setup for the simultaneous measurement of the thermoelectric power (TEP) of two samples in the temperature range from 77 K to 500 K using optimum electronic instruments. The setup consists of two rectangular copper bars in a bridge arrangement for sample mounting, two surface mount (SM) chip resistors for creating alternate temperature gradient, and a type E thermocouple in differential geometry for gradient temperature (ΔT) measurement across the samples. In addition, a diode arrangement has been made for the alternate heating of SM resistors using only one DC current source. The measurement accuracy of ΔT increases with the differential thermocouple arrangement. For the calibration of the setup, measurements of TEP on a high purity (99.99%) platinum wire and type K thermocouple wires Chromel and Alumel have been performed from 77 K to 500 K with respect to copper lead wires. Additionally, this setup can be utilized to calibrate an unknown sample against a sample of known absolute TEP.

  20. Survey of Magnetic Fields Near BPA 230-kV and 500-kV Transmission Lines.

    SciTech Connect

    Perrin, Nancy; Aggarwal, Rajinder Pal; Bracken, T. Daniel

    1991-05-20

    The purpose of this study was to characterize typical levels and variability of 60Hz magnetic fields at the centerline and edge of right-of-way of Bonneville Power Administration (BPA) 230-kV and 500-kV transmission lines. This was accomplished by taking magnetic field measurements at over 800 spans in Oregon and Washington. The spans were sampled using a stratified random sampling procedure with region (East vs. West), voltage (230-kV vs 500-kV), and circuit configuration as strata. There were five different circuit configuration groups for each region/voltage category requiring a total of 200 strata. Magnetic field measurements were taken at 13 locations under each span using an EMDEX-C as a survey meter. Additional information recorded for each span included conductor height (at 10 locations), right-of-way width, longitudinal and lateral slope, time of day, vegetation, terrain, weather conditions, temperature, wind speed, span length and presence of other lines in the corridor. 9 refs., 17 figs., 26 tabs.

  1. Advanced Photovoltaic Inverter Functionality using 500 kW Power Hardware-in-Loop Complete System Laboratory Testing: Preprint

    SciTech Connect

    Mather, B. A.; Kromer, M. A.; Casey, L.

    2013-01-01

    With the increasing penetration of distribution connected photovoltaic (PV) systems, more and more PV developers and utilities are interested in easing future PV interconnection concerns by mitigating some of the impacts of PV integration using advanced PV inverter controls and functions. This paper describes the testing of a 500 kW PV inverter using Power Hardware-in-Loop (PHIL) testing techniques. The test setup is described and the results from testing the inverter in advanced functionality modes, not commonly used in currently interconnected PV systems, are presented. PV inverter operation under PHIL evaluation that emulated both the DC PV array connection and the AC distribution level grid connection are shown for constant power factor (PF) and constant reactive power (VAr) control modes. The evaluation of these modes was completed under varying degrees of modeled PV variability.

  2. Design studies on a 500 kV DC gun photo-injector for the BXERL test facility

    NASA Astrophysics Data System (ADS)

    Liu, Sheng-Guang; Xu, Jin-Qiang

    2011-01-01

    BXERL is a proposal for a test facility (Beijing X-ray Energy Recovery Linac), which requires its injector to provide an electron beam of 5 MeV, 77 pC/bunch at a repetition rate of 130 MHz (average current of 10 mA). In this paper, we present the design of the injector, which consists of a 500 kV photocathode DC gun equipped with a GaAs cathode preparation device, a 1.3 GHz normal conducting RF buncher, two solenoids, and one cryomodule containing two 1.3 GHz 2-cell superconducting RF cavities as the energy booster. The detailed beam dynamics show that the injector can generate electron bunches with a RMS normalized emittance of 1.49 πmm·mrad, a bunch length of 0.67 mm, a beam energy of 5 MeV and an energy spread of 0.72%.

  3. Development of 500-kV AC cable employing laminar insulation of other than conventional cellulosic paper. Final report

    SciTech Connect

    Bahder, G.; Eager, G.S. Jr.; Walker, J.J.; Dima, A.F.

    1980-09-01

    The results of an investigation to develop a 500 kV ac laminar dielectric power cable and joint having insulation with lower losses than conventional cellulosic paper insulation are presented. Background information is presented on proposed low-loss synthetic and composite synthetic/cellulosic paper insulations. From these studies, fibrous polypropylene paper tape and cellulosic paper-polypropylene film-cellulosic paper composite paper (PPP) were chosen. Extensive testing of hand-wrapped cable models fabricated with each type of tape served to eliminate the fibrous polypropylene paper tape from further consideration. Cable model tests indicate that the PPP tape is satisfactory for insulation in 500 kV ac cable, and that oil impregnants now used in conventional cellulosic paper insulated cables are unsuitable, but that silicone oil with an additive is satisfactory for PPP tapes. Laboratory data indicate that it may be necessary with the PPP tapes to use a significantly lower viscosity impregnating oil which has a greater tendency to drain from pipe-type cables than conventional oil. This may require a modification of the moisture seal. Four final pipe-type cables having a conventional moisture seal were manufactured for possible future field testing. The dielectric loss of the final cables is one-fifth that of conventional cellulosic paper insulated cables. The estimated installed cost per MVA-mile of the PPP insulated cable, neglecting losses, is higher than cellulosic insulated cables impregnated with conventional mineral oil. However, the capacitance of the cable insulated with PPP tape is 25% lower than conventional cable, and therefore, the reactance necessary to compensate for the cable charging current is significantly reduced.

  4. Absolute rate constants for O + NO + M /= He, Ne, Ar, Kr/ yields NO2 + M from 217-500 K

    NASA Technical Reports Server (NTRS)

    Michael, J. V.; Payne, W. A.; Whytock, D. A.

    1976-01-01

    Rate constants for the reaction O + NO + M yields NO2 + M have been obtained at temperatures from 217-500 K in four different rare gases by a method combining flash photolysis with time resolved detection of O(3-P) by resonance fluorescence. The measured rate constants in Arrhenius form are (10.8 plus or minus 1.2) x 10 to the -33rd exp(1040 plus or minus 60/1.987 T) for helium; (9.01 plus or minus 1.16) x 10 to the -33rd exp(1180 plus or minus 70/1.987 T) for argon; (9.33 plus or minus 1.10) x 10 to the -33rd exp(1030 plus or minus 60/1.987 T) for neon; and (9.52 plus or minus 1.10) x 10 to the -33rd exp(1140 plus or minus 70/1.987 T) for krypton in units of cm to the 6th/sq molecule/s.

  5. Final phase testing and evaluation of the 500 kW direct contact pilot plant at East Mesa

    SciTech Connect

    Olander, R.; Oshmyansky, S.; Nichols, K.; Werner, D.

    1983-12-01

    The testing performed during the last phase of the geothermal direct contact heat exchanger program utilizing the 500 kW pilot plant provided more insight into the capabilities and limits of the direct contact approach and showed that more work needs to be done to understand the inner workings of a large direct contact heat exchanger if they are to be modeled analytically. Testing of the column demonstrated that the performance was excellent and that the sizing criteria is conservative. The system operated smoothly and was readily controlled over a wide range of operating conditions. Performance evaluation showed pinch differentials of 4/sup 0/F or less and better than predicted heat transfer capability. Testing during this final phase was directed towards establishing the limits of the column to transfer heat. The working column height was shortened progressively to approximately 16 feet from a design length of 28 feet. The short column performed as well as a full length column and there are indications that the column could have been shortened even more without affecting its ability to transfer heat. The column's ability to perform as well with shortened lengths indicates that the heat transfer coefficients and criteria derived from the small scale tests are very conservative.

  6. Genome-wide linkage analysis of a Parkinsonian-pyramidal syndrome pedigree by 500 K SNP arrays.

    PubMed

    Shojaee, Seyedmehdi; Sina, Farzad; Banihosseini, Setareh Sadat; Kazemi, Mohammad Hossein; Kalhor, Reza; Shahidi, Gholam-Ali; Fakhrai-Rad, Hossein; Ronaghi, Mostafa; Elahi, Elahe

    2008-06-01

    Robust SNP genotyping technologies and data analysis programs have encouraged researchers in recent years to use SNPs for linkage studies. Platforms used to date have been 10 K chip arrays, but the possible value of interrogating SNPs at higher densities has been considered. Here, we present a genome-wide linkage analysis by means of a 500 K SNP platform. The analysis was done on a large pedigree affected with Parkinsonian-pyramidal syndrome (PPS), and the results showed linkage to chromosome 22. Sequencing of candidate genes revealed a disease-associated homozygous variation (R378G) in FBXO7. FBXO7 codes for a member of the F-box family of proteins, all of which may have a role in the ubiquitin-proteosome protein-degradation pathway. This pathway has been implicated in various neurodegenerative diseases, and identification of FBXO7 as the causative gene of PPS is expected to shed new light on its role. The performance of the array was assessed and systematic analysis of effects of SNP density reduction was performed with the real experimental data. Our results suggest that linkage in our pedigree may have been missed had we used chips containing less than 100,000 SNPs across the genome. PMID:18513678

  7. Seasonal Patterns of Melatonin, Cortisol, and Progesterone Secretion in Female Lambs Raised Beneath a 500-kV Transmission Line.

    SciTech Connect

    Lee, Jack M.

    1992-06-01

    Although several kinds of biological effects of electric and magnetic fields have been reported from laboratory studies, few have been independently replicated. When this study was being planned, the suppression of nighttime melatonin in rodents was thought to represent one of the strongest known effects of these fields. The effect had been replicated by a single laboratory for 60-Hz electric fields, and by multiple laboratories for d-c magnetic fields. The primary objective of this study was to determine whether the effect of electric and magnetic fields on melatonin would also occur in sheep exposed to a high voltage transmission line. The specific hypothesis tested by this experiment was as follows: The electrical environment produced by a 60-Hz, 500-kV transmission line causes a depression in nocturnal melatonin in chronically exposed female lambs. This may mimic effects of pinealectomy or constant long-day photoperiods, thus delaying the onset of reproductive cycles. Results of the study do not provide evidence to support the hypothesis. Melatonin concentrations in the sheep exposed to the transmission line showed the normal pattern of low daytime and high nighttime serum levels. As compared to the control group, there were no statistically significant group differences in the mean amplitude, phase, or duration of the nighttime melatonin elevation.

  8. Agarose and Polyacrylamide Gel Electrophoresis Methods for Molecular Mass Analysis of 5–500 kDa Hyaluronan

    PubMed Central

    Bhilocha, Shardul; Amin, Ripal; Pandya, Monika; Yuan, Han; Tank, Mihir; LoBello, Jaclyn; Shytuhina, Anastasia; Wang, Wenlan; Wisniewski, Hans-Georg; de la Motte, Carol; Cowman, Mary K.

    2011-01-01

    Agarose and polyacrylamide gel electrophoresis systems for the molecular mass-dependent separation of hyaluronan (HA) in the size range of approximately 5–500 kDa have been investigated. For agarose-based systems, the suitability of different agarose types, agarose concentrations, and buffers systems were determined. Using chemoenzymatically synthesized HA standards of low polydispersity, the molecular mass range was determined for each gel composition, over which the relationship between HA mobility and logarithm of the molecular mass was linear. Excellent linear calibration was obtained for HA molecular mass as low as approximately 9 kDa in agarose gels. For higher resolution separation, and for extension to molecular masses as low as approximately 5 kDa, gradient polyacrylamide gels were superior. Densitometric scanning of stained gels allowed analysis of the range of molecular masses present in a sample, and calculation of weight-average and number-average values. The methods were validated for polydisperse HA samples with viscosity-average molecular masses of 112, 59, 37, and 22 kDa, at sample loads of 0.5 µg (for polyacrylamide) to 2.5 µg (for agarose). Use of the methods for electrophoretic mobility shift assays was demonstrated for binding of the HA-binding region of aggrecan (recombinant human aggrecan G1-IGD-G2 domains) to a 150 kDa HA standard. PMID:21684248

  9. A calorimetric study of energy conversion efficiency of a sonochemical reactor at 500 kHz for organic solvents.

    PubMed

    Toma, Maricela; Fukutomi, Satoshi; Asakura, Yoshiyuki; Koda, Shinobu

    2011-01-01

    It would seem that the economic viability is yet to be established for a great number of sonochemical processes, owning to their perfectible ultrasonic equipments. Industrial scale sonoreactors may become more important as a result of mastering the parameters with influence on their energy balance. This work related the solvent type to the energy efficiency as the first step of a complex study aiming to assess the energy balance of sonochemical reactors at 500 kHz. Quantitative measurements of ultrasonic power for water and 10 pure organic solvents were performed by calorimetry for a cylindrically shaped sonochemical reactor with a bottom mounted vibrating plate. It was found that the ultrasonic power is strongly related to the solvent, the energy conversion for organic liquids is half from that of water and there is a drop in energy efficiency for filling levels up to 250 mm organic solvents. Surface tension, viscosity and vapor pressure influence the energy conversion for organic solvents, but it is difficult explain these findings based on physical properties of solvents alone. The apparent intensity of the atomization process shows a good agreement with the experimentally determined values for energy conversion for water and the solvent group studied here. This study revealed that to attain the same ultrasonic power level, more electrical energy is need for organic solvents as compared to water. The energy balance equation has been defined based on these findings by considering an energy term for atomization. PMID:20655791

  10. Hunter survey final report, Phase I - baseline study. Garrison-Spokane 500-kV transmission project

    SciTech Connect

    Allen, S.

    1984-11-01

    The State of Montana, in cooperation with the US Forest Service and the Bonneville Power Administration, is conducting a five-year study on the impacts on elk security habitat and hunter opportunity in western Montana of a 500 kV transmission line. Potential impacts stem from the new and upgraded access roads required for the line, which may reduce summer/fall security habitat and make hunting areas less remote. The line itself could affect the aesthetics of popular hunting areas located along the route. As part of this monitoring program, the Montana Department of Natural Resources and Conservation is surveying hunters at seven check stations in the project's two study areas. The hunter survey research has three phases. Phase I was conducted in fall, 1983, to collect baseline data on hunting use and quality in the study areas. After the line is constructed and energized, the Phase II survey, scheduled for fall, 1985, will test hypotheses developed from baseline data to assess the project's impacts on hunting use. During Phase III, scheduled for fall, 1986, the persistence of any impacts identified will be measured. Reports from each phase will be issued to the Interagency Wildlife Technical Committee (chaired by the Bonneville Power Administration). The data will also be used by the Montana Department of Fish, Wildlife, and Parks, both to help manage elk and to assist in US Forest Service Land management planning. Over 600 hunters were interviewed using a questionnaire developed by DNRC and reviewed extensively by state and federal agencies. The survey form contained questions on hunters' reasons for choosing the study areas as places to hunt, hunting success and related information, previous hunting experience, hunting area evaluations, place of residence, and age. The data were tabulated to describe the 1983 baseline data, and then subjected to cluster analysis. 36 references, 1 figure, 9 tables. (ACR)

  11. SFP Genotyping from Affymetrix Arrays is Robust but Largely Detects Cis-acting Expression Regulators

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The recent development of Affymetrix chips designed from assembled EST sequences has spawned considerable interest in identifying single-feature polymorphisms (SFPs) from transcriptome data. SFPs are valuable genetic markers that potentially offer a physical link to the structural genes themselves....

  12. Association between Genetic Subgroups of Pancreatic Ductal Adenocarcinoma Defined by High Density 500 K SNP-Arrays and Tumor Histopathology

    PubMed Central

    Gutiérrez, María Laura; Muñoz-Bellvis, Luís; Abad, María del Mar; Bengoechea, Oscar; González-González, María

    2011-01-01

    The specific genes and genetic pathways associated with pancreatic ductal adenocarcinoma are still largely unknown partially due to the low resolution of the techniques applied so far to their study. Here we used high-density 500 K single nucleotide polymorphism (SNP)-arrays to define those chromosomal regions which most commonly harbour copy number (CN) alterations and loss of heterozygozity (LOH) in a series of 20 PDAC tumors and we correlated the corresponding genetic profiles with the most relevant clinical and histopathological features of the disease. Overall our results showed that primary PDAC frequently display (>70%) extensive gains of chromosomes 1q, 7q, 8q and 20q, together with losses of chromosomes 1p, 9p, 12q, 17p and 18q, such chromosomal regions harboring multiple cancer- and PDAC-associated genes. Interestingly, these alterations clustered into two distinct genetic profiles characterized by gains of the 2q14.2, 3q22.1, 5q32, 10q26.13, 10q26.3, 11q13.1, 11q13.3, 11q13.4, 16q24.1, 16q24.3, 22q13.1, 22q13.31 and 22q13.32 chromosomal regions (group 1; n = 9) versus gains at 1q21.1 and losses of the 1p36.11, 6q25.2, 9p22.1, 9p24.3, 17p13.3 and Xp22.33 chromosomal regions (group 2; n = 11). From the clinical and histopathological point of view, group 1 cases were associated with smaller and well/moderately-differentiated grade I/II PDAC tumors, whereas and group 2 PDAC displayed a larger size and they mainly consisted of poorly-differentiated grade III carcinomas. These findings confirm the cytogenetic complexity and heterogenity of PDAC and provide evidence for the association between tumor cytogenetics and its histopathological features. In addition, we also show that the altered regions identified harbor multiple cancer associate genes that deserve further investigation to determine their relevance in the pathogenesis of PDAC. PMID:21811587

  13. Software comparison for evaluating genomic copy number variation for Affymetrix 6.0 SNP array platform

    PubMed Central

    2011-01-01

    Background Copy number data are routinely being extracted from genome-wide association study chips using a variety of software. We empirically evaluated and compared four freely-available software packages designed for Affymetrix SNP chips to estimate copy number: Affymetrix Power Tools (APT), Aroma.Affymetrix, PennCNV and CRLMM. Our evaluation used 1,418 GENOA samples that were genotyped on the Affymetrix Genome-Wide Human SNP Array 6.0. We compared bias and variance in the locus-level copy number data, the concordance amongst regions of copy number gains/deletions and the false-positive rate amongst deleted segments. Results APT had median locus-level copy numbers closest to a value of two, whereas PennCNV and Aroma.Affymetrix had the smallest variability associated with the median copy number. Of those evaluated, only PennCNV provides copy number specific quality-control metrics and identified 136 poor CNV samples. Regions of copy number variation (CNV) were detected using the hidden Markov models provided within PennCNV and CRLMM/VanillaIce. PennCNV detected more CNVs than CRLMM/VanillaIce; the median number of CNVs detected per sample was 39 and 30, respectively. PennCNV detected most of the regions that CRLMM/VanillaIce did as well as additional CNV regions. The median concordance between PennCNV and CRLMM/VanillaIce was 47.9% for duplications and 51.5% for deletions. The estimated false-positive rate associated with deletions was similar for PennCNV and CRLMM/VanillaIce. Conclusions If the objective is to perform statistical tests on the locus-level copy number data, our empirical results suggest that PennCNV or Aroma.Affymetrix is optimal. If the objective is to perform statistical tests on the summarized segmented data then PennCNV would be preferred over CRLMM/VanillaIce. Specifically, PennCNV allows the analyst to estimate locus-level copy number, perform segmentation and evaluate CNV-specific quality-control metrics within a single software package

  14. Development of compact 500 kV 8000 A gas insulated transmission line-dust control during field jointing and method for detecting conductive particles

    SciTech Connect

    Kaminaga, K.; Koshiishi, M.; Hayashi, T.; Matsuki, M.; Hara, T.; Sugiyama, N.

    1987-10-01

    This paper describes the results of studies made on dust control during field jointing and a method for detecting conductive particles after installation in the development of a compact 500 kV 8000 A gas insulated transmission line (GIL). The study on dust control during field jointing proved that field jointing of the compact GIL can be done like conventional GIL in an easily fabricated vinyl shelter without a clean air flow. Harmful conductive particles can be detected with an Acoustic Emission (AE) sensor. This sensor is effective in improving the reliability of the compact GIL when used with a suitable ac voltage during field test. A 120 m long test line of compact 500 kV 8000 A GIL was constructed and, in a long-term field test, proved to have properties sufficient for practical use.

  15. Innovation on Energy Power Technology (23)Completion of Installation of 500kV Cable along the Large-scale Bridges

    NASA Astrophysics Data System (ADS)

    Maekawa, Yuichi

    This paper describes an outline of the Honshu-Shikoku Interconnecting Transmission Line which includes the first large-scale cable line. The most significant feature of this transmission line is the installation of 500kV cables along various types of bridges. This brought many previously unknown technical hurdles such as techniques to overcome movements and vibrations of a series of large bridges. These hurdles were cleared through various efforts and techniques by the concerned parties.

  16. Normalization of Affymetrix miRNA Microarrays for the Analysis of Cancer Samples.

    PubMed

    Wu, Di; Gantier, Michael P

    2016-01-01

    microRNA (miRNA) microarray normalization is a critical step for the identification of truly differentially expressed miRNAs. This is particularly important when dealing with cancer samples that have a global miRNA decrease. In this chapter, we provide a simple step-by-step procedure that can be used to normalize Affymetrix miRNA microarrays, relying on robust normal-exponential background correction with cyclic loess normalization. PMID:25971910

  17. A comparison of statistical tests for detecting differential expression using Affymetrix oligonucleotide microarrays.

    PubMed

    Vardhanabhuti, Saran; Blakemore, Steven J; Clark, Steven M; Ghosh, Sujoy; Stephens, Richard J; Rajagopalan, Dilip

    2006-01-01

    Signal quantification and detection of differential expression are critical steps in the analysis of Affymetrix microarray data. Many methods have been proposed in the literature for each of these steps. The goal of this paper is to evaluate several signal quantification methods (GCRMA, RSVD, VSN, MAS5, and Resolver) and statistical methods for differential expression (t test, Cyber-T, SAM, LPE, RankProducts, Resolver RatioBuild). Our particular focus is on the ability to detect differential expression via statistical tests. We have used two different datasets for our evaluation. First, we have used the HG-U133 Latin Square spike in dataset developed by Affymetrix. Second, we have used data from an in-house rat liver transcriptomics study following 30 different drug treatments generated using the Affymetrix RAE230A chip. Our overall recommendation based on this study is to use GCRMA for signal quantification. For detection of differential expression, GCRMA coupled with Cyber-T or SAM is the best approach, as measured by area under the receiver operating characteristic (ROC) curve. The integrated pipeline in Resolver RatioBuild combining signal quantification and detection of differential expression is an equally good alternative for detecting differentially expressed genes. For most of the differential expression algorithms we considered, the performance using MAS5 signal quantification was inferior to that of the other methods we evaluated. PMID:17233564

  18. High-peak-power optically pumped AlGaInAs eye-safe laser at 500-kHz repetition rate with an intracavity diamond heat spreader

    NASA Astrophysics Data System (ADS)

    Chen, Y.-F.; Su, K. W.; Chen, W. L.; Huang, K. F.; Chen, Y. F.

    2012-08-01

    We report on a compact efficient high-repetition-rate (>100 kHz) optically pumped AlGaInAs nanosecond eye-safe laser at 1525 nm. A diamond heat spreader bonded to the gain chip is employed to improve the heat removal. At a pump power of 13.3 W, the average output power at a repetition rate 200 kHz is up to 3.12 W, corresponding to a peak output power of 560 W. At a repetition rate 500 kHz, the maximum average power and peak power are found to be 2.32 W and 170 W, respectively.

  19. 1 mJ, 500 kHz Nd:YAG/Nd:YVO4 MOPA laser with a Nd:YAG cavity-dumping seed laser

    NASA Astrophysics Data System (ADS)

    Fu, X.; Liu, Q.; Yan, X.; Cui, J.; Gong, M.

    2010-08-01

    We report a high-repetition-rate, high-pulse-energy master oscillator power amplifier (MOPA) laser system, in which the seed laser from the Nd:YAG rod-based oscillator cavity dumped at 500 kHz, was scaled up consecutively by a four-stage Nd:YVO4 preamplifier and a two-stage Nd:YAG zigzag slab main amplifier. The laser pulsed output with the average power of 510 W was achieved, with the efficiency extraction of 26.6% at the main amplifier stage and the single-pulse energy of 1.02 mJ.

  20. Fast wavelength-swept dispersion-tuned fiber laser over 500kHz using a wideband chirped fiber Bragg grating

    NASA Astrophysics Data System (ADS)

    Yamashita, Shinji; Takubo, Yuya

    2011-05-01

    We proposed a wide and fast wavelength-swept fiber lasers based on the dispersion tuning for the optical coherence tomography (OCT) applications. So far, we have achieved the sweep rate of ~200kHz at the sweep bandwidth of ~180nm. The sweep rate is only limited by the photon lifetime, which is proportional to the cavity length. Since we used a dispersion compensating fiber (DCF) as the dispersive medium, the long cavity length (~100m) was the limit of the sweep rate. In this paper, we demonstrate faster sweep rate up to ~500kHz by using a wideband chirped fiber Bragg grating (CFBG).

  1. Proposed amendment to presidential permit PP-63 and associated modifications to 500 kV international transmission line, Forbes, Minnesota to Manitoba, Canada. [Forbes Substation

    SciTech Connect

    Not Available

    1992-10-01

    This Addendum to the Final Environmental Assessment for the Proposed Amendment to Presidential Permit PP-63 and Associated Modifications to 500 kV International Transmission Line: Forbes, Minnesota to Manitoba, Canada (DOE/EA-587) addresses Northern States Power Company's (NSP) proposed expansion of the Forbes Substation. The applicant has requested that the expansion take place on the west side of the substation, within the existing property line, instead of on the north side as originally proposed. All of the proposed construction would take place on property already owned by NSP. DOE has reviewed the environmental impacts associated with this minor modification and has determined that the conclusions reached in the environmental assessment and Finding of No Significant Impact prepared in connection with NSP's original amendment request remain valid.

  2. Diode-pumped, ultrafast, multi-octave supercontinuum source at repetition rates between 500 kHz and 20 MHz using Yb:glass lasers and tapered fibers.

    PubMed

    Teipel, Jörn; Türke, Diana; Giessen, Harald; Killi, Alexander; Morgner, Uwe; Lederer, Max; Kopf, Daniel; Kolesik, Miroslav

    2005-03-01

    We present a compact, all diode-pumped supercontinuum source based on a SESAM mode-locked Yb:glass oscillator at 1040 nm and a tapered fiber. The oscillator has a repetition rate of 20 MHz, a pulse duration of 200 fs, and a maximum pulse energy of about 15 nJ. This system delivers an 1100 nm broad spectrum with an output power of more than 100 mW. Decreasing the repetition rate to 500 kHz by cavity-dumping results in a supercontinuum with a high pulse energy of about 50 nJ. Furthermore, using the frequency-doubled output of this laser at 520 nm with 300 fs pulse duration resulted in supercontinua in the near-UV and visible spectral region. We compare the experimental spectra with theoretical simulations. PMID:19495023

  3. 500 kHz OPCPA delivering tunable sub-20 fs pulses with 15 W average power based on an all-ytterbium laser.

    PubMed

    Puppin, Michele; Deng, Yunpei; Prochnow, Oliver; Ahrens, Jan; Binhammer, Thomas; Morgner, Uwe; Krenz, Marcel; Wolf, Martin; Ernstorfer, Ralph

    2015-01-26

    An optical parametric chirped pulse amplifier fully based on Yb lasers at 500 kHz is described. Passive optical-synchronization is achieved between a fiber laser-pumped white-light and a 515 nm pump produced with a 200 W picosecond Yb:YAG InnoSlab amplifier. An output power up to 19.7 W with long-term stability of 0.3% is demonstrated for wavelength tunable pulses between 680 nm and 900 nm and spectral stability of 0.2%; 16.5 W can be achieved with a bandwidth supporting 5.4 fs pulses. We demonstrate compression of 30 µJ pulses to sub-20 fs duration with a prism compressor, suitable for high harmonic generation. PMID:25835905

  4. Summary of Static power converters of 500 kW or less serving as the relay interface package for non-conventional generators''

    SciTech Connect

    Ball, G.J.; Blackburn, D.C. Jr.; Gish, W.

    1994-07-01

    The special publication was prepared by the Power System Relaying Committee of the IEEE to assist people involved in the installation, application, and operation of utility-interconnected dispersed storage and generation (DSG) systems of 500 kW or less. The energy sources considered are batteries, fuel cells, windmills and photovoltaic arrays. In most cases, the electrical energy produced is direct current, dc, which must be converted to alternating current, ac, for connection to the electric utility network. The interface between the dc source and the utility ac is often a static power converter (SPC). The purpose of the publication is to illustrate those SPC characteristics that can obviate the need for the interface relay protection package normally required by a utility. A qualifying SPC can detect utility system disturbances or other conditions that would require generator separation in addition to its normal function of protection and control of the DSG.

  5. Improvements in 500-kHz Ultrasonic Phased-Array Probe Designs for Evaluation of Thick Section Cast Austenitic Stainless Steel Piping Welds

    SciTech Connect

    Crawford, Susan L.; Cinson, Anthony D.; Moran, Traci L.; Anderson, Michael T.; Diaz, Aaron A.

    2011-02-01

    PNNL has been studying and performing confirmatory research on the inspection of piping welds in coarse-grained steels for over 30 years. More recent efforts have been the application of low frequency phased array technology to this difficult to inspect material. The evolution of 500 kHz PA probes and the associated electronics and scanning protocol are documented in this report. The basis for the probe comparisons are responses from one mechanical fatigue crack and two thermal fatigue cracks in large-bore cast mockup specimens on loan from the Electric Power Research Institution. One of the most significant improvements was seen in the use of piezo-composite elements in the later two probes instead of the piezo-ceramic material used in the prototype array. This allowed a reduction in system gain of 30 dB and greatly reduced electronic noise. The latest probe had as much as a 5 dB increase in signal to noise, adding to its flaw discrimination capability. The system electronics for the latest probe were fully optimized for a 500 kHz center frequency, however significant improvements were not observed in the center frequency of the flaw responses. With improved scanner capabilities, smaller step sizes were used, allowing both line and raster data improvements to be made with the latest probe. The small step sizes produce high resolution images that improve flaw discrimination and, along with the increased signal-to-noise ratio inherent in the latest probe design, enhanced detection of the upper regions of the flaw make depth sizing more plausible. Finally, the physical sizes of the probes were progressively decreased allowing better access to the area of interest on specimens with weld crowns, and the latest probe was designed with non-integral wedges providing flexibility in focusing on different specimen geometries.

  6. Evaluation of the Affymetrix CytoScan® Dx Assay for Developmental Delay

    PubMed Central

    Webb, Bryn D.; Scharf, Rebecca J.; Spear, Emily A.; Edelmann, Lisa J.; Stroustrup, Annemarie

    2015-01-01

    The goal of molecular cytogenetic testing for children presenting with developmental delay is to identify or exclude genetic abnormalities that are associated with cognitive, behavioral, and/or motor symptoms. Until 2010, chromosome analysis was the standard first-line genetic screening test for evaluation of patients with developmental delay when a specific syndrome was not suspected. In 2010, The American College of Medical Genetics and several other groups recommended chromosomal microarray (CMA) as the first-line test in children with developmental delays, multiple congenital anomalies, and/or autism. This test is able to detect regions of genomic imbalances at a much finer resolution than G-banded karyotyping. Until recently, no CMA testing had been approved by the United States Food and Drug Administration (FDA). This review will focus on the use of the Affymetrix CytoScan® Dx Assay, the first CMA to receive FDA approval for the genetic evaluation of individuals with developmental delay. PMID:25350348

  7. Exon array data analysis using Affymetrix power tools and R statistical software

    PubMed Central

    2011-01-01

    The use of microarray technology to measure gene expression on a genome-wide scale has been well established for more than a decade. Methods to process and analyse the vast quantity of expression data generated by a typical microarray experiment are similarly well-established. The Affymetrix Exon 1.0 ST array is a relatively new type of array, which has the capability to assess expression at the individual exon level. This allows a more comprehensive analysis of the transcriptome, and in particular enables the study of alternative splicing, a gene regulation mechanism important in both normal conditions and in diseases. Some aspects of exon array data analysis are shared with those for standard gene expression data but others present new challenges that have required development of novel tools. Here, I will introduce the exon array and present a detailed example tutorial for analysis of data generated using this platform. PMID:21498550

  8. Impact Mitigation and Monitoring of the BPA 500-kV Garrison-Taft Transmission Line : Effects on Elk Security and Hunter Opportunity, Final Report.

    SciTech Connect

    Canfield, Jodie E.

    1988-11-01

    This study was conducted by the Montana Department of Fish, Wildlife and Parks from 1984--1988 to assess the impacts of the Garrison-Taft segment of a 500-kV powerline on elk summer-fall habitat. Construction of the powerline began in 1983, and the powerline was energized in 1985. The Garrison-Taft powerline corridor crossed 251 km of mountainous terrain in western Montana; about 465 km of new roads were constructed to provide permanent access to the powerline towers. The objectives of the study were: (1) to monitor the effectiveness of mitigation measures, including timing restrictions on construction activities and road closures on newly-built access roads, and (2) to determine if opening previously-unroaded elk security habitats to hunters by powerline access roads affected elk habitat use, distribution, use of security areas, or elk harvest. In addition, both the potential for accelerated timber harvest in areas crossed by the powerline that would not have otherwise been logged because of marginal economics and lack of haul roads and the potential effect of powerline flashovers on future prescribed burning of elk winter-ranges were evaluated. 83 refs., 88 figs., 15 tabs.

  9. Design and Construction of a 500 kW CW, 400 MHz Klystron to be used as RF Power Source for LHC/RF Component Tests

    NASA Astrophysics Data System (ADS)

    Frischholz, H.; Fowkes, W. R.; Pearson, C.

    1997-05-01

    A 500 kW CW klystron operating at 400 MHz was jointly developed and constructed by CERN and SLAC for use as a high power source at CERN for testing LHC/RF components such as circulators, RF absorbers and superconducting cavities with their input couplers. The design is a modification of the 353 MHz SLAC PEP-I klystron which resulted in lower engineering costs as well as reduced development and construction time. More than 80% of the original PEP-I tube parts could be incorporated in the LHC test klystron. The physical length between cathode plane and upper pole plate was kept unchanged so that a PEP-I tube focusing frame, available at CERN, could be re-used. With the aid of the klystron simulation codes JPNDISK and CONDOR, the design of the LHC tube was accomplished, which resulted in a tube with noticeably higher efficiency than its predecessor, the PEP-I klystron. The integrated cavities were redesigned by using SUPERFISH and the output coupling circuit, which also required redesigning, was done with the aid of MAFIA. Details of the tube development and test results are presented. Finally the set-up of the LHC/RF test stand and the features of its auxiliary high-power RF equipment, such as circulator and absorber, are described.

  10. Modeling of collision-induced infrared absorption spectra of H2 pairs in the first overtone band at temperatures from 20 to 500 K

    NASA Technical Reports Server (NTRS)

    Zheng, Chunguang; Borysow, Aleksandra

    1995-01-01

    A simple formalism is presented that permits quick computations of the low-resolution, rotovibrational collision-induced absorption (RV CIA) spectra of H2 pairs in the first overtone band of hydrogen, at temperatures from 20 to 500 K. These spectra account for the free-free transitions. The sharp dimer features, originating from the bound-free, free-bound, and bound-bound transitions are ignored, though their integrated intensities are properly accounted for. The method employs spectral model line- shapes with parameters computed from the three lowest spectral moments. The moments are obtained from first principles expressed as analytical functions of temperature. Except for the sharp dimer features, which are absent in this model, the computed spectra reproduce closely the results of exact quantum mechanical lineshape computations. Comparisons of the computed spectra with existing experimental data also show good agreement. The work interest for the modeling of the atmospheres of the outer planets in the near-infrared region of the spectrum. The user-friendly Fortran program developed here is available on request from the authors.

  11. Measuring ~10 T B-Fields Using Zeeman Splitting of Sodium Emission Lines on a 500 kA Pulsed Power Machine

    NASA Astrophysics Data System (ADS)

    Banasek, Jacob; Engelbrecht, Joseph; Hammer, David; Pikuz, Sergei; Shelkovenko, Tatiana

    2015-11-01

    Following earlier work by M. Gomez et al., we have shown that Zeeman splitting of the Sodium (Na) D-lines at 5890 Å and 5896 Å can be used to measure the magnetic field (B-field) produced in high current pulsed power experiments. In the present experiments, we have measured the B-field next to a return current post during hybrid X-pinch experiments near peak current. These measurements were performed at 500 kA current on the XP machine at Cornell University using a 150 ns current rise time. Na was added to the system by applying a few drops of a NaCl solution onto the inner surface of one of two 4 mm radius return current posts, located about 4 cm away from the hybrid X-pinch. The Na is desorbed from the return current post by radiation from the hybrid x-pinch, enabling observation of the Na vapor's spectral lines. Measurements have shown a B-field of 10-15 T near the return current post, which is consistent with the calculated B-field. Future experiments will explore applying this approach to regions of higher B-field in higher current machines. This research is supported by the NNSA Stewardship Sciences Academic Programs under DOE Cooperative Agreement DE-NA0001836.

  12. The Affymetrix DMET Plus Platform Reveals Unique Distribution of ADME-Related Variants in Ethnic Arabs

    PubMed Central

    Wakil, Salma M.; Nguyen, Cao; Muiya, Nzioka P.; Andres, Editha; Lykowska-Tarnowska, Agnieszka; Baz, Batoul; Meyer, Brian F.; Morahan, Grant

    2015-01-01

    Background. The Affymetrix Drug Metabolizing Enzymes and Transporters (DMET) Plus Premier Pack has been designed to genotype 1936 gene variants thought to be essential for screening patients in personalized drug therapy. These variants include the cytochrome P450s (CYP450s), the key metabolizing enzymes, many other enzymes involved in phase I and phase II pharmacokinetic reactions, and signaling mediators associated with variability in clinical response to numerous drugs not only among individuals, but also between ethnic populations. Materials and Methods. We genotyped 600 Saudi individuals for 1936 variants on the DMET platform to evaluate their clinical potential in personalized medicine in ethnic Arabs. Results. Approximately 49% each of the 437 CYP450 variants, 56% of the 581 transporters, 56% of 419 transferases, 48% of the 104 dehydrogenases, and 58% of the remaining 390 variants were detected. Several variants, such as rs3740071, rs6193, rs258751, rs6199, rs11568421, and rs8187797, exhibited significantly either higher or lower minor allele frequencies (MAFs) than those in other ethnic groups. Discussion. The present study revealed some unique distribution trends for several variants in Arabs, which displayed partly inverse allelic prevalence compared to other ethnic populations. The results point therefore to the need to verify and ascertain the prevalence of a variant as a prerequisite for engaging it in clinical routine screening in personalized medicine in any given population. PMID:25802476

  13. Calibration of miniature medical ultrasonic hydrophones for frequencies in the range 100 to 500 kHz using an ultrasonically absorbing waveguide.

    PubMed

    Rajagopal, Srinath; Zeqiri, Bajram; Gélat, Pierre N

    2014-05-01

    Enhancements to the existing primary standard optical interferometer and narrowband tone-burst comparison calibration methods for miniature medical ultrasonic hydrophones of the membrane type over the frequency range 100 to 500 kHz are described. Improvements were realized through application of an ultrasonically absorbing waveguide made of a low-frequency-absorbing tile used in sonar applications which narrows the spatial extent of the broad acoustic field. The waveguide was employed in conjunction with a sonar multilayered polyvinylidene difluoride (PVDF) hydrophone used as a transmitting transducer covering a frequency range of 100 kHz to 1 MHz. The acoustic field emanating from the ultrasonically absorbing waveguide reduced the significance of diffracted acoustic waves from the membrane hydrophone ring and the consequent interference of this wave with the direct acoustic wave received by the active element of the hydrophone during calibration. Four membrane hydrophone make/ models with ring sizes (defined as the inner diameter of the annular mounting ring of the hydrophone) in the range 50 to 100 mm were employed along with a needle hydrophone. A reference membrane hydrophone, calibrated using the NPL primary standard optical interferometer in combination with the ultrasonically absorbing waveguide, was subsequently used to calibrate the other four hydrophones by comparison, again using the ultrasonically absorbing waveguide. In comparison to existing methods, the use of the ultrasonically absorbing waveguide enabled the low-frequency calibration limit of a membrane hydrophone with a ring diameter of 50 mm to be reduced from 400 kHz to 200 kHz. PMID:24803021

  14. Ploidy status and copy number aberrations in primary glioblastomas defined by integrated analysis of allelic ratios, signal ratios and loss of heterozygosity using 500K SNP Mapping Arrays

    PubMed Central

    Gardina, Paul J; Lo, Ken C; Lee, Walter; Cowell, John K; Turpaz, Yaron

    2008-01-01

    Background Genomic hybridization platforms, including BAC-CGH and genotyping arrays, have been used to estimate chromosome copy number (CN) in tumor samples by detecting the relative strength of genomic signal. The methods rely on the assumption that the predominant chromosomal background of the samples is diploid, an assumption that is frequently incorrect for tumor samples. In addition to generally greater resolution, an advantage of genotyping arrays over CGH arrays is the ability to detect signals from individual alleles, allowing estimation of loss-of-heterozygosity (LOH) and allelic ratios to enhance the interpretation of copy number alterations. Copy number events associated with LOH potentially have the same genetic consequences as deletions. Results We have utilized allelic ratios to detect patterns that are indicative of higher ploidy levels. An integrated analysis using allelic ratios, total signal and LOH indicates that many or most of the chromosomes from 24 glioblastoma tumors are in fact aneuploid. Some putative whole-chromosome losses actually represent trisomy, and many apparent sub-chromosomal losses are in fact relative losses against a triploid or tetraploid background. Conclusion These results suggest a re-interpretation of previous findings based only on total signal ratios. One interesting observation is that many single or multiple-copy deletions occur at common putative tumor suppressor sites subsequent to chromosomal duplication; these losses do not necessarily result in LOH, but nonetheless occur in conspicuous patterns. The 500 K Mapping array was also capable of detecting many sub-mega base losses and gains that were overlooked by CGH-BAC arrays, and was superior to CGH-BAC arrays in resolving regions of complex CN variation. PMID:18928532

  15. Transcript Profiling of Common Bean (Phaseolus vulgaris) Using the GeneChip Soybean Genome Array: Optimizing Analysis by Masking Biased Probes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Common bean (Phaseolus vulgaris) and soybean (Glycine max) both belong to the Phaseoleae tribe and share significant coding sequence homology. To evaluate the utility of the soybean GeneChip for transcript profiling of common bean, we hybridized cRNAs purified from nodule, leaf, and root of common b...

  16. The Properties of the 500 K Dwarf UGPS J072227.51-054031.2 and a Study of the Far-red Flux of Cold Brown Dwarfs

    NASA Astrophysics Data System (ADS)

    Leggett, S. K.; Saumon, D.; Marley, M. S.; Lodders, K.; Canty, J.; Lucas, P.; Smart, R. L.; Tinney, C. G.; Homeier, D.; Allard, F.; Burningham, Ben; Day-Jones, A.; Fegley, B.; Ishii, Miki; Jones, H. R. A.; Marocco, F.; Pinfield, D. J.; Tamura, M.

    2012-04-01

    We present i and z photometry for 25 T dwarfs and 1 L dwarf. Combined with published photometry, the data show that the i - z, z - Y, and z - J colors of T dwarfs are very red, and continue to increase through to the late-type T dwarfs, with a hint of a saturation for the latest types with T eff ≈ 600 K. We present new 0.7-1.0 μm and 2.8-4.2 μm spectra for the very late type T dwarf UGPS J072227.51-054031.2, as well as improved astrometry for this dwarf. Examination of the spectral energy distribution using new and published data, with Saumon & Marley models, shows that the dwarf has T eff = 505 ± 10 K, a mass of 3-11 M Jupiter, and an age between 60 Myr and 1 Gyr. This young age is consistent with the thin disk kinematics of the dwarf. The mass range overlaps with that usually considered to be planetary, despite this being an unbound object discovered in the field near the Sun. This apparently young rapid rotator is also undergoing vigorous atmospheric mixing, as determined by the IRAC and WISE 4.5 μm photometry and the Saumon & Marley models. The optical spectrum for this 500 K object shows clearly detected lines of the neutral alkalis Cs and Rb, which are emitted from deep atmospheric layers with temperatures of 900-1200 K. Based on observations obtained at the Gemini Observatory, which is operated by the Association of Universities for Research in Astronomy, Inc., under a cooperative agreement with the NSF on behalf of the Gemini partnership: the National Science Foundation (United States), the Science and Technology Facilities Council (United Kingdom), the National Research Council (Canada), CONICYT (Chile), the Australian Research Council (Australia), Ministério da Ciência e Tecnologia (Brazil), and Ministerio de Ciencia, Tecnología e Innovación Productiva (Argentina); also based on data collected at Subaru Telescope, which is operated by the National Astronomical Observatory of Japan; and also based on observations made at the UK Infrared Telescope

  17. Proposed amendment for Presidential Permit PP-63 and associated modifications to 500 kV international transmission line, Forbes, Minnesota to Manitoba, Canada Northern States Power Company. Final Environmental Assessment

    SciTech Connect

    Not Available

    1992-02-01

    Northern States Power Company, (NSP), a Minnesota investor owned utility has applied to the Office of Fossil Energy, United States Department of Energy, to amend Presidential Permit PP-63 to allow for alterations to the 500 kV transmission line and as sedated facilities currently regulated by this permit. The alterations proposed for the 500 kV line owned by NSP are part of a long term effort sponsored by NSP to upgrade the existing NSP transmission system to allow for increased exchange of electricity with the Manitoba Hydro-Electric Board. Presidential Permit PP-63 authorized NSP to construct, connect, operate and maintain a 500 kV line at the United States/Canadian border approximately seven-and-a-half miles west of Warroad in Roseau County, Minnesota. This line connects with a 500 kV line owned and operated by the Manitoba Hydro-Electric Board (MHEB), which extends from Dorsey, Manitoba, Canada to the United States/Canadian border. NSP proposes to increase the electricity transfer capability of this transmission facility by constructing a new 80-acre substation on the existing 500 kV line in Roseau County, Minnesota, and upgrading the existing substation at Forbes, Minnesota. The proposed Roseau substation would contain two 41.5 ohm series capacitor banks. In addition, static VAR compensators are to be installed at the existing Forbes Substation. Approximately 5 acres would be added to the 30-acre Forbes site to house the additional equipment. No new lines would enter or exit the facility. NSP proposes to place the new Roseau Substation in service in May 1993 and to complete the upgrading of the Forbes Substation in March 1994. The primary, initial purpose of these modifications is to enable NSP to import 400 megawatts of electric power from MHEB during the summer months to meet peak electrical demand in the Minneapolis-St. Paul area. It is expected that this power transfer would begin in 1993.

  18. High Fidelity Copy Number Analysis of Formalin-Fixed and Paraffin-Embedded Tissues Using Affymetrix Cytoscan HD Chip

    PubMed Central

    Yu, Yan P.; Michalopoulos, Amantha; Ding, Ying; Tseng, George; Luo, Jian-Hua

    2014-01-01

    Detection of human genome copy number variation (CNV) is one of the most important analyses in diagnosing human malignancies. Genome CNV detection in formalin-fixed and paraffin-embedded (FFPE) tissues remains challenging due to suboptimal DNA quality and failure to use appropriate baseline controls for such tissues. Here, we report a modified method in analyzing CNV in FFPE tissues using microarray with Affymetrix Cytoscan HD chips. Gel purification was applied to select DNA with good quality and data of fresh frozen and FFPE tissues from healthy individuals were included as baseline controls in our data analysis. Our analysis showed a 91% overlap between CNV detection by microarray with FFPE tissues and chromosomal abnormality detection by karyotyping with fresh tissues on 8 cases of lymphoma samples. The CNV overlap between matched frozen and FFPE tissues reached 93.8%. When the analyses were restricted to regions containing genes, 87.1% concordance between FFPE and fresh frozen tissues was found. The analysis was further validated by Fluorescence In Situ Hybridization on these samples using probes specific for BRAF and CITED2. The results suggested that the modified method using Affymetrix Cytoscan HD chip gave rise to a significant improvement over most of the previous methods in terms of accuracy in detecting CNV in FFPE tissues. This FFPE microarray methodology may hold promise for broad application of CNV analysis on clinical samples. PMID:24699316

  19. Gene Expression in the Rat Brain during Sleep Deprivation and Recovery Sleep: An Affymetrix GeneChip® Study

    PubMed Central

    Terao, A.; Wisor, J.P.; Peyron, C.; Apte-Deshpande, A.; Wurts, S.W.; Edgar, D.M.; Kilduff, T.S.

    2016-01-01

    Previous studies have demonstrated that macromolecular synthesis in the brain is modulated in association with the occurrence of sleep and wakefulness. Similarly, the spectral composition of electroencephalographic activity that occurs during sleep is dependent on the duration of prior wakefulness. Since this homeostatic relationship between wake and sleep is highly conserved across mammalian species, genes that are truly involved in the electroencephalographic response to sleep deprivation (SD) might be expected to be conserved across mammalian species. Therefore, in the rat cerebral cortex, we have studied the effects of SD on the expression of immediate early gene (IEG) and heat shock protein (HSP) mRNAs previously shown to be upregulated in the mouse brain in SD and in recovery sleep (RS) after SD. We find that the molecular response to SD and RS in the brain is highly conserved between these two mammalian species, at least in terms of expression of IEG and HSP family members. Using Affymetrix Neurobiology U34 GeneChips®, we also screened the rat cerebral cortex, basal forebrain, and hypothalamus for other genes whose expression may be modulated by SD or RS. We find that the response of the basal forebrain to SD is more similar to that of the cerebral cortex than to the hypothalamus. Together, these results suggest that sleep-dependent changes in gene expression in the cerebral cortex are similar across rodent species and therefore may underlie sleep history-dependent changes in sleep electroencephalographic activity. PMID:16257491

  20. MMBGX: a method for estimating expression at the isoform level and detecting differential splicing using whole-transcript Affymetrix arrays

    PubMed Central

    Turro, Ernest; Lewin, Alex; Rose, Anna; Dallman, Margaret J.; Richardson, Sylvia

    2010-01-01

    Affymetrix has recently developed whole-transcript GeneChips—‘Gene’ and ‘Exon’ arrays—which interrogate exons along the length of each gene. Although each probe on these arrays is intended to hybridize perfectly to only one transcriptional target, many probes match multiple transcripts located in different parts of the genome or alternative isoforms of the same gene. Existing statistical methods for estimating expression do not take this into account and are thus prone to producing inflated estimates. We propose a method, Multi-Mapping Bayesian Gene eXpression (MMBGX), which disaggregates the signal at ‘multi-match’ probes. When applied to Gene arrays, MMBGX removes the upward bias of gene-level expression estimates. When applied to Exon arrays, it can further disaggregate the signal between alternative transcripts of the same gene, providing expression estimates of individual splice variants. We demonstrate the performance of MMBGX on simulated data and a tissue mixture data set. We then show that MMBGX can estimate the expression of alternative isoforms within one experimental condition, confirming our results by RT-PCR. Finally, we show that our method for detecting differential splicing has a lower error rate than standard exon-level approaches on a previously validated colon cancer data set. PMID:19854940

  1. Proposed amendment to presidential permit PP-63 and associated modifications to 500 kV international transmission line, Forbes, Minnesota to Manitoba, Canada. Addendum to the final environmental assessment

    SciTech Connect

    Not Available

    1992-10-01

    This Addendum to the Final Environmental Assessment for the Proposed Amendment to Presidential Permit PP-63 and Associated Modifications to 500 kV International Transmission Line: Forbes, Minnesota to Manitoba, Canada (DOE/EA-587) addresses Northern States Power Company`s (NSP) proposed expansion of the Forbes Substation. The applicant has requested that the expansion take place on the west side of the substation, within the existing property line, instead of on the north side as originally proposed. All of the proposed construction would take place on property already owned by NSP. DOE has reviewed the environmental impacts associated with this minor modification and has determined that the conclusions reached in the environmental assessment and Finding of No Significant Impact prepared in connection with NSP`s original amendment request remain valid.

  2. Proposed Amendment to Presidential Permit PP-63 and Associated Modifications to 500-kV International Transmission Line: Forbes, Minnesota to Manitoba, Canada, Northern States Power Company. Addendum to the final Environmental Assessment

    SciTech Connect

    Not Available

    1992-10-01

    This Addendum to the Final Environmental Assessment for the Proposed Amendment to Presidential Permit PP-63 and Associated Modifications to 500 kV International Transmission Line: Forbes, Minnesota to Manitoba, Canada (DOE/EA-587) addresses Northern States Power Company`s (NSP) proposed expansion of the Forbes Substation. The applicant has requested that the expansion take place on the west side of the substation, within the existing property line, instead of on the north side as originally proposed. All of the proposed construction would take place on property already owned by NSP. DOE has reviewed the environmental impacts associated with this minor modification and has determined that the conclusions reached in the environmental assessment and Finding of No Significant Impact prepared in connection with NSP`s original amendment request remain valid.

  3. Imputing amino acid polymorphisms in human leukocyte antigens.

    PubMed

    Jia, Xiaoming; Han, Buhm; Onengut-Gumuscu, Suna; Chen, Wei-Min; Concannon, Patrick J; Rich, Stephen S; Raychaudhuri, Soumya; de Bakker, Paul I W

    2013-01-01

    DNA sequence variation within human leukocyte antigen (HLA) genes mediate susceptibility to a wide range of human diseases. The complex genetic structure of the major histocompatibility complex (MHC) makes it difficult, however, to collect genotyping data in large cohorts. Long-range linkage disequilibrium between HLA loci and SNP markers across the major histocompatibility complex (MHC) region offers an alternative approach through imputation to interrogate HLA variation in existing GWAS data sets. Here we describe a computational strategy, SNP2HLA, to impute classical alleles and amino acid polymorphisms at class I (HLA-A, -B, -C) and class II (-DPA1, -DPB1, -DQA1, -DQB1, and -DRB1) loci. To characterize performance of SNP2HLA, we constructed two European ancestry reference panels, one based on data collected in HapMap-CEPH pedigrees (90 individuals) and another based on data collected by the Type 1 Diabetes Genetics Consortium (T1DGC, 5,225 individuals). We imputed HLA alleles in an independent data set from the British 1958 Birth Cohort (N = 918) with gold standard four-digit HLA types and SNPs genotyped using the Affymetrix GeneChip 500 K and Illumina Immunochip microarrays. We demonstrate that the sample size of the reference panel, rather than SNP density of the genotyping platform, is critical to achieve high imputation accuracy. Using the larger T1DGC reference panel, the average accuracy at four-digit resolution is 94.7% using the low-density Affymetrix GeneChip 500 K, and 96.7% using the high-density Illumina Immunochip. For amino acid polymorphisms within HLA genes, we achieve 98.6% and 99.3% accuracy using the Affymetrix GeneChip 500 K and Illumina Immunochip, respectively. Finally, we demonstrate how imputation and association testing at amino acid resolution can facilitate fine-mapping of primary MHC association signals, giving a specific example from type 1 diabetes. PMID:23762245

  4. Analysis of the Metabolic Pathways Affected by Poly(γ-glutamic Acid) in Arabidopsis thaliana Based on GeneChip Microarray.

    PubMed

    Xu, Zongqi; Lei, Peng; Feng, Xiaohai; Li, Sha; Xu, Hong

    2016-08-17

    Plant growth is promoted by poly(γ-glutamic acid) (γ-PGA). However, the molecular mechanism underlying such promotion is not yet well understood. Therefore, we used GeneChip microarrays to explore the effects of γ-PGA on gene transcription in Arabidopsis thaliana. Our results revealed 299 genes significantly regulated by γ-PGA. These differently expressed genes participate mainly in metabolic and cellular processes and in stimuli responses. The metabolic pathways linked to these differently expressed genes were also investigated. A total of 64 of the 299 differently expressed genes were shown to be directly involved in 24 pathways such as brassinosteroid biosynthesis, α-linolenic acid metabolism, phenylpropanoid biosynthesis, and nitrogen metabolism, all of which were influenced by γ-PGA. The analysis demonstrated that γ-PGA promoted nitrogen assimilation and biosynthesis of brassinosteroids, jasmonic acid, and lignins, providing a better explanation for why γ-PGA promotes growth and enhances stress tolerance in plants. PMID:27465513

  5. The efficacy of detecting variants with small effects on the Affymetrix 6.0 platform using pooled DNA

    PubMed Central

    Chiang, Charleston W. K.; Gajdos, Zofia K. Z.; Butler, Johannah L.; Hackett, Rachel; Guiducci, Candace; Nguyen, Thutrang T.; Wilks, Rainford; Forrester, Terrence; Henderson, Katherine D.; Le Marchand, Loic; Henderson, Brian E.; Haiman, Christopher A.; Cooper, Richard S.; Lyon, Helen N.; Zhu, Xiaofeng; McKenzie, Colin A.; Palmer, Mark R.; Hirschhorn, Joel N.

    2012-01-01

    Genome-wide genotyping of a cohort using pools rather than individual samples has long been proposed as a cost-saving alternative for performing genome-wide association (GWA) studies. However, successful disease gene mapping using pooled genotyping has thus far been limited to detecting common variants with large effect sizes, which tend not to exist for many complex common diseases or traits. Therefore, for DNA pooling to be a viable strategy for conducting GWA studies, it is important to determine whether commonly used genome-wide SNP array platforms such as the Affymetrix 6.0 array can reliably detect common variants of small effect sizes using pooled DNA. Taking obesity and age at menarche as examples of human complex traits, we assessed the feasibility of genome-wide genotyping of pooled DNA as a single-stage design for phenotype association. By individually genotyping the top associations identified by pooling, we obtained a 14- to 16-fold enrichment of SNPs nominally associated with the phenotype, but we likely missed the top true associations. In addition, we assessed whether genotyping pooled DNA can serve as an inexpensive screen as the second stage of a multi-stage design with a large number of samples by comparing the most cost-effective 3-stage designs with 80% power to detect common variants with genotypic relative risk of 1.1, with and without pooling. Given the current state of the specific technology we employed and the associated genotyping costs, we showed through simulation that a design involving pooling would be 1.07 times more expensive than a design without pooling. Thus, while a significant amount of information exists within the data from pooled DNA, our analysis does not support genotyping pooled DNA as a means to efficiently identify common variants contributing small effects to phenotypes of interest. While our conclusions were based on the specific technology and study design we employed, the approach presented here will be useful for

  6. Automated setup for magnetic hysteresis characterization based on a voltage controlled current source with 500 kHz full power bandwidth and 10 A peak-to-peak current

    SciTech Connect

    Calabrese, G.; Capineri, L.; Granato, M.; Frattini, G.

    2015-04-15

    This paper describes the design of a system for the characterization of magnetic hysteresis behavior in soft ferrite magnetic cores. The proposed setup can test magnetic materials exciting them with controlled arbitrary magnetic field waveforms, including the capability of providing a DC bias, in a frequency bandwidth up to 500 kHz, with voltages up to 32 V peak-to-peak, and currents up to 10 A peak-to-peak. In order to have an accurate control of the magnetic field waveform, the system is based on a voltage controlled current source. The electronic design is described focusing on closed loop feedback stabilization and passive components choice. The system has real-time hysteretic loop acquisition and visualization. The comparisons between measured hysteresis loops of sample magnetic materials and datasheet available ones are shown. Results showing frequency and thermal behavior of the hysteresis of a test sample prove the system capabilities. Moreover, the B-H loops obtained with a multiple waveforms excitation signal, including DC bias, are reported. The proposal is a low-cost and replicable solution for hysteresis characterization of magnetic materials used in power electronics.

  7. Kinetics following addition of sulfur fluorides to a weakly ionized plasma from 300 to 500 K: rate constants and product determinations for ion-ion mutual neutralization and thermal electron attachment to SF5, SF3, and SF2.

    PubMed

    Shuman, Nicholas S; Miller, Thomas M; Hazari, Nilay; Luzik, Eddie D; Viggiano, A A

    2010-12-21

    Rate constants for several processes including electron attachment to SF(2), SF(3), and SF(5) and individual product channels of ion-ion mutual neutralization between SF(6)(-), SF(5)(-), and SF(4)(-) with Ar(+) were determined by variable electron and neutral density attachment mass spectrometry. The experiments were conducted with a series of related neutral precursors (SF(6), SF(4), SF(5)Cl, SF(5)C(6)H(5), and SF(3)C(6)F(5)) over a temperature range of 300-500 K. Mutual neutralization rate constants for SF(6)(-), SF(5)(-), and SF(4)(-) with Ar(+) are reported with uncertainties of 10-25% and show temperature dependencies in agreement with the theoretical value of T(-0.5). Product branching in the mutual neutralizations is temperature independent and dependent on the electron binding energy of the anion. A larger fraction of product neutrals from the SF(6)(-) mutual neutralization (0.9 ± 0.1) are dissociated than in the SF(5)(-) mutual neutralization (0.65 ± 0.2), with the SF(4)(-) (0.7 ± 0.3) likely lying in between. Electron attachment to SF(5) (k = 2.0 × 10(-8) ±(1)(2) cm(3) s(-1) at 300 K) and SF(3) (4 ± 3 × 10(-9) cm(3) s(-1) at 300 K) show little temperature dependence. Rate constants of electron attachment to closed-shell SF(n) species decrease as the complexity of the neutral decreases. PMID:21186868

  8. A model of binding on DNA microarrays: understanding the combined effect of probe synthesis failure, cross-hybridization, DNA fragmentation and other experimental details of affymetrix arrays

    PubMed Central

    2012-01-01

    Background DNA microarrays are used both for research and for diagnostics. In research, Affymetrix arrays are commonly used for genome wide association studies, resequencing, and for gene expression analysis. These arrays provide large amounts of data. This data is analyzed using statistical methods that quite often discard a large portion of the information. Most of the information that is lost comes from probes that systematically fail across chips and from batch effects. The aim of this study was to develop a comprehensive model for hybridization that predicts probe intensities for Affymetrix arrays and that could provide a basis for improved microarray analysis and probe development. The first part of the model calculates probe binding affinities to all the possible targets in the hybridization solution using the Langmuir isotherm. In the second part of the model we integrate details that are specific to each experiment and contribute to the differences between hybridization in solution and on the microarray. These details include fragmentation, wash stringency, temperature, salt concentration, and scanner settings. Furthermore, the model fits probe synthesis efficiency and target concentration parameters directly to the data. All the parameters used in the model have a well-established physical origin. Results For the 302 chips that were analyzed the mean correlation between expected and observed probe intensities was 0.701 with a range of 0.88 to 0.55. All available chips were included in the analysis regardless of the data quality. Our results show that batch effects arise from differences in probe synthesis, scanner settings, wash strength, and target fragmentation. We also show that probe synthesis efficiencies for different nucleotides are not uniform. Conclusions To date this is the most complete model for binding on microarrays. This is the first model that includes both probe synthesis efficiency and hybridization kinetics/cross-hybridization. These

  9. GeneChip expression profiling reveals the alterations of energy metabolism related genes in osteocytes under large gradient high magnetic fields.

    PubMed

    Wang, Yang; Chen, Zhi-Hao; Yin, Chun; Ma, Jian-Hua; Li, Di-Jie; Zhao, Fan; Sun, Yu-Long; Hu, Li-Fang; Shang, Peng; Qian, Ai-Rong

    2015-01-01

    The diamagnetic levitation as a novel ground-based model for simulating a reduced gravity environment has recently been applied in life science research. In this study a specially designed superconducting magnet with a large gradient high magnetic field (LG-HMF), which can provide three apparent gravity levels (μ-g, 1-g, and 2-g), was used to simulate a space-like gravity environment. Osteocyte, as the most important mechanosensor in bone, takes a pivotal position in mediating the mechano-induced bone remodeling. In this study, the effects of LG-HMF on gene expression profiling of osteocyte-like cell line MLO-Y4 were investigated by Affymetrix DNA microarray. LG-HMF affected osteocyte gene expression profiling. Differentially expressed genes (DEGs) and data mining were further analyzed by using bioinfomatic tools, such as DAVID, iReport. 12 energy metabolism related genes (PFKL, AK4, ALDOC, COX7A1, STC1, ADM, CA9, CA12, P4HA1, APLN, GPR35 and GPR84) were further confirmed by real-time PCR. An integrated gene interaction network of 12 DEGs was constructed. Bio-data mining showed that genes involved in glucose metabolic process and apoptosis changed notablly. Our results demostrated that LG-HMF affected the expression of energy metabolism related genes in osteocyte. The identification of sensitive genes to special environments may provide some potential targets for preventing and treating bone loss or osteoporosis. PMID:25635858

  10. GeneChip Expression Profiling Reveals the Alterations of Energy Metabolism Related Genes in Osteocytes under Large Gradient High Magnetic Fields

    PubMed Central

    Wang, Yang; Chen, Zhi-Hao; Yin, Chun; Ma, Jian-Hua; Li, Di-Jie; Zhao, Fan; Sun, Yu-Long; Hu, Li-Fang; Shang, Peng; Qian, Ai-Rong

    2015-01-01

    The diamagnetic levitation as a novel ground-based model for simulating a reduced gravity environment has recently been applied in life science research. In this study a specially designed superconducting magnet with a large gradient high magnetic field (LG-HMF), which can provide three apparent gravity levels (μ-g, 1-g, and 2-g), was used to simulate a space-like gravity environment. Osteocyte, as the most important mechanosensor in bone, takes a pivotal position in mediating the mechano-induced bone remodeling. In this study, the effects of LG-HMF on gene expression profiling of osteocyte-like cell line MLO-Y4 were investigated by Affymetrix DNA microarray. LG-HMF affected osteocyte gene expression profiling. Differentially expressed genes (DEGs) and data mining were further analyzed by using bioinfomatic tools, such as DAVID, iReport. 12 energy metabolism related genes (PFKL, AK4, ALDOC, COX7A1, STC1, ADM, CA9, CA12, P4HA1, APLN, GPR35 and GPR84) were further confirmed by real-time PCR. An integrated gene interaction network of 12 DEGs was constructed. Bio-data mining showed that genes involved in glucose metabolic process and apoptosis changed notablly. Our results demostrated that LG-HMF affected the expression of energy metabolism related genes in osteocyte. The identification of sensitive genes to special environments may provide some potential targets for preventing and treating bone loss or osteoporosis. PMID:25635858

  11. Characterization of Capsicum annuum Genetic Diversity and Population Structure Based on Parallel Polymorphism Discovery with a 30K Unigene Pepper GeneChip

    PubMed Central

    Hill, Theresa A.; Ashrafi, Hamid; Reyes-Chin-Wo, Sebastian; Yao, JiQiang; Stoffel, Kevin; Truco, Maria-Jose; Kozik, Alexander; Michelmore, Richard W.; Van Deynze, Allen

    2013-01-01

    The widely cultivated pepper, Capsicum spp., important as a vegetable and spice crop world-wide, is one of the most diverse crops. To enhance breeding programs, a detailed characterization of Capsicum diversity including morphological, geographical and molecular data is required. Currently, molecular data characterizing Capsicum genetic diversity is limited. The development and application of high-throughput genome-wide markers in Capsicum will facilitate more detailed molecular characterization of germplasm collections, genetic relationships, and the generation of ultra-high density maps. We have developed the Pepper GeneChip® array from Affymetrix for polymorphism detection and expression analysis in Capsicum. Probes on the array were designed from 30,815 unigenes assembled from expressed sequence tags (ESTs). Our array design provides a maximum redundancy of 13 probes per base pair position allowing integration of multiple hybridization values per position to detect single position polymorphism (SPP). Hybridization of genomic DNA from 40 diverse C. annuum lines, used in breeding and research programs, and a representative from three additional cultivated species (C. frutescens, C. chinense and C. pubescens) detected 33,401 SPP markers within 13,323 unigenes. Among the C. annuum lines, 6,426 SPPs covering 3,818 unigenes were identified. An estimated three-fold reduction in diversity was detected in non-pungent compared with pungent lines, however, we were able to detect 251 highly informative markers across these C. annuum lines. In addition, an 8.7 cM region without polymorphism was detected around Pun1 in non-pungent C. annuum. An analysis of genetic relatedness and diversity using the software Structure revealed clustering of the germplasm which was confirmed with statistical support by principle components analysis (PCA) and phylogenetic analysis. This research demonstrates the effectiveness of parallel high-throughput discovery and application of genome

  12. Characterization of Capsicum annuum genetic diversity and population structure based on parallel polymorphism discovery with a 30K unigene Pepper GeneChip.

    PubMed

    Hill, Theresa A; Ashrafi, Hamid; Reyes-Chin-Wo, Sebastian; Yao, JiQiang; Stoffel, Kevin; Truco, Maria-Jose; Kozik, Alexander; Michelmore, Richard W; Van Deynze, Allen

    2013-01-01

    The widely cultivated pepper, Capsicum spp., important as a vegetable and spice crop world-wide, is one of the most diverse crops. To enhance breeding programs, a detailed characterization of Capsicum diversity including morphological, geographical and molecular data is required. Currently, molecular data characterizing Capsicum genetic diversity is limited. The development and application of high-throughput genome-wide markers in Capsicum will facilitate more detailed molecular characterization of germplasm collections, genetic relationships, and the generation of ultra-high density maps. We have developed the Pepper GeneChip® array from Affymetrix for polymorphism detection and expression analysis in Capsicum. Probes on the array were designed from 30,815 unigenes assembled from expressed sequence tags (ESTs). Our array design provides a maximum redundancy of 13 probes per base pair position allowing integration of multiple hybridization values per position to detect single position polymorphism (SPP). Hybridization of genomic DNA from 40 diverse C. annuum lines, used in breeding and research programs, and a representative from three additional cultivated species (C. frutescens, C. chinense and C. pubescens) detected 33,401 SPP markers within 13,323 unigenes. Among the C. annuum lines, 6,426 SPPs covering 3,818 unigenes were identified. An estimated three-fold reduction in diversity was detected in non-pungent compared with pungent lines, however, we were able to detect 251 highly informative markers across these C. annuum lines. In addition, an 8.7 cM region without polymorphism was detected around Pun1 in non-pungent C. annuum. An analysis of genetic relatedness and diversity using the software Structure revealed clustering of the germplasm which was confirmed with statistical support by principle components analysis (PCA) and phylogenetic analysis. This research demonstrates the effectiveness of parallel high-throughput discovery and application of genome

  13. A Single-Array-Based Method for Detecting Copy Number Variants Using Affymetrix High Density SNP Arrays and its Application to Breast Cancer

    PubMed Central

    Li, Ming; Wen, Yalu; Fu, Wenjiang

    2014-01-01

    Cumulative evidence has shown that structural variations, due to insertions, deletions, and inversions of DNA, may contribute considerably to the development of complex human diseases, such as breast cancer. High-throughput genotyping technologies, such as Affymetrix high density single-nucleotide polymorphism (SNP) arrays, have produced large amounts of genetic data for genome-wide SNP genotype calling and copy number estimation. Meanwhile, there is a great need for accurate and efficient statistical methods to detect copy number variants. In this article, we introduce a hidden-Markov-model (HMM)-based method, referred to as the PICR-CNV, for copy number inference. The proposed method first estimates copy number abundance for each single SNP on a single array based on the raw fluorescence values, and then standardizes the estimated copy number abundance to achieve equal footing among multiple arrays. This method requires no between-array normalization, and thus, maintains data integrity and independence of samples among individual subjects. In addition to our efforts to apply new statistical technology to raw fluorescence values, the HMM has been applied to the standardized copy number abundance in order to reduce experimental noise. Through simulations, we show our refined method is able to infer copy number variants accurately. Application of the proposed method to a breast cancer dataset helps to identify genomic regions significantly associated with the disease. PMID:26279618

  14. Evaluating the Influence of Quality Control Decisions and Software Algorithms on SNP Calling for the Affymetrix 6.0 SNP Array Platform

    PubMed Central

    de Andrade, Mariza; Atkinson, Elizabeth J.; Bamlet, William R.; Matsumoto, Martha E.; Maharjan, Sooraj; Slager, Susan L.; Vachon, Celine M.; Cunningham, Julie M.; Kardia, Sharon L.R.

    2011-01-01

    Objective Our goal was to evaluate the influence of quality control (QC) decisions using two genotype calling algorithms, CRLMM and Birdseed, designed for the Affymetrix SNP Array 6.0. Methods Various QC options were tried using the two algorithms and comparisons were made on subject and call rate and on association results using two data sets. Results For Birdseed, we recommend using the contrast QC instead of QC call rate for sample QC. For CRLMM, we recommend using the signal-to-noise rate ≥4 for sample QC and a posterior probability of 90% for genotype accuracy. For both algorithms, we recommend calling the genotype separately for each plate, and dropping SNPs with a lower call rate (<95%) before evaluating samples with lower call rates. To investigate whether the genotype calls from the two algorithms impacted the genome-wide association results, we performed association analysis using data from the GENOA cohort; we observed that the number of significant SNPs were similar using either CRLMM or Birdseed. Conclusions Using our suggested workflow both algorithms performed similarly; however, fewer samples were removed and CRLMM took half the time to run our 854 study samples (4.2 h) compared to Birdseed (8.4 h). PMID:21734406

  15. Clover Biotechnology Research at FAPRU

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Randy Dinkins (USDA-ARS-FAPRU) is conducting research to determine the utility of using the Medicago Affymetrix Genechip for use with red clover (Trifolium pretense). The Medicago Affymetrix Genechip contains approximately 51,000 probe sets that are derived from Medicago truncatula, 1,800 from Medi...

  16. The 100-500 kWe NEP systems

    NASA Technical Reports Server (NTRS)

    George, Jeffrey A.

    1993-01-01

    Systems technology for nuclear electric propulsion (NEP) vehicles is discussed. The following topics are discussed: the SP-100 reactor; dynamic power conversion; heat rejection; and krypton ion thrusters. The discussion is presented in vugraph form.

  17. Kinetics following addition of sulfur fluorides to a weakly ionized plasma from 300 to 500 K: Rate constants and product determinations for ion-ion mutual neutralization and thermal electron attachment to SF{sub 5}, SF{sub 3}, and SF{sub 2}

    SciTech Connect

    Shuman, Nicholas S.; Miller, Thomas M.; Viggiano, A. A.; Hazari, Nilay; Luzik, Eddie D. Jr.

    2010-12-21

    Rate constants for several processes including electron attachment to SF{sub 2}, SF{sub 3}, and SF{sub 5} and individual product channels of ion-ion mutual neutralization between SF{sub 6}{sup -}, SF{sub 5}{sup -}, and SF{sub 4}{sup -} with Ar{sup +} were determined by variable electron and neutral density attachment mass spectrometry. The experiments were conducted with a series of related neutral precursors (SF{sub 6}, SF{sub 4}, SF{sub 5}Cl, SF{sub 5}C{sub 6}H{sub 5}, and SF{sub 3}C{sub 6}F{sub 5}) over a temperature range of 300-500 K. Mutual neutralization rate constants for SF{sub 6}{sup -}, SF{sub 5}{sup -}, and SF{sub 4}{sup -} with Ar{sup +} are reported with uncertainties of 10-25% and show temperature dependencies in agreement with the theoretical value of T{sup -0.5}. Product branching in the mutual neutralizations is temperature independent and dependent on the electron binding energy of the anion. A larger fraction of product neutrals from the SF{sub 6}{sup -} mutual neutralization (0.9 {+-}0.1) are dissociated than in the SF{sub 5}{sup -} mutual neutralization (0.65 {+-} 0.2), with the SF{sub 4}{sup -} (0.7 {+-} 0.3) likely lying in between. Electron attachment to SF{sub 5} (k= 2.0 x 10{sup -8} {+-}{sub 1}{sup 2} cm{sup 3} s{sup -1} at 300 K) and SF{sub 3} (4 {+-} 3 x 10{sup -9} cm{sup 3} s{sup -1} at 300 K) show little temperature dependence. Rate constants of electron attachment to closed-shell SF{sub n} species decrease as the complexity of the neutral decreases.

  18. Arabidopsis transcriptional responses differentiating closely related chemicals (herbicides) and cross-species extrapolation to Brassica

    EPA Science Inventory

    Using whole genome Affymetrix ATH1 GeneChips we characterized the transcriptional response of Arabidopsis thaliana Columbia 24 hours after treatment with five different herbicides. Four of them (chloransulam, imazapyr, primisulfuron, sulfometuron) inhibit acetolactate synthase (A...

  19. MOLCARE development towards MCFC commercial power plants based on 500 kW standard modules

    SciTech Connect

    Torazza, A.; Dufour, A.; Perfumo, A.; Ricerche, A.; Gegundez, J.; Sanson, F.; Moreno, A.

    1998-07-01

    Fuel cells technologies for stationary applications are expected to play a remarkable role in the field of next decade energy production systems ranging from some hundreds kW to some MW. The interest in using fuel cells to produce electric energy comes from the advantages that fuel cells offer in terms of high efficiency, good behavior at base and partial load, very low emissions, modularity (easy adjustment of plant capacity to power-demand increase), and reduced time to be spent for plant erection. At least four types of fuel cells can be considered suitable for stationary applications. With reference to their electrolyte they can be classified as: Polymeric Electrolyte Membrane Fuel Cells (PEMFC), Phosphoric Acid Fuel Cells (PAFC), Molten Carbonate Fuel Cells (MCFC) and Solid Oxide Fuel Cells (SOFC). Each of them works at a temperature level that is depending on the type of electrolyte. From a general point of view all the fuel cell technologies present, at various extents, the above listed advantages. Nevertheless specific features of each fuel cell type suggest to identify a specific field of application for each type of solution, in order to stress the potential advantages of any technology and minimize its possible drawbacks. Anyway the different level of maturity for the various fuel cell technologies does not allow an homogeneous comparison of technical and economical key parameters. PAFCs, due to their present commercial availability and operation experience, are well outlined in terms of performance and costs; on the contrary with regard to the other technologies--PEMFC, MCFC and SOFC--which are still under development, their commercialization is expected within a period of 7 to 13 years according to single technology maturity level (MCFC level seems to be more ready), kind of application, competitors, environmental constraints, etc.

  20. The system Fe-Si-O: Oxygen buffer calibrations to 1,500K

    NASA Astrophysics Data System (ADS)

    Myers, J.; Eugster, H. P.

    1983-03-01

    The five solid-phase oxygen buffers of the system Fe-Si-O, iron-wuestite (IW), wuestite-magnetite (WM), magnetite-hematite (MH), quartz-iron-fayalite (QIF) and fayalite-magnetite-quartz (FMQ) have been recalibrated at 1 atm pressure and temperatures from 800° 1,300° C, using a thermogravimetric gas mixing furnace. The oxygen fugacity, f_{{text{O}}_{text{2}} } was measured with a CaO-doped ZrO2 electrode. Measurements were made also for wuestite solid solutions in order to determine the redox behavior of wuestites with O/Fe ratios varying from 1.05 to 1.17. For FMQ, additional determinations were carried out at 1 kb over a temperature range of 600° to 800° C, using a modified Shaw membrane. Results agree reasonably well with published data and extrapolations. The reaction parameters K, Δ G {r/o}, Δ H {r/o}, and Δ S {r/o}were calculated from the following log f_{{text{O}}_{text{2}} }/ T relations (T in K): 410_2004_Article_BF00371177_TeX2GIFE1.gif begin{gathered} {text{IW }}log f_{{text{O}}_{text{2}} } = - 26,834.7/T + 6.471left( { ± 0.058} right) \\ {text{ }}left( {{text{800}} - 1,260{text{ C}}} right), \\ {text{WM }}log f_{{text{O}}_{text{2}} } = - 36,951.3/T + 16.092left( { ± 0.045} right) \\ {text{ }}left( {{text{1,000}} - 1,300{text{ C}}} right), \\ {text{MH }}log f_{{text{O}}_{text{2}} } = - 23,847.6/T + 13.480left( { ± 0.055} right) \\ {text{ }}left( {{text{1,040}} - 1,270{text{ C}}} right), \\ {text{QIF }}log f_{{text{O}}_{text{2}} } = - 27,517.5/T + 6.396left( { ± 0.049} right) \\ {text{ }}left( {{text{960}} - 1,140{text{ C}}} right), \\ {text{FMQ }}log f_{{text{O}}_{text{2}} } = - 24,441.9/T + 8.290left( { ± 0.167} right) \\ {text{ }}left( {{text{600}} - 1,140{text{ C}}} right). \\ These experimentally determined reaction parameters were combined with published 298 K data to determine the parameters Gf, Hf, and Sf for the phases wuestite, magnetite, hematite, and fayalite from 298 K to the temperatures of the experiments. The T-f_{{text{O}}_{text{2}} } data for wuestite solid solutions were used to obtain activities, excess free energies and Margules mixing parameters. The new data provide a more reliable, consistent and complete reference set for the interpretation of redox reactions at elevated temperatures in experiments and field settings encompassing the crust, mantle and core as well as extraterrestrial environments.

  1. Integrated mixed signal control IC for 500-kHz switching frequency buck regulator

    NASA Astrophysics Data System (ADS)

    Chen, Keng; Zhang, Hong

    2015-12-01

    The main purpose for this work is to study the challenges of designing a digital buck regulator using pipelined analog to digital converter (ADC). Although pipelined ADC can achieve high sampling speed, it will introduce additional phase lag to the buck circuit. Along with the latency brought by processing time of additional digital circuits, as well as the time delay associated with the switching frequency, the closed loop will be unstable; moreover, raw ADC outputs have low signal-to-noise ratio, which usually need back-end calibration. In order to compensate these phase lag and make control loop unconditional stable, as well as boost up signal-to-noise ratio of the ADC block with cost-efficient design, a finite impulse response filter followed by digital proportional-integral-derivative blocks were designed. All these digital function blocks were optimised with processing speed. In the system simulation, it can be found that this controller achieved output regulation within 10% of nominal 5 V output voltage under 1 A/µs load transient condition; moreover, with the soft-start method, there is no turn-on overshooting. The die size of this controller is controlled within 3 mm2 by using 180 nm CMOS technology.

  2. Cathode pressure modeling of the Buckeye Bullet II 500kW PEM fuel cell system

    NASA Astrophysics Data System (ADS)

    Hillstrom, Edward T.

    This dissertation details the development of a model that simulates the pressure dynamics of the cathode supply system for the Buckeye Bullet 2, the worlds fastest hydrogen fuel cell vehicle. Due to the extreme power levels of the BB2 system, and the unique use of heliox as the oxidant supply, it is shown that existing system level models for predicting the fuel cell pressure dynamics do not adequately capture the dynamics of the BB2 system. Several modeling attempts are evaluated, and eventually the most robust model is a model which is derived from a rational system decomposition of the cathode system. By separating the major losses of the cathode system into an upstream and downstream resistance, the performance of the model is significantly improved. It is shown that the rate at which water exits the cathode plays a significant role accurately capturing the pressure dynamics. With this in mind, a distributed parameter model is developed to provide estimates of how the rate of liquid water removal from cathode changes with time. The results of this model are validated through physical testing. The resulting model relies on five empirically tunable parameters to tune the model performance to match that of the system. The method of calibrating these parameters is outlined, and the resulting model developed with stationary test data is compared to data from the actual BB2 race data. Only a few parameters need to be recalibrated, which is due to physical system differences between the data from the stationary tests and the race data.

  3. PB500, 500kW Utility-Scale PowerBuoy Project

    SciTech Connect

    Hart, Philip R.

    2011-09-27

    This presentation from the Water Peer Review highlights one of the program's marine and hyrokinetics device development projects in which Ocean Power Technologies will advance the current PowerBuoy design for commercial readiness.

  4. Rate constant for the fraction of atomic chlorine with formaldehyde from 200 to 500K

    NASA Technical Reports Server (NTRS)

    Michael, J. V.; Nava, D. F.; Payne, W. A.; Stief, L. J.

    1978-01-01

    A flash photolysis - resonance fluorescence technique was used to measure rate constant. The results were independent of substantial variations in H2CO, total pressure (Ar), and flash intensity (i.e., initial Cl). The rate constant was shown to be invariant with temperature, the best representation for this temperature range being K = (7.48 + or - 0.50) x 10 to the minus 11 power cu cm molecule-1 s-1 where the error is one standard deviation. The rate constant is theoretically discussed and the potential importance of the reaction in stratospheric chemistry is considered.

  5. Who are the Okinawans? Ancestry, genome diversity, and implications for the genetic study of human longevity from a geographically isolated population.

    PubMed

    Bendjilali, Nasrine; Hsueh, Wen-Chi; He, Qimei; Willcox, D Craig; Nievergelt, Caroline M; Donlon, Timothy A; Kwok, Pui-Yan; Suzuki, Makoto; Willcox, Bradley J

    2014-12-01

    Isolated populations have advantages for genetic studies of longevity from decreased haplotype diversity and long-range linkage disequilibrium. This permits smaller sample sizes without loss of power, among other utilities. Little is known about the genome of the Okinawans, a potential population isolate, recognized for longevity. Therefore, we assessed genetic diversity, structure, and admixture in Okinawans, and compared this with Caucasians, Chinese, Japanese, and Africans from HapMap II, genotyped on the same Affymetrix GeneChip Human Mapping 500K array. Principal component analysis, haplotype coverage, and linkage disequilibrium decay revealed a distinct Okinawan genome-more homogeneity, less haplotype diversity, and longer range linkage disequilibrium. Population structure and admixture analyses utilizing 52 global reference populations from the Human Genome Diversity Cell Line Panel demonstrated that Okinawans clustered almost exclusively with East Asians. Sibling relative risk (λs) analysis revealed that siblings of Okinawan centenarians have 3.11 times (females) and 3.77 times (males) more likelihood of centenarianism. These findings suggest that Okinawans are genetically distinct and share several characteristics of a population isolate, which are prone to develop extreme phenotypes (eg, longevity) from genetic drift, natural selection, and population bottlenecks. These data support further exploration of genetic influence on longevity in the Okinawans. PMID:24444611

  6. Computational method for estimating DNA copy numbers in normal samples, cancer cell lines, and solid tumors using array comparative genomic hybridization.

    PubMed

    Abkevich, Victor; Iliev, Diana; Timms, Kirsten M; Tran, Thanh; Skolnick, Mark; Lanchbury, Jerry S; Gutin, Alexander

    2010-01-01

    Genomic copy number variations are a typical feature of cancer. These variations may influence cancer outcomes as well as effectiveness of treatment. There are many computational methods developed to detect regions with deletions and amplifications without estimating actual copy numbers (CN) in these regions. We have developed a computational method capable of detecting regions with deletions and amplifications as well as estimating actual copy numbers in these regions. The method is based on determining how signal intensity from different probes is related to CN, taking into account changes in the total genome size, and incorporating into analysis contamination of the solid tumors with benign tissue. Hidden Markov Model is used to obtain the most likely CN solution. The method has been implemented for Affymetrix 500K GeneChip arrays and Agilent 244K oligonucleotide arrays. The results of CN analysis for normal cell lines, cancer cell lines, and tumor samples are presented. The method is capable of detecting copy number alterations in tumor samples with up to 80% contamination with benign tissue. Analysis of 178 cancer cell lines reveals multiple regions of common homozygous deletions and strong amplifications encompassing known tumor suppressor genes and oncogenes as well as novel cancer related genes. PMID:20706610

  7. Genome-wide and fine-resolution association analysis of malaria in West Africa

    PubMed Central

    Jallow, Muminatou; Teo, Yik Ying; Small, Kerrin S; Rockett, Kirk A; Deloukas, Panos; Clark, Taane G; Kivinen, Katja; Bojang, Kalifa A; Conway, David J; Pinder, Margaret; Sirugo, Giorgio; Sisay-Joof, Fatou; Usen, Stanley; Auburn, Sarah; Bumpstead, Suzannah J; Campino, Susana; Coffey, Alison; Dunham, Andrew; Fry, Andrew E; Green, Angela; Gwilliam, Rhian; Hunt, Sarah E; Inouye, Michael; Jeffreys, Anna E; Mendy, Alieu; Palotie, Aarno; Potter, Simon; Ragoussis, Jiannis; Rogers, Jane; Rowlands, Kate; Somaskantharajah, Elilan; Whittaker, Pamela; Widden, Claire; Donnelly, Peter; Howie, Bryan; Marchini, Jonathan; Morris, Andrew; SanJoaquin, Miguel; Achidi, Eric Akum; Agbenyega, Tsiri; Allen, Angela; Amodu, Olukemi; Corran, Patrick; Djimde, Abdoulaye; Dolo, Amagana; Doumbo, Ogobara K; Drakeley, Chris; Dunstan, Sarah; Evans, Jennifer; Farrar, Jeremy; Fernando, Deepika; Hien, Tran Tinh; Horstmann, Rolf D; Ibrahim, Muntaser; Karunaweera, Nadira; Kokwaro, Gilbert; Koram, Kwadwo A; Lemnge, Martha; Makani, Julie; Marsh, Kevin; Michon, Pascal; Modiano, David; Molyneux, Malcolm E; Mueller, Ivo; Parker, Michael; Peshu, Norbert; Plowe, Christopher V; Puijalon, Odile; Reeder, John; Reyburn, Hugh; Riley, Eleanor M; Sakuntabhai, Anavaj; Singhasivanon, Pratap; Sirima, Sodiomon; Tall, Adama; Taylor, Terrie E; Thera, Mahamadou; Troye-Blomberg, Marita; Williams, Thomas N; Wilson, Michael; Kwiatkowski, Dominic P

    2009-01-01

    We report a genome-wide association (GWA) study of severe malaria in The Gambia. The initial GWA scan included 2,500 children genotyped on the Affymetrix 500K GeneChip, and a replication study included 3,400 children. We used this to examine the performance of GWA methods in Africa. We found considerable population stratification, and also that signals of association at known malaria resistance loci were greatly attenuated owing to weak linkage disequilibrium (LD). To investigate possible solutions to the problem of low LD, we focused on the HbS locus, sequencing this region of the genome in 62 Gambian individuals and then using these data to conduct multipoint imputation in the GWA samples. This increased the signal of association, from P = 4 × 10−7 to P = 4 × 10−14, with the peak of the signal located precisely at the HbS causal variant. Our findings provide proof of principle that fine-resolution multipoint imputation, based on population-specific sequencing data, can substantially boost authentic GWA signals and enable fine mapping of causal variants in African populations. PMID:19465909

  8. Who Are the Okinawans? Ancestry, Genome Diversity, and Implications for the Genetic Study of Human Longevity From a Geographically Isolated Population

    PubMed Central

    Hsueh, Wen-Chi; He, Qimei; Willcox, D. Craig; Nievergelt, Caroline M.; Donlon, Timothy A.; Kwok, Pui-Yan; Suzuki, Makoto; Willcox, Bradley J.

    2014-01-01

    Isolated populations have advantages for genetic studies of longevity from decreased haplotype diversity and long-range linkage disequilibrium. This permits smaller sample sizes without loss of power, among other utilities. Little is known about the genome of the Okinawans, a potential population isolate, recognized for longevity. Therefore, we assessed genetic diversity, structure, and admixture in Okinawans, and compared this with Caucasians, Chinese, Japanese, and Africans from HapMap II, genotyped on the same Affymetrix GeneChip Human Mapping 500K array. Principal component analysis, haplotype coverage, and linkage disequilibrium decay revealed a distinct Okinawan genome—more homogeneity, less haplotype diversity, and longer range linkage disequilibrium. Population structure and admixture analyses utilizing 52 global reference populations from the Human Genome Diversity Cell Line Panel demonstrated that Okinawans clustered almost exclusively with East Asians. Sibling relative risk (λs) analysis revealed that siblings of Okinawan centenarians have 3.11 times (females) and 3.77 times (males) more likelihood of centenarianism. These findings suggest that Okinawans are genetically distinct and share several characteristics of a population isolate, which are prone to develop extreme phenotypes (eg, longevity) from genetic drift, natural selection, and population bottlenecks. These data support further exploration of genetic influence on longevity in the Okinawans. PMID:24444611

  9. Genome-wide and fine-resolution association analysis of malaria in West Africa.

    PubMed

    Jallow, Muminatou; Teo, Yik Ying; Small, Kerrin S; Rockett, Kirk A; Deloukas, Panos; Clark, Taane G; Kivinen, Katja; Bojang, Kalifa A; Conway, David J; Pinder, Margaret; Sirugo, Giorgio; Sisay-Joof, Fatou; Usen, Stanley; Auburn, Sarah; Bumpstead, Suzannah J; Campino, Susana; Coffey, Alison; Dunham, Andrew; Fry, Andrew E; Green, Angela; Gwilliam, Rhian; Hunt, Sarah E; Inouye, Michael; Jeffreys, Anna E; Mendy, Alieu; Palotie, Aarno; Potter, Simon; Ragoussis, Jiannis; Rogers, Jane; Rowlands, Kate; Somaskantharajah, Elilan; Whittaker, Pamela; Widden, Claire; Donnelly, Peter; Howie, Bryan; Marchini, Jonathan; Morris, Andrew; SanJoaquin, Miguel; Achidi, Eric Akum; Agbenyega, Tsiri; Allen, Angela; Amodu, Olukemi; Corran, Patrick; Djimde, Abdoulaye; Dolo, Amagana; Doumbo, Ogobara K; Drakeley, Chris; Dunstan, Sarah; Evans, Jennifer; Farrar, Jeremy; Fernando, Deepika; Hien, Tran Tinh; Horstmann, Rolf D; Ibrahim, Muntaser; Karunaweera, Nadira; Kokwaro, Gilbert; Koram, Kwadwo A; Lemnge, Martha; Makani, Julie; Marsh, Kevin; Michon, Pascal; Modiano, David; Molyneux, Malcolm E; Mueller, Ivo; Parker, Michael; Peshu, Norbert; Plowe, Christopher V; Puijalon, Odile; Reeder, John; Reyburn, Hugh; Riley, Eleanor M; Sakuntabhai, Anavaj; Singhasivanon, Pratap; Sirima, Sodiomon; Tall, Adama; Taylor, Terrie E; Thera, Mahamadou; Troye-Blomberg, Marita; Williams, Thomas N; Wilson, Michael; Kwiatkowski, Dominic P

    2009-06-01

    We report a genome-wide association (GWA) study of severe malaria in The Gambia. The initial GWA scan included 2,500 children genotyped on the Affymetrix 500K GeneChip, and a replication study included 3,400 children. We used this to examine the performance of GWA methods in Africa. We found considerable population stratification, and also that signals of association at known malaria resistance loci were greatly attenuated owing to weak linkage disequilibrium (LD). To investigate possible solutions to the problem of low LD, we focused on the HbS locus, sequencing this region of the genome in 62 Gambian individuals and then using these data to conduct multipoint imputation in the GWA samples. This increased the signal of association, from P = 4 × 10(-7) to P = 4 × 10(-14), with the peak of the signal located precisely at the HbS causal variant. Our findings provide proof of principle that fine-resolution multipoint imputation, based on population-specific sequencing data, can substantially boost authentic GWA signals and enable fine mapping of causal variants in African populations. PMID:19465909

  10. Comparison of Comparative Genomic Hybridization Technologies across Microarray Platforms

    EPA Science Inventory

    In the 2007 Association of Biomolecular Resource Facilities (ABRF) Microarray Research Group (MARG) project, we analyzed HL-60 DNA with five platforms: Agilent, Affymetrix 500K, Affymetrix U133 Plus 2.0, Illumina, and RPCI 19K BAC arrays. Copy number variation (CNV) was analyzed ...

  11. Using The Affymetrix Wheat Microarray As An Oat Expression Platform

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent advances in sequencing have resulted in the sequence of a large number of plant expressed sequence tags (ESTs) to entire plant genomes. Using these EST sequences, oligonucleotide microarray chips have been developed for several species including barley (Hordeum vulgare), maize (Zea mays), ric...

  12. Lr34-mediated leaf rust resistance in wheat: transcript profiling reveals a high energetic demand supported by transient recruitment of multiple metabolic pathways

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The wheat gene Lr34 confers partial resistance to all races of Puccinia triticina, the causal agent of wheat leaf rust. However, the biological basis for the exceptional durability of Lr34 is unclear. We used the Affymetrix GeneChip Wheat Genome Array to compare transcriptional changes of wheat in a...

  13. Surveying expression level polymorphism and single-feature polymorphism in near-isogenic wheat lines differing for the Yr5 stripe rust resistance locus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    DNA polymorphisms are valuable for several applications including genotyping, molecular mapping and marker-assisted selection. The Affymetrix Wheat GeneChip was used to survey expression level polymorphisms (ELPs) and single-feature polymorphisms (SFPs) between two near-isogenic wheat genotypes (BC7...

  14. Surveying expression level polymorphism and single-feature polymorphism in near-isogenic wheat lines differing for the Yr5 stripe rust resistance locus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    DNA polymorphisms are valuable for several applications including genotyping, molecular mapping and marker-assisted selection. The Affymetrix Wheat GeneChip was used to survey expression level polymorphisms (ELPs) and single-feature polymorphisms (SFPs) between two near-isogenic wheat genotypes (BC...

  15. Characterizing the porcine transcriptional regulatory response to infection by Salmonella: identifying putative new NFkB direct targets through comparative bioinformatics.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have collected data on host response to infection from RNA prepared from mesenteric lymph node of swine infected with either Salmonella enterica serovar Typhimurium (ST) or S. Choleraesuis (SC) using the porcine Affymetrix GeneChip. We identified 848 (ST) and 1,853 (SC) genes with statistical evi...

  16. GENE EXPRESSION ANALYSIS OF CONIDIUM MATURATION AND GERMINATION IN FUSARIUM GRAMINEARUM

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To understand the infection cycle of the head blight pathogen F. graminearum, gene expression profiles were monitored in newly formed conidia, conidia that had been desiccated for 10 days and germinating conidia using the 18K feature F. graminearum Affymetrix GeneChip. A total of 6,384 positive sign...

  17. Gene Expression Profiling and Functional Analysis of Spore Germination in Fusarium graminearum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A full genome study on conidia and ascospores has been carried out using F. graminearum Affymetrix GeneChips to compare gene expression during germination in complete medium at 0, 2, 8, 24 hours and after 10 days of drought stress. The total number of genes detected in at least one time point was si...

  18. Computational Integration of Structural and Functional Genomics Data Across Species to Develop Information on Porcine Inflammatory Gene Regulatory Pathway

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Comparative integration of structural and functional genomic data across species holds great promise in finding genes controlling disease resistance. We are investigating the porcine gut immune response to infection through gene expression profiling. We have collected porcine Affymetrix GeneChip da...

  19. BIOINFORMATIC INTEGRATION OF STRUCTURAL AND FUNCTIONAL GENOMICS DATA ACROSS SPECIES TO DEVELOP PORCINE INFLAMMATORY GENE REGULATORY PATHWAY INFORMATION

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Integration of structural and functional genomic data across species holds great promise in finding genes controlling disease resistance. We are investigating the porcine gut immune response to infection through gene expression profiling. We have collected porcine Affymetrix GeneChip data from RNA ...

  20. Computational Integration Of Structural And Functional Genomics Data Across Species To Develop Porcine Inflammatory Gene Regulatory Pathway Information

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Comparative integration of structural and functional genomic data across species holds great promise in finding genes controlling disease resistance. We are investigating the porcine gut immune response to infection through gene expression profiling. We have collected porcine Affymetrix GeneChip da...

  1. Global changes in expression of grapefruit peel tissue in response to the yeast biocontrol agent, Metschnikowia fructicola

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To gain a better understanding of the molecular changes taking place in citrus fruit tissue following the application of the yeast biocontrol agent, Metschnikowia fructicola, microarray analysis was performed on grapefruit surface wounds using an Affymetrix Citrus GeneChip. Using a cut off of p<0.0...

  2. Differential Regulation of Genes of Metabolic Pathways during Wheat-Hessian Fly Interactions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Hessian fly is one of the most destructive pests of wheat worldwide. Virulent larvae cause stunting and yield loss to susceptible plants whereas avirulent larvae die within a few days of infesting resistant plants. We employed the Affymetrix GeneChip Wheat Genome Array to examine the temporal di...

  3. Microarray-Based Genetic Mapping Using Soybean Near-Isogenic Lines and Generation of SNP Markers in the Rag1 Aphid-Resistance Interval

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A strategy using near-isogenic lines (NILs) and Affymetrix Soybean GeneChip microarrays was employed to identify genetic markers closely linked to the soybean aphid [Aphis glycines Matsumura (Hemiptera: Aphididae)] resistance gene Rag1 in soybean [Glycine max (L.) Merr.]. Genomic DNA from the aphid ...

  4. Arabidopsis transcriptional responses differentiate between O3 and herbicides

    EPA Science Inventory

    Using published data based on Affymetrix ATH1 Gene-Chips we characterized the transcriptional response of Arabidopsis thaliana Columbia to O3 and a few other major environmental stresses including oxidative stress . A set of 101 markers could be extracted which provided a compo...

  5. Electrical injection and detection of spin accumulation in silicon at 500 K with magnetic metal/silicon dioxide contacts.

    PubMed

    Li, C H; van 't Erve, O M J; Jonker, B T

    2011-01-01

    The International Technology Roadmap for Semiconductors has identified the electron's spin angular momentum as a new state variable that should be explored as an alternative to the electron's charge for use beyond the size scaling of Moore's Law. A major obstacle has been achieving control of the spin variable at temperatures required for practical applications. Here we demonstrate electrical injection, detection and precession of spin accumulation in silicon, the cornerstone material of device technology, at temperatures that easily exceed these requirements. We observe Hanle precession of electron spin accumulation in silicon for a wide range of bias, show that the magnitude of the Hanle signal agrees well with theory, and that the spin lifetime varies with silicon carrier density. These results confirm spin accumulation in the silicon transport channel to 500 K rather than trapping in localized interface states, and enable utilization of the spin variable in practical device applications. PMID:21427716

  6. A Novel 500kW High-Speed Turbine PM Synchronous Generator Set for Distributed Power Generation

    NASA Astrophysics Data System (ADS)

    Wendt, Sven; Benecke, Frank; Güldner, Henry

    The paper presents a power generation system based on the cogeneration of heat and electricity with a novel high speed turbogenerator. The machine consists of a single stage steam turbine and a directly coupled permanent magnet synchronous generator in one constructional unit. A PWM IGBT rectifier is the load to the generator and a PWM IGBT three-phase four-wire inverter feeds the power into the low voltage mains. In order to increase the turbine efficiency at light load, variable speed operation of the turbogenerator is realized. Different control schemes for mains parallel operation and stand alone operation are presented. The control schemes allow for the use of a lookup table based control with a speed-power-characteristic or for the use of a maximum power point tracker. Measurement results from the successfully tested turbogenerator set are presented.

  7. 75 FR 3486 - Susquehanna to Roseland 500kV Transmission Line, Environmental Impact Statement, Delaware Water...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-21

    ...Pursuant to National Environmental Policy Act of 1969, 42 U.S.C. 4332(2)(C), the National Park Service (NPS) is preparing an Environmental Impact Statement (EIS) and conducting public scoping meetings for a construction and right-of-way permit requested from Delaware Water Gap National Recreation Area, Middle Delaware National Scenic and Recreational River, and Appalachian National Scenic......

  8. Genomic characterization of esophageal squamous cell carcinoma from a high-risk population in China

    PubMed Central

    Hu, Nan; Wang, Chaoyu; Ng, David; Clifford, Robert; Yang, Howard H; Tang, Ze-Zhong; Wang, Quan-Hong; Han, Xiao-You; Giffen, Carol; Goldstein, Alisa M; Taylor, Philip R; Lee, Maxwell P

    2009-01-01

    Genomic instability plays an important role in most human cancers. To characterize genomic instability in esophageal squamous cell carcinoma (ESCC), we examined loss of heterozygosity (LOH), copy number (CN) loss, CN gain, and gene expression using the Affymetrix GeneChip Human Mapping 500K (n=30 cases) and Human U133A (n=17 cases) arrays in ESCC cases from a high-risk region of China. We found that genomic instability measures varied widely among cases and separated them into two groups: a high-frequency instability group (two-thirds of all cases with one or more instability category ≥ 10%) and a low-frequency instability group (one-third of cases with instability < 10%). Genomic instability also varied widely across chromosomal arms, with the highest frequency of LOH on 9p (33% of informative single nucleotide polymorphisms (SNPs)), CN loss on 3p (33%), and CN gain on 3q (48%). Twenty-two LOH regions were identified: four on 9p, seven on 9q, four on 13q, two on 17p, and five on 17q. Three CN loss regions – 3p12.3, 4p15.1, and 9p21.3 – were detected. Twelve CN gain regions were found, including six on 3q, one on 7q, four on 8q, and one on 11q. One of the most gene-rich of these CN gain regions was 11q13.1-13.4, where 26 genes also had RNA expression data available. CN gain was significantly correlated with increased RNA expression in over 80% of these genes. Our findings demonstrate the potential utility of combining CN analysis and gene expression data to identify genes involved in esophageal carcinogenesis. PMID:19584285

  9. Genome-wide patterns of population structure and admixture in West Africans and African Americans.

    PubMed

    Bryc, Katarzyna; Auton, Adam; Nelson, Matthew R; Oksenberg, Jorge R; Hauser, Stephen L; Williams, Scott; Froment, Alain; Bodo, Jean-Marie; Wambebe, Charles; Tishkoff, Sarah A; Bustamante, Carlos D

    2010-01-12

    Quantifying patterns of population structure in Africans and African Americans illuminates the history of human populations and is critical for undertaking medical genomic studies on a global scale. To obtain a fine-scale genome-wide perspective of ancestry, we analyze Affymetrix GeneChip 500K genotype data from African Americans (n = 365) and individuals with ancestry from West Africa (n = 203 from 12 populations) and Europe (n = 400 from 42 countries). We find that population structure within the West African sample reflects primarily language and secondarily geographical distance, echoing the Bantu expansion. Among African Americans, analysis of genomic admixture by a principal component-based approach indicates that the median proportion of European ancestry is 18.5% (25th-75th percentiles: 11.6-27.7%), with very large variation among individuals. In the African-American sample as a whole, few autosomal regions showed exceptionally high or low mean African ancestry, but the X chromosome showed elevated levels of African ancestry, consistent with a sex-biased pattern of gene flow with an excess of European male and African female ancestry. We also find that genomic profiles of individual African Americans afford personalized ancestry reconstructions differentiating ancient vs. recent European and African ancestry. Finally, patterns of genetic similarity among inferred African segments of African-American genomes and genomes of contemporary African populations included in this study suggest African ancestry is most similar to non-Bantu Niger-Kordofanian-speaking populations, consistent with historical documents of the African Diaspora and trans-Atlantic slave trade. PMID:20080753

  10. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.

    PubMed

    2007-06-01

    There is increasing evidence that genome-wide association (GWA) studies represent a powerful approach to the identification of genes involved in common human diseases. We describe a joint GWA study (using the Affymetrix GeneChip 500K Mapping Array Set) undertaken in the British population, which has examined approximately 2,000 individuals for each of 7 major diseases and a shared set of approximately 3,000 controls. Case-control comparisons identified 24 independent association signals at P < 5 x 10(-7): 1 in bipolar disorder, 1 in coronary artery disease, 9 in Crohn's disease, 3 in rheumatoid arthritis, 7 in type 1 diabetes and 3 in type 2 diabetes. On the basis of prior findings and replication studies thus-far completed, almost all of these signals reflect genuine susceptibility effects. We observed association at many previously identified loci, and found compelling evidence that some loci confer risk for more than one of the diseases studied. Across all diseases, we identified a large number of further signals (including 58 loci with single-point P values between 10(-5) and 5 x 10(-7)) likely to yield additional susceptibility loci. The importance of appropriately large samples was confirmed by the modest effect sizes observed at most loci identified. This study thus represents a thorough validation of the GWA approach. It has also demonstrated that careful use of a shared control group represents a safe and effective approach to GWA analyses of multiple disease phenotypes; has generated a genome-wide genotype database for future studies of common diseases in the British population; and shown that, provided individuals with non-European ancestry are excluded, the extent of population stratification in the British population is generally modest. Our findings offer new avenues for exploring the pathophysiology of these important disorders. We anticipate that our data, results and software, which will be widely available to other investigators, will provide a

  11. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls

    PubMed Central

    2009-01-01

    There is increasing evidence that genome-wide association (GWA) studies represent a powerful approach to the identification of genes involved in common human diseases. We describe a joint GWA study (using the Affymetrix GeneChip 500K Mapping Array Set) undertaken in the British population, which has examined ~2,000 individuals for each of 7 major diseases and a shared set of ~3,000 controls. Case-control comparisons identified 24 independent association signals at P<5×10-7: 1 in bipolar disorder, 1 in coronary artery disease, 9 in Crohn’s disease, 3 in rheumatoid arthritis, 7 in type 1 diabetes and 3 in type 2 diabetes. On the basis of prior findings and replication studies thus-far completed, almost all of these signals reflect genuine susceptibility effects. We observed association at many previously identified loci, and found compelling evidence that some loci confer risk for more than one of the diseases studied. Across all diseases, we identified a large number of further signals (including 58 loci with single-point P values between 10-5 and 5×10-7) likely to yield additional susceptibility loci. The importance of appropriately large samples was confirmed by the modest effect sizes observed at most loci identified. This study thus represents a thorough validation of the GWA approach. It has also demonstrated that careful use of a shared control group represents a safe and effective approach to GWA analyses of multiple disease phenotypes; has generated a genome-wide genotype database for future studies of common diseases in the British population; and shown that, provided individuals with non-European ancestry are excluded, the extent of population stratification in the British population is generally modest. Our findings offer new avenues for exploring the pathophysiology of these important disorders. We anticipate that our data, results and software, which will be widely available to other investigators, will provide a powerful resource for human genetics

  12. The prevalence of chromosomal aberrations associated with myelodysplastic syndromes in China.

    PubMed

    Hu, Qinyong; Chu, Yuxin; Song, Qibin; Yao, Yi; Yang, Weihong; Huang, Shiang

    2016-08-01

    This study aims to investigate the prevalence and distribution of diverse chromosomal aberrations associated with myelodysplastic syndromes (MDS) in China. Bone marrow samples were collected from multiple cities in China. Metaphase cytogenetic (MC) analysis and fluorescence in situ hybridization (FISH) were initially used to test chromosomal lesions. Affymetrix CytoScan 750 K genechip platform performed a genome-wide detection of chromosomal aberrations. Chromosomal gain was identified in 76 patients; the most prevalent was trisomy 8(17.9 %). New chromosomal gain was detected on chromosome 9, 19p, and X. Chromosomal loss was detected in 101 patients. The most frequent was loss 5q (21.0 %). Some loss and gain were not identified by MC or FISH but identified by genechip. UPD was solely identified by genechip in 51 patients; the most prevalent were UPD 7q (4.94 %) and UPD 17p (4.32 %). Furthermore, complex chromosomal aberrations were detected in 56 patients. In conclusion, Affymetrix CytoScan 750 K genechip was more precise than MC and FISH in detection of cryptic chromosomal aberrations relevant to MDS. Analysis of the prevalence and distribution of diverse chromosomal aberrations in China may improve strategies for MDS diagnosis and therapies. PMID:27225263

  13. Identifying the genes regulated by IDH1 via gene-chip in glioma cell U87

    PubMed Central

    Ren, Jie; Lou, Meiqing; Shi, Jinlong; Xue, Yajun; Cui, Daming

    2015-01-01

    Glioma is the most common form of primary brain tumor. Increasing evidence show that IDH1 gene mutation is implicated in glioma. However, the mechanism involved in the progression of glioma remains unclear until now. In the study reported here, we used gene chip to identifying the genes regulated with IDH mutanted at R132. The results showed that IDH1-mutant leads to 1255 up-regulated genes and 1862 down-regulated genes in U87 cell lines. Meanwhile, GO and gene-network was performed and shown IDH1-mutant mainly affect small molecule metabolic process, mitotic cell cycle and apoptosis. This result will lay a foundation for further study of IDH1 gene function in the future. PMID:26770405

  14. Topographic map of the western region of Dao Vallis in Hellas Planitia, Mars; MTM 500k -40/082E OMKT

    USGS Publications Warehouse

    Rosiek, Mark R.; Redding, Bonnie L.; Galuszka, Donna M.

    2006-01-01

    This map, compiled photogrammetrically from Viking Orbiter stereo image pairs, is part of a series of topographic maps of areas of special scientific interest on Mars. Contours were derived from a digital terrain model (DTM) compiled on a digital photogrammetric workstation using Viking Orbiter stereo image pairs with orientation parameters derived from an analytic aerotriangulation. The image base for this map employs Viking Orbiter images from orbits 406 and 363. An orthophotomosaic was created on the digital photogrammetric workstation using the DTM compiled from stereo models.

  15. 78 FR 68467 - Notice of Availability of the Record of Decision for the Gateway West 230/345/500-kV Transmission...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-14

    ... Register on May 16, 2008 (73 FR 28425), stating its intent to prepare an Environmental Impact Statement... Draft EIS in the Federal Register (76 FR 45609), starting a 90-day public comment period. On June 29... amendments. On April 26, 2013, the BLM published the Notice of Availability of the Final EIS (78 FR...

  16. The e-SCRUB Machine: an 800-kV, 500-kW average power pulsed electron beam generator for flue-gas scrubbing

    NASA Astrophysics Data System (ADS)

    Cooper, James R.; Briggs, Ray; Crewson, Walter F.; Johnson, R. D.; Ratafia-Brown, J. A.; Richardson, W. K.; Rienstra, W. W.; Ballard, Perry G.; Cukr, Jeffrey; Cassel, R. L.; Schlitt, Leland; Genuario, R. D.; Morgan, R. D.; Tripoli, G. A.

    1995-03-01

    This paper gives an overview of electron beam dry scrubbing (EBDS) to remove SOx and NOx from flue gases of coal-fired power plants. It also describes the e-SCRUB program, a program currently underway to commercialize this process with an integrated pulsed electron beam. The electron beam, together with injected water and ammonia, causes chemical reactions which convert the SOx and NOx into commercial grade agricultural fertilizer, a usable byproduct. The e-SCRUB facility is a test bed to demonstrate the feasibility and performance of a repetitive, reliable pulsed electron beam generator operating at average power levels of up to 1 MW. This facility contains the electron beam generator and all the auxiliary and support systems required by the machine, including a computer driven central experiment control system, a 100,000 SCFM flowing dry nitrogen load which simulates the characteristics of a power plant flue, and a 2 MVA dedicated electrical service to power the machine. The e-SCRUB electron beam machine is designed to produce an 800 kV pulsed electron beam with a repetition rate of 667 pps. The energy per pulse deposited into the flue gas is approximately 750 J. The pulsed power system converts the utility power input to a 667 pps, 800 kV pulse train which powers the electron gun. The functional units of the pulsed power system will be discussed in the paper, along with some preliminary experimental results.

  17. Si-N membrane microcalorimetry: Thermal conductivity and specific heat of thin films from 2-500K in magnetic fields to 8 Tesla.

    NASA Astrophysics Data System (ADS)

    Zink, Barry

    2003-03-01

    Understanding the thermal behavior of mesoscopic systems and thin films is a critical issue of both fundamental and technological solid state science. Despite the wealth of knowledge in principle available from accurate measurement of specific heat and thermal conductivity of thin films, there are relatively few results of this type, due to the difficulty of isolating the small heat capacities and thermal conductivities from the typically large background contribution of conventional apparatus. Our group at UC San Diego uses amorphous Si-N membranes to thermally isolate small samples from their environment and allow accurate thermal measurements. Recent work adds the ability to measure thermal conductivity of films as thin as 150 Angstrom over a broad temperature range [1] to our well-established techniques for measuring Cp of small samples.[2] Our microcalorimeter is also particularly well-suited for measurements of both Cp and k in high magnetic fields [3]. The micromachining techniques used to fabricate the calorimeter allow production of significant numbers of calorimeters with well-controlled dimensions and highly reproducible properties which facilitates studies of the thermal properties of thin film and tiny crystals. In this talk I will briefly review the fabrication of our microcalorimeter and the techniques for measuring Cp and k. I will present example data and results of numerical heat flow simulations used to further our understanding of heat flow in the microcalorimeter [1] B. L. Zink, B. Revaz, J. J. Cherry and F. Hellman, Submitted to RSI, Sept. 2002 [2] D. W. Denlinger et al., Rev. Sci. Inst 65, 946-59 (1994) [3] B. L. Zink, B. Revaz, R. Sappey and F. Hellman, Rev. Sci. Instrum. 73, 1841 (2002)

  18. Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data

    PubMed Central

    2010-01-01

    Background Chromatin immunoprecipitation combined with DNA microarrays (ChIP-chip) is an assay used for investigating DNA-protein-binding or post-translational chromatin/histone modifications. As with all high-throughput technologies, it requires thorough bioinformatic processing of the data for which there is no standard yet. The primary goal is to reliably identify and localize genomic regions that bind a specific protein. Further investigation compares binding profiles of functionally related proteins, or binding profiles of the same proteins in different genetic backgrounds or experimental conditions. Ultimately, the goal is to gain a mechanistic understanding of the effects of DNA binding events on gene expression. Results We present a free, open-source R/Bioconductor package Starr that facilitates comparative analysis of ChIP-chip data across experiments and across different microarray platforms. The package provides functions for data import, quality assessment, data visualization and exploration. Starr includes high-level analysis tools such as the alignment of ChIP signals along annotated features, correlation analysis of ChIP signals with complementary genomic data, peak-finding and comparative display of multiple clusters of binding profiles. It uses standard Bioconductor classes for maximum compatibility with other software. Moreover, Starr automatically updates microarray probe annotation files by a highly efficient remapping of microarray probe sequences to an arbitrary genome. Conclusion Starr is an R package that covers the complete ChIP-chip workflow from data processing to binding pattern detection. It focuses on the high-level data analysis, e.g., it provides methods for the integration and combined statistical analysis of binding profiles and complementary functional genomics data. Starr enables systematic assessment of binding behaviour for groups of genes that are alingned along arbitrary genomic features. PMID:20398407

  19. Nine susceptibility loci for hepatitis B virus-related hepatocellular carcinoma identified by a pilot two-stage genome-wide association study

    PubMed Central

    QU, LI-SHUAI; JIN, FEI; GUO, YAN-MEI; LIU, TAO-TAO; XUE, RU-YI; HUANG, XIAO-WU; XU, MIN; CHEN, TAO-YANG; NI, ZHENG-PING; SHEN, XI-ZHONG

    2016-01-01

    Previous studies have indicated that complex interactions among viral, environmental and genetic factors lead to hepatocellular carcinoma (HCC). To identify susceptibility alleles for hepatitis B virus (HBV)-related HCC, the present study conducted a pilot two-phase genome-wide association study (GWAS) in 660 Han Chinese individuals. In phase 1, a total of 500,447 single-nucleotide polymorphisms (SNPs) were genotyped in 50 HCC cases and 50 controls using Affymetrix GeneChip 500k Array Set. In phase 2, 1,152 SNPs were selected from phase 1 and genotyped in 282 cases and 278 controls using the Illumina GoldenGate platform. The prior probability of HCC in control subjects was assigned at 0.01, and false-positive report probability (FPRP) was utilized to evaluate the statistical significance. In phase 1, one SNP (rs2212522) showed a significant association with HCC (Pallele=5.23×10−8; ORallele=4.96; 95% CI, 2.72–9.03). In phase 2, among 27 SNPs with unadjusted Pallele<0.05, 9 SNPs were associated with HCC based on FPRP criteria (FPRP <0.20). The strongest statistical evidence for an association signal was with rs2120243 (combined ORallele=1.76; 95% CI, 1.39–2.22; P=2.00×10−6), which maps within the fourth intron of VEPH1. The second strongest statistical evidence for an association was identified for rs1350171 (combined ORallele=1.66; 95% CI, 1.33–2.07; P=6.48×10−6), which maps to the region downstream of the FZD4 gene. The other potential susceptibility genes included PCDH9, PRMT6, LHX1, KIF2B and L3MBTL4. In conclusion, this pilot two-phase GWAS provides the evidence for the existence of common susceptibility loci for HCC. These genes involved various signaling pathways, including those associated with transforming growth factor β, insulin/phosphoinositide 3 kinase, Wnt and epidermal growth factor receptor. These associations must be replicated and validated in larger studies. PMID:26870257

  20. Association of genetic variants with myocardial infarction in Japanese individuals with or without metabolic syndrome

    PubMed Central

    KAWAMIYA, TOSHIKI; KATO, KIMIHIKO; HORIBE, HIDEKI; YOKOI, KIYOSHI; OGURI, MITSUTOSHI; YOSHIDA, TETSURO; FUJIMAKI, TETSUO; WATANABE, SACHIRO; SATOH, KEI; AOYAGI, YUKITOSHI; NOZAWA, YOSHINORI; MUROHARA, TOYOAKI; YAMADA, YOSHIJI

    2010-01-01

    The etiology of metabolic syndrome (MetS) is highly complex, with both genetic and environmental factors being thought to play an important role. Although MetS has been recognized as a risk factor for myocardial infarction (MI), the genetic risk for MI in individuals with or without MetS has remained uncharacterized. We examined a possible association of genetic variants with MI in individuals with or without MetS separately. The study population comprised 4,424 individuals, including 1,918 individuals with MetS (903 subjects with MI and 1,015 controls) and 2,506 individuals without MetS (499 subjects with MI and 2,007 controls). The 150 polymorphisms examined in the present study were selected by genome-wide association studies of MI and ischemic stroke with the use of Affymetrix GeneChip Human Mapping 500K Array Set. Initial screening by the Chi-square test revealed that the C→T polymorphism (rs1794429) of LRPAP1, the A→G polymorphism (rs12373237) of LAMA3 and the A→G polymorphism (rs3782257) of NCOR2 were significantly (false discovery rate of <0.05) associated with MI for individuals with MetS, and that the C→G polymorphism (rs13051704) of TFF1 was significantly related to MI for individuals without MetS. Subsequent multivariable logistic analysis with adjustment for covariates revealed that rs1794429 of LRPAP1 (recessive model; P=0.0218; odds ratio=0.71) and rs3782257 of NCOR2 (dominant model; P=0.0057; odds ratio=1.94) were significantly associated with MI among individuals with MetS, and that rs13051704 of TFF1 (additive model; P=0.0100; odds ratio=0.55) was significantly associated with MI among individuals without MetS. The genetic variants that confer susceptibility to MI differ between individuals with or without MetS. Stratification of subjects according to the presence or absence of MetS may thus be important for personalized prevention of MI based on genetic information. PMID:22993627

  1. Genetic risk for myocardial infarction in Japanese individuals with or without chronic kidney disease.

    PubMed

    Fujimaki, Tetsuo; Kato, Kimihiko; Yokoi, Kiyoshi; Yoshida, Tetsuro; Oguri, Mitsutoshi; Watanabe, Sachiro; Metoki, Norifumi; Yoshida, Hidemi; Satoh, Kei; Aoyagi, Yukitoshi; Nozawa, Yoshinori; Yamada, Yoshiji

    2010-05-01

    Although chronic kidney disease (CKD) is recognized as an important risk factor for myocardial infarction (MI), genetic factors underlying predisposition to MI in individuals with or without CKD remain largely unknown. The aim of the present study was to identify genetic variants that confer susceptibility to MI in individuals with or without CKD in order to allow prediction of genetic risk for such individuals separately. The study population comprised a total of 4344 individuals, including 1247 individuals with CKD (506 subjects with MI and 741 controls) and 3097 individuals without CKD (833 subjects with MI and 2264 controls). The 150 polymorphisms examined in this study were selected by genome-wide association studies of ischemic stroke and MI with the use of the GeneChip Human Mapping 500K Array Set (Affymetrix) and determined by a method that combines the polymerase chain reaction and sequence-specific oligonucleotide probes with suspension array technology. In individuals with CKD, no polymorphism was significantly related to MI. In individuals without CKD, an initial screen by the Chi-square test revealed that the Cyright curved arrow T polymorphism of CLEC16A (rs9925481) and the Aright curved arrow G polymorphism of LAMA3 (rs12373237) were significantly (false discovery rate for allele frequencies of <0.05) associated with MI. Subsequent multivariable logistic regression analysis with adjustment for covariates revealed that the Cright curved arrow T polymorphism of CLEC16A (dominant model; P=0.0003; odds ratio, 0.66) and the Aright curved arrow G polymorphism of LAMA3 (recessive model; P=0.0087; odds ratio, 0.75) were significantly (P<0.05) associated with MI. A stepwise forward selection procedure also revealed that these polymorphisms were significant and independent determinants of MI. CLEC16A and LAMA3 may be susceptibility loci for MI in Japanese individuals without CKD. Determination of genotypes for CLEC16A and LAMA3 may prove informative for

  2. Association of genetic variants with myocardial infarction in Japanese individuals with or without metabolic syndrome.

    PubMed

    Kawamiya, Toshiki; Kato, Kimihiko; Horibe, Hideki; Yokoi, Kiyoshi; Oguri, Mitsutoshi; Yoshida, Tetsuro; Fujimaki, Tetsuo; Watanabe, Sachiro; Satoh, Kei; Aoyagi, Yukitoshi; Nozawa, Yoshinori; Murohara, Toyoaki; Yamada, Yoshiji

    2010-11-01

    The etiology of metabolic syndrome (MetS) is highly complex, with both genetic and environmental factors being thought to play an important role. Although MetS has been recognized as a risk factor for myocardial infarction (MI), the genetic risk for MI in individuals with or without MetS has remained uncharacterized. We examined a possible association of genetic variants with MI in individuals with or without MetS separately. The study population comprised 4,424 individuals, including 1,918 individuals with MetS (903 subjects with MI and 1,015 controls) and 2,506 individuals without MetS (499 subjects with MI and 2,007 controls). The 150 polymorphisms examined in the present study were selected by genome-wide association studies of MI and ischemic stroke with the use of Affymetrix GeneChip Human Mapping 500K Array Set. Initial screening by the Chi-square test revealed that the C→T polymorphism (rs1794429) of LRPAP1, the A→G polymorphism (rs12373237) of LAMA3 and the A→G polymorphism (rs3782257) of NCOR2 were significantly (false discovery rate of <0.05) associated with MI for individuals with MetS, and that the C→G polymorphism (rs13051704) of TFF1 was significantly related to MI for individuals without MetS. Subsequent multivariable logistic analysis with adjustment for covariates revealed that rs1794429 of LRPAP1 (recessive model; P=0.0218; odds ratio=0.71) and rs3782257 of NCOR2 (dominant model; P=0.0057; odds ratio=1.94) were significantly associated with MI among individuals with MetS, and that rs13051704 of TFF1 (additive model; P=0.0100; odds ratio=0.55) was significantly associated with MI among individuals without MetS. The genetic variants that confer susceptibility to MI differ between individuals with or without MetS. Stratification of subjects according to the presence or absence of MetS may thus be important for personalized prevention of MI based on genetic information. PMID:22993627

  3. Nanobarcode gene expression monitoring system for potential miniaturized space applications

    NASA Astrophysics Data System (ADS)

    Ruan, Weiming; Eastman, P. Scott; Cooke, Patrick A.; Park, Jennifer S.; Chu, Julia S. F.; Gray, Joe W.; Li, Song; Chen, Fanqing Frank

    Manned mission to space has been threatened by various cosmos risks including radiation, mirogravity, vacuum, confinement, etc., which may cause genetic variations of astronauts and eventually lead to damages of their health. Thus, the development of small biomedical devices, which can monitor astronaut gene expression changes, is useful for future long-term space missions. Using magnetic microbeads packed with nanocrystal quantum dots at controlled ratios, we were able to generate highly multiplexed nanobarcodes, which can encode a flexible panel of genes. Also, by using a reporter quantum dot, this nanobarcode platform can monitor and quantify gene expression level with improved speed and sensitivity. As a comparison, we studied TGF-β1 induced transcription changes in human bone marrow mesenchymal stem cells with both the nanobarcode microbead system and the Affymetrix GeneChip ® HTA system, which is currently considered as the industrial standard. Though using only 1/20 of the sample RNA, the nanobarcode system showed sensitivity equivalent to Affymetrix GeneChip ® system. The coefficient of variation, dynamic range, and accuracy of the nanobarcodes measurement is equivalent to that of the GeneChip ® HTA system. Therefore, this newly invented nanobarcode microbead platform is thought to be sensitive, flexible, cost-effective and accurate in a level equivalent to the conventional methods. As an extension of the use of this new platform, spacecrafts may carry this miniaturized system as a diagnostic tool for the astronauts.

  4. CGO: utilizing and integrating gene expression microarray data in clinical research and data management.

    PubMed

    Bumm, Klaus; Zheng, Mingzhong; Bailey, Clyde; Zhan, Fenghuang; Chiriva-Internati, M; Eddlemon, Paul; Terry, Julian; Barlogie, Bart; Shaughnessy, John D

    2002-02-01

    Clinical GeneOrganizer (CGO) is a novel windows-based archiving, organization and data mining software for the integration of gene expression profiling in clinical medicine. The program implements various user-friendly tools and extracts data for further statistical analysis. This software was written for Affymetrix GeneChip *.txt files, but can also be used for any other microarray-derived data. The MS-SQL server version acts as a data mart and links microarray data with clinical parameters of any other existing database and therefore represents a valuable tool for combining gene expression analysis and clinical disease characteristics. PMID:11847084

  5. Soybean GeneChip hybridizations to RNA isolated from root pieces colonized by soybean cyst nematode, Heterodera glycines

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The roots of susceptible 14 day-old soybean plants (cv. Williams) were inoculated with J2 soybean cyst nematodes, Heterodera glycines. After 8, 12 and 16 dpi the roots were placed under a stereomicroscope and root pieces (1 to 5 mm) that displayed 1 to many swollen SCN females were dissected out, l...

  6. EFFECTS OF STORAGE, RNA EXTRACTION, GENECHIP TYPE, AND DONOR SEX ON GENE EXPRESSION PROFILING OF HUMAN WHOLE BLOOD

    EPA Science Inventory

    Background: Gene expression profiling of whole blood may be useful for monitoring toxicological exposure and for diagnosis and monitoring of various diseases. Several methods are available that can be used to transport, store, and extract RNA from whole blood, but it is not clear...

  7. IT'S IN THE CHIPS: DEVELOPMENT OF A MICROARRAY GENECHIP APPROACH TO DETE T AND TYPE WATERBORNE VIRUSES

    EPA Science Inventory

    Human caliciviruses, specifically members of the genus Norovirus, have been documented as a culprit for drinking water-related outbreaks of acute gastroenteritis in the United States. In addition, these viruses are believed to be one of the major causes of waterborne disease. D...

  8. Comparison of Gene Expression in Leymus Tiller and Rhizome Meristems Using Heterologous Affymetrix Wheat and Barley Gene Chips

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Perennial Leymus wildrye tillers and rhizomes develop from similar underground axillary meristems, but display different response to gravity and perhaps other cues that govern branch angle and overall patterns of subterranean growth. Corresponding variation in growth habit is an important component...

  9. Comparison of L1000 and Affymetrix Microarray for In Vitro Concentration-Response Gene Expression Profiling (SOT)

    EPA Science Inventory

    Advances in high-throughput screening technologies and in vitro systems have opened doors for cost-efficient evaluation of chemical effects on a diversity of biological endpoints. However, toxicogenomics platforms remain too costly to evaluate large libraries of chemicals in conc...

  10. Splicy: a web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data

    PubMed Central

    Rambaldi, Davide; Felice, Barbara; Praz, Viviane; Bucher, Philip; Cittaro, Davide; Guffanti, Alessandro

    2007-01-01

    Background The Affymetrix™ technology is nowadays a well-established method for the analysis of gene expression profiles in cancer research studies. However, changes in gene expression levels are not the only way to link genes and disease. The existence of gene isoforms specifically linked with cancer or apoptosis is increasingly found in literature. Hence it is of great interest to associate the results of a gene expression study with updated evidences on the transcript structure and its possible variants. Results We present here a web-based software tool, Splicy, whose primary task is to retrieve data on the mapping of Affymetrix™ probes to single exons of gene transcripts and displaying graphically this information projected on the gene physical structure. Starting from a list of Affymetrix™ probesets the program produces a series of graphical displays, each relative to a transcript associated with the gene targeted by a given probe. The information on the transcript-by-transcript and exon-by-exon mapping of probe pairs can be retrieved both graphically and in the form of tab-separated files. The mapping of single probes to NCBI RefSeq or EMBL cDNAs is handled by the ISREC mapping tables used in the CleanEx Expression Reference Database Project. We currently maintain these mappings for most popular human and mouse Affymetrix™ chips, and Splicy can be queried for matches with human and mouse NCBI RefSeq or EMBL cDNAs. Conclusion Splicy generates probeset annotations and images describing the relation between the single probes and intron/exon structure of the target transcript in all its known variants. We think that Splicy will be useful for giving to the researcher a clearer picture of the possible transcript variants linked with a given gene and an additional view on the interpretation of microarray experiment data. Splicy is publicly available and has been realized in the framework of a bioinformatics grant from the Italian Cancer Research Association. PMID:17430561

  11. An overview of custom array sequencing.

    PubMed

    Kothiyal, Prachi; Cox, Stephanie; Ebert, Jonathan; Aronow, Bruce J; Greinwald, John H; Rehm, Heidi L

    2009-04-01

    This unit provides an overview of oligo hybridization-based resequencing and a wide range of considerations for implementing the technology and analyzing the resulting data. The specific technology discussed is the Affymetrix GeneChip CustomSeq Resequencing Array platform. Concepts related to array design, experimental protocols, and base-calling using existing algorithms are presented. Details that should be evaluated during development of sequence tiling, target amplification, and PCR protocols are addressed. An overview of the Affymetrix GeneChip Sequence Analysis Software (GSEQ) is provided, along with factors that influence base-calling coverage and accuracy. Also outlined are performance measures that can be used to characterize base-calling with resequencing arrays, as well as factors known to affect their performance. Limitations associated with detection of insertions and deletions (indels) are discussed, with empirical data from our experiments used to outline possible approaches to indel detection. Critical topics in the design, implementation, and analysis of targeted sequencing arrays not previously discussed in detail are highlighted. PMID:19360699

  12. The heat capacities of osumilite from 298.15 to 1000 K, the thermodynamic properties of two natural chlorites to 500 K, and the thermodynamic properties of petalite to 1800 K.

    USGS Publications Warehouse

    Hemingway, B.S.; Robie, R.A.; Kittrick, J.A.; Grew, E.S.; Nelen, J.A.; London, D.

    1984-01-01

    Modifications to an automated low-T, adiabatic calorimeter are described. Thermodynamic data obtained with this instrument are reported for minerals from metamorphic terrains. (U.S. Bureau of Mines Report of Investigations 8451)-J.A.Z.

  13. Power enhancement via multivariate outlier testing with gene expression arrays

    PubMed Central

    Asare, Adam L.; Carey, Vincent J.; Wang, Richard; Seyfert-Margolis, Vicki

    2009-01-01

    Motivation: As the use of microarrays in human studies continues to increase, stringent quality assurance is necessary to ensure accurate experimental interpretation. We present a formal approach for microarray quality assessment that is based on dimension reduction of established measures of signal and noise components of expression followed by parametric multivariate outlier testing. Results: We applied our approach to several data resources. First, as a negative control, we found that the Affymetrix and Illumina contributions to MAQC data were free from outliers at a nominal outlier flagging rate of α=0.01. Second, we created a tunable framework for artificially corrupting intensity data from the Affymetrix Latin Square spike-in experiment to allow investigation of sensitivity and specificity of quality assurance (QA) criteria. Third, we applied the procedure to 507 Affymetrix microarray GeneChips processed with RNA from human peripheral blood samples. We show that exclusion of arrays by this approach substantially increases inferential power, or the ability to detect differential expression, in large clinical studies. Availability: http://bioconductor.org/packages/2.3/bioc/html/arrayMvout.html and http://bioconductor.org/packages/2.3/bioc/html/affyContam.html affyContam (credentials: readonly/readonly) Contact: aasare@immunetolerance.org; stvjc@channing.harvard.edu PMID:19015138

  14. Comparative Transcriptional Profiling of Two Wheat Genotypes, with Contrasting Levels of Minerals in Grains, Shows Expression Differences during Grain Filling

    PubMed Central

    Singh, Sudhir P.; Jeet, Raja; Kumar, Jitendra; Shukla, Vishnu; Srivastava, Rakesh; Mantri, Shrikant S.; Tuli, Rakesh

    2014-01-01

    Wheat is one of the most important cereal crops in the world. To identify the candidate genes for mineral accumulation, it is important to examine differential transcriptome between wheat genotypes, with contrasting levels of minerals in grains. A transcriptional comparison of developing grains was carried out between two wheat genotypes- Triticum aestivum Cv. WL711 (low grain mineral), and T. aestivum L. IITR26 (high grain mineral), using Affymetrix GeneChip Wheat Genome Array. The study identified a total of 580 probe sets as differentially expressed (with log2 fold change of ≥2 at p≤0.01) between the two genotypes, during grain filling. Transcripts with significant differences in induction or repression between the two genotypes included genes related to metal homeostasis, metal tolerance, lignin and flavonoid biosynthesis, amino acid and protein transport, vacuolar-sorting receptor, aquaporins, and stress responses. Meta-analysis revealed spatial and temporal signatures of a majority of the differentially regulated transcripts. PMID:25364903

  15. Cloning and characterization of the drought-resistance OsRCI2-5 gene in rice (Oryza sativa L.).

    PubMed

    Li, L; Li, N; Song, S F; Li, Y X; Xia, X J; Fu, X Q; Chen, G H; Deng, H F

    2014-01-01

    The genomic expression profile of the super-hybrid rice Liangyoupeijiu female parent Pei'ai 64S in different tissues at different developmental stages under low temperature, drought, and high temperature stresses were detected using an Affymetrix GeneChip Rice Genome Array to screen upregulated and downregulated genes. In this study, we screened the drought-resistant gene OsRCI2-5, after which a constitutive OsRCI2-5 construct was created and transferred into Nipponbare. After polyethylene glycol-6000 and drought treatment, we found that the OsRCI2-5 gene improved the drought resistance of Nipponbare. Gene expression profiling showed that the OsRCI2-5 gene was expressed in the rice leaves, stems, and flower organs. Subcellular localization revealed that the gene was located in the membranes, and hence, we can deduce that a membrane signal peptide was responsible for signal transduction. PMID:24938613

  16. Global gene expression profiling of JMJD6- and JMJD4-depleted mouse NIH3T3 fibroblasts

    PubMed Central

    Hu, Yu-Jie; Imbalzano, Anthony N.

    2016-01-01

    Emerging evidence suggests Jumonji domain-containing proteins are epigenetic regulators in diverse biological processes including cellular differentiation and proliferation. RNA interference-based analyses combined with gene expression profiling can effectively characterize the cellular functions of these enzymes. We found that the depletion of Jumonji domain-containing protein 6 (JMJD6) and its paralog protein Jumonji domain-containing protein 4 (JMJD4) individually by small hairpin RNAs (shRNAs) slowed cell proliferation of mouse NIH3T3 fibroblasts. We subsequently performed gene expression profiling on both JMJD6- and JMJD4-depleted mouse NIH3T3 fibroblasts using the Affymetrix GeneChip Mouse Exon 1.0 ST Array. Here we report the gene profiling datasets along with the experimental procedures. The information can be used to further investigate how JMJD6 and JMJD4 affect gene expression and cellular physiology. PMID:27071056

  17. Genetic Aberrations in Childhood Acute Lymphoblastic Leukaemia: Application of High-Density Single Nucleotide Polymorphism Array

    PubMed Central

    Sulong, Sarina

    2010-01-01

    Screening of the entire human genome using high-density single nucleotide polymorphism array (SNPA) has become a powerful technique used in cancer genetics and population genetics studies. The GeneChip® Mapping Array, introduced by Affymetrix, is one SNPA platform utilised for genotyping studies. This GeneChip system allows researchers to gain a comprehensive view of cancer biology on a single platform for the quantification of chromosomal amplifications, deletions, and loss of heterozygosity or for allelic imbalance studies. Importantly, this array analysis has the potential to reveal novel genetic findings involved in the multistep development of cancer. Given the importance of genetic factors in leukaemogenesis and the usefulness of screening the whole genome, SNPA analysis has been utilised in many studies to characterise genetic aberrations in childhood acute lymphoblastic leukaemia. PMID:22135543

  18. Homozygosity Mapping in Leber Congenital Amaurosis and Autosomal Recessive Retinitis Pigmentosa in South Indian Families

    PubMed Central

    Srilekha, Sundaramurthy; Arokiasamy, Tharigopala; Srikrupa, Natarajan N.; Umashankar, Vetrivel; Meenakshi, Swaminathan; Sen, Parveen; Kapur, Suman; Soumittra, Nagasamy

    2015-01-01

    Leber congenital amaurosis (LCA) and retinitis pigmentosa (RP) are retinal degenerative diseases which cause severe retinal dystrophy affecting the photoreceptors. LCA is predominantly inherited as an autosomal recessive trait and contributes to 5% of all retinal dystrophies; whereas RP is inherited by all the Mendelian pattern of inheritance and both are leading causes of visual impairment in children and young adults. Homozygosity mapping is an efficient strategy for mapping both known and novel disease loci in recessive conditions, especially in a consanguineous mating, exploiting the fact that the regions adjacent to the disease locus will also be homozygous by descent in such inbred children. Here we have studied eleven consanguineous LCA and one autosomal recessive RP (arRP) south Indian families to know the prevalence of mutations in known genes and also to know the involvement of novel loci, if any. Complete ophthalmic examination was done for all the affected individuals including electroretinogram, fundus photograph, fundus autofluorescence, and optical coherence tomography. Homozygosity mapping using Affymetrix 250K HMA GeneChip on eleven LCA families followed by screening of candidate gene(s) in the homozygous block identified mutations in ten families; AIPL1 – 3 families, RPE65- 2 families, GUCY2D, CRB1, RDH12, IQCB1 and SPATA7 in one family each, respectively. Six of the ten (60%) mutations identified are novel. Homozygosity mapping using Affymetrix 10K HMA GeneChip on the arRP family identified a novel nonsense mutation in MERTK. The mutations segregated within the family and was absent in 200 control chromosomes screened. In one of the eleven LCA families, the causative gene/mutation was not identified but many homozygous blocks were noted indicating that a possible novel locus/gene might be involved. The genotype and phenotype features, especially the fundus changes for AIPL1, RPE65, CRB1, RDH12 genes were as reported earlier. PMID:26147992

  19. Gene expression profile of bladder tissue of patients with ulcerative interstitial cystitis

    PubMed Central

    Gamper, Marianne; Viereck, Volker; Geissbühler, Verena; Eberhard, Jakob; Binder, Jochen; Moll, Carlo; Rehrauer, Hubert; Moser, René

    2009-01-01

    Background Interstitial cystitis (IC), a chronic bladder disease with an increasing incidence, is diagnosed using subjective symptoms in combination with cystoscopic and histological evidence. By cystoscopic examination, IC can be classified into an ulcerative and a non-ulcerative subtype. To better understand this debilitating disease on a molecular level, a comparative gene expression profile of bladder biopsies from patients with ulcerative IC and control patients has been performed. Results Gene expression profiles from bladder biopsies of five patients with ulcerative IC and six control patients were generated using Affymetrix GeneChip expression arrays (Affymetrix – GeneChip® Human Genome U133 Plus 2.0). More than 31,000 of > 54,000 tested probe sets were present (detection p-value < 0.05). The difference between the two groups was significant for over 3,500 signals (t-test p-value < 0.01), and approximately 2,000 of the signals (corresponding to approximately 1,000 genes) showed an IC-to-healthy expression ratio greater than two. The IC pattern had similarities to patterns from immune system, lymphatic, and autoimmune diseases. The dominant biological processes were the immune and inflammatory responses. Many of the up-regulated genes were expressed in leukocytes, suggesting that leukocyte invasion into the bladder wall is a dominant feature of ulcerative IC. Histopathological data supported these findings. Conclusion GeneChip expression arrays present a global picture of ulcerative IC and provide us with a series of marker genes characteristic for this subtype of the disease. Evaluation of biopsies from other bladder patients with similar symptoms (e.g. patients with non-ulcerative IC) will further indicate whether the data presented here will be valuable for the diagnosis of IC. PMID:19400928

  20. Comparison of Nanostring nCounter® Data on FFPE Colon Cancer Samples and Affymetrix Microarray Data on Matched Frozen Tissues

    PubMed Central

    Chen, Xi; Deane, Natasha G.; Lewis, Keeli B.; Li, Jiang; Zhu, Jing; Washington, M. Kay; Beauchamp, R. Daniel

    2016-01-01

    The prognosis of colorectal cancer (CRC) stage II and III patients remains a challenge due to the difficulties of finding robust biomarkers suitable for testing clinical samples. The majority of published gene signatures of CRC have been generated on fresh frozen colorectal tissues. Because collection of frozen tissue is not practical for routine surgical pathology practice, a clinical test that improves prognostic capabilities beyond standard pathological staging of colon cancer will need to be designed for formalin-fixed paraffin-embedded (FFPE) tissues. The NanoString nCounter® platform is a gene expression analysis tool developed for use with FFPE-derived samples. We designed a custom nCounter® codeset based on elements from multiple published fresh frozen tissue microarray-based prognostic gene signatures for colon cancer, and we used this platform to systematically compare gene expression data from FFPE with matched microarray array data from frozen tissues. Our results show moderate correlation of gene expression between two platforms and discovery of a small subset of genes as candidate biomarkers for colon cancer prognosis that are detectable and quantifiable in FFPE tissue sections. PMID:27176004

  1. Construction and Validation of the Rhodobacter sphaeroides 2.4.1 DNA Microarray: Transcriptome Flexibility at Diverse Growth Modes

    SciTech Connect

    Pappas, Christopher T.; Sram, Jakub; Moskvin, Oleg V.; Ivanov, Pavel S.; Mackenzie, Christopher; Choudhary, Madhusudan; Land, Miriam L; Larimer, Frank W; Kaplan, Samuel; Gomelsky, Mark

    2004-07-01

    A high-density oligonucleotide DNA microarray, a genechip, representing the 4.6-Mb genome of the facultative phototrophic proteobacterium, Rhodobacter sphaeroides 2.4.1, was custom-designed and manufactured by Affymetrix, Santa Clara, Calif. The genechip contains probe sets for 4,292 open reading frames (ORFs), 47 rRNA and tRNA genes, and 394 intergenic regions. The probe set sequences were derived from the genome annotation generated by Oak Ridge National Laboratory after extensive revision, which was based primarily upon codon usage characteristic of this GC-rich bacterium. As a result of the revision, numerous missing ORFs were uncovered, nonexistent ORFs were deleted, and misidentified start codons were corrected. To evaluate R. sphaeroides transcriptome flexibility, expression profiles for three diverse growth modes-aerobic respiration, anaerobic respiration in the dark, and anaerobic photosynthesis-were generated. Expression levels of one-fifth to one-third of the R. sphaeroides ORFs were significantly different in cells under any two growth modes. Pathways involved in energy generation and redox balance maintenance under three growth modes were reconstructed. Expression patterns of genes involved in these pathways mirrored known functional changes, suggesting that massive changes in gene expression are the major means used by R. sphaeroides in adaptation to diverse conditions. Differential expression was observed for genes encoding putative new participants in these pathways (additional photosystem genes, duplicate NADH dehydrogenase, ATP synthases), whose functionality has yet to be investigated. The DNA microarray data correlated well with data derived from quantitative reverse transcription-PCR, as well as with data from the literature, thus validating the R. sphaeroides genechip as a powerful and reliable tool for studying unprecedented metabolic versatility of this bacterium.

  2. Transcriptome Analysis of Nodes and Buds from High and Low Tillering Switchgrass Inbred Lines

    PubMed Central

    Wang, Yixing; Zeng, Xin; Peal, Lila; Tang, Yuhong; Wu, Yanqi; Mahalingam, Ramamurthy

    2013-01-01

    In the last two decades switchgrass has received increasing attention as a promising bioenergy feedstock. Biomass is the principal trait for improvement in switchgrass breeding programs and tillering is an important component of biomass yield. Switchgrass inbred lines derived from a single parent showing vast variation in tiller number trait was used in this study. Axillary buds, which can develop into tillers, and node tissues, which give rise to axillary buds, were collected from high and low tillering inbred lines growing in field conditions. RNA from buds and nodes from the contrasting inbred lines were used for transcriptome profiling with switchgrass Affymetrix genechips. Nearly 7% of the probesets on the genechip exhibited significant differential expression in these lines. Real-time PCR analysis of 30 genes confirmed the differential expression patterns observed with genechips. Cluster analysis aided in identifying probesets unique to high or low tillering lines as well as those specific to buds or nodes of high tillering lines. Rice orthologs of the switchgrass genes were used for gene ontology (GO) analysis with AgriGO. Enrichment of genes associated with amino acid biosynthesis, lipid transport and vesicular transport were observed in low tillering lines. Enrichment of GOs for translation, RNA binding and gene expression in high tillering lines were indicative of active metabolism associated with rapid growth and development. Identification of different classes of transcription factor genes suggests that regulation of many genes determines the complex process of axillary bud initiation and development. Genes identified in this study will complement the current ongoing efforts in quantitative trait loci mapping of tillering in switchgrass. PMID:24386276

  3. A new diagnostic workflow for patients with mental retardation and/or multiple congenital abnormalities: test arrays first

    PubMed Central

    Gijsbers, Antoinet CJ; Lew, Janet YK; Bosch, Cathy AJ; Schuurs-Hoeijmakers, Janneke HM; van Haeringen, Arie; den Hollander, Nicolette S; Kant, Sarina G; Bijlsma, Emilia K; Breuning, Martijn H; Bakker, Egbert; Ruivenkamp, Claudia AL

    2009-01-01

    High-density single-nucleotide polymorphism (SNP) genotyping technology enables extensive genotyping as well as the detection of increasingly smaller chromosomal aberrations. In this study, we assess molecular karyotyping as first-round analysis of patients with mental retardation and/or multiple congenital abnormalities (MR/MCA). We used different commercially available SNP array platforms, the Affymetrix GeneChip 262K NspI, the Genechip 238K StyI, the Illumina HumanHap 300 and HumanCNV 370 BeadChip, to detect copy number variants (CNVs) in 318 patients with unexplained MR/MCA. We found abnormalities in 22.6% of the patients, including six CNVs that overlap known microdeletion/duplication syndromes, eight CNVs that overlap recently described syndromes, 63 potentially pathogenic CNVs (in 52 patients), four large segments of homozygosity and two mosaic trisomies for an entire chromosome. This study shows that high-density SNP array analysis reveals a much higher diagnostic yield as that of conventional karyotyping. SNP arrays have the potential to detect CNVs, mosaics, uniparental disomies and loss of heterozygosity in one experiment. We, therefore, propose a novel diagnostic approach to all MR/MCA patients by first analyzing every patient with an SNP array instead of conventional karyotyping. PMID:19436329

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

    SciTech Connect

    Railo, Antti; Pajunen, Antti; Itaeranta, Petri; Naillat, Florence; Vuoristo, Jussi; Kilpelaeinen, Pekka; Vainio, Seppo

    2009-10-01

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

  5. Whole genome association analysis shows that ACE is a risk factor for Alzheimer's disease and fails to replicate most candidates from Meta-analysis.

    PubMed

    Webster, Jennifer; Reiman, Eric M; Zismann, Victoria L; Joshipura, Keta D; Pearson, John V; Hu-Lince, Diane; Huentelman, Matthew J; Craig, David W; Coon, Keith D; Beach, Thomas; Rohrer, Kristen C; Zhao, Alice S; Leung, Doris; Bryden, Leslie; Marlowe, Lauren; Kaleem, Mona; Mastroeni, Diego; Grover, Andrew; Rogers, Joseph; Heun, Reinhard; Jessen, Frank; Kölsch, Heike; Heward, Christopher B; Ravid, Rivka; Hutton, Michael L; Melquist, Stacey; Petersen, Ron C; Caselli, Richard J; Papassotiropoulos, Andreas; Stephan, Dietrich A; Hardy, John; Myers, Amanda

    2010-01-01

    For late onset Alzheimer's disease (LOAD), the only confirmed, genetic association is with the apolipoprotein E (APOE) locus on chromosome 19. Meta-analysis is often employed to sort the true associations from the false positives. LOAD research has the advantage of a continuously updated meta-analysis of candidate gene association studies in the web-based AlzGene database. The top 30 AlzGene loci on May 1(st), 2007 were investigated in our whole genome association data set consisting of 1411 LOAD cases and neuropathoiogicaiiy verified controls genotyped at 312,316 SNPs using the Affymetrix 500K Mapping Platform. Of the 30 "top AlzGenes", 32 SNPs in 24 genes had odds ratios (OR) whose 95% confidence intervals that did not include 1. Of these 32 SNPs, six were part of the Affymetrix 500K Mapping panel and another ten had proxies on the Affymetrix array that had >80% power to detect an association with α=0.001. Two of these 16 SNPs showed significant association with LOAD in our sample series. One was rs4420638 at the APOE locus (uncorrected p-value=4.58E-37) and the other was rs4293, located in the angiotensin converting enzyme (ACE) locus (uncorrected p-value=0.014). Since this result was nominally significant, but did not survive multiple testing correction for 16 independent tests, this association at rs4293 was verified in a geographically distinct German cohort (p-value=0.03). We present the results of our ACE replication aiongwith a discussion of the statistical limitations of multiple test corrections in whole genome studies. PMID:21537449

  6. Gene Expression and Genetic Variation in Human Atria

    PubMed Central

    Lin, Honghuang; Dolmatova, Elena V.; Morley, Michael P.; Lunetta, Kathryn L.; McManus, David D.; Magnani, Jared W.; Margulies, Kenneth B.; Hakonarson, Hakon; del Monte, Federica; Benjamin, Emelia J.; Cappola, Thomas P.; Ellinor, Patrick T.

    2013-01-01

    Background The human left and right atria have different susceptibilities to develop atrial fibrillation (AF). However, the molecular events related to structural and functional changes that enhance AF susceptibility are still poorly understood. Objective To characterize gene expression and genetic variation in human atria. Methods We studied the gene expression profiles and genetic variations in 53 left atrial and 52 right atrial tissue samples collected from the Myocardial Applied Genomics Network (MAGNet) repository. The tissues were collected from heart failure patients undergoing transplantation and from unused organ donor hearts with normal ventricular function. Gene expression was profiled using the Affymetrix GeneChip Human Genome U133A Array. Genetic variation was profiled using the Affymetrix Genome-Wide Human SNP Array 6.0. Results We found that 109 genes were differentially expressed between left and right atrial tissues. A total of 187 and 259 significant cis-associations between transcript levels and genetic variants were identified in left and right atrial tissues, respectively. We also found that a SNP at a known AF locus, rs3740293, was associated with the expression of MYOZ1 in both left and right atrial tissues. Conclusion We found a distinct transcriptional profile between the right and left atrium, and extensive cis-associations between atrial transcripts and common genetic variants. Our results implicate MYOZ1 as the causative gene at the chromosome 10q22 locus for AF. PMID:24177373

  7. Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements

    PubMed Central

    Mecham, Brigham H.; Klus, Gregory T.; Strovel, Jeffrey; Augustus, Meena; Byrne, David; Bozso, Peter; Wetmore, Daniel Z.; Mariani, Thomas J.; Kohane, Isaac S.; Szallasi, Zoltan

    2004-01-01

    Cancer derived microarray data sets are routinely produced by various platforms that are either commercially available or manufactured by academic groups. The fundamental difference in their probe selection strategies holds the promise that identical observations produced by more than one platform prove to be more robust when validated by biology. However, cross-platform comparison requires matching corresponding probe sets. We are introducing here sequence-based matching of probes instead of gene identifier-based matching. We analyzed breast cancer cell line derived RNA aliquots using Agilent cDNA and Affymetrix oligonucleotide microarray platforms to assess the advantage of this method. We show, that at different levels of the analysis, including gene expression ratios and difference calls, cross-platform consistency is significantly improved by sequence- based matching. We also present evidence that sequence-based probe matching produces more consistent results when comparing similar biological data sets obtained by different microarray platforms. This strategy allowed a more efficient transfer of classification of breast cancer samples between data sets produced by cDNA microarray and Affymetrix gene-chip platforms. PMID:15161944

  8. Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements.

    PubMed

    Mecham, Brigham H; Klus, Gregory T; Strovel, Jeffrey; Augustus, Meena; Byrne, David; Bozso, Peter; Wetmore, Daniel Z; Mariani, Thomas J; Kohane, Isaac S; Szallasi, Zoltan

    2004-01-01

    Cancer derived microarray data sets are routinely produced by various platforms that are either commercially available or manufactured by academic groups. The fundamental difference in their probe selection strategies holds the promise that identical observations produced by more than one platform prove to be more robust when validated by biology. However, cross-platform comparison requires matching corresponding probe sets. We are introducing here sequence-based matching of probes instead of gene identifier-based matching. We analyzed breast cancer cell line derived RNA aliquots using Agilent cDNA and Affymetrix oligonucleotide microarray platforms to assess the advantage of this method. We show, that at different levels of the analysis, including gene expression ratios and difference calls, cross-platform consistency is significantly improved by sequence- based matching. We also present evidence that sequence-based probe matching produces more consistent results when comparing similar biological data sets obtained by different microarray platforms. This strategy allowed a more efficient transfer of classification of breast cancer samples between data sets produced by cDNA microarray and Affymetrix gene-chip platforms. PMID:15161944

  9. The Medicago truncatula gene expression atlas web server

    PubMed Central

    2009-01-01

    Background Legumes (Leguminosae or Fabaceae) play a major role in agriculture. Transcriptomics studies in the model legume species, Medicago truncatula, are instrumental in helping to formulate hypotheses about the role of legume genes. With the rapid growth of publically available Affymetrix GeneChip Medicago Genome Array GeneChip data from a great range of tissues, cell types, growth conditions, and stress treatments, the legume research community desires an effective bioinformatics system to aid efforts to interpret the Medicago genome through functional genomics. We developed the Medicago truncatula Gene Expression Atlas (MtGEA) web server for this purpose. Description The Medicago truncatula Gene Expression Atlas (MtGEA) web server is a centralized platform for analyzing the Medicago transcriptome. Currently, the web server hosts gene expression data from 156 Affymetrix GeneChip® Medicago genome arrays in 64 different experiments, covering a broad range of developmental and environmental conditions. The server enables flexible, multifaceted analyses of transcript data and provides a range of additional information about genes, including different types of annotation and links to the genome sequence, which help users formulate hypotheses about gene function. Transcript data can be accessed using Affymetrix probe identification number, DNA sequence, gene name, functional description in natural language, GO and KEGG annotation terms, and InterPro domain number. Transcripts can also be discovered through co-expression or differential expression analysis. Flexible tools to select a subset of experiments and to visualize and compare expression profiles of multiple genes have been implemented. Data can be downloaded, in part or full, in a tabular form compatible with common analytical and visualization software. The web server will be updated on a regular basis to incorporate new gene expression data and genome annotation, and is accessible at: http

  10. Identification of TTP mRNA targets in human dendritic cells reveals TTP as a critical regulator of dendritic cell maturation.

    PubMed

    Emmons, Jillian; Townley-Tilson, W H Davin; Deleault, Kristen M; Skinner, Stephen J; Gross, Robert H; Whitfield, Michael L; Brooks, Seth A

    2008-05-01

    Dendritic cells provide a critical link between innate and adaptive immunity and are essential to prime a naive T-cell response. The transition from immature dendritic cells to mature dendritic cells involves numerous changes in gene expression; however, the role of post-transcriptional changes in this process has been largely ignored. Tristetraprolin is an AU-rich element mRNA-binding protein that has been shown to regulate the stability of a number of cytokines and chemokines of mRNAs. Using TTP immunoprecipitations and Affymetrix GeneChips, we identified 393 messages as putative TTP mRNA targets in human dendritic cells. Gene ontology analysis revealed that approximately 25% of the identified mRNAs are associated with protein synthesis. We also identified six MHC Class I alleles, five MHC Class II alleles, seven chemokine and chemokine receptor genes, indoleamine 2,3 dioxygenase, and CD86 as putative TTP ligands. Real-time PCR was used to validate the GeneChip data for 15 putative target genes and functional studies performed for six target genes. These data establish that TTP regulates the expression of DUSP1, IDO, SOD2, CD86, and MHC Class I-B and F via the 3'-untranslated region of each gene. A novel finding is the demonstration that TTP can interact with and regulate the expression of non-AU-rich element-containing messages. The data implicate TTP as having a broader role in regulating and limiting the immune response than previously suspected. PMID:18367721

  11. Quality Control Usage in High-Density Microarrays Reveals Differential Gene Expression Profiles in Ovarian Cancer.

    PubMed

    Villegas-Ruiz, Vanessa; Moreno, Jose; Jacome-Lopez, Karina; Zentella-Dehesa, Alejandro; Juarez-Mendez, Sergio

    2016-01-01

    There are several existing reports of microarray chip use for assessment of altered gene expression in different diseases. In fact, there have been over 1.5 million assays of this kind performed over the last twenty years, which have influenced clinical and translational research studies. The most commonly used DNA microarray platforms are Affymetrix GeneChip and Quality Control Software along with their GeneChip Probe Arrays. These chips are created using several quality controls to confirm the success of each assay, but their actual impact on gene expression profiles had not been previously analyzed until the appearance of several bioinformatics tools for this purpose. We here performed a data mining analysis, in this case specifically focused on ovarian cancer, as well as healthy ovarian tissue and ovarian cell lines, in order to confirm quality control results and associated variation in gene expression profiles. The microarray data used in our research were downloaded from ArrayExpress and Gene Expression Omnibus (GEO) and analyzed with Expression Console Software using RMA, MAS5 and Plier algorithms. The gene expression profiles were obtained using Partek Genomics Suite v6.6 and data were visualized using principal component analysis, heat map, and Venn diagrams. Microarray quality control analysis showed that roughly 40% of the microarray files were false negative, demonstrating over- and under-estimation of expressed genes. Additionally, we confirmed the results performing second analysis using independent samples. About 70% of the significant expressed genes were correlated in both analyses. These results demonstrate the importance of appropriate microarray processing to obtain a reliable gene expression profile. PMID:27268623

  12. Comparative analysis of temporal gene expression patterns in the developing ovary of the embryonic chicken

    PubMed Central

    YU, Minli; XU, Yali; YU, Defu; YU, Debing; DU, Wenxing

    2015-01-01

    Many genes participate in the process of ovarian germ cell development, while the combined action mechanisms of these molecular regulators still need clarification. The present study was focused on determination of differentially expressed genes and gene functions at four critical time points in chicken ovarian development. Comparative transcriptional profiling of ovaries from embryonic day 5.5 (E5.5), E12.5, E15.5 and E18.5 was performed using an Affymetrix GeneChip chicken genome microarray. Differential expression patterns for genes specifically depleted and enriched in each stage were identified. The results showed that most of the up- and downregulated genes were involved in the metabolism of retinoic acid (RA) and synthesis of hormones. Among them, a higher number of up- and downregulated genes in the E15.5 ovary were identified as being involved in steroid biosynthesis and retinol metabolism, respectively. To validate gene changes, expressions of twelve candidate genes related to germ cell development were examined by real-time PCR and found to be consistent with the of GeneChip data. Moreover, the immunostaining results suggested that ovarian development during different stages was regulated by different genes. Furthermore, a Raldh2 knockdown chicken model was produced to investigate the fundamental role of Raldh2 in meiosis initiation. It was found that meiosis occurred abnormally in Raldh2 knockdown ovaries, but the inhibitory effect on meiosis was reversed by the addition of exogenous RA. This study offers insights into the profile of gene expression and mechanisms regulating ovarian development, especially the notable role of Raldh2 in meiosis initiation in the chicken. PMID:25736178

  13. MIMAS 3.0 is a Multiomics Information Management and Annotation System

    PubMed Central

    Gattiker, Alexandre; Hermida, Leandro; Liechti, Robin; Xenarios, Ioannis; Collin, Olivier; Rougemont, Jacques; Primig, Michael

    2009-01-01

    Background DNA sequence integrity, mRNA concentrations and protein-DNA interactions have been subject to genome-wide analyses based on microarrays with ever increasing efficiency and reliability over the past fifteen years. However, very recently novel technologies for Ultra High-Throughput DNA Sequencing (UHTS) have been harnessed to study these phenomena with unprecedented precision. As a consequence, the extensive bioinformatics environment available for array data management, analysis, interpretation and publication must be extended to include these novel sequencing data types. Description MIMAS was originally conceived as a simple, convenient and local Microarray Information Management and Annotation System focused on GeneChips for expression profiling studies. MIMAS 3.0 enables users to manage data from high-density oligonucleotide SNP Chips, expression arrays (both 3'UTR and tiling) and promoter arrays, BeadArrays as well as UHTS data using MIAME-compliant standardized vocabulary. Importantly, researchers can export data in MAGE-TAB format and upload them to the EBI's ArrayExpress certified data repository using a one-step procedure. Conclusion We have vastly extended the capability of the system such that it processes the data output of six types of GeneChips (Affymetrix), two different BeadArrays for mRNA and miRNA (Illumina) and the Genome Analyzer (a popular Ultra-High Throughput DNA Sequencer, Illumina), without compromising on its flexibility and user-friendliness. MIMAS, appropriately renamed into Multiomics Information Management and Annotation System, is currently used by scientists working in approximately 50 academic laboratories and genomics platforms in Switzerland and France. MIMAS 3.0 is freely available via . PMID:19450266

  14. Neuroprotective changes of striatal degeneration-related gene expression by acupuncture in an MPTP mouse model of Parkinsonism: microarray analysis.

    PubMed

    Choi, Yeong-Gon; Yeo, Sujung; Hong, Yeon-Mi; Lim, Sabina

    2011-04-01

    Acupuncture at acupoints GB34 and LR3 has been reported to inhibit nigrostriatal degeneration in Parkinsonism models, yet the genes related to this preventive effect of acupuncture on the nigrostriatal dopaminergic system remain elusive. This study investigated gene expression profile changes in the striatal region of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced Parkinsonism models after acupuncture at the acupoints GB34 and LR3 using a whole transcript genechip microarray (Affymetrix genechip mouse gene 1.0 ST array). It was confirmed that acupuncture at these acupoints could inhibit the decrease of tyrosine hydroxylase and dopamine transporter in the nigrostriatal region of the MPTP model while acupuncture at the non-acupoints could not counteract this decrease. Genechip gene array analysis (fold change cutoff 1.3 and P < 0.05) showed that 12 of the 69 probes up-regulated in MPTP when compared to the control were down-regulated by acupuncture at the acupoints. Of these 12 probes, 11 probes (nine annotated genes) were exclusively down-regulated by acupuncture only at the acupoints; the Gfral gene was excluded because it was commonly down-regulated by acupuncture at both the acupoints and the non-acupoints. In addition, 28 of the 189 probes down-regulated in MPTP when compared to the control were up-regulated by acupuncture at the acupoints. Of these 28 probes, 19 probes (seven annotated genes) were exclusively up-regulated by acupuncture only at the acupoints while nine probes were commonly up-regulated by acupuncture at both the acupoints and the non-acupoints. The regulation patterns of representative genes in real-time RT-PCR correlated with those of the genes in the microarray. These results suggest that the 30 probes (16 annotated genes), which are affected by MPTP and acupuncture only at the acupoints, are responsible for exerting in the striatal regions the inhibitory effect of acupuncture at the acupoints on MPTP-induced striatal

  15. New insights into the pathogenesis of cystic follicles in cattle: microarray analysis of gene expression in granulosa cells.

    PubMed

    Grado-Ahuir, J A; Aad, P Y; Spicer, L J

    2011-06-01

    Ovarian follicular growth and development are regulated by extraovarian and intraovarian factors, which influence granulosa cell proliferation and differentiation. However, the molecular mechanisms that drive follicular growth are not completely understood. Ovarian follicular cysts are one of the most common causes of reproductive failure in dairy cattle. Nevertheless, the primary cause of cyst formation has not been clearly established. A gene expression comparison may aid in elucidating the causes of ovarian cyst disease. Our objective was to identify differentially expressed genes in ovarian granulosa cells between normal dominant and cystic follicles of cattle. Granulosa cells and follicular fluid were isolated from dominant and cystic follicles collected via either ultrasound-guided aspiration from dairy cows (n = 24) or slaughterhouse ovaries from beef cows (n = 23). Hormonal analysis for progesterone, estradiol, and androstenedione in follicular fluid was performed by RIA. Total RNA was extracted and hybridized to 6 Affymetrix GeneChip Bovine Genome Arrays (Affymetrix, Santa Clara, CA). Abundance of mRNA for differentially expressed selected genes was determined through quantitative real-time reverse-transcription PCR. Follicular cysts showed greater (P < 0.05) progesterone, lesser (P < 0.05) estradiol, and no differences (P > 0.10) in androstenedione concentrations compared with noncystic follicles. A total of 163 gene sequences were differentially expressed (P < 0.01), with 19 upregulated and 144 downregulated. From selected target genes, quantitative real-time reverse-transcription PCR confirmed angiogenin, PGE(2) receptor 4, and G-protein coupled receptor 34 genes as upregulated in cystic follicles, and Indian hedgehog protein precursor and secreted frizzled-related protein 4 genes as downregulated in cystic follicles. Further research is required to elucidate the role of these factors in follicular development and cyst formation. PMID:21239663

  16. Microarray analysis of microRNA expression in mouse fetus at 13.5 and 14.5 days post-coitum in ear and back skin tissues.

    PubMed

    Torres, Leda; Juárez, Ulises; García, Laura; Miranda-Ríos, Juan; Frias, Sara

    2016-09-01

    There is no information regarding the role of microRNAs in the development of the external ear in mammals. The purpose of this study was to determine the stage-specific expression of microRNA during external ear development in mice under normal conditions. GeneChip miRNA 3.0 arrays by Affymetrix were used to obtain miRNA expression profiles from mice fetal pinnae and back skin tissues at 13.5 days-post-coitum (dpc) and 14.5 dpc. Biological triplicates for each tissue were analyzed; one litter represents one biological replica, each litter had 16 fetuses on average. The results were analyzed with Affymetrix's Transcriptome Analysis Console software to identify differentially expressed miRNAs. The inquiry showed significant differential expression of 25 miRNAs at 13.5 dpc and 31 at 14.5 dpc, some of these miRNAs were predicted to target genes implicated in external ear development. One example is mmu-miR-10a whose low expression in pinnae is known to impact ear development by modulating Hoxa1 mRNA levels Garzon et al. (2006), Gavalas et al. (1998) [1], [2]. Other findings like the upregulation of mmu-miR-200c and mmu-miR-205 in the pinnae tissues of healthy mice are in agreement with what has been reported in human patients with microtia, in which down regulation of both miRNAs has been found Li et al. (2013) [3]. This study uncovered a spatiotemporal pattern of miRNA expression in the external ear, which results from continuous transcriptional changes during normal development of body structures. All microarray data are available at the Gene Expression Omnibus (GEO) at NCBI under accession number GSE64945. PMID:27408816

  17. Gene Expression Changes With Time in Skeletal Muscle of Severely Burned Children

    PubMed Central

    Dasu, Mohan R. K.; Barrow, Robert E.; Herndon, David N.

    2005-01-01

    Objective: The purpose of this study was to identify gene-expression changes in leg muscle for up to 24 months after a severe thermal injury. Summary Background Data: Hypermetabolism associated with severe burns was thought to cease with wound healing and closure. It has been recently shown that hypermetabolism does not completely resolve after healing, and muscle catabolism continues after hospital discharge; however, just how long after discharge has not been established. Methods: Six children, admitted to our hospital within 1 week after injury, were studied. Patients ranged in age from 3 to 18 years, with flame or scald burns covering more than 40% of their body surface area. At 1.5, 6, 12, 18, and 24 months postburn, a biopsy of the vastus lateralis muscle was taken and snap frozen at −80°C. Total RNA was isolated and in vitro transcribed and hybridized to HG-U95 Av.2 Affymetrix arrays. The images were scanned and analyzed using Affymetrix GeneChip Analysis Suite 5.2 and dChip programs. Using 1 to 7 days after injury as baseline, comparisons were made of expression profiles at the various time intervals after injury. Results: When comparisons are made to nonburned children, 38 genes were significantly altered at 1.5 months, 10 genes remained altered at 6 months, 4 remained altered at 12 months, and 2 at 18 months. No differences could be shown at 24 months. Western blot analysis of β-2 microglobulin and myosin light chain was used to corroborate the microarray data. Conclusions: Gene changes can be identified for up to 18 months after burn but not at 24 months. These gene changes may provide information concerning what genes in skeletal muscle contribute to recovery from burn trauma. PMID:15798467

  18. Gene expression profiling in adipose tissue from growing broiler chickens

    PubMed Central

    Hausman, Gary J; Barb, C Rick; Fairchild, Brian D; Gamble, John; Lee-Rutherford, Laura

    2014-01-01

    In this study, total RNA was collected from abdominal adipose tissue samples obtained from ten broiler chickens at 3, 4, 5, and 6 weeks of age and prepared for gene microarray analysis with Affymetrix GeneChip Chicken Genome Arrays (Affymetrix) and quantitative real-time PCR analysis. Studies of global gene expression in chicken adipose tissue were initiated since such studies in many animal species show that adipose tissue expresses and secretes many factors that can influence growth and physiology. Microarray results indicated 333 differentially expressed adipose tissue genes between 3 and 6 wk, 265 differentially expressed genes between 4 and 6 wk and 42 differentially expressed genes between 3 and 4 wk. Enrichment scores of Gene Ontology Biological Process categories indicated strong age upregulation of genes involved in the immune system response. In addition to microarray analysis, quantitative real-time PCR analysis was used to confirm the influence of age on the expression of adipose tissue CC chemokine ligands (CCL), toll-like receptor (TLR)-2, lipopolysaccharide-induced TNF factor (LITAF), chemokine (C-C motif) receptor 8 (CCR8), and several other genes. Between 3 and 6 wk of age CCL5, CCL1, and CCR8 expression increased (P = 0.0001) with age. Furthermore, TLR2, CCL19, and LITAF expression increased between 4 and 6 wk of age (P = 0.001). This is the first demonstration of age related changes in CCL, LITAF, and TLR2 gene expression in chicken adipose tissue. Future studies are needed to elucidate the role of these adipose tissue genes in growth and the immune system. PMID:26317054

  19. High-resolution SNP arrays in mental retardation diagnostics: how much do we gain?

    PubMed Central

    Bernardini, Laura; Alesi, Viola; Loddo, Sara; Novelli, Antonio; Bottillo, Irene; Battaglia, Agatino; Digilio, Maria Cristina; Zampino, Giuseppe; Ertel, Adam; Fortina, Paolo; Surrey, Saul; Dallapiccola, Bruno

    2010-01-01

    We used Affymetrix 6.0 GeneChip SNP arrays to characterize copy number variations (CNVs) in a cohort of 70 patients previously characterized on lower-density oligonucleotide arrays affected by idiopathic mental retardation and dysmorphic features. The SNP array platform includes ∼900 000 SNP probes and 900 000 non-SNP oligonucleotide probes at an average distance of 0.7 Kb, which facilitates coverage of the whole genome, including coding and noncoding regions. The high density of probes is critical for detecting small CNVs, but it can lead to data interpretation problems. To reduce the number of false positives, parameters were set to consider only imbalances >75 Kb encompassing at least 80 probe sets. The higher resolution of the SNP array platform confirmed the increased ability to detect small CNVs, although more than 80% of these CNVs overlapped to copy number ‘neutral' polymorphism regions and 4.4% of them did not contain known genes. In our cohort of 70 patients, of the 51 previously evaluated as ‘normal' on the Agilent 44K array, the SNP array platform disclosed six additional CNV changes, including three in three patients, which may be pathogenic. This suggests that about 6% of individuals classified as ‘normal' using the lower-density oligonucleotide array could be found to be affected by a genomic disorder when evaluated with the higher-density microarray platforms. PMID:19809473

  20. Endophytic colonization of barley (Hordeum vulgare) roots by the nematophagous fungus Pochonia chlamydosporia reveals plant growth promotion and a general defense and stress transcriptomic response.

    PubMed

    Larriba, Eduardo; Jaime, María D L A; Nislow, Corey; Martín-Nieto, José; Lopez-Llorca, Luis Vicente

    2015-07-01

    Plant crop yields are negatively conditioned by a large set of biotic and abiotic factors. An alternative to mitigate these adverse effects is the use of fungal biological control agents and endophytes. The egg-parasitic fungus Pochonia chlamydosporia has been traditionally studied because of its potential as a biological control agent of plant-parasitic nematodes. This fungus can also act as an endophyte in monocot and dicot plants, and has been shown to promote plant growth in different agronomic crops. An Affymetrix 22K Barley GeneChip was used in this work to analyze the barley root transcriptomic response to P. chlamydosporia root colonization. Functional gene ontology (GO) and gene set enrichment analyses showed that genes involved in stress response were enriched in the barley transcriptome under endophytism. An 87.5% of the probesets identified within the abiotic stress response group encoded heat shock proteins. Additionally, we found in our transcriptomic analysis an up-regulation of genes implicated in the biosynthesis of plant hormones, such as auxin, ethylene and jasmonic acid. Along with these, we detected induction of brassinosteroid insensitive 1-associated receptor kinase 1 (BR1) and other genes related to effector-triggered immunity (ETI) and pattern-triggered immunity (PTI). Our study supports at the molecular level the growth-promoting effect observed in plants endophytically colonized by P. chlamydosporia, which opens the door to further studies addressing the capacity of this fungus to mitigate the negative effects of biotic and abiotic factors on plant crops. PMID:25982739

  1. Homozygous sequence variants in the FKBP10 gene underlie osteogenesis imperfecta in consanguineous families.

    PubMed

    Umair, Muhammad; Hassan, Annum; Jan, Abid; Ahmad, Farooq; Imran, Muhammad; Samman, Muhammad I; Basit, Sulman; Ahmad, Wasim

    2016-03-01

    Osteogenesis imperfecta (OI, MIM 610968) is a genetically and clinically heterogeneous disorder characterized by bone fragility. It is one of the rare forms of skeletal deformity caused by sequence variants in at least 14 different genes, including FKBP10 (MIM 607063) encoding protein FKBP65. Here we present three consanguineous families of Pakistani origin segregating OI in an autosomal-recessive pattern. Genotyping using either single-nucleotide polymorphism markers by Affymetrix GeneChip Human Mapping 250K Nsp array or polymorphic microsatellite markers revealed a homozygous region, containing a candidate gene FKBP10, among affected members on chromosome 17q21.2. Sequencing the FKBP10 gene revealed a homozygous novel nonsense variant (c.1490G>A, p.Trp497*) in the family A and two previously reported variants, including a missense (c.344G>A, p.Arg115Gln), in the family B and duplication of a nucleotide C (c.831dupC, p.Gly278ArgfsX295) in the family C. Our findings further extend the body of evidence that supports the importance of FKBP10 gene in the development of skeletal system. PMID:26538303

  2. Differential Tomato Transcriptomic Responses Induced by Pepino Mosaic Virus Isolates with Differential Aggressiveness1[W][OA

    PubMed Central

    Hanssen, Inge M.; Peter van Esse, H.; Ballester, Ana-Rosa; Hogewoning, Sander W.; Parra, Nelia Ortega; Paeleman, Anneleen; Lievens, Bart; Bovy, Arnaud G.; Thomma, Bart P.H.J.

    2011-01-01

    Pepino mosaic virus (PepMV) is a highly infectious potexvirus and a major disease of greenhouse tomato (Solanum lycopersicum) crops worldwide. Damage and economic losses caused by PepMV vary greatly and can be attributed to differential symptomatology caused by different PepMV isolates. Here, we used a custom-designed Affymetrix tomato GeneChip array with probe sets to interrogate over 22,000 tomato transcripts to study transcriptional changes in response to inoculation of tomato seedlings with a mild and an aggressive PepMV isolate that share 99.4% nucleotide sequence identity. The two isolates induced a different transcriptomic response, despite accumulating to similar viral titers. PepMV inoculation resulted in repression of photosynthesis. In addition, defense responses were stronger upon inoculation with the aggressive isolate, in both cases mediated by salicylic acid signaling rather than by jasmonate signaling. Our results furthermore show that PepMV differentially regulates the RNA silencing pathway, suggesting a role for a PepMV-encoded silencing suppressor. Finally, perturbation of pigment biosynthesis, as shown by differential regulation of the flavonoid and lycopene biosynthesis pathways, was monitored. Metabolite analyses on mature fruits of PepMV-infected tomato plants, which showed typical fruit marbling, revealed a decrease in carotenoids, likely responsible for the marbled phenotype, and an increase in alkaloids and phenylpropanoids that are associated with pathogen defense in the yellow sectors of the fruit. PMID:21427280

  3. Gene Expression Signatures in Polyarticular Juvenile Idiopathic Arthritis Demonstrate Disease Heterogeneity and Offer a Molecular Classification of Disease Subsets

    PubMed Central

    Griffin, Thomas A.; Barnes, Michael G.; Ilowite, Norman T.; Olson, Judyann C.; Sherry, David D.; Gottlieb, Beth S.; Aronow, Bruce J.; Pavlidis, Paul; Hinze, Claas; Thornton, Sherry; Thompson, Susan D.; Grom, Alexei A.; Colbert, Robert A.; Glass, David N.

    2009-01-01

    Objective Microarray analysis was used to determine whether children with recent onset polyarticular juvenile idiopathic arthritis (JIA) exhibit biologically or clinically informative gene expression signatures in peripheral blood mononuclear cells (PBMC). Methods Peripheral blood samples were obtained from 59 healthy children and 61 children with polyarticular JIA prior to treatment with second-line medications, such as methotrexate or biological agents. RNA was extracted from Ficoll-isolated mononuclear cells, fluorescently labeled and hybridized to Affymetrix U133 Plus 2.0 GeneChips. Data were analyzed using ANOVA at a 5% false discovery rate threshold after Robust Multi-Array Average pre-processing and Distance Weighted Discrimination normalization. Results Initial analysis revealed 873 probe sets for genes that were differentially expressed between polyarticular JIA and controls. Hierarchical clustering of these probe sets distinguished three subgroups within polyarticular JIA. Prototypical subjects within each subgroup were identified and used to define subgroup-specific gene expression signatures. One of these signatures was associated with monocyte markers, another with transforming growth factor β-inducible genes, and a third with immediate-early genes. Correlation of gene expression signatures with clinical and biological features of JIA subgroups suggests relevance to aspects of disease activity and supports the division of polyarticular JIA into distinct subsets. Conclusions PBMC gene expression signatures in recent onset polyarticular JIA reflect discrete disease processes and offer a molecular classification of disease. PMID:19565504

  4. Arabidopsis gene expression patterns during spaceflight

    NASA Astrophysics Data System (ADS)

    Paul, A.-L.; Ferl, R. J.

    The exposure of Arabidopsis thaliana (Arabidopsis) plants to spaceflight environments resulted in the differential expression of hundreds of genes. A 5 day mission on orbiter Columbia in 1999 (STS-93) carried transgenic Arabidopsis plants engineered with a transgene composed of the alcohol dehydrogenase (Adh) gene promoter linked to the β -Glucuronidase (GUS) reporter gene. The plants were used to evaluate the effects of spaceflight on two fronts. First, expression patterns visualized with the Adh/GUS transgene were used to address specifically the possibility that spaceflight induces a hypoxic stress response, and to assess whether any spaceflight response was similar to control terrestrial hypoxia-induced gene expression patterns. (Paul et al., Plant Physiol. 2001, 126:613). Second, genome-wide patterns of native gene expression were evaluated utilizing the Affymetrix ATH1 GeneChip? array of 8,000 Arabidopsis genes. As a control for the veracity of the array analyses, a selection of genes identified with the arrays was further characterized with quantitative Real-Time RT PCR (ABI - TaqmanTM). Comparison of the patterns of expression for arrays of hybridized with RNA isolated from plants exposed to spaceflight compared to the control arrays revealed hundreds of genes that were differentially expressed in response to spaceflight, yet most genes that are hallmarks of hypoxic stress were unaffected. These results will be discussed in light of current models for plant responses to the spaceflight environment, and with regard to potential future flight opportunities.

  5. Fine mapping of stable QTLs related to eating quality in rice (Oryza sativa L.) by CSSLs harboring small target chromosomal segments

    PubMed Central

    Li, Jingjing; Zhang, Wenwei; Wu, Hongkai; Guo, Tao; Liu, Xiaolu; Wan, Xiangyuan; Jin, Jiansheng; Hanh, Than Thi Thu; Thoa, Nguyen Thi Nhu; Chen, Mingjiang; Liu, Shijia; Chen, Liangming; Liu, Xi; Wang, Jiankang; Zhai, Huqu; Wan, Jianmin

    2011-01-01

    Amylose content (AC) and viscosity profile are primary indices for evaluating eating and cooking qualities of rice grain. Using chromosome segment substitution lines (CSSLs), previous studies identified a QTL cluster of genes for rice eating and cooking quality in the interval R727–G1149 on chromosome 8. In this study we report two QTLs for viscosity parameters, respectively controlling setback viscosity (SBV) and consistency viscosity (CSV), located in the same interval using rapid viscosity analyzer (RVA) profile as an indicator of eating quality. Previously reported QTL for AC was dissected into two components with opposite genetic effects. Of four QTLs, qCSV-8 and qAC-8-2 had stable genetic effects across three and four environments, respectively. qSBV-8, qCSV-8 and qAC-8-1 partly overlapped, but were separated from qAC-8-2. Based on data from an Affymetrix rice GeneChip, two genes related to starch biosynthesis at the qAC-8-2 locus were chosen for further quantitative expression analysis. Both genes showed enhanced expression in sub-CSSLs carrying the target qAC-8-2 allele, but not in sub-CSSLs without the target qAC-8-2 allele, indicating their possible role in rice quality determination. Molecular markers closely linked to the two stable QTL provide the opportunity for marker-assisted selection (MAS) in breeding high quality rice. PMID:23136470

  6. Gene Expression Profiling of Microdissected Pancreatic Ductal Carcinomas Using High-Density DNA Microarrays1,3

    PubMed Central

    Grützmann, Robert; Pilarsky, Christian; Ammerpohl, Ole; Lüttges, Jutta; Böhme, Armin; Sipos, Bence; Foerder, Melanie; Alldinger, Ingo; Jahnke, Beatrix; Schackert, Hans Konrad; Kalthoff, Holger; Kremer, Bernd; Klöppel, Günter; Saeger, Hans Detlev

    2004-01-01

    Abstract Pancreatic ductal adenocarcinoma (PDAC) remains an important cause of malignancy-related death and is the eighth most common cancer with the lowest overall 5-year relative survival rate. To identify new molecular markers and candidates for new therapeutic regimens, we investigated the gene expression profile of microdissected cells from 11 normal pancreatic ducts, 14 samples of PDAC, and 4 well-characterized pancreatic cancer cell lines using the Affymetrix U133 GeneChip set. RNA was extracted from microdissected samples and cell lines, amplified, and labeled using a repetitive in vitro transcription protocol. Differentially expressed genes were identified using the significance analysis of microarrays program. We found 616 differentially expressed genes. Within these, 140 were also identified in PDAC by others, such as Galectin-1, Galectin-3, and MT-SP2. We validated the differential expression of several genes (e.g., CENPF, MCM2, MCM7, RAMP, IRAK1, and PTTG1) in PDAC by immunohistochemistry and reverse transcription polymerase chain reaction. We present a whole genome expression study of microdissected tissues from PDAC, from microdissected normal ductal pancreatic cells and pancreatic cancer cell lines using highdensity microarrays. Within the panel of genes, we identified novel differentially expressed genes, which have not been associated with the pathogenesis of PDAC before. PMID:15548371

  7. Molecular subtypes of serous borderline ovarian tumor show distinct expression patterns of benign tumor and malignant tumor-associated signatures.

    PubMed

    Curry, Edward W J; Stronach, Euan A; Rama, Nona R; Wang, Yuepeng Y P; Gabra, Hani; El-Bahrawy, Mona A

    2014-03-01

    Borderline ovarian tumors show heterogeneity in clinical behavior. Most have excellent prognosis, although a small percentage show recurrence or progressive disease, usually to low-grade serous carcinoma. The aim of this study was to understand the molecular relationship between these entities and identify potential markers of tumor progression and therapeutic targets. We studied gene expression using Affymetrix HGU133plus2 GeneChip microarrays in 3 low-grade serous carcinomas, 13 serous borderline tumors and 8 serous cystadenomas. An independent data set of 18 serous borderline tumors and 3 low-grade serous carcinomas was used for validation. Unsupervised clustering revealed clear separation of benign and malignant tumors, whereas borderline tumors showed two distinct groups, one clustering with benign and the other with malignant tumors. The segregation into benign- and malignant-like borderline molecular subtypes was reproducible on applying the same analysis to an independent publicly available data set. We identified 50 genes that separate borderline tumors into their subgroups. Functional enrichment analysis of genes that separate borderline tumors to the two subgroups highlights a cell adhesion signature for the malignant-like subset, with Claudins particularly prominent. This is the first report of molecular subtypes of borderline tumors based on gene expression profiling. Our results provide the basis for identification of biomarkers for the malignant potential of borderline ovarian tumor and potential therapeutic targets for low-grade serous carcinoma. PMID:23948749

  8. Gene expression from plants grown on the International Space Station

    NASA Astrophysics Data System (ADS)

    Stimpson, Alexander; Pereira, Rhea; Kiss, John Z.; Correll, Melanie

    Three experiments were performed on the International Space Station (ISS) in 2006 as part of the TROPI experiments. These experiments were performed to study graviTROPIsm and photoTROPIsm responses of Arabidopsis in microgravity (µg). Seedlings were grown with a variety of light and gravitational treatments for approximately five days. The frozen samples were returned to Earth during three space shuttle missions in 2007 and stored at -80° C. Due to the limited amount of plant biomass returned, new protocols were developed to minimize the amount of material needed for RNA extraction as a preparation for microarray analysis. Using these new protocols, RNA was extracted from several sets of seedlings grown in red light followed by blue light with one sample from 1.0g treatment and the other at µg. Using a 2-fold change criterion, microarray (Affymetrix, GeneChip) results showed that 613 genes were upregulated in the µg sample while 757 genes were downregulated. Upregulated genes in response to µg included transcription factors from the WRKY (15 genes), MYB (3) and ZF (8) families as well as those that are involved in auxin responses (10). Downregulated genes also included transcription factors such as MYB (5) and Zinc finger (10) but interestingly only two WRKY family genes were down-regulated during the µg treatment. Studies are underway to compare these results with other samples to identify the genes involved in the gravity and light signal transduction pathways (this project is Supported By: NASA NCC2-1200).

  9. A roadmap for zinc trafficking in the developing barley grain based on laser capture microdissection and gene expression profiling

    PubMed Central

    Tauris, Birgitte; Borg, Søren; Gregersen, Per L.; Holm, Preben B.

    2009-01-01

    Nutrients destined for the developing cereal grain encounter several restricting barriers on their path towards their final storage sites in the grain. In order to identify transporters and chelating agents that may be involved in transport and deposition of zinc in the barley grain, expression profiles have been generated of four different tissue types: the transfer cells, the aleurone layer, the endosperm, and the embryo. Cells from these tissues were isolated with the ‘laser capture microdissection’ technology and the extracted RNA was subjected to three rounds of T7-based amplification. The amplified RNA was subsequently hybridized to Affymetrix 22K Barley GeneChips. Due to the short average length of the amplified transcripts and the positioning of numerous probe sets at locations more than 400 base pairs (bp) from the poly(A)-tail, a normalization approach was used where the probe positions were taken into account. On the basis of the expression levels of a number of metal homeostasis genes, a working model is proposed for the translocation of zinc from the phloem to the storage sites in the developing grain. PMID:19297552

  10. Characterization of DNA reactive and non-DNA reactive anticancer drugs by gene expression profiling.

    PubMed

    Le Fevre, Anne-Celine; Boitier, Eric; Marchandeau, Jean-Pierre; Sarasin, Alain; Thybaud, Veronique

    2007-06-01

    Gene expression profiling technology is expected to advance our understanding of genotoxic mechanisms involving direct or indirect interaction with DNA. We exposed human lymphoblastoid TK6 cells to 14 anticancer drugs (vincristine, paclitaxel, etoposide, daunorubicin, camptothecin, amsacrine, cytosine arabinoside, hydroxyurea, methotrexate, 5-fluorouracil, cisplatin, 1-(2-chloroethyl)-3-cyclohexyl-1-nitrosourea (CCNU), 1,3-bis (2-chloroethyl)-1-nitrosourea (BCNU), and bleomycin) for 4-h and examined them immediately or after a 20-h recovery period. Cytotoxicity and genotoxicity, respectively, were evaluated by cell counting and by in vitro micronucleus assay at 24h. Effects on the cell cycle were determined by flow cytometry at 4 and 24h. Gene expression was profiled at both sampling times by using human Affymetrix U133A GeneChips (22K). Bioanalysis was done with Resolver/Rosetta software and an in-house annotation program. Cell cycle analysis and gene expression profiling allowed us to classify the drugs according to their mechanisms of action. The molecular signature is composed of 28 marker genes mainly involved in signal transduction and cell cycle pathways. Our results suggest that these marker genes could be used as a predictive model to classify genotoxins according to their direct or indirect interaction with DNA. PMID:17374387

  11. Global gene expression profiling in larval zebrafish exposed to microcystin-LR and microcystis reveals endocrine disrupting effects of Cyanobacteria.

    PubMed

    Rogers, Emily D; Henry, Theodore B; Twiner, Michael J; Gouffon, Julia S; McPherson, Jackson T; Boyer, Gregory L; Sayler, Gary S; Wilhelm, Steven W

    2011-03-01

    Microcystis blooms occur worldwide and threaten aquatic ecosystems and human health. Sublethal effects on early developmental stages of fish are largely unknown, and research has mainly focused on microcystin toxins (such as MC-LR) rather than Microcystis cells. We exposed (96 h) zebrafish larvae to purified MC-LR (0-1000 μg/L) or lyophilized Microcystis aeruginosa containing 4.5 μg/L MC-LR and evaluated changes in global gene expression (Affymetrix GeneChip zebrafish genome arrays). Significant changes in gene expression (≥ 1.7-fold change, p < 0.0001) were determined with Rosetta Resolver 7.0, and ontology analysis was conducted with the DAVID bioinformatics tool. The number of differentially expressed genes relative to control increased with MC-LR concentration and included genes related to known mechanisms of action for MC-LR in mammals and older life stages of fish, as well as genes unique to larval zebrafish. Up-regulation of vitellogenin genes (vtg) (19.2-fold to >100-fold on arrays; 619.3-fold confirmed by quantitative PCR) was observed in Microcystis-exposed larvae but not in larvae exposed to MC-LR. Up-regulation of vtg indicates exposure to estrogenic substance(s) and suggests that Microcystis may be a natural source of environmental estrogens. Concerns about effects of Microcystis blooms may extend beyond those associated with the microcystin toxin. PMID:21280650

  12. Age and Diet Affect Gene Expression Profile in Canine Skeletal Muscle

    PubMed Central

    Middelbos, Ingmar S.; Vester, Brittany M.; Karr-Lilienthal, Lisa K.; Schook, Lawrence B.; Swanson, Kelly S.

    2009-01-01

    We evaluated gene transcription in canine skeletal muscle (biceps femoris) using microarray analysis to identify effects of age and diet on gene expression. Twelve female beagles were used (six 1-year olds and six 12-year olds) and they were fed one of two experimental diets for 12 months. One diet contained primarily plant-based protein sources (PPB), whereas the second diet contained primarily animal-based protein sources (APB). Affymetrix GeneChip Canine Genome Arrays were used to hybridize extracted RNA. Age had the greatest effect on gene transcription (262 differentially expressed genes), whereas the effect of diet was relatively small (22 differentially expressed genes). Effects of age (regardless of diet) were most notable on genes related to metabolism, cell cycle and cell development, and transcription function. All these genes were predominantly down-regulated in geriatric dogs. Age-affected genes that were differentially expressed on only one of two diets were primarily noted in the PPB diet group (144/165 genes). Again, genes related to cell cycle (22/35) and metabolism (15/19) had predominantly decreased transcription in geriatric dogs, but 6/8 genes related to muscle development had increased expression. Effects of diet on muscle gene expression were mostly noted in geriatric dogs, but no consistent patterns in transcription were observed. The insight these data provide into gene expression profiles of canine skeletal muscle as affected by age, could serve as a foundation for future research pertaining to age-related muscle diseases. PMID:19221602

  13. Asymmetric Lower-Limb Malformations in Individuals with Homeobox PITX1 Gene Mutation

    PubMed Central

    Gurnett, Christina A.; Alaee, Farhang; Kruse, Lisa M.; Desruisseau, David M.; Hecht, Jacqueline T.; Wise, Carol A.; Bowcock, Anne M.; Dobbs, Matthew B.

    2008-01-01

    Clubfoot is one of the most common severe musculoskeletal birth defects, with a worldwide incidence of 1 in 1000 live births. In the present study, we describe a five-generation family with asymmetric right-sided predominant idiopathic clubfoot segregating as an autosomal-dominant condition with incomplete penetrance. Other lower-limb malformations, including patellar hypoplasia, oblique talus, tibial hemimelia, developmental hip dysplasia, and preaxial polydactyly, were also present in some family members. Genome-wide linkage analysis with Affymetrix GeneChip Mapping 10K mapping data from 13 members of this family revealed a multipoint LODmax of 3.31 on chromosome 5q31. A single missense mutation (c.388G→A) was identified in PITX1, a bicoid-related homeodomain transcription factor critical for hindlimb development, and segregated with disease in this family. The PITX1 E130K mutation is located in the highly conserved homeodomain and reduces the ability of PITX1 to transactivate a luciferase reporter. The PITX1 E130K mutation also suppresses wild-type PITX1 activity in a dose-dependent manner, suggesting dominant-negative effects on transcription. The propensity for right-sided involvement in tibial hemimelia and clubfoot suggests that PITX1, or pathways involving PITX1, may be involved in their etiology. Implication of a gene involved in early limb development in clubfoot pathogenesis also suggests additional pathways for future investigations of idiopathic clubfoot etiology in humans. PMID:18950742

  14. Comparative Microarray Analysis of Proliferating and Differentiating Murine ENS Progenitor Cells

    PubMed Central

    Neckel, Peter Helmut; Mohr, Roland; Zhang, Ying; Hirt, Bernhard; Just, Lothar

    2016-01-01

    Postnatal neural progenitor cells of the enteric nervous system are a potential source for future cell replacement therapies of developmental dysplasia like Hirschsprung's disease. However, little is known about the molecular mechanisms driving the homeostasis and differentiation of this cell pool. In this work, we conducted Affymetrix GeneChip experiments to identify differences in gene regulation between proliferation and early differentiation of enteric neural progenitors from neonatal mice. We detected a total of 1333 regulated genes that were linked to different groups of cellular mechanisms involved in cell cycle, apoptosis, neural proliferation, and differentiation. As expected, we found an augmented inhibition in the gene expression of cell cycle progression as well as an enhanced mRNA expression of neuronal and glial differentiation markers. We further found a marked inactivation of the canonical Wnt pathway after the induction of cellular differentiation. Taken together, these data demonstrate the various molecular mechanisms taking place during the proliferation and early differentiation of enteric neural progenitor cells. PMID:26697082

  15. Differing transcriptional responses to pulsed or continuous estradiol exposure in human umbilical vein endothelial cells.

    PubMed

    Li, Jin; Wang, Hongliang; Johnson, Suzanne M; Horner-Glister, Emma; Thompson, John; White, Ian N H; Al-Azzawi, Farook

    2008-07-01

    This study used human umbilical vein endothelial cells (HUVECs) that were treated with 17beta-estradiol for 5 days as 1h pulse or 24h continuous treatment at concentrations such that the 24h exposure (concentration x time) was identical in both conditions. Cell proliferation was studied and gene expression profiling was carried out using the Affymetrix GeneChip microarray analysis. Changes in morphology and apoptosis in HUVECs were examined with electron microscopy. Time-course studies of expression of genes vascular endothelial growth factor (VEGF), inducible nitric oxide synthase (iNOS) and endothelial nitric oxide synthase (eNOS) were performed by quantitative PCR. We observed that cell proliferation was significantly decreased over days 3-5 with pulsed estradiol treatment relative to constant exposure. Microarray results showed that after 5 days, 801 genes differed (P<0.05) between continuous versus pulsed estradiol treatment. Functional analysis showed a significant number of genes to be associated with apoptosis and cell cycle pathways. We did not find any evidence of apoptosis from flow cytometry or electron microscopy examination. Our study highlights a large number of significantly different molecular responses to estradiol depending upon the mode of administration of estradiol. Significant changes were observed in genes involved in apoptosis and proliferation including VEGF, IGF receptors, and tumor protein p53. PMID:18562193

  16. Dietary Inulin Supplementation Modifies Significantly the Liver Transcriptomic Profile of Broiler Chickens

    PubMed Central

    Sevane, Natalia; Bialade, Federica; Velasco, Susana; Rebolé, Almudena; Rodríguez, Maria Luisa; Ortiz, Luís T.; Cañón, Javier; Dunner, Susana

    2014-01-01

    Inclusion of prebiotics in the diet is known to be advantageous, with positive influences both on health and growth. The current study investigated the differences in the hepatic transcriptome profiles between chickens supplemented with inulin (a storage carbohydrate found in many plants) and controls. Liver is a major metabolic organ and has been previously reported to be involved in the modification of the lipid metabolism in chickens fed with inulin. A nutrigenomic approach through the analysis of liver RNA hybridized to the Affymetrix GeneChip Chicken Genome Array identified 148 differentially expressed genes among both groups: 104 up-regulated (≥1.4-fold) and 44 down-regulated (≤0.6-fold). Quantitative real-time PCR analysis validated the microarray expression results for five out of seven genes tested. The functional annotation analyses revealed a number of genes, processes and pathways with putative involvement in chicken growth and performance, while reinforcing the immune status of animals, and fostering the production of long chain fatty acids in broilers supplemented with 5 g of inulin kg−1 diet. As far as we are aware, this is the first report of a microarray based gene expression study on the effect of dietary inulin supplementation, supporting further research on the use of this prebiotic on chicken diets as a useful alternative to antibiotics for improving performance and general immunity in poultry farming, along with a healthier meat lipid profile. PMID:24915441

  17. A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma

    PubMed Central

    Stewart, Paul A.; Parapatics, Katja; Welsh, Eric A.; Müller, André C.; Cao, Haoyun; Fang, Bin; Koomen, John M.; Eschrich, Steven A.; Bennett, Keiryn L.; Haura, Eric B.

    2015-01-01

    We performed a pilot proteogenomic study to compare lung adenocarcinoma to lung squamous cell carcinoma using quantitative proteomics (6-plex TMT) combined with a customized Affymetrix GeneChip. Using MaxQuant software, we identified 51,001 unique peptides that mapped to 7,241 unique proteins and from these identified 6,373 genes with matching protein expression for further analysis. We found a minor correlation between gene expression and protein expression; both datasets were able to independently recapitulate known differences between the adenocarcinoma and squamous cell carcinoma subtypes. We found 565 proteins and 629 genes to be differentially expressed between adenocarcinoma and squamous cell carcinoma, with 113 of these consistently differentially expressed at both the gene and protein levels. We then compared our results to published adenocarcinoma versus squamous cell carcinoma proteomic data that we also processed with MaxQuant. We selected two proteins consistently overexpressed in squamous cell carcinoma in all studies, MCT1 (SLC16A1) and GLUT1 (SLC2A1), for further investigation. We found differential expression of these same proteins at the gene level in our study as well as in other public gene expression datasets. These findings combined with survival analysis of public datasets suggest that MCT1 and GLUT1 may be potential prognostic markers in adenocarcinoma and druggable targets in squamous cell carcinoma. Data are available via ProteomeXchange with identifier PXD002622. PMID:26539827

  18. High-Throughput Quantitative Analysis of the Human Intestinal Microbiota with a Phylogenetic Microarray▿

    PubMed Central

    Paliy, Oleg; Kenche, Harshavardhan; Abernathy, Frank; Michail, Sonia

    2009-01-01

    Gut microbiota carry out key functions in health and participate in the pathogenesis of a growing number of diseases. The aim of this study was to develop a custom microarray that is able to identify hundreds of intestinal bacterial species. We used the Entrez nucleotide database to compile a data set of bacterial 16S rRNA gene sequences isolated from human intestinal and fecal samples. Identified sequences were clustered into separate phylospecies groups. Representative sequences from each phylospecies were used to develop a microbiota microarray based on the Affymetrix GeneChip platform. The designed microbiota array contains probes to 775 different bacterial phylospecies. In our validation experiments, the array correctly identified genomic DNA from all 15 bacterial species used. Microbiota array has a detection sensitivity of at least 1 pg of genomic DNA and can detect bacteria present at a 0.00025% level of overall sample. Using the developed microarray, fecal samples from two healthy children and two healthy adults were analyzed for bacterial presence. Between 227 and 232 species were detected in fecal samples from children, whereas 191 to 208 species were found in adult stools. The majority of identified phylospecies belonged to the classes Clostridia and Bacteroidetes. The microarray revealed putative differences between the gut microbiota of healthy children and adults: fecal samples from adults had more Clostridia and less Bacteroidetes and Proteobacteria than those from children. A number of other putative differences were found at the genus level. PMID:19363078

  19. Transcriptional response of susceptible and tolerant citrus to infection with Candidatus Liberibacter asiaticus.

    PubMed

    Albrecht, Ute; Bowman, Kim D

    2012-04-01

    Candidatus Liberibacter asiaticus (Las), a non-culturable phloem-limited bacterium, is the suspected causal agent of huanglongbing (HLB) in Florida. HLB is one of the most devastating diseases of citrus and no resistant cultivars have been identified to date, though tolerance has been observed in the genus Poncirus and some of its hybrids. This study compares transcriptional changes in tolerant US-897 (Citrus reticulata Blanco×Poncirus trifoliata L. Raf.) and susceptible 'Cleopatra' mandarin (C. reticulata) seedlings in response to infection with Las using the Affymetrix GeneChip citrus array, with the main objective of identifying genes associated with tolerance to HLB. Microarray analysis identified 326 genes which were significantly upregulated by at least 4-fold in the susceptible genotype, compared with only 17 genes in US-897. Exclusively upregulated in US-897 was a gene for a 2-oxoglutarate (2OG) and Fe(II)-dependant oxygenase, an important enzyme involved in the biosynthesis of plant secondary metabolites. More than eight hundred genes were expressed at much higher levels in US-897 independent of infection with Las. Among these, genes for a constitutive disease resistance protein (CDR1) were notable. The possible involvement of these and other detected genes in tolerance to HLB and their possible use for biotechnology are discussed. PMID:22325873

  20. The transcription factor ccaat/enhancer binding protein β (C/EBPβ) and miR-27a regulate the expression of porcine Dickkopf2 (DKK2)

    PubMed Central

    Tao, Hu; Wang, Lei; Zhou, Jiawei; Pang, Panfei; Cai, Shanzhi; Li, Jialian; Mei, Shuqi; Li, Fenge

    2015-01-01

    Using Affymetrix porcine Gene-Chip analyses, we found that Dickkopf2 (DKK2), a WNT antagonist, is differentially expressed in pre-ovulatory follicles between Large White and Chinese Taihu sows. This study aims to identify the regulatory factors responsible for DKK2 expression. Deletion fragment and mutation analyses identified DKK2-D3 as the porcine DKK2 core promoter. There were four C/EBPβ binding sites within the DKK2 core promoter. The C allele that results from a spontaneous alteration (DKK2 c.−1130 T > C) in the core promoter was associated with a higher total number born (TNB) and a higher number born alive (NBA) in all parities in a synthetic pig population. This was possibly the result of a change in C/EBPβ binding ability, which was confirmed using chromatin immunoprecipitation (ChIP) and electrophoretic mobility shift assays (EMSA). Moreover, C/EBPβ specifically bound to and activated the DKK2 promoter, as revealed by mutation analysis, overexpression and RNA interference (RNAi) experiments. We also confirmed that miR-27a is a negative regulator of the DKK2 gene using miR-27a overexpression and inhibition experiments and mutation analyses. RTCA xCELLigence experiments showed that miR-27a suppressed Chinese hamster ovary (CHO) cell proliferation by down-regulating DKK2 gene expression. Taken together, our findings suggest that C/EBPβ and miR-27a control DKK2 transcription. PMID:26656471

  1. The transcription factor ccaat/enhancer binding protein β (C/EBPβ) and miR-27a regulate the expression of porcine Dickkopf2 (DKK2).

    PubMed

    Tao, Hu; Wang, Lei; Zhou, Jiawei; Pang, Panfei; Cai, Shanzhi; Li, Jialian; Mei, Shuqi; Li, Fenge

    2015-01-01

    Using Affymetrix porcine Gene-Chip analyses, we found that Dickkopf2 (DKK2), a WNT antagonist, is differentially expressed in pre-ovulatory follicles between Large White and Chinese Taihu sows. This study aims to identify the regulatory factors responsible for DKK2 expression. Deletion fragment and mutation analyses identified DKK2-D3 as the porcine DKK2 core promoter. There were four C/EBPβ binding sites within the DKK2 core promoter. The C allele that results from a spontaneous alteration (DKK2 c.-1130 T > C) in the core promoter was associated with a higher total number born (TNB) and a higher number born alive (NBA) in all parities in a synthetic pig population. This was possibly the result of a change in C/EBPβ binding ability, which was confirmed using chromatin immunoprecipitation (ChIP) and electrophoretic mobility shift assays (EMSA). Moreover, C/EBPβ specifically bound to and activated the DKK2 promoter, as revealed by mutation analysis, overexpression and RNA interference (RNAi) experiments. We also confirmed that miR-27a is a negative regulator of the DKK2 gene using miR-27a overexpression and inhibition experiments and mutation analyses. RTCA xCELLigence experiments showed that miR-27a suppressed Chinese hamster ovary (CHO) cell proliferation by down-regulating DKK2 gene expression. Taken together, our findings suggest that C/EBPβ and miR-27a control DKK2 transcription. PMID:26656471

  2. Transcriptional Profiling of Canker-Resistant Transgenic Sweet Orange (Citrus sinensis Osbeck) Constitutively Overexpressing a Spermidine Synthase Gene

    PubMed Central

    Fu, Xing-Zheng; Liu, Ji-Hong

    2013-01-01

    Citrus canker disease caused by Xanthomonas citri subsp. citri (Xcc) is one of the most devastating diseases affecting the citrus industry worldwide. In our previous study, the canker-resistant transgenic sweet orange (Citrus sinensis Osbeck) plants were produced via constitutively overexpressing a spermidine synthase. To unravel the molecular mechanisms underlying Xcc resistance of the transgenic plants, in the present study global transcriptional profiling was compared between untransformed line (WT) and the transgenic line (TG9) by hybridizing with Affymetrix Citrus GeneChip. In total, 666 differentially expressed genes (DEGs) were identified, 448 upregulated, and 218 downregulated. The DEGs were classified into 33 categories after Gene ontology (GO) annotation, in which 68 genes are in response to stimulus and involved in immune system process, 12 genes are related to cell wall, and 13 genes belong to transcription factors. These genes and those related to starch and sucrose metabolism, glutathione metabolism, biosynthesis of phenylpropanoids, and plant hormones were hypothesized to play major roles in the canker resistance of TG9. Semiquantitative RT-PCR analysis showed that the transcript levels of several candidate genes in TG9 were significantly higher than in WT both before and after Xcc inoculation, indicating their potential association with canker disease. PMID:23509803

  3. Different Transcriptional Response to Xanthomonas citri subsp. citri between Kumquat and Sweet Orange with Contrasting Canker Tolerance

    PubMed Central

    Fu, Xing-Zheng; Gong, Xiao-Qing; Zhang, Yue-Xin; Wang, Yin; Liu, Ji-Hong

    2012-01-01

    Citrus canker disease caused by Xanthomonas citri subsp. citri (Xcc) is one of the most devastating biotic stresses affecting the citrus industry. Meiwa kumquat (Fortunella crassifolia) is canker-resistant, while Newhall navel orange (Citrus sinensis Osbeck) is canker-sensitive. To understand the molecular mechanisms underlying the differences in responses to Xcc, transcriptomic profiles of these two genotypes following Xcc attack were compared by using the Affymetrix citrus genome GeneChip. A total of 794 and 1324 differentially expressed genes (DEGs) were identified as canker-responsive genes in Meiwa and Newhall, respectively. Of these, 230 genes were expressed in common between both genotypes, while 564 and 1094 genes were only significantly expressed in either Meiwa or Newhall. Gene ontology (GO) annotation and Singular Enrichment Analysis (SEA) of the DEGs showed that genes related to the cell wall and polysaccharide metabolism were induced for basic defense in both Meiwa and Newhall, such as chitinase, glucanase and thaumatin-like protein. Moreover, apart from inducing basic defense, Meiwa showed specially upregulated expression of several genes involved in the response to biotic stimulus, defense response, and cation binding as comparing with Newhall. And in Newhall, abundant photosynthesis-related genes were significantly down-regulated, which may be in order to ensure the basic defense. This study revealed different molecular responses to canker disease in Meiwa and Newhall, affording insight into the response to canker and providing valuable information for the identification of potential genes for engineering canker tolerance in the future. PMID:22848606

  4. Genome-wide analysis of DNA methylation and gene expression patterns in purified, uncultured human liver cells and activated hepatic stellate cells

    PubMed Central

    Reiner, Andrew H.; Coll, Mar; Verhulst, Stefaan; Mannaerts, Inge; Øie, Cristina I.; Smedsrød, Bård; Najimi, Mustapha; Sokal, Etienne; Luttun, Aernout; Sancho-Bru, Pau; Collas, Philippe; van Grunsven, Leo A.

    2015-01-01

    Background & Aims Liver fibrogenesis – scarring of the liver that can lead to cirrhosis and liver cancer – is characterized by hepatocyte impairment, capillarization of liver sinusoidal endothelial cells (LSECs) and hepatic stellate cell (HSC) activation. To date, the molecular determinants of a healthy human liver cell phenotype remain largely uncharacterized. Here, we assess the transcriptome and the genome-wide promoter methylome specific for purified, non-cultured human hepatocytes, LSECs and HSCs, and investigate the nature of epigenetic changes accompanying transcriptional changes associated with activation of HSCs. Material and methods Gene expression profile and promoter methylome of purified, uncultured human liver cells and culture-activated HSCs were respectively determined using Affymetrix HG-U219 genechips and by methylated DNA immunoprecipitation coupled to promoter array hybridization. Histone modification patterns were assessed at the single-gene level by chromatin immunoprecipitation and quantitative PCR. Results We unveil a DNA-methylation-based epigenetic relationship between hepatocytes, LSECs and HSCs despite their distinct ontogeny. We show that liver cell type-specific DNA methylation targets early developmental and differentiation-associated functions. Integrative analysis of promoter methylome and transcriptome reveals partial concordance between DNA methylation and transcriptional changes associated with human HSC activation. Further, we identify concordant histone methylation and acetylation changes in the promoter and putative novel enhancer elements of genes involved in liver fibrosis. Conclusions Our study provides the first epigenetic blueprint of three distinct freshly isolated, human hepatic cell types and of epigenetic changes elicited upon HSC activation. PMID:26353929

  5. USH1G with unique retinal findings caused by a novel truncating mutation identified by genome-wide linkage analysis

    PubMed Central

    Taibah, Khalid; Bin-Khamis, Ghada; Kennedy, Shelley; Hemidan, Amal; Al-Qahtani, Faisal; Tabbara, Khalid; Mubarak, Bashayer Al; Ramzan, Khushnooda; Meyer, Brian F.; Al-Owain, Mohammed

    2012-01-01

    Purpose Usher syndrome (USH) is an autosomal recessive disorder divided into three distinct clinical subtypes based on the severity of the hearing loss, manifestation of vestibular dysfunction, and the age of onset of retinitis pigmentosa and visual symptoms. To date, mutations in seven different genes have been reported to cause USH type 1 (USH1), the most severe form. Patients diagnosed with USH1 are known to be ideal candidates to benefit from cochlear implantation. Methods Genome-wide linkage analysis using Affymetrix GeneChip Human Mapping 10K arrays were performed in three cochlear implanted Saudi siblings born from a consanguineous marriage, clinically diagnosed with USH1 by comprehensive clinical, audiological, and ophthalmological examinations. From the linkage results, the USH1G gene was screened for mutations by direct sequencing of the coding exons. Results We report the identification of a novel p.S243X truncating mutation in USH1G that segregated with the disease phenotype and was not present in 300 ethnically matched normal controls. We also report on the novel retinal findings and the outcome of cochlear implantation in the affected individuals. Conclusions In addition to reporting a novel truncating mutation, this report expands the retinal phenotype in USH1G and presents the first report of successful cochlear implants in this disease. PMID:22876113

  6. Gene Expression Analysis of Peripheral Cells for Subclassification of Pediatric Inflammatory Bowel Disease in Remission

    PubMed Central

    van Lierop, Pieter P. E.; Swagemakers, Sigrid M.; de Bie, Charlotte I.; Middendorp, Sabine; van Baarlen, Peter; Samsom, Janneke N.; van IJcken, Wilfred F. J.; Escher, Johanna C.; van der Spek, Peter J.; Nieuwenhuis, Edward E. S.

    2013-01-01

    Objective In current clinical practice, optimal treatment of inflammatory bowel disease (IBD) aims at the induction and maintenance of clinical remission. Clinical remission is apparent when laboratory markers of inflammation are normal and clinical symptoms are absent. However, sub-clinical inflammation can still be present. A detailed analysis of the immune status during this inactive state of disease may provide a useful tool to categorize patients with clinical remission into subsets with variable states of immune activation. Design By using Affymetrix GeneChips, we analysed RNA gene expression profiles of peripheral blood leukocytes from pediatric IBD patients in clinical remission and controls. We performed (un)supervised clustering analysis of IBD-associated genes and applied Ingenuity® pathway software to identify specific molecular profiles between patients. Results Pediatric IBD patients with disease in clinical remission display heterogeneously distributed gene expression profiles that are significantly distinct from controls. We identified three clusters of IBD patients, each displaying specific expression profiles of IBD-associated genes. Conclusion The expression of immune- and IBD-associated genes in peripheral blood leukocytes from pediatric IBD patients in clinical remission was different from healthy controls, indicating that sub-clinical immune mechanisms are still active during remission. As such, RNA profiling of peripheral blood may allow for non-invasive patient subclassification and new perspectives in treatment regimes of IBD patients in the future. PMID:24260248

  7. The Arabidopsis cold-responsive transcriptome and its regulation by ICE1.

    PubMed

    Lee, Byeong-ha; Henderson, David A; Zhu, Jian-Kang

    2005-11-01

    To understand the gene network controlling tolerance to cold stress, we performed an Arabidopsis thaliana genome transcript expression profile using Affymetrix GeneChips that contain approximately 24,000 genes. We statistically determined 939 cold-regulated genes with 655 upregulated and 284 downregulated. A large number of early cold-responsive genes encode transcription factors that likely control late-responsive genes, suggesting a multitude of transcriptional cascades. In addition, many genes involved in chromatin level and posttranscriptional regulation were also cold regulated, suggesting their involvement in cold-responsive gene regulation. A number of genes important for the biosynthesis or signaling of plant hormones, such as abscisic acid, gibberellic acid, and auxin, are regulated by cold stress, which is of potential importance in coordinating cold tolerance with growth and development. We compared the cold-responsive transcriptomes of the wild type and inducer of CBF expression 1 (ice1), a mutant defective in an upstream transcription factor required for chilling and freezing tolerance. The transcript levels of many cold-responsive genes were altered in the ice1 mutant not only during cold stress but also before cold treatments. Our study provides a global picture of the Arabidopsis cold-responsive transcriptome and its control by ICE1 and will be valuable for understanding gene regulation under cold stress and the molecular mechanisms of cold tolerance. PMID:16214899

  8. Noncoder: a web interface for exon array-based detection of long non-coding RNAs

    PubMed Central

    Gellert, Pascal; Ponomareva, Yuliya; Braun, Thomas; Uchida, Shizuka

    2013-01-01

    Due to recent technical developments, a high number of long non-coding RNAs (lncRNAs) have been discovered in mammals. Although it has been shown that lncRNAs are regulated differently among tissues and disease statuses, functions of these transcripts are still unknown in most cases. GeneChip Exon 1.0 ST Arrays (exon arrays) from Affymetrix, Inc. have been used widely to profile genome-wide expression changes and alternative splicing of protein-coding genes. Here, we demonstrate that re-annotation of exon array probes can be used to profile expressions of tens of thousands of lncRNAs. With this annotation, a detailed inspection of lncRNAs and their isoforms is possible. To allow for a general usage to the research community, we developed a user-friendly web interface called ‘noncoder’. By uploading CEL files from exon arrays and with a few mouse clicks and parameter settings, exon array data will be normalized and analysed to identify differentially expressed lncRNAs. Noncoder provides the detailed annotation information of lncRNAs and is equipped with unique features to allow for an efficient search for interesting lncRNAs to be studied further. The web interface is available at http://noncoder.mpi-bn.mpg.de. PMID:23012263

  9. Invasion of Normal Human Fibroblasts Induced by v-Fos Is Independent of Proliferation, Immortalization, and the Tumor Suppressors p16INK4a and p53

    PubMed Central

    Scott, Linda A.; Vass, J. Keith; Parkinson, E. Kenneth; Gillespie, David A. F.; Winnie, Joseph N.; Ozanne, Bradford W.

    2004-01-01

    Invasion is generally perceived to be a late event during the progression of human cancer, but to date there are no consistent reports of alterations specifically associated with malignant conversion. We provide evidence that the v-Fos oncogene induces changes in gene expression that render noninvasive normal human diploid fibroblasts highly invasive, without inducing changes in growth factor requirements or anchorage dependence for proliferation. Furthermore, v-Fos-stimulated invasion is independent of the pRb/p16INK4a and p53 tumor suppressor pathways and telomerase. We have performed microarray analysis using Affymetrix GeneChips, and the gene expression profile of v-Fos transformed cells supports its role in the regulation of invasion, independent from proliferation. We also demonstrate that invasion, but not proliferation, is dependent on the activity of the up-regulated epidermal growth factor receptor. Taken together, these results indicate that AP-1-directed invasion could precede deregulated proliferation during tumorigenesis and that sustained activation of AP-1 could be the epigenetic event required for conversion of a benign tumor into a malignant one, thereby explaining why many malignant human tumors present without an obvious premalignant hyperproliferative dysplastic lesion. PMID:14749371

  10. Fibroblasts from patients with Diamond-Blackfan anaemia show abnormal expression of genes involved in protein synthesis, amino acid metabolism and cancer

    PubMed Central

    Avondo, Federica; Roncaglia, Paola; Crescenzio, Nicoletta; Krmac, Helena; Garelli, Emanuela; Armiraglio, Marta; Castagnoli, Carlotta; Campagnoli, Maria Francesca; Ramenghi, Ugo; Gustincich, Stefano; Santoro, Claudio; Dianzani, Irma

    2009-01-01

    Background Diamond-Blackfan anaemia (DBA) is a rare inherited red cell hypoplasia characterised by a defect in the maturation of erythroid progenitors and in some cases associated with malformations. Patients have an increased risk of solid tumors. Mutations have been found in several ribosomal protein (RP) genes, i.e RPS19, RPS24, RPS17, RPL5, RPL11, RPL35A. Studies in haematopoietic progenitors from patients show that haplo-insufficiency of an RP impairs rRNA processing and ribosome biogenesis. DBA lymphocytes show reduced protein synthesis and fibroblasts display abnormal rRNA processing and impaired proliferation. Results To evaluate the involvement of non-haematopoietic tissues in DBA, we have analysed global gene expression in fibroblasts from DBA patients compared to healthy controls. Microarray expression profiling using Affymetrix GeneChip Human Genome U133A 2.0 Arrays revealed that 421 genes are differentially expressed in DBA patient fibroblasts. These genes include a large cluster of ribosomal proteins and factors involved in protein synthesis and amino acid metabolism, as well as genes associated to cell death, cancer and tissue development. Conclusion This analysis reports for the first time an abnormal gene expression profile in a non-haematopoietic cell type in DBA. These data support the hypothesis that DBA may be due to a defect in general or specific protein synthesis. PMID:19765279

  11. Rice transcriptome analysis to identify possible herbicide quinclorac detoxification genes

    PubMed Central

    Xu, Wenying; Di, Chao; Zhou, Shaoxia; Liu, Jia; Li, Li; Liu, Fengxia; Yang, Xinling; Ling, Yun; Su, Zhen

    2015-01-01

    Quinclorac is a highly selective auxin-type herbicide and is widely used in the effective control of barnyard grass in paddy rice fields, improving the world's rice yield. The herbicide mode of action of quinclorac has been proposed, and hormone interactions affecting quinclorac signaling has been identified. Because of widespread use, quinclorac may be transported outside rice fields with the drainage waters, leading to soil and water pollution and other environmental health problems. In this study, we used 57K Affymetrix rice whole-genome array to identify quinclorac signaling response genes to study the molecular mechanisms of action and detoxification of quinclorac in rice plants. Overall, 637 probe sets were identified with differential expression levels under either 6 or 24 h of quinclorac treatment. Auxin-related genes such as GH3 and OsIAAs responded to quinclorac treatment. Gene Ontology analysis showed that genes of detoxification-related family genes were significantly enriched, including cytochrome P450, GST, UGT, and ABC and drug transporter genes. Moreover, real-time RT-PCR analysis showed that top candidate genes of P450 families such as CYP81, CYP709C, and CYP72A were universally induced by different herbicides. Some Arabidopsis genes of the same P450 family were up-regulated under quinclorac treatment. We conducted rice whole-genome GeneChip analysis and the first global identification of quinclorac response genes. This work may provide potential markers for detoxification of quinclorac and biomonitors of environmental chemical pollution. PMID:26483837

  12. Gene family analysis of the Arabidopsis pollen transcriptome reveals biological implications for cell growth, division control, and gene expression regulation.

    PubMed

    Pina, Cristina; Pinto, Francisco; Feijó, José A; Becker, Jörg D

    2005-06-01

    Upon germination, pollen forms a tube that elongates dramatically through female tissues to reach and fertilize ovules. While essential for the life cycle of higher plants, the genetic basis underlying most of the process is not well understood. We previously used a combination of flow cytometry sorting of viable hydrated pollen grains and GeneChip array analysis of one-third of the Arabidopsis (Arabidopsis thaliana) genome to define a first overview of the pollen transcriptome. We now extend that study to approximately 80% of the genome of Arabidopsis by using Affymetrix Arabidopsis ATH1 arrays and perform comparative analysis of gene family and gene ontology representation in the transcriptome of pollen and vegetative tissues. Pollen grains have a smaller and overall unique transcriptome (6,587 genes expressed) with greater proportions of selectively expressed (11%) and enriched (26%) genes than any vegetative tissue. Relative gene ontology category representations in pollen and vegetative tissues reveal a functional skew of the pollen transcriptome toward signaling, vesicle transport, and the cytoskeleton, suggestive of a commitment to germination and tube growth. Cell cycle analysis reveals an accumulation of G2/M-associated factors that may play a role in the first mitotic division of the zygote. Despite the relative underrepresentation of transcription-associated transcripts, nonclassical MADS box genes emerge as a class with putative unique roles in pollen. The singularity of gene expression control in mature pollen grains is further highlighted by the apparent absence of small RNA pathway components. PMID:15908605

  13. Intestinal gene expression profiles of piglets benefit from maternal supplementation with a yeast mannan-rich fraction during gestation and lactation.

    PubMed

    Graugnard, D E; Samuel, R S; Xiao, R; Spangler, L F; Brennan, K M

    2015-04-01

    The objective was to study the effect of maternal supplementation with a yeast cell wall-based product containing a mannan-rich fraction (MRF) during gestation and lactation on piglet intestinal gene expression. First parity sows were fed experimental gestation and lactation diets with or without MRF (900 mg/kg). After farrowing, piglets were fostered within treatment, as necessary. Sow and litter production performance data were collected until weaning. On day 10 post farrowing, jejunum samples from piglets were collected for gene expression analysis using the Affymetrix Porcine GeneChip array. Most performance parameters did not differ between the treatments. However, protein (P<0.01), total solids less fat (P<0.03) and the concentration of immunoglobulin G (IgG) in milk were greater (P<0.05) in the MRF-supplemented group. Gene expression results using hierarchical clustering revealed an overall dietary effect. Further analysis elucidated activation of pathways involved in tissue development, functioning and immunity, as well as greater cell proliferation and less migration of cells in the jejunum tissue. In conclusion, feeding the sow MRF during pregnancy and lactation was an effective nutritional strategy to bolster colostrum and milk IgG that are essential for development of piglet immune system and gut. In addition, the gene expression patterns affected by the passive immunity transfer showed indicators that could benefit animal performance long term. PMID:25482612

  14. CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis.

    PubMed

    Rainer, Johannes; Sanchez-Cabo, Fatima; Stocker, Gernot; Sturn, Alexander; Trajanoski, Zlatko

    2006-07-01

    CARMAweb (Comprehensive R-based Microarray Analysis web service) is a web application designed for the analysis of microarray data. CARMAweb performs data preprocessing (background correction, quality control and normalization), detection of differentially expressed genes, cluster analysis, dimension reduction and visualization, classification, and Gene Ontology-term analysis. This web application accepts raw data from a variety of imaging software tools for the most widely used microarray platforms: Affymetrix GeneChips, spotted two-color microarrays and Applied Biosystems (ABI) microarrays. R and packages from the Bioconductor project are used as an analytical engine in combination with the R function Sweave, which allows automatic generation of analysis reports. These report files contain all R commands used to perform the analysis and guarantee therefore a maximum transparency and reproducibility for each analysis. The web application is implemented in Java based on the latest J2EE (Java 2 Enterprise Edition) software technology. CARMAweb is freely available at https://carmaweb.genome.tugraz.at. PMID:16845058

  15. Analysis of Gene Expression Profiling in Meningioma: Deregulated Signaling Pathways Associated with Meningioma and EGFL6 Overexpression in Benign Meningioma Tissue and Serum

    PubMed Central

    Wang, Xuanchun; Gong, Ye; Wang, Daijun; Xie, Qing; Zheng, Mingzhe; Zhou, Yu; Li, Qin; Yang, Zhen; Tang, Hailiang; Li, Yiming; Hu, Renming; Chen, Xiancheng; Mao, Ying

    2012-01-01

    Molecular mechanisms underlying the pathogenesis of meningioma are not fully elucidated. In this study, we established differential gene expression profiles between meningiomas and brain arachnoidal tissue by using Affymetrix GeneChip Human U133 Plus 2.0 Array. KEGG pathway analysis demonstrated that PI3K/Akt and TGFβ signaling pathways were up-regulated in fibroblastic meningioma, and focal adhesion and ECM-receptor interaction pathways were activated in anaplastic meningioma. EGFL6 was one of the most up-regulated genes in fibroblastic meningioma by microarray analysis. Quantitative real-time PCR demonstrated that benign meningiomas had significantly higher levels of EGFL6 mRNA than brain arachnoidal tissue and atypical and anaplastic meningiomas (P<0.001). EGFL6 gene was also highly expressed in ovarian cancer, but expressed lowly in other investigated tumors. ELISA analysis showed that patients with benign meningiomas and ovarian cancers had the highest serum levels of EGFL6 (mean concentration: 672 pg/ml for benign meningiomas, and 616 pg/ml for ovarian cancers). Healthy people and patients with other tumors, however, had low levels of serum EGFL6. In conclusion, we proposed that activation of PI3K/Akt and integrin-mediated signaling pathways was involved in the pathogenesis of benign and anaplastic meningiomas, respectively. We also presented evidence that EGFL6 was overexpressed in benign meningioma tissues and serum. PMID:23285163

  16. Removal of hybridization and scanning noise from microarrays.

    PubMed

    Gopalappa, Chaitra; Das, Tapas K; Enkemann, Steven; Eschrich, Steven

    2009-09-01

    Microarray technology for measuring gene expression values has created significant opportunities for advances in disease diagnosis and individualized treatment planning. However, the random noise introduced by the sample preparation, hybridization, and scanning stages of microarray processing creates significant inaccuracies in the gene expression levels, and hence presents a major barrier in realizing the anticipated advances. Literature presents several methodologies for noise reduction, which can be broadly categorized as: 1) model based approaches for estimation and removal of hybridization noise; 2) approaches using commonly available image denoising tools; and 3) approaches involving the need for control sample(s). In this paper, we present a novel methodology for identifying and removing hybridization and scanning noise from microarray images, using a dual-tree-complex-wavelet-transform-based multiresolution analysis coupled with bivariate shrinkage thresholding. The key features of our methodology include consideration of inherent features and type of noise specific to microarray images, and the ability to work with a single microarray without needing a control. Our methodology is first benchmarked on a fabricated dataset that mimics a real microarray probe dataset. Thereafter, our methodology is tested on datasets obtained from a number of Affymetrix GeneChip human genome HG-U133 Plus 2.0 arrays, processed on HCT-116 cell line at the Microarray Core Facility of Moffitt Cancer Center and Research Institute. The results indicate an appreciable improvement in the quality of the microarray data. PMID:20051337

  17. Classification and Subtype Prediction of Adult Soft Tissue Sarcoma by Functional Genomics

    PubMed Central

    Segal, Neil H.; Pavlidis, Paul; Antonescu, Cristina R.; Maki, Robert G.; Noble, William S.; DeSantis, Diann; Woodruff, James M.; Lewis, Jonathan J.; Brennan, Murray F.; Houghton, Alan N.; Cordon-Cardo, Carlos

    2003-01-01

    Adult soft tissue sarcomas are a heterogeneous group of tumors, including well-described subtypes by histological and genotypic criteria, and pleomorphic tumors typically characterized by non-recurrent genetic aberrations and karyotypic heterogeneity. The latter pose a diagnostic challenge, even to experienced pathologists. We proposed that gene expression profiling in soft tissue sarcoma would identify a genomic-based classification scheme that is useful in diagnosis. RNA samples from 51 pathologically confirmed cases, representing nine different histological subtypes of adult soft tissue sarcoma, were examined using the Affymetrix U95A GeneChip. Statistical tests were performed on experimental groups identified by cluster analysis, to find discriminating genes that could subsequently be applied in a support vector machine algorithm. Synovial sarcomas, round-cell/myxoid liposarcomas, clear-cell sarcomas and gastrointestinal stromal tumors displayed remarkably distinct and homogenous gene expression profiles. Pleomorphic tumors were heterogeneous. Notably, a subset of malignant fibrous histiocytomas, a controversialhistological subtype, was identified as a distinct genomic group. The support vector machine algorithm supported a genomic basis for diagnosis, with both high sensitivity and specificity. In conclusion, we showed gene expression profiling to be useful in classification and diagnosis, providing insights into pathogenesis and pointing to potential new therapeutic targets of soft tissue sarcoma. PMID:12875988

  18. Microarray analysis of immune challenged Drosophila hemocytes.

    PubMed

    Johansson, Karin C; Metzendorf, Christoph; Söderhäll, Kenneth

    2005-04-15

    Insect hemocytes play multiple roles in immunity and carry out cellular responses like phagocytosis, encapsulation and melanization as well as producing humoral effector proteins in the first line of defense after injury and invasion of microorganisms. In this work, we used the Drosophila melanogaster hemocyte-like cell line mbn-2 and Affymetrix Drosophila GeneChips to investigate the transcriptome of a single type of immune competent tissue exposed to Gram-negative cell wall components (crude LPS) or high dose infection with live Escherichia coli. We found that gene expression profiles of both treatments overlap but show important differences in expression levels of several genes involved in immunity. In addition, cell morphology during infection was monitored and revealed distinct alterations in cell shape and adhesion. Presence of large numbers of bacteria also increased the number of cells taking on crystal cell fate. Taken together, our results indicate that hemocytes sense and respond differently to purified bacterial surface molecules and infection with live and actively growing bacteria both at the level of gene expression and in cell behavior. PMID:15777795

  19. A Microarray-Based Gene Expression Analysis to Identify Diagnostic Biomarkers for Unknown Primary Cancer

    PubMed Central

    Kurahashi, Issei; Fujita, Yoshihiko; Arao, Tokuzo; Kurata, Takayasu; Koh, Yasuhiro; Sakai, Kazuko; Matsumoto, Koji; Tanioka, Maki; Takeda, Koji; Takiguchi, Yuichi; Yamamoto, Nobuyuki; Tsuya, Asuka; Matsubara, Nobuaki; Mukai, Hirofumi; Minami, Hironobu; Chayahara, Naoko; Yamanaka, Yasuhiro; Miwa, Keisuke; Takahashi, Shin; Takahashi, Shunji; Nakagawa, Kazuhiko; Nishio, Kazuto

    2013-01-01

    Background The biological basis for cancer of unknown primary (CUP) at the molecular level remains largely unknown, with no evidence of whether a common biological entity exists. Here, we assessed the possibility of identifying a common diagnostic biomarker for CUP using a microarray gene expression analysis. Methods Tumor mRNA samples from 60 patients with CUP were analyzed using the Affymetrix U133A Plus 2.0 GeneChip and were normalized by asinh (hyperbolic arc sine) transformation to construct a mean gene-expression profile specific to CUP. A gene-expression profile specific to non-CUP group was constructed using publicly available raw microarray datasets. The t-tests were performed to compare the CUP with non-CUP groups and the top 59 CUP specific genes with the highest fold change were selected (p-value<0.001). Results Among the 44 genes that were up-regulated in the CUP group, 6 genes for ribosomal proteins were identified. Two of these genes (RPS7 and RPL11) are known to be involved in the Mdm2–p53 pathway. We also identified several genes related to metastasis and apoptosis, suggesting a biological attribute of CUP. Conclusions The protein products of the up-regulated and down-regulated genes identified in this study may be clinically useful as unique biomarkers for CUP. PMID:23671674

  20. The transcriptome of syncytia induced by the cyst nematode Heterodera schachtii in Arabidopsis roots

    PubMed Central

    Szakasits, Dagmar; Heinen, Petra; Wieczorek, Krzysztof; Hofmann, Julia; Wagner, Florian; Kreil, David P; Sykacek, Peter; Grundler, Florian M W; Bohlmann, Holger

    2009-01-01

    Arabidopsis thaliana is a host for the sugar beet cyst nematode Heterodera schachtii. Juvenile nematodes invade the roots and induce the development of a syncytium, which functions as a feeding site for the nematode. Here, we report on the transcriptome of syncytia induced in the roots of Arabidopsis. Microaspiration was employed to harvest pure syncytium material, which was then used to prepare RNA for hybridization to Affymetrix GeneChips. Initial data analysis showed that the gene expression in syncytia at 5 and 15 days post-infection did not differ greatly, and so both time points were compared together with control roots. Out of a total of 21 138 genes, 18.4% (3893) had a higher expression level and 15.8% (3338) had a lower expression level in syncytia, as compared with control roots, using a multiple-testing corrected false discovery rate of below 5%. A gene ontology (GO) analysis of up- and downregulated genes showed that categories related to high metabolic activity were preferentially upregulated. A principal component analysis was applied to compare the transcriptome of syncytia with the transcriptome of different Arabidopsis organs (obtained by the AtGenExpress project), and with specific root tissues. This analysis revealed that syncytia are transcriptionally clearly different from roots (and all other organs), as well as from other root tissues. PMID:18980640

  1. A genome-wide study of preferential amplification/hybridization in microarray-based pooled DNA experiments

    PubMed Central

    Yang, H.-C.; Liang, Y.-J.; Huang, M.-C.; Li, L.-H.; Lin, C.-H.; Wu, J.-Y.; Chen, Y.-T.; Fann, C.S.J.

    2006-01-01

    Microarray-based pooled DNA methods overcome the cost bottleneck of simultaneously genotyping more than 100 000 markers for numerous study individuals. The success of such methods relies on the proper adjustment of preferential amplification/hybridization to ensure accurate and reliable allele frequency estimation. We performed a hybridization-based genome-wide single nucleotide polymorphisms (SNPs) genotyping analysis to dissect preferential amplification/hybridization. The majority of SNPs had less than 2-fold signal amplification or suppression, and the lognormal distributions adequately modeled preferential amplification/hybridization across the human genome. Comparative analyses suggested that the distributions of preferential amplification/hybridization differed among genotypes and the GC content. Patterns among different ethnic populations were similar; nevertheless, there were striking differences for a small proportion of SNPs, and a slight ethnic heterogeneity was observed. To fulfill appropriate and gratuitous adjustments, databases of preferential amplification/hybridization for African Americans, Caucasians and Asians were constructed based on the Affymetrix GeneChip Human Mapping 100 K Set. The robustness of allele frequency estimation using this database was validated by a pooled DNA experiment. This study provides a genome-wide investigation of preferential amplification/hybridization and suggests guidance for the reliable use of the database. Our results constitute an objective foundation for theoretical development of preferential amplification/hybridization and provide important information for future pooled DNA analyses. PMID:16931491

  2. Global regulation of Staphylococcus aureus genes by Rot.

    PubMed

    Saïd-Salim, B; Dunman, P M; McAleese, F M; Macapagal, D; Murphy, E; McNamara, P J; Arvidson, S; Foster, T J; Projan, S J; Kreiswirth, B N

    2003-01-01

    Staphylococcus aureus produces a wide array of cell surface and extracellular proteins involved in virulence. Expression of these virulence factors is tightly controlled by numerous regulatory loci, including agr, sar, sigB, sae, and arl, as well as by a number of proteins with homology to SarA. Rot (repressor of toxins), a SarA homologue, was previously identified in a library of transposon-induced mutants created in an agr-negative strain by screening for restored protease and alpha-toxin. To date, all of the SarA homologues have been shown to act as global regulators of virulence genes. Therefore, we investigated the extent of transcriptional regulation of staphylococcal genes by Rot. We compared the transcriptional profile of a rot agr double mutant to that of its agr parental strain by using custom-made Affymetrix GeneChips. Our findings indicate that Rot is not only a repressor but a global regulator with both positive and negative effects on the expression of S. aureus genes. Our data also indicate that Rot and agr have opposing effects on select target genes. These results provide further insight into the role of Rot in the regulatory cascade of S. aureus virulence gene expression. PMID:12511508

  3. Global Profiling in Vestibular Schwannomas Shows Critical Deregulation of MicroRNAs and Upregulation in Those Included in Chromosomal Region 14q32

    PubMed Central

    Torres-Martin, Miguel; Lassaletta, Luis; de Campos, Jose M.; Isla, Alberto; Gavilan, Javier; Pinto, Giovanny R.; Burbano, Rommel R.; Latif, Farida; Melendez, Barbara; Castresana, Javier S.; Rey, Juan A.

    2013-01-01

    Background Vestibular schwannomas are benign tumors that arise from Schwann cells in the VIII cranial pair and usually present NF2 gene mutations and/or loss of heterozygosity on chromosome 22q. Deregulation has also been found in several genes, such as ERBB2 and NRG1. MicroRNAs are non-coding RNAs approximately 21 to 23 nucleotides in length that regulate mRNAs, usually by degradation at the post-transcriptional level. Methods We used microarray technology to test the deregulation of miRNAs and other non-coding RNAs present in GeneChip miRNA 1.0 (Affymetrix) over 16 vestibular schwannomas and 3 control-nerves, validating 10 of them by qRT-PCR. Findings Our results showed the deregulation of 174 miRNAs, including miR-10b, miR-206, miR-183 and miR-204, and the upregulation of miR-431, miR-221, miR-21 and miR-720, among others. The results also showed an aberrant expression of other non-coding RNAs. We also found a general upregulation of the miRNA cluster located at chromosome 14q32. Conclusion Our results suggest that several miRNAs are involved in tumor formation and/or maintenance and that global upregulation of the 14q32 chromosomal site contains miRNAs that may represent a therapeutic target for this neoplasm. PMID:23776562

  4. KARMA: a web server application for comparing and annotating heterogeneous microarray platforms.

    PubMed

    Cheung, Kei-Hoi; Hager, Janet; Pan, Deyun; Srivastava, Ranjana; Mane, Shrikant; Li, Yuli; Miller, Perry; Williams, Kenneth R

    2004-07-01

    We have developed a universal web server application (KARMA) that allows comparison and annotation of user-defined pairs of microarray platforms based on diverse types of genome annotation data (across different species) collected from multiple sources. The application is an effective tool for diverse microarray platforms, including arrays that are provided by (i) the Keck Microarray Resource at Yale, (ii) commercially available Affymetrix GeneChips and spotted arrays and (iii) custom arrays made by individual academics. The tool provides a web interface that allows users to input pairs of test files that represent diverse array platforms for either single or multiple species. The program dynamically identifies analogous DNA fragments spotted or synthesized on multiple microarray platforms based on the following types of information: (i) NCBI-Unigene identifiers, if the platforms being compared are within the same species or (ii) NCBI-Homologene data, if they are cross-species. The single-species comparison is implemented based on set operations: intersection, union and difference. Other forms of retrievable annotation data, including LocusLink, SwissProt and Gene Ontology (GO), are collected from multiple remote sites and stored in an integrated fashion using an Oracle database. The KARMA database, which is updated periodically, is available on line at the following URL: http://ymd.med.yale.edu/karma/cgi-bin/karma.pl. PMID:15215426

  5. Phycocyanobilin promotes PC12 cell survival and modulates immune and inflammatory genes and oxidative stress markers in acute cerebral hypoperfusion in rats.

    PubMed

    Marín-Prida, Javier; Pavón-Fuentes, Nancy; Llópiz-Arzuaga, Alexey; Fernández-Massó, Julio R; Delgado-Roche, Liván; Mendoza-Marí, Yssel; Santana, Seydi Pedroso; Cruz-Ramírez, Alieski; Valenzuela-Silva, Carmen; Nazábal-Gálvez, Marcelo; Cintado-Benítez, Alberto; Pardo-Andreu, Gilberto L; Polentarutti, Nadia; Riva, Federica; Pentón-Arias, Eduardo; Pentón-Rol, Giselle

    2013-10-01

    Since the inflammatory response and oxidative stress are involved in the stroke cascade, we evaluated here the effects of Phycocyanobilin (PCB, the C-Phycocyanin linked tetrapyrrole) on PC12 cell survival, the gene expression and the oxidative status of hypoperfused rat brain. After the permanent bilateral common carotid arteries occlusion (BCCAo), the animals were treated with saline or PCB, taking samples 24h post-surgery. Global gene expression was analyzed with GeneChip Rat Gene ST 1.1 from Affymetrix; the expression of particular genes was assessed by the Fast SYBR Green RT-PCR Master Mix and Bioplex methods; and redox markers (MDA, PP, CAT, SOD) were evaluated spectrophotometrically. The PCB treatment prevented the H2O2 and glutamate induced PC12 cell injury assessed by the MTT assay, and modulated 190 genes (93 up- and 97 down-regulated) associated to several immunological and inflammatory processes in BCCAo rats. Furthermore, PCB positively modulated 19 genes mostly related to a detrimental pro-inflammatory environment and counteracted the oxidative imbalance in the treated BCCAo animals. Our results support the view of an effective influence of PCB on major inflammatory mediators in acute cerebral hypoperfusion. These results suggest that PCB has a potential to be a treatment for ischemic stroke for which further studies are needed. PMID:23732081

  6. Analysis of cell death inducing compounds.

    PubMed

    Spicker, Jeppe S; Pedersen, Henrik Toft; Nielsen, Henrik Bjørn; Brunak, Søren

    2007-11-01

    Biomarkers for early detection of toxicity hold the promise of improving the failure rates in drug development. In the present study, gene expression levels were measured using full-genome RAE230 version 2 Affymetrix GeneChips on rat liver tissue 48 h after administration of six different compounds, three toxins (ANIT, DMN and NMF) and three non-toxins (Caeruelein, Dinitrophenol and Rosiglitazone). We identified three gene transcripts with exceptional predictive performance towards liver toxicity and/or changes in histopathology. The three genes were: glucokinase regulatory protein (GCKR), ornithine aminotransferase (OAT) and Cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase) (Cyp2C29). RT-PCR for these three genes was performed and four additional compounds were included for validation. The quantitative RT-PCR analysis confirmed the findings based on the microarray data and using the three genes a classification rate of 55 of 57 samples was achieved for the classification of not toxic versus toxic. The single most promising biomarker (OAT) alone resulted in a surprisingly 100% correctly classified samples. OAT has not previously been linked to toxicity and cell death in the literature and the novel finding represents a putative hepatotoxicity biomarker. PMID:17503021

  7. Reverse engineering and analysis of large genome-scale gene networks

    PubMed Central

    Aluru, Maneesha; Zola, Jaroslaw; Nettleton, Dan; Aluru, Srinivas

    2013-01-01

    Reverse engineering the whole-genome networks of complex multicellular organisms continues to remain a challenge. While simpler models easily scale to large number of genes and gene expression datasets, more accurate models are compute intensive limiting their scale of applicability. To enable fast and accurate reconstruction of large networks, we developed Tool for Inferring Network of Genes (TINGe), a parallel mutual information (MI)-based program. The novel features of our approach include: (i) B-spline-based formulation for linear-time computation of MI, (ii) a novel algorithm for direct permutation testing and (iii) development of parallel algorithms to reduce run-time and facilitate construction of large networks. We assess the quality of our method by comparison with ARACNe (Algorithm for the Reconstruction of Accurate Cellular Networks) and GeneNet and demonstrate its unique capability by reverse engineering the whole-genome network of Arabidopsis thaliana from 3137 Affymetrix ATH1 GeneChips in just 9 min on a 1024-core cluster. We further report on the development of a new software Gene Network Analyzer (GeNA) for extracting context-specific subnetworks from a given set of seed genes. Using TINGe and GeNA, we performed analysis of 241 Arabidopsis AraCyc 8.0 pathways, and the results are made available through the web. PMID:23042249

  8. The Effect of an Obesogenic Maternal Environment on Expression of Fetal Umbilical Cord Blood miRNA

    PubMed Central

    Parry, Samuel; Elovitz, Michal A.; Durnwald, Celeste P.

    2015-01-01

    Objective: Exposure to maternal obesity in utero predisposes offspring to obesity and metabolic disease. This study investigated whether maternal obesity is associated with alterations in expression of fetal microRNA (miRNA). Study Design: A cohort study of women with body mass index (BMI) ≥35 kg/m2 (n = 16) versus those with normal BMI 20 to 24.9 (n = 20) was performed. All participants had normal glucose tolerance (1-hour glucose challenge test <130) and normally grown neonates (2700-3500 g). Umbilical cord samples were collected immediately after delivery. Expression of miRNA was assessed using Affymetrix GeneChip miRNA 3.0 Arrays. Differential miRNA expression was determined using Student t tests with Benjamini-Hocherg correction. Results: For 1733 human mature miRNAs, the expression levels were not statistically different in umbilical cord blood samples from pregnancies of obese women compared to controls. Conclusion: Expression of fetal miRNA is not altered in umbilical cord blood in response to in utero exposure to obesity. Alternate mechanisms underlying the fetal effects of maternal obesity should be explored. PMID:25544675

  9. Transcriptomes reveal alterations in gravity impact circadian clocks and activate mechanotransduction pathways with adaptation through epigenetic change.

    PubMed

    Casey, Theresa; Patel, Osman V; Plaut, Karen

    2015-04-01

    Few studies have investigated the impact of alterations in gravity on mammalian transcriptomes. Here, we describe the impact of spaceflight on mammary transcriptome of late pregnant rats and the effect of hypergravity exposure on mammary, liver, and adipose transcriptomes in late pregnancy and at the onset of lactation. RNA was isolated from mammary collected on pregnancy day 20 from rats exposed to spaceflight from days 11 to 20 of gestation. To measure the impact of hypergravity on mammary, liver, and adipose transcriptomes we isolated RNA from tissues collected on P20 and lactation day 1 from rats exposed to hypergravity beginning on pregnancy day 9. Gene expression was measured with Affymetrix GeneChips. Microarray analysis of variance revealed alterations in gravity affected the expression of genes that regulate circadian clocks and activate mechanotransduction pathways. Changes in these systems may explain global gene expression changes in immune response, metabolism, and cell proliferation. Expression of genes that modify chromatin structure and methylation was affected, suggesting adaptation to gravity alterations may proceed through epigenetic change. Altered gravity experiments offer insights into the role of forces omnipresent on Earth that shape genomes in heritable ways. Our study is the first to analyze the impact of alterations in gravity on transcriptomes of pregnant and lactating mammals. Findings provide insight into systems that sense gravity and the way in which they affect phenotype, as well as the possibility of sustaining life beyond Earth's orbit. PMID:25649141

  10. Reference genes identified in SH-SY5Y cells using custom-made gene arrays with validation by quantitative polymerase chain reaction.

    PubMed

    Hoerndli, Frédéric J; Toigo, Marco; Schild, Andreas; Götz, Jürgen; Day, Philip J

    2004-12-01

    Transcriptomic methods are widely used as an initial approach to gain a mechanistic insight into physiological and pathological processes. Because differences in gene regulation to be assessed by RNA screening methods (e.g., SAGE, Affymetrix GeneChips) can be very subtle, these techniques require stable reference genes for accurate normalization. It is widely known that housekeeping genes, which are routinely used for normalization, can vary significantly depending on the tissue, and experimental test. In this study, we aimed at identifying stable reference genes for a fibrillar Abeta(42) peptide-treated, human tau-expressing SH-SY5Y neuroblastoma cell line derived to model aspects of Alzheimer's disease in tissue culture. We selected genes exhibiting potential normalization characteristics from public databases to create a custom-made microarray allowing the identification of reference genes for low, intermediate, and abundant mRNAs. A subset of these candidates was subjected to quantitative real-time polymerase chain reaction and was analyzed with geNorm software. By doing so, we were able to identify GAPD, M-RIP, and POLR2F as stable and usable reference genes irrespective of differentiation status and Abeta(42) treatment. PMID:15519568

  11. Gene expression profiling in the skin of zebrafish infected with Citrobacter freundii.

    PubMed

    Lü, Aijun; Hu, Xiucai; Xue, Jun; Zhu, Jingrong; Wang, Yi; Zhou, Guangzhou

    2012-02-01

    Skin is considered the largest immunologically active organ, but its molecular mechanism remains unclear in fish. Here, Affymetrix Zebrafish GeneChip was used to assess gene expression in the skin of zebrafish (Danio rerio) infected with the bacterium Citrobacter freundii. The results showed that 229 genes were differentially expressed, of which 196 genes were upregulated and 33 genes were downregulated. Gene Ontology and KEGG pathway analyses indicated 88 genes significantly associated with skin immunity involved in complement activation and acute phase response, defense and immune response, response to stress and stimulus, antigen processing and presentation, cell adhesion and migration, platelet activation and coagulation factors, regulation of autophagy and apoptosis. When compared with transcriptional profiles of previously reported carp (Cyprinus carpio) skin, a similar innate immunity (e.g., interferon, lectin, heat shock proteins, complements), and several different acute phase proteins (transferrin, ceruloplasmin, vitellogenin and alpha-1-microglobulin, etc.) were detected in zebrafish skin. The validity of the microarray results was verified by quantitative real-time PCR analysis of nine representative genes. This is first report that skin play important roles in innate immune responses to bacterial infection, which contribute to understanding the defense mechanisms of the skin in fish. PMID:22155693

  12. Whole-genome transcriptional analysis of heavy metal stresses inCaulobacter crescentus

    SciTech Connect

    Hu, Ping; Brodie, Eoin L.; Suzuki, Yohey; McAdams, Harley H.; Andersen, Gary L.

    2005-09-21

    The bacterium Caulobacter crescentus and related stalkbacterial species are known for their distinctive ability to live in lownutrient environments, a characteristic of most heavy metal contaminatedsites. Caulobacter crescentus is a model organism for studying cell cycleregulation with well developed genetics. We have identified the pathwaysresponding to heavy metal toxicity in C. crescentus to provide insightsfor possible application of Caulobacter to environmental restoration. Weexposed C. crescentus cells to four heavy metals (chromium, cadmium,selenium and uranium) and analyzed genome wide transcriptional activitiespost exposure using a Affymetrix GeneChip microarray. C. crescentusshowed surprisingly high tolerance to uranium, a possible mechanism forwhich may be formation of extracellular calcium-uranium-phosphateprecipitates. The principal response to these metals was protectionagainst oxidative stress (up-regulation of manganese-dependent superoxidedismutase, sodA). Glutathione S-transferase, thioredoxin, glutaredoxinsand DNA repair enzymes responded most strongly to cadmium and chromate.The cadmium and chromium stress response also focused on reducing theintracellular metal concentration, with multiple efflux pumps employed toremove cadmium while a sulfate transporter was down-regulated to reducenon-specific uptake of chromium. Membrane proteins were also up-regulatedin response to most of the metals tested. A two-component signaltransduction system involved in the uranium response was identified.Several differentially regulated transcripts from regions previously notknown to encode proteins were identified, demonstrating the advantage ofevaluating the transcriptome using whole genome microarrays.

  13. Beryllium-induced lung disease exhibits expression profiles similar to sarcoidosis.

    PubMed

    Li, Li; Silveira, Lori J; Hamzeh, Nabeel; Gillespie, May; Mroz, Peggy M; Mayer, Annyce S; Fingerlin, Tasha E; Maier, Lisa A

    2016-06-01

    A subset of beryllium-exposed workers develop beryllium sensitisation (BeS) which precedes chronic beryllium disease (CBD). We conducted an in-depth analysis of differentially expressed candidate genes in CBD.We performed Affymetrix GeneChip 1.0 ST array analysis on peripheral blood mononuclear cells (PBMCs) from 10 CBD, 10 BeS and 10 beryllium-exposed, nondiseased controls stimulated with BeSO4 or medium. The differentially expressed genes were validated by high-throughput real-time PCR in this group and in an additional group of cases and nonexposed controls. The functional roles of the top candidate genes in CBD were assessed using a pharmacological inhibitor. CBD gene expression data were compared with whole blood and lung tissue in sarcoidosis from the Gene Expression Omnibus.We confirmed almost 450 genes that were significantly differentially expressed between CBD and controls. The top enrichment of genes was for JAK (Janus kinase)-STAT (signal transducer and activator of transcription) signalling. A JAK2 inhibitor significantly decreased tumour necrosis factor-α and interferon-γ production. Furthermore, we found 287 differentially expressed genes overlapped in CBD/sarcoidosis. The top shared pathways included cytokine-cytokine receptor interactions, and Toll-like receptor, chemokine and JAK-STAT signalling pathways.We show that PBMCs demonstrate differentially expressed gene profiles relevant to the immunnopathogenesis of CBD. CBD and sarcoidosis share similar differential expression of pathogenic genes and pathways. PMID:27103383

  14. Microarray analysis of responsible genes in increased growth rate in the subline of HL60 (HL60RG) cells.

    PubMed

    Luan, Yang; Kogi, Mieko; Rajaguru, Palanisamy; Ren, Jin; Yamaguchi, Teruhide; Suzuki, Kazuhiro; Suzuki, Takayoshi

    2012-03-01

    HL60RG, a subline of human promyelocytic leukemia HL60 cells, has a increased growth rate than their parental cells. To gain information of the mechanisms involved in the increased growth rate of HL60RG, we performed a multiplex fluorescence in situ hybridization (M-FISH), standard cytogenetics analysis (G-banding) and genome scan using 10K SNP mapping array on both cell types. Characteristic genomic alterations in HL60RG cells were identified including uniparental disomy (UPD) of chromosome 1, and hemizygous deletion in 10p and 11p. However, no such defects were observed in HL60 cells. Changes in gene expression in HL60RG cells were determined using expression arrays (Affymetrix GeneChip, HU133A). Candidate genes associated with the rapid growth of HL60RG cells were identified. Two tumor necrosis factor receptors, TNFRSF1B (type II tumor necrosis factor-α receptor) and TNFRSF8 (also known as a tumor marker CD30), which are adjacently located on chromosome 1 showed opposing changes in gene expression in HL60RG cells-over-expression of TNFRSF8 and repression of TNFRSF1B. Differences in the DNA methylation status in the transcriptional regulatory regions of both genes between HL60 and HL60RG was detected by a methylation-specific PCR assay. In conclusion, alterations in chromosome and gene expression in HL60RG may be associated with increased growth rate. PMID:22032829

  15. Association of ADAM10 and CAMK2A polymorphisms with conduct disorder: evidence from family-based studies.

    PubMed

    Jian, Xue-Qiu; Wang, Ke-Sheng; Wu, Tie-Jian; Hillhouse, Joel J; Mullersman, Jerald E

    2011-08-01

    Twin and family studies have shown that genetic factors play a role in the development of conduct disorder (CD). The purpose of this study was to identify genetic variants associated with CD using a family-based association study. We used 4,720 single nucleotide polymorphisms (SNPs) from the Illumina Panel and 11,120 SNPs from the Affymetrix 10K GeneChips genotyped in 155 Caucasian nuclear families from Genetic Analysis Workshop (GAW) 14, a subset from the Collaborative Study on the Genetics of Alcoholism (COGA). 20 SNPs had suggestive associations with CD (p<10(-3)), nine of which were located in known genes, including ADAM10 (rs383902, p=0.00036) and CAMK2A (rs2053053, p=0.00098). Our results were verified using the International Multi-Center ADHD Genetics Project (IMAGE) dataset. In conclusion, we identified several loci associated with CD. Especially, the two genes (ADAM10 and CAMK2A) have been reported to be associated with Alzheimer's disease, bipolar disorder and depression. These findings may serve as a resource for replication in other populations. PMID:21611732

  16. Dietary inulin supplementation modifies significantly the liver transcriptomic profile of broiler chickens.

    PubMed

    Sevane, Natalia; Bialade, Federica; Velasco, Susana; Rebolé, Almudena; Rodríguez, Maria Luisa; Ortiz, Luís T; Cañón, Javier; Dunner, Susana

    2014-01-01

    Inclusion of prebiotics in the diet is known to be advantageous, with positive influences both on health and growth. The current study investigated the differences in the hepatic transcriptome profiles between chickens supplemented with inulin (a storage carbohydrate found in many plants) and controls. Liver is a major metabolic organ and has been previously reported to be involved in the modification of the lipid metabolism in chickens fed with inulin. A nutrigenomic approach through the analysis of liver RNA hybridized to the Affymetrix GeneChip Chicken Genome Array identified 148 differentially expressed genes among both groups: 104 up-regulated (≥ 1.4-fold) and 44 down-regulated (≤ 0.6-fold). Quantitative real-time PCR analysis validated the microarray expression results for five out of seven genes tested. The functional annotation analyses revealed a number of genes, processes and pathways with putative involvement in chicken growth and performance, while reinforcing the immune status of animals, and fostering the production of long chain fatty acids in broilers supplemented with 5 g of inulin kg(-1) diet. As far as we are aware, this is the first report of a microarray based gene expression study on the effect of dietary inulin supplementation, supporting further research on the use of this prebiotic on chicken diets as a useful alternative to antibiotics for improving performance and general immunity in poultry farming, along with a healthier meat lipid profile. PMID:24915441

  17. Differential gene expression in mouse liver associated with the hepatoprotective effect of clofibrate

    SciTech Connect

    Moffit, Jeffrey S.; Koza-Taylor, Petra H.; Holland, Ricky D.; Thibodeau, Michael S.; Beger, Richard D.; Lawton, Michael P.; Manautou, Jose E. . E-mail: jose.manautou@uconn.edu

    2007-07-15

    Pretreatment of mice with the peroxisome proliferator clofibrate (CFB) protects against acetaminophen (APAP)-induced hepatotoxicity. Previous studies have shown that activation of the nuclear peroxisome proliferator activated receptor-alpha (PPAR{alpha}) is required for this effect. The present study utilizes gene expression profile analysis to identify potential pathways contributing to PPAR{alpha}-mediated hepatoprotection. Gene expression profiles were compared between wild type and PPAR{alpha}-null mice pretreated with vehicle or CFB (500 mg/kg, i.p., daily for 10 days) and then challenged with APAP (400 mg/kg, p.o.). Total hepatic RNA was isolated 4 h after APAP treatment and hybridized to Affymetrix Mouse Genome MGU74 v2.0 GeneChips. Gene expression analysis was performed utilizing GeneSpring (registered) software. Our analysis identified 53 genes of interest including vanin-1, cell cycle regulators, lipid-metabolizing enzymes, and aldehyde dehydrogenase 2, an acetaminophen binding protein. Vanin-1 could be important for CFB-mediated hepatoprotection because this protein is involved in the synthesis of cysteamine and cystamine. These are potent antioxidants capable of ameliorating APAP toxicity in rodents and humans. HPLC-ESI/MS/MS analysis of liver extracts indicates that enhanced vanin-1 gene expression results in elevated cystamine levels, which could be mechanistically associated with CFB-mediated hepatoprotection.

  18. Gene Expression Profiling on the Molecular Action of Danshen-Gegen Formula in a Randomized Placebo-Controlled Trial of Postmenopausal Women with Hypercholesterolemia

    PubMed Central

    Koon, Chi-Man; Ko, Chun-Hay; Sun, Xu-Xu; Hoi, Sandy Wan-Heng; Tam, Jacqueline Chor-Wing; Cheung, David Wing-Shing; Cheng, King-Fai; Pang, Suet-Yee; Lo, Wing-Man; Chook, Ping; Lau, Clara Bik-San; Chan, Wai-Yee; Leung, Ping-Chung; Kwok, Timothy Chi-Yui; Fung, Kwok-Pui

    2013-01-01

    The Danshen-Gegen formula (DG) is a traditional Chinese herbal formula which has long been used to treat cardiovascular disease. DG was found to be a cardiovascular tonic in our recent research. However, a comprehensive investigation of the molecular mechanism of DG in cardiovascular disease has not been performed. The aim of this study was to clarify the transcriptional profiling of genes modulated by DG on postmenopausal women by using DNAmicroarray technology. We obtained 29 whole blood samples both from DG-treated and placebo-treated subjects. Blood lipid profile and intima-media thickness (IMT) were measured. Affymetrix GeneChip was used to identify differentially expressed genes (DEGs), followed by validation by the real-time PCR method. The results showed that DG-treated group has a significant improvement in IMT and lipid profile as compared to placebo-treated group. For the genomic study, the DG-treated group has a higher number of DEGs identified as compared to the placebo-treated group. Two important biological processes of “regulation of systemic arterial blood pressure by hormone” and “regulation of smooth muscle proliferation” have been identified by GePS in the DG-treated group. No significant biological process and cellular components were identified in the placebo-treated group. This genomic study on the molecular action of DG in postmenopausal women gathered sufficient molecular targets and pathways to reveal that DG could improve neointima thickening and hypertension. PMID:24174980

  19. Water deficit modulates the response of Vitis vinifera to the Pierce's disease pathogen Xylella fastidiosa.

    PubMed

    Choi, Hong-Kyu; Iandolino, Alberto; da Silva, Francisco Goes; Cook, Douglas R

    2013-06-01

    Pierce's disease, caused by the bacterium Xylella fastidiosa, is one of the most devastating diseases of cultivated grape, currently restricted to the Americas. To test the long-standing hypothesis that Pierce's disease results from pathogen-induced drought stress, we used the Affymetrix Vitis GeneChip to compare the transcriptional response of Vitis vinifera to Xylella infection, water deficit, or a combination of the two stresses. The results reveal a redirection of gene transcription involving 822 genes with a minimum twofold change (P < 0.05), including the upregulation of transcripts for phenylpropanoid and flavonoid biosynthesis, pathogenesis-related proteins, abscisic acid- and jasmonic acid-responsive biosynthesis, and downregulation of transcripts related to photosynthesis, growth, and nutrition. Although the transcriptional response of plants to Xylella infection was largely distinct from the response of healthy plants to water stress, we find that 138 of the pathogen-induced genes exhibited a significantly stronger transcriptional response when plants were simultaneously exposed to infection and drought stress, suggesting a strong interaction between disease and water deficit. This interaction between drought stress and disease was mirrored in planta at the physiological level for aspects of water relations and photosynthesis and in terms of the severity of disease symptoms and the extent of pathogen colonization, providing a molecular correlate of the classical concept of the disease triangle in which environment impacts disease severity. PMID:23425100

  20. Vibration mechanosignals superimposed to resistive exercise result in baseline skeletal muscle transcriptome profiles following chronic disuse in bed rest

    PubMed Central

    Salanova, Michele; Gambara, Guido; Moriggi, Manuela; Vasso, Michele; Ungethuem, Ute; Belavý, Daniel L.; Felsenberg, Dieter; Cerretelli, Paolo; Gelfi, Cecilia; Blottner, Dieter

    2015-01-01

    Disuse-induced muscle atrophy is a major concern in aging, in neuromuscular diseases, post-traumatic injury and in microgravity life sciences affecting health and fitness also of crew members in spaceflight. By using a laboratory analogue to body unloading we perform for the first time global gene expression profiling joined to specific proteomic analysis to map molecular adaptations in disused (60 days of bed rest) human soleus muscle (CTR) and in response to a resistive exercise (RE) countermeasure protocol without and with superimposed vibration mechanosignals (RVE). Adopting Affymetrix GeneChip technology we identified 235 differently transcribed genes in the CTR group (end- vs. pre-bed rest). RE comprised 206 differentially expressed genes, whereas only 51 changed gene transcripts were found in RVE. Most gene transcription and proteomic changes were linked to various key metabolic pathways (glycolysis, oxidative phosphorylation, tricarboxylic acid (TCA) cycle, lipid metabolism) and to functional contractile structures. Gene expression profiling in bed rest identified a novel set of genes explicitly responsive to vibration mechanosignals in human soleus. This new finding highlights the efficacy of RVE protocol in reducing key signs of disuse maladaptation and atrophy, and to maintain a close-to-normal skeletal muscle quality outcome following chronic disuse in bed rest. PMID:26596638

  1. Pulmonary arteriole gene expression signature in idiopathic pulmonary fibrosis.

    PubMed

    Patel, Nina M; Kawut, Steven M; Jelic, Sanja; Arcasoy, Selim M; Lederer, David J; Borczuk, Alain C

    2013-06-01

    A third of patients with idiopathic pulmonary fibrosis (IPF) develop pulmonary hypertension (PH-IPF), which is associated with increased mortality. Whether an altered gene expression profile in the pulmonary vasculature precedes the clinical onset of PH-IPF is unknown. We compared gene expression in the pulmonary vasculature of IPF patients with and without PH with controls. Pulmonary arterioles were isolated using laser capture microdissection from 16 IPF patients: eight with PH (PH-IPF) and eight with no PH (NPH-IPF), and seven controls. Probe was prepared from extracted RNA, and hybridised to Affymetrix Hu133 2.0 Plus genechips. Biometric Research Branch array tools and Ingenuity Pathway Analysis software were used for analysis of the microarray data. Univariate analysis revealed 255 genes that distinguished IPF arterioles from controls (p<0.001). Mediators of vascular smooth muscle and endothelial cell proliferation, Wnt signalling and apoptosis were differentially expressed in IPF arterioles. Unsupervised and supervised clustering analyses revealed similar gene expression in PH-IPF and NPH-IPF arterioles. The pulmonary arteriolar gene expression profile is similar in IPF patients with and without coexistent PH. Pathways involved in vascular proliferation and aberrant apoptosis, which may contribute to pulmonary vascular remodelling, are activated in IPF patients. PMID:23728404

  2. Human Dendritic Cells exhibit a pronounced type I IFN signature following Leishmania major infection that is required for IL-12 induction1.

    PubMed Central

    Favila, Michelle A.; Geraci, Nicholas S.; Zeng, Erliang; Harker, Brent; Condon, David; Cotton, Rachel N.; Jayakumar, Asha; Tripathi, Vinita; McDowell, Mary Ann

    2014-01-01

    Leishmania major infected human dendritic cells (DCs) exhibit a marked induction of IL-12, ultimately promoting a robust Th1-mediated response associated with parasite killing and protective immunity. The host cell transcription machinery associated with the specific IL-12 induction observed during L. major infection remains to be thoroughly elucidated. In this study, we utilized Affymetrix Genechips to globally assess the host cell genes and pathways associated with early L. major infection in human myeloid-derived DCs. Our data revealed 728 genes were significantly differentially expressed and molecular signaling pathway revealed that the type I IFN pathway was significantly enriched. Addition of a neutralizing type I IFN decoy receptor blocked the expression of IRF7 and IL-12p40 during DC infection, indicating the L. major induced expression of IL-12p40 is dependent upon the type I IFN signaling pathway. In stark contrast, IL-12p40 expression is not elicited by Leishmania donovani, the etiological agent of deadly visceral leishmaniasis. Therefore, we examined the gene expression profile for several IFN response genes in L. major versus L. donovani DC infections. Our data revealed that L. major, but not L. donovani, induces expression of IRF2, IRF7, and IFIT5, implicating the regulation of type I IFN associated signaling pathways as mediating factors toward the production of IL-12. PMID:24808365

  3. Effect of Chronic Pioglitazone Treatment on Hepatic Gene Expression Profile in Obese C57BL/6J Mice

    PubMed Central

    Jia, Chunming; Huan, Yi; Liu, Shuainan; Hou, Shaocong; Sun, Sujuan; Li, Caina; Liu, Quan; Jiang, Qian; Wang, Yue; Shen, Zhufang

    2015-01-01

    Pioglitazone, a selective ligand of peroxisome proliferator-activated receptor gamma (PPARγ), is an insulin sensitizer drug that is being used in a number of insulin-resistant conditions, including non-alcoholic fatty liver disease (NAFLD). However, there is a discrepancy between preclinical and clinical data in the literature and the benefits of pioglitazone treatment as well as the precise mechanism of action remain unclear. In the present study, we determined the effect of chronic pioglitazone treatment on hepatic gene expression profile in diet-induced obesity (DIO) C57BL/6J mice in order to understand the mechanisms of NAFLD induced by PPARγ agonists. DIO mice were treated with pioglitazone (25 mg/kg/day) for 38 days, the gene expression profile in liver was evaluated using Affymetrix Mouse GeneChip 1.0 ST array. Pioglitazone treatment resulted in exacerbated hepatic steatosis and increased hepatic triglyceride and free fatty acids concentrations, though significantly increased the glucose infusion rate in hyperinsulinemic-euglycemic clamp test. The differentially expressed genes in liver of pioglitazone treated vs. untreated mice include 260 upregulated and 86 downregulated genes. Gene Ontology based enrichment analysis suggests that inflammation response is transcriptionally downregulated, while lipid metabolism is transcriptionally upregulated. This may underlie the observed aggravating liver steatosis and ameliorated systemic insulin resistance in DIO mice. PMID:26035752

  4. Gene expression profiling of dengue infected human primary cells identifies secreted mediators in vivo

    PubMed Central

    Becerra, Aniuska; Warke, Rajas V.; Martin, Katherine; Xhaja, Kris; de Bosch, Norma; Rothman, Alan L.; Bosch, Irene

    2009-01-01

    We used gene expression profiling of human primary cells infected in vitro with dengue virus (DENV) as a tool to identify secreted mediators induced in response to the acute infection. Affymetrix Genechip analysis of human primary monocytes, B cells and dendritic cells infected with DENV in vitro revealed a strong induction of monocyte chemotactic protein 2 (MCP-2/CCL8), interferon gamma-induced protein 10 (IP-10/CXCL10) and tumor necrosis factor-related apoptosis-inducing ligand (TRAIL/TNFSF10). The expression of these genes was confirmed in dendritic cells infected with DENV in vitro at mRNA and protein levels. A prospectively enrolled cohort of DENV-infected Venezuelan patients was used to measure the levels of these proteins in serum during three different periods of the disease. Results showed significant increase of MCP-2, IP-10 and TRAIL levels in DENV-infected patients during the febrile period, when compared to healthy donors and patients with other febrile illnesses. MCP-2 and IP-10 levels were still elevated during the post-febrile period while TRAIL levels dropped close to normal after defervescense. Patients with primary infections had higher TRAIL levels than patients with secondary infections during the febrile period of the disease. Increased levels of IP-10, TRAIL and MCP-2 in acute DENV infections suggest a role for these mediators in the immune response to the infection. PMID:19551822

  5. A Global Survey of Gene Regulation during Cold Acclimation in Arabidopsis thaliana

    PubMed Central

    Hannah, Matthew A; Heyer, Arnd G; Hincha, Dirk K

    2005-01-01

    Many temperate plant species such as Arabidopsis thaliana are able to increase their freezing tolerance when exposed to low, nonfreezing temperatures in a process called cold acclimation. This process is accompanied by complex changes in gene expression. Previous studies have investigated these changes but have mainly focused on individual or small groups of genes. We present a comprehensive statistical analysis of the genome-wide changes of gene expression in response to 14 d of cold acclimation in Arabidopsis, and provide a large-scale validation of these data by comparing datasets obtained for the Affymetrix ATH1 Genechip and MWG 50-mer oligonucleotide whole-genome microarrays. We combine these datasets with existing published and publicly available data investigating Arabidopsis gene expression in response to low temperature. All data are integrated into a database detailing the cold responsiveness of 22,043 genes as a function of time of exposure at low temperature. We concentrate our functional analysis on global changes marking relevant pathways or functional groups of genes. These analyses provide a statistical basis for many previously reported changes, identify so far unreported changes, and show which processes predominate during different times of cold acclimation. This approach offers the fullest characterization of global changes in gene expression in response to low temperature available to date. PMID:16121258

  6. Genetics and genomics of Drosophila mating behavior

    PubMed Central

    Mackay, Trudy F. C.; Heinsohn, Stefanie L.; Lyman, Richard F.; Moehring, Amanda J.; Morgan, Theodore J.; Rollmann, Stephanie M.

    2005-01-01

    The first steps of animal speciation are thought to be the development of sexual isolating mechanisms. In contrast to recent progress in understanding the genetic basis of postzygotic isolating mechanisms, little is known about the genetic architecture of sexual isolation. Here, we have subjected Drosophila melanogaster to 29 generations of replicated divergent artificial selection for mating speed. The phenotypic response to selection was highly asymmetrical in the direction of reduced mating speed, with estimates of realized heritability averaging 7%. The selection response was largely attributable to a reduction in female receptivity. We assessed the whole genome transcriptional response to selection for mating speed using Affymetrix GeneChips and a rigorous statistical analysis. Remarkably, >3,700 probe sets (21% of the array elements) exhibited a divergence in message levels between the Fast and Slow replicate lines. Genes with altered transcriptional abundance in response to selection fell into many different biological process and molecular function Gene Ontology categories, indicating substantial pleiotropy for this complex behavior. Future functional studies are necessary to test the extent to which transcript profiling of divergent selection lines accurately predicts genes that directly affect the selected trait. PMID:15851659

  7. A Pooled Genome-Wide Association Study of Asperger Syndrome

    PubMed Central

    Warrier, Varun; Chakrabarti, Bhismadev; Murphy, Laura; Chan, Allen; Craig, Ian; Mallya, Uma; Lakatošová, Silvia; Rehnstrom, Karola; Wheelwright, Sally; Allison, Carrie; Fisher, Simon E.; Baron-Cohen, Simon

    2015-01-01

    Asperger Syndrome (AS) is a neurodevelopmental condition characterized by impairments in social interaction and communication, alongside the presence of unusually repetitive, restricted interests and stereotyped behaviour. Individuals with AS have no delay in cognitive and language development. It is a subset of Autism Spectrum Conditions (ASC), which are highly heritable and has a population prevalence of approximately 1%. Few studies have investigated the genetic basis of AS. To address this gap in the literature, we performed a genome-wide pooled DNA association study to identify candidate loci in 612 individuals (294 cases and 318 controls) of Caucasian ancestry, using the Affymetrix GeneChip Human Mapping version 6.0 array. We identified 11 SNPs that had a p-value below 1x10-5. These SNPs were independently genotyped in the same sample. Three of the SNPs (rs1268055, rs7785891 and rs2782448) were nominally significant, though none remained significant after Bonferroni correction. Two of our top three SNPs (rs7785891 and rs2782448) lie in loci previously implicated in ASC. However, investigation of the three SNPs in the ASC genome-wide association dataset from the Psychiatric Genomics Consortium indicated that these three SNPs were not significantly associated with ASC. The effect sizes of the variants were modest, indicating that our study was not sufficiently powered to identify causal variants with precision. PMID:26176695

  8. Conidial germination in the filamentous fungus Fusarium graminearum.

    PubMed

    Seong, Kye-Yong; Zhao, Xinhua; Xu, Jin-Rong; Güldener, Ulrich; Kistler, H Corby

    2008-04-01

    The ascomycetous fungus Fusarium graminearum is an important plant pathogen causing Fusarium head blight disease of wheat and barley. To understand early developmental stages of this organism, we followed the germination of macroconidia microscopically to understand the timing of key events. These events, recorded after suspension of spores in liquid germination medium, included spore swelling at 2h, germination tube emergence and elongation from conidia at 8h and hyphal branching at 24h. To understand changes in gene expression during these developmental changes, RNA was isolated from spores and used to interrogate the F. graminearum Affymetrix GeneChip. RNAs corresponding to 5813 genes were detected in fresh spores and 5146, 5249 and 5993, respectively, in spores incubated in germination medium after 2, 8 or 24h (P<0.001). Gene expression data were used to predict the cellular and physiological state of each developmental stage for known processes. Predictions were confirmed microscopically for several previously unreported developmental events such as manifestation of peroxisomes in fresh spores and nuclear division resulting in binuclear cells within macroconidia prior to spore germination. Knowledge of stage-specific gene expression and changes in gene expression levels between developmental stages are an important first step to understanding the molecular mechanisms responsible for spore germination and development. PMID:17950638

  9. Prevalence of gene expression additivity in genetically stable wheat allohexaploids.

    PubMed

    Chelaifa, Houda; Chagué, Véronique; Chalabi, Smahane; Mestiri, Imen; Arnaud, Dominique; Deffains, Denise; Lu, Yunhai; Belcram, Harry; Huteau, Virginie; Chiquet, Julien; Coriton, Olivier; Just, Jérémy; Jahier, Joseph; Chalhoub, Boulos

    2013-02-01

    The reprogramming of gene expression appears as the major trend in synthetic and natural allopolyploids where expression of an important proportion of genes was shown to deviate from that of the parents or the average of the parents. In this study, we analyzed gene expression changes in previously reported, highly stable synthetic wheat allohexaploids that combine the D genome of Aegilops tauschii and the AB genome extracted from the natural hexaploid wheat Triticum aestivum. A comprehensive genome-wide analysis of transcriptional changes using the Affymetrix GeneChip Wheat Genome Array was conducted. Prevalence of gene expression additivity was observed where expression does not deviate from the average of the parents for 99.3% of 34,820 expressed transcripts. Moreover, nearly similar expression was observed (for 99.5% of genes) when comparing these synthetic and natural wheat allohexaploids. Such near-complete additivity has never been reported for other allopolyploids and, more interestingly, for other synthetic wheat allohexaploids that differ from the ones studied here by having the natural tetraploid Triticum turgidum as the AB genome progenitor. Our study gave insights into the dynamics of additive gene expression in the highly stable wheat allohexaploids. PMID:23278496

  10. Shades of gray: A comparison of linkage disequilibrium between Hutterites and Europeans

    PubMed Central

    Thompson, Emma E; Sun, Ying; Nicolae, Dan; Ober, Carole

    2014-01-01

    Founder or isolated populations have advantages for genetic studies due to decreased genetic and environmental heterogeneity. However, whereas longer range linkage disequilibrium (LD) in these populations is expected to facilitate gene localization, extensive LD may actually limit the ability for gene discovery. The North American Hutterite population is one of the best characterized young founder populations and members of this isolate have been the subjects of our studies of complex traits, including fertility, asthma and cardiovascular disease, for >20 years. Here, we directly assess the patterns and extent of global LD using single nucleotide polymorphism (SNP) genotypes with minor allele frequencies (MAFs) ≥5% from the Affymetrix GeneChip® Mapping 500K array in 60 relatively unrelated Hutterites and 60 unrelated Europeans (HapMap CEU). Although LD among some marker pairs extends further in the Hutterites than in Europeans, the pattern of LD and minor allele frequencies are surprisingly similar. These results indicate that 1) identifying disease genes should be no more difficult in the Hutterites than in outbred European populations, 2) the same common susceptibility alleles for complex diseases should be present in the Hutterites and outbred European populations, and 3) imputation algorithms based on HapMap CEU should be applicable to the Hutterites. PMID:19697328

  11. Loss of heterozygosity and transcriptome analyses of a 1.2 Mb candidate ovarian cancer tumor suppressor locus region at 17q25.1-q25.2.

    PubMed

    Presneau, Nadège; Dewar, Ken; Forgetta, Vince; Provencher, Diane; Mes-Masson, Anne-Marie; Tonin, Patricia N

    2005-07-01

    Loss of heterozygosity (LOH) analysis was performed in epithelial ovarian cancers (EOC) to further characterize a previously identified candidate tumor suppressor gene (TSG) region encompassing D17S801 at chromosomal region 17q25.1. LOH of at least one informative marker was observed for 100 (71%) of 140 malignant EOC samples in an analysis of 6 polymorphic markers (cen-D17S1839-D17S785-D17S1817-D17S801-D17S751-D17S722-tel). The combined LOH analysis revealed a 453 kilobase (Kb) minimal region of deletion (MRD) bounded by D17S1817 and D17S751. Human and mouse genome assemblies were used to resolve marker inconsistencies in the D17S1839-D17S722 interval and identify candidates. The region contains 32 known and strongly predicted genes, 9 of which overlap the MRD. The reference genomic sequences share nearly identical gene structures and the organization of the region is highly collinear. Although, the region does not show any large internal duplications, a 1.5 Kb inverted duplicated sequence of 87% nucleotide identity was observed in a 13 Kb region surrounding D17S801. Transcriptome analysis by Affymetrix GeneChip and reverse transcription (RT)-polymerase chain reaction (PCR) methods of 3 well characterized EOC cell lines and primary cultures of normal ovarian surface epithelial (NOSE) cells was performed with 32 candidates spanning D17S1839-D17S722 interval. RT-PCR analysis of 8 known or strongly predicted genes residing in the MRD in 10 EOC samples, that exhibited LOH of the MRD, identified FLJ22341 as a strong candidate TSG. The proximal repeat sequence of D17S801 occurs 8 Kb upstream of the putative promoter region of FLJ22341. RT-PCR analysis of the EOC samples and cell lines identified DKFZP434P0316 that maps proximal to the MRD, as a candidate. While Affymetrix technology was useful for initially eliminating less promising candidates, subsequent RT-PCR analysis of well-characterized EOC samples was essential to prioritize TSG candidates for further study

  12. Microarray profiling for differential gene expression in PMSG-hCG stimulated preovulatory ovarian follicles of Chinese Taihu and Large White sows

    PubMed Central

    2011-01-01

    Background The Chinese Taihu is one of the most prolific pig breeds in the world, which farrows at least five more piglets per litter than Western pig breeds partly due to a greater ovulation rate. Variation of ovulation rate maybe associated with the differences in the transcriptome of Chinese Taihu and Large White ovaries. In order to understand the molecular basis of the greater ovulation rate of Chinese Taihu sows, expression profiling experiments were conducted to identify differentially expressed genes in ovarian follicles at the preovulatory stage of a PMSG-hCG stimulated estrous cycle from 3 Chinese Taihu and 3 Large White cycling sows by using the Affymetrix Porcine Genechip™. Results One hundred and thirty-three differentially expressed genes were identified between Chinese Taihu and Large White sows by using Affymetrix porcine GeneChip (p ≤ 0.05, Fold change ≥ 2 or ≤ 0.5). Gene Ontology (GO) analysis revealed that these genes belonged to the class of genes that participated in regulation of cellular process, regulation of biological process, biological regulation, developmental process, cell communication and signal transduction and so on. Significant differential expression of 6 genes including WNT10B and DKK2 in the WNT signaling pathway was detected. Real-time RT-PCR confirmed the expression pattern in seven of eight selected genes. A search of chromosomal location revealed that 92 differentially expressed transcripts located to the intervals of quantitative trait loci (QTLs) for reproduction traits. Furthermore, SNPs of two differentially expressed genes- BAX and BMPR1B were showed to be associated with litter size traits in Large White pigs and Chinese DIV line pigs (p ≤ 0.1 or p ≤ 0.05). Conclusions Our study detected many genes that showed differential expression between ovary follicles of two divergent breeds of pigs. Genes involved with regulation of cellular process, regulation of biological process, in addition to several genes not

  13. The periparturient period is associated with structural and transcriptomic adaptations of rumen papillae in dairy cattle.

    PubMed

    Steele, M A; Schiestel, C; AlZahal, O; Dionissopoulos, L; Laarman, A H; Matthews, J C; McBride, B W

    2015-04-01

    The structural and functional adaption of the rumen epithelium during the transition period is largely undescribed. To characterize the adaptation of the rumen epithelium during transition, multiparous dairy cattle (n=12) fitted with rumen fistulas and fed a low-energy dry cow diet (1.37 Mcal/kg, net energy for lactation) were transitioned abruptly to a high-energy lactating cow diet (1.68 Mcal/kg, net energy for lactation) immediately after parturition. Rumen papillae were biopsied at -3, +1, and +6 wk relative to calving. The histology of morphology of the rumen papillae was evaluated under the light microscope and electron microscope, and mRNA profiling was performed using an Affymetrix GeneChip Bovine Gene 1.0 ST Array (Affymetrix, Santa Clara, CA). Data preprocessing was conducted using the robust multi-array average method, and detection of significant genes was conducted using ANOVA. Also, the Benjamini-Hochberg false discovery rate of 0.1 was applied. Microscopic examination of rumen papillae revealed an increase in epithelial desquamation during early lactation as sloughing scores increased from 1.7 ± 0.2 at -3 wk to 4.1 ± 0.3 and 3.4 ± 0.2 at +1 and + 6 wk, respectively. A total of 1,011 (-3 vs. +1 wk) and 729 (-3 vs. +6 wk) differentially expressed genes were identified (false discovery rate of 0.10, P<10(-3), fold-change ± 1.2 cut-off). A group of differentially expressed genes involved in desmosome assembly (DSG1, CDSN), epidermal growth factor signaling (EGFR, EREG), transforming growth factor β signaling (TGFB1), and the insulin-like growth factor-axis (GHR, IGFBP2, IGFBP3, CTGF) was also validated using PCR. Gene network analysis found that EGFR, GHR, and TGFB1 were focal points of the top pathways, thereby supporting the importance of these regulatory genes to the adaptive response of rumen papillae in early lactation. The microscopic and transcriptomic changes in this study provide insight into the mechanisms responsible for the rapid rate of

  14. VTCdb: a gene co-expression database for the crop species Vitis vinifera (grapevine)

    PubMed Central

    2013-01-01

    Background Gene expression datasets in model plants such as Arabidopsis have contributed to our understanding of gene function and how a single underlying biological process can be governed by a diverse network of genes. The accumulation of publicly available microarray data encompassing a wide range of biological and environmental conditions has enabled the development of additional capabilities including gene co-expression analysis (GCA). GCA is based on the understanding that genes encoding proteins involved in similar and/or related biological processes may exhibit comparable expression patterns over a range of experimental conditions, developmental stages and tissues. We present an open access database for the investigation of gene co-expression networks within the cultivated grapevine, Vitis vinifera. Description The new gene co-expression database, VTCdb (http://vtcdb.adelaide.edu.au/Home.aspx), offers an online platform for transcriptional regulatory inference in the cultivated grapevine. Using condition-independent and condition-dependent approaches, grapevine co-expression networks were constructed using the latest publicly available microarray datasets from diverse experimental series, utilising the Affymetrix Vitis vinifera GeneChip (16 K) and the NimbleGen Grape Whole-genome microarray chip (29 K), thus making it possible to profile approximately 29,000 genes (95% of the predicted grapevine transcriptome). Applications available with the online platform include the use of gene names, probesets, modules or biological processes to query the co-expression networks, with the option to choose between Affymetrix or Nimblegen datasets and between multiple co-expression measures. Alternatively, the user can browse existing network modules using interactive network visualisation and analysis via CytoscapeWeb. To demonstrate the utility of the database, we present examples from three fundamental biological processes (berry development, photosynthesis and

  15. Potential Factors for the Differentiation of ESCs/iPSCs Into Insulin-Producing Cells.

    PubMed

    Tsugata, Takako; Nikoh, Naruo; Kin, Tatsuya; Saitoh, Issei; Noguchi, Yasufumi; Ueki, Hideo; Watanabe, Masami; James Shapiro, Andrew M; Noguchi, Hirofumi

    2015-02-01

    The low efficiency of in vitro differentiation of human embryonic stem cells (ESCs) or human induced pluripotent stem cells (iPSCs) into insulin-producing cells thus creates a crucial hurdle for the clinical implementation of human pluripotent stem cells (PSCs). In this study, we investigated the key factors for the differentiation of PSCs into insulin-producing cells. We obtained microarray data of HUES8 and HUES6 from two GeneChips (GPL3921: Affymetrix HT Human Genome U133A Array, GPL570: Affymetrix Human Genome U133 Plus 2.0 Array) in a database of GEO (NCBI), since HUES8 can differentiate into pancreatic cells, while HUES6 hardly demonstrates any differentiation at all. The genes with more than fourfold higher expressions in HUES8 compared to HUES6 included RPS4Y1, DDX3Y, EIF1AY, GREM1, GATA6, and NLGN4Y. Since there were four genes, RPS4Y1, DDX3Y, EIF1AY, and NLGN4Y, on the Y chromosome and HUES8 was a male cell line and HUES6 was a female cell line, we excluded these genes in this study. On the other hand, genes with more than fourfold higher expressions in HUES6 compared to HUES8 included NLRP2, EGR1, and SMC3. We next compared iPSCs derived from pancreatic cells (PiPSCs) and iPSCs derived from fibroblasts (FiPSCs). PiPSCs differentiated into insulin-producing cells more easily than FiPSCs because of their epigenetic memory. The gene expressions of GREM1, GATA6, NLRP2, EGR1, and SMC3 in PiPSCs and FiPSCs were also investigated. The expression level of GREM1 and GATA6 in PiPSCs were higher than in FiPSCs. On the other hand, EGR1, which was lower in HUES8 than in HUES6, was predictably lower in PiPSCs than FiPSCs, while NLRP2 and SMC3 were higher in PiPSCs than FiPSCs. These data suggest that the expression of GATA6 and GREM1 and the inhibition of EGR1 may be important factors for the differentiation of PSCs into insulin-producing cells. PMID:26858897

  16. Identification of diagnostic markers in colorectal cancer via integrative epigenomics and genomics data

    PubMed Central

    KOK-SIN, TEOW; MOKHTAR, NORFILZA MOHD; HASSAN, NUR ZARINA ALI; SAGAP, ISMAIL; ROSE, ISA MOHAMED; HARUN, ROSLAN; JAMAL, RAHMAN

    2015-01-01

    Apart from genetic mutations, epigenetic alteration is a common phenomenon that contributes to neoplastic transformation in colorectal cancer. Transcriptional silencing of tumor-suppressor genes without changes in the DNA sequence is explained by the existence of promoter hypermethylation. To test this hypothesis, we integrated the epigenome and transcriptome data from a similar set of colorectal tissue samples. Methylation profiling was performed using the Illumina InfiniumHumanMethylation27 BeadChip on 55 paired cancer and adjacent normal epithelial cells. Fifteen of the 55 paired tissues were used for gene expression profiling using the Affymetrix GeneChip Human Gene 1.0 ST array. Validation was carried out on 150 colorectal tissues using the methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) technique. PCA and supervised hierarchical clustering in the two microarray datasets showed good separation between cancer and normal samples. Significant genes from the two analyses were obtained based on a ≥2-fold change and a false discovery rate (FDR) P-value of <0.05. We identified 1,081 differentially hypermethylated CpG sites and 36 hypomethylated CpG sites. We also found 709 upregulated and 699 downregulated genes from the gene expression profiling. A comparison of the two datasets revealed 32 overlapping genes with 27 being hypermethylated with downregulated expression and 4 hypermethylated with upregulated expression. One gene was found to be hypomethylated and downregulated. The most enriched molecular pathway identified was cell adhesion molecules that involved 4 overlapped genes, JAM2, NCAM1, ITGA8 and CNTN1. In the present study, we successfully identified a group of genes that showed methylation and gene expression changes in well-defined colorectal cancer tissues with high purity. The integrated analysis gives additional insight regarding the regulation of colorectal cancer-associated genes and their underlying mechanisms that

  17. OpaR Controls a Network of Downstream Transcription Factors in Vibrio parahaemolyticus BB22OP

    PubMed Central

    Kernell Burke, Alison; Guthrie, Leah T. C.; Modise, Thero; Cormier, Guy; Jensen, Roderick V.; McCarter, Linda L.; Stevens, Ann M.

    2015-01-01

    Vibrio parahaemolyticus is an emerging world-wide human pathogen that is associated with food-borne gastroenteritis when raw or undercooked seafood is consumed. Expression of virulence factors in this organism is modulated by the phenomenon known as quorum sensing, which permits differential gene regulation at low versus high cell density. The master regulator of quorum sensing in V. parahaemolyticus is OpaR. OpaR not only controls virulence factor gene expression, but also the colony and cellular morphology associated with growth on a surface and biofilm formation. Whole transcriptome Next Generation sequencing (RNA-Seq) was utilized to determine the OpaR regulon by comparing strains BB22OP (opaR+, LM5312) and BB22TR (∆opaR1, LM5674). This work, using the published V. parahaemolyticus BB22OP genome sequence, confirms and expands upon a previous microarray analysis for these two strains that used an Affymetrix GeneChip designed from the closely related V. parahaemolyticus RIMD2210633 genome sequence. Overall there was excellent correlation between the microarray and RNA-Seq data. Eleven transcription factors under OpaR control were identified by both methods and further confirmed by quantitative reverse transcription PCR (qRT-PCR) analysis. Nine of these transcription factors were demonstrated to be direct OpaR targets via in vitro electrophoretic mobility shift assays with purified hexahistidine-tagged OpaR. Identification of the direct and indirect targets of OpaR, including small RNAs, will enable the construction of a network map of regulatory interactions important for the switch between the nonpathogenic and pathogenic states. PMID:25901572

  18. Form-Deprivation Myopia in Chick Induces Limited Changes in Retinal Gene Expression

    PubMed Central

    McGlinn, Alice M.; Baldwin, Donald A.; Tobias, John W.; Budak, Murat T.; Khurana, Tejvir S.; Stone, Richard A.

    2007-01-01

    Purpose Evidence has implicated the retina as a principal controller of refractive development. In the present study, the retinal transcriptome was analyzed to identify alterations in gene expression and potential signaling pathways involved in form-deprivation myopia of the chick. Methods One-week-old white Leghorn chicks wore a unilateral image-degrading goggle for 6 hours or 3 days (n = 6 at each time). Total RNA from the retina/(retinal pigment epithelium) was used for expression profiling with chicken gene microarrays (Chicken GeneChips; Affymetrix, Santa Clara, CA). To identify gene expression level differences between goggled and contralateral nongoggled eyes, normalized microarray signal intensities were analyzed by the significance analysis of microarrays (SAM) approach. Differentially expressed genes were validated by real-time quantitative reverse transcription–polymerase chain reaction (qPCR) in independent biological replicates. Results Small changes were detected in differentially expressed genes in form-deprived eyes. In chickens that had 6 hours of goggle wear, downregulation of bone morphogenetic protein 2 and connective tissue growth factor was validated. In those with 3 days of goggle wear, downregulation of bone morphogenetic protein 2, vasoactive intestinal peptide, preopro-urotensin II–related peptide and mitogen-activated protein kinase phosphatase 2 was validated, and upregulation of endothelin receptor type B and interleukin-18 was validated. Conclusions Form-deprivation myopia, in its early stages, is associated with only minimal changes in retinal gene expression at the level of the transcriptome. While the list of validated genes is short, each merits further study for potential involvement in the signaling cascade mediating myopia development. PMID:17652709

  19. Changes of gene expression profiles in the cervical spinal cord by acupuncture in an MPTP-intoxicated mouse model: microarray analysis.

    PubMed

    Choi, Yeong-Gon; Yeo, Sujung; Hong, Yeon-Mi; Kim, Sung-Hoon; Lim, Sabina

    2011-07-15

    It has been shown that acupuncture at acupoints GB34 and LR3 inhibits the degeneration of nigrostriatal neurons in a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) mouse model of Parkinson's disease. The degeneration of spinal cord was reported to be induced in the MPTP-treated pre-symptomatic mouse. In this study, the gene expression profile changes following acupuncture at the acupoints were investigated in the cervical spinal cord of an MPTP-induced parkinsonism model using a whole transcript array (Affymetrix GeneChip mouse gene 1.0 ST array). It was shown that 8 of the probes up-regulated in MPTP, as compared to the control, were down-regulated after acupuncture at the acupoints. Of these 8 probes, 6 probes (4 annotated genes in 6 probes: Ctla2a, EG383229, Ppbp and Ube2l6) were exclusively down-regulated by acupuncture at the specific acupoints except for 2 probes as these 2 probes were commonly down-regulated by acupuncture at both the acupoints and the non-acupoints. In addition, 11 of the probes down-regulated in MPTP, as compared to the control, were up-regulated by acupuncture at the acupoints. Of these 11 probes, 10 probes (5 annotated genes in 10 probes: EG665033, ENSMUSG00000055323, Obox6, Pbp2 and Tmem150) were exclusively up-regulated by acupuncture at the specific acupoints except for the Fut11 because the Fut11 was commonly up-regulated by acupuncture at both the acupoints and the non-acupoints. The expression levels of the representative genes in the microarray were validated by real-time RT-PCR. These data suggest that the expression of these exclusively regulated 16 probes (9 genes) may be, at least in part, affected by acupuncture at the acupoints in the cervical spinal cord which can be damaged by MPTP intoxication. PMID:21440609

  20. Ochratoxin a lowers mRNA levels of genes encoding for key proteins of liver cell metabolism.

    PubMed

    Hundhausen, Christoph; Boesch-Saadatmandi, Christine; Matzner, Nicole; Lang, Florian; Blank, Ralf; Wolffram, Siegfried; Blaschek, Wolfgang; Rimbach, Gerald

    2008-01-01

    Ochratoxin A (OTA) is a nephro- and hepatotoxic mycotoxin that frequently contaminates food and feedstuffs. Although recent studies have indicated that OTA modulates renal gene expression, little is known regarding its impact on differential gene expression in the liver. Therefore a microarray study of the HepG2 liver cell transcriptome in response to OTA exposure (0, 0.25, 2.5 micromol/l for 24 h) was performed using Affymetrix GeneChip technology. Selected microarray results were verified by real-time PCR and Western blotting as independent methods. Out of 14,500 genes present on the microarray, 13 and 250 genes were down-regulated by 0.25 and 2.5 micromol/l OTA, respectively. Reduced mRNA levels of calcineurin A beta (PPP3CB), which regulates inflammatory signalling pathways in immune cells, and of the uncoupling protein 2 (UCP2), which has been suggested to control the production of reactive oxygen species (ROS), were observed in response to 0.25 micromol/l OTA. A particularly strong down-regulation due to 2.5 micromol/l OTA was evident for the mRNA levels of insulin-like growth factor binding protein 1 (IGFBP1) and tubulin beta 1 (TUBB1) which have been demonstrated to function as a pro-survival factor in hepatocytes and as an important cytoskeletal component, respectively. In addition, many genes involved in energy and xenobiotic metabolism, including phosphoglycerate kinase 1 (PGK1), stearoyl-Coenzyme A desaturase 1 (SCD), and glutathione S-transferase omega 1 (GSTO1), were down-regulated by OTA. Furthermore, OTA significantly inhibited the capacitative calcium entry into the HepG2 cells, indicating an alteration of calcium homeostasis. Overall, OTA dose-dependently affects multiple genes encoding for key proteins of liver cell metabolism. PMID:19287073

  1. Mechanism-based biomarker gene sets for glutathione depletion-related hepatotoxicity in rats

    SciTech Connect

    Gao Weihua; Mizukawa, Yumiko; Nakatsu, Noriyuki; Minowa, Yosuke; Yamada, Hiroshi; Ohno, Yasuo; Urushidani, Tetsuro

    2010-09-15

    Chemical-induced glutathione depletion is thought to be caused by two types of toxicological mechanisms: PHO-type glutathione depletion [glutathione conjugated with chemicals such as phorone (PHO) or diethyl maleate (DEM)], and BSO-type glutathione depletion [i.e., glutathione synthesis inhibited by chemicals such as L-buthionine-sulfoximine (BSO)]. In order to identify mechanism-based biomarker gene sets for glutathione depletion in rat liver, male SD rats were treated with various chemicals including PHO (40, 120 and 400 mg/kg), DEM (80, 240 and 800 mg/kg), BSO (150, 450 and 1500 mg/kg), and bromobenzene (BBZ, 10, 100 and 300 mg/kg). Liver samples were taken 3, 6, 9 and 24 h after administration and examined for hepatic glutathione content, physiological and pathological changes, and gene expression changes using Affymetrix GeneChip Arrays. To identify differentially expressed probe sets in response to glutathione depletion, we focused on the following two courses of events for the two types of mechanisms of glutathione depletion: a) gene expression changes occurring simultaneously in response to glutathione depletion, and b) gene expression changes after glutathione was depleted. The gene expression profiles of the identified probe sets for the two types of glutathione depletion differed markedly at times during and after glutathione depletion, whereas Srxn1 was markedly increased for both types as glutathione was depleted, suggesting that Srxn1 is a key molecule in oxidative stress related to glutathione. The extracted probe sets were refined and verified using various compounds including 13 additional positive or negative compounds, and they established two useful marker sets. One contained three probe sets (Akr7a3, Trib3 and Gstp1) that could detect conjugation-type glutathione depletors any time within 24 h after dosing, and the other contained 14 probe sets that could detect glutathione depletors by any mechanism. These two sets, with appropriate scoring

  2. The global role of ppGpp synthesis in morphological differentiation and antibiotic production in Streptomyces coelicolor A3(2)

    PubMed Central

    Hesketh, Andrew; Chen, Wenqiong Joan; Ryding, Jamie; Chang, Sherman; Bibb, Mervyn

    2007-01-01

    Background Regulation of production of the translational apparatus via the stringent factor ppGpp in response to amino acid starvation is conserved in many bacteria. However, in addition to this core function, it is clear that ppGpp also exhibits genus-specific regulatory effects. In this study we used Affymetrix GeneChips to more fully characterize the regulatory influence of ppGpp synthesis on the biology of Streptomyces coelicolor A3(2), with emphasis on the control of antibiotic biosynthesis and morphological differentiation. Results Induction of ppGpp synthesis repressed transcription of the major sigma factor hrdB, genes with functions associated with active growth, and six of the thirteen conservons present in the S. coelicolor genome. Genes induced following ppGpp synthesis included the alternative sigma factor SCO4005, many for production of the antibiotics CDA and actinorhodin, the regulatory genes SCO4198 and SCO4336, and two alternative ribosomal proteins. Induction of the CDA and actinorhodin clusters was accompanied by an increase in transcription of the pathway regulators cdaR and actII-ORF4, respectively. Comparison of transcriptome profiles of a relA null strain, M570, incapable of ppGpp synthesis with its parent M600 suggested the occurrence of metabolic stress in the mutant. The failure of M570 to sporulate was associated with a stalling between production of the surfactant peptide SapB, and of the hydrophobins: it overproduced SapB but failed to express the chaplin and rodlin genes. Conclusion In S. coelicolor, ppGpp synthesis influences the expression of several genomic elements that are particularly characteristic of streptomycete biology, notably antibiotic gene clusters, conservons, and morphogenetic proteins. PMID:17683547

  3. Comparison of TCDD-elicited genome-wide hepatic gene expression in Sprague–Dawley rats and C57BL/6 mice

    PubMed Central

    Nault, Rance; Kim, Suntae; Zacharewski, Timothy R.

    2014-01-01

    Although the structure and function of the AhR are conserved, emerging evidence suggests that downstream effects are species-specific. In this study, rat hepatic gene expression data from the DrugMatrix database (National Toxicology Program) were compared to mouse hepatic whole-genome gene expression data following treatment with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). For the DrugMatrix study, male Sprague–Dawley rats were gavaged daily with 20 μg/kg TCDD for 1, 3 and 5 days, while female C57BL/6 ovariectomized mice were examined 1, 3 and 7 days after a single oral gavage of 30 μg/kg TCDD. A total of 649 rat and 1386 mouse genes (|fold change|≥1.5, P1(t)≥0.99) were differentially expressed following treatment. HomoloGene identified 11,708 orthologs represented across the rat Affymetrix 230 2.0 GeneChip (12,310 total orthologs), and the mouse 4×44K v.1 Agilent oligonucleotide array (17,578 total orthologs). Comparative analysis found 563 and 922 orthologs differentially expressed in response to TCDD in the rat and mouse, respectively, with 70 responses associated with immune function and lipid metabolism in common to both. Moreover, QRTPCR analysis of Ceacam1, showed divergent expression (induced in rat; repressed in mouse) functionally consistent with TCDD-elicited hepatic steatosis in the mouse but not the rat. Functional analysis identified orthologs involved in nucleotide binding and acetyltransferase activity in rat, while mouse-specific responses were associated with steroid, phospholipid, fatty acid, and carbohydrate metabolism. These results provide further evidence that TCDD elicits species-specific regulation of distinct gene networks, and outlines considerations for future comparisons of publicly available microarray datasets. PMID:23238561

  4. The Sterolgene v0 cDNA microarray: a systemic approach to studies of cholesterol homeostasis and drug metabolism

    PubMed Central

    Režen, Tadeja; Juvan, Peter; Fon Tacer, Klementina; Kuzman, Drago; Roth, Adrian; Pompon, Denis; Aggerbeck, Lawrence P; Meyer, Urs A; Rozman, Damjana

    2008-01-01

    Background Cholesterol homeostasis and xenobiotic metabolism are complex biological processes, which are difficult to study with traditional methods. Deciphering complex regulation and response of these two processes to different factors is crucial also for understanding of disease development. Systems biology tools as are microarrays can importantly contribute to this knowledge and can also discover novel interactions between the two processes. Results We have developed a low density Sterolgene v0 cDNA microarray dedicated to studies of cholesterol homeostasis and drug metabolism in the mouse. To illustrate its performance, we have analyzed mouse liver samples from studies focused on regulation of cholesterol homeostasis and drug metabolism by diet, drugs and inflammation. We observed down-regulation of cholesterol biosynthesis during fasting and high-cholesterol diet and subsequent up-regulation by inflammation. Drug metabolism was down-regulated by fasting and inflammation, but up-regulated by phenobarbital treatment and high-cholesterol diet. Additionally, the performance of the Sterolgene v0 was compared to the two commercial high density microarray platforms: the Agilent cDNA (G4104A) and the Affymetrix MOE430A GeneChip. We hybridized identical RNA samples to the commercial microarrays and showed that the performance of Sterolgene is comparable to commercial arrays in terms of detection of changes in cholesterol homeostasis and drug metabolism. Conclusion Using the Sterolgene v0 microarray we were able to detect important changes in cholesterol homeostasis and drug metabolism caused by diet, drugs and inflammation. Together with its next generations the Sterolgene microarrays represent original and dedicated tools enabling focused and cost effective studies of cholesterol homeostasis and drug metabolism. These microarrays have the potential of being further developed into screening or diagnostic tools. PMID:18261244

  5. Genetic associations with neuroendocrine tumor risk: results from a genome-wide association study.

    PubMed

    Du, Yeting; Ter-Minassian, Monica; Brais, Lauren; Brooks, Nichole; Waldron, Amanda; Chan, Jennifer A; Lin, Xihong; Kraft, Peter; Christiani, David C; Kulke, Matthew H

    2016-08-01

    The etiology of neuroendocrine tumors remains poorly defined. Although neuroendocrine tumors are in some cases associated with inherited genetic syndromes, such syndromes are rare. The majority of neuroendocrine tumors are thought to be sporadic. We performed a genome-wide association study (GWAS) to identify potential genetic risk factors for sporadic neuroendocrine tumors. Using germline DNA from blood specimens, we genotyped 909,622 SNPs using the Affymetrix 6.0 GeneChip, in a cohort comprising 832 neuroendocrine tumor cases from Dana-Farber Cancer Institute and Massachusetts General Hospital and 4542 controls from the Harvard School of Public Health. An additional 241 controls from Dana-Farber Cancer Institute were used for quality control. We assessed risk associations in the overall cohort, and in neuroendocrine tumor subgroups. We identified no potential risk associations in the cohort overall. In the small intestine neuroendocrine tumor subgroup, comprising 293 cases, we identified risk associations with three SNPs on chromosome 12, all in strong LD. The three SNPs are located upstream of ELK3, a transcription factor implicated in angiogenesis. We did not identify clear risk associations in the bronchial or pancreatic neuroendocrine subgroups. This large-scale study provides initial evidence that presumed sporadic small intestine neuroendocrine tumors may have a genetic etiology. Our results provide a basis for further exploring the role of genes implicated in this analysis, and for replication studies to confirm the observed associations. Additional studies to evaluate potential genetic risk factors for sporadic pancreatic and bronchial neuroendocrine tumors are warranted. PMID:27492634

  6. Gene Expression Profiling of NF1-Associated and Sporadic Pilocytic Astrocytoma Identifies Aldehyde Dehydrogenase 1 Family, Member L1 (ALDH1L1) as an Underexpressed Candidate Biomarker in Aggressive Subtypes

    PubMed Central

    Rodriguez, Fausto J.; Giannini, Caterina; Asmann, Yan W.; Sharma, Mukesh K.; Perry, Arie; Tibbetts, Kathleen M.; Jenkins, Robert B.; Scheithauer, Bernd W.; Anant, Shrikant; Jenkins, Sarah; Eberhart, Charles G.; Sarkaria, Jann N.; Gutmann, David H.

    2009-01-01

    Pilocytic astrocytomas (PAs) are WHO grade I gliomas; they most often affect children and young adults and occur in patients with neurofibromatosis type 1 (NF-1). To identify genes that are differentially expressed in sporadic (S-PA) versus NF-1-associated PAs (NF1-PAs) and those that might reflect differences in clinical behavior, we performed gene expression profiling using Affymetrix U133 Plus2.0 GeneChip arrays in 36 S-PAs and 11 NF1-PAs. Thirteen genes were over-expressed and another 13 genes were under-expressed in NF1-associated PAs relative to S-PAs. Immunohistochemical studies performed on 103 tumors, representing 2 independently generated tissue microarrays, confirmed the differential expression of CUGBP2 (p = 0.0014), RANBP9 (p = 0.0075), ITGAV1 (p = 0.0001), and INFGR1 (p = 0.024) proteins. One of the underexpressed genes, aldehyde dehydrogenase 1 family, member L1 (ALDH1L1), was also reduced in clinically aggressive compared to typical PAs (p = 0.01) and in PAs with increased cellularity and necrosis. Furthermore, in an additional independent set of tumors, weak to absent ALDH1L1 expression was found in 13/18 (72%) clinically aggressive PAs, in 8/9 (89%) PAs with pilomyxoid features, in 7/10 (70%) PAs with anaplastic transformation and in 16/21 (76%) diffusely infiltrating astrocytomas of various grades. In summary, we have identified a molecular signature that distinguishes NF1-PA from S-PA, and found that ALDH1L1 underexpression is associated with aggressive histology and/or biological behavior. PMID:19018242

  7. Modeling Oncogenic Signaling in Colon Tumors by Multidirectional Analyses of Microarray Data Directed for Maximization of Analytical Reliability

    PubMed Central

    Rubel, Tymon; Paziewska, Agnieszka; Mikula, Michal; Jarosz, Dorota; Pachlewski, Jacek; Oledzki, Janusz; Ostrowsk, Jerzy

    2010-01-01

    Background Clinical progression of colorectal cancers (CRC) may occur in parallel with distinctive signaling alterations. We designed multidirectional analyses integrating microarray-based data with biostatistics and bioinformatics to elucidate the signaling and metabolic alterations underlying CRC development in the adenoma-carcinoma sequence. Methodology/Principal Findings Studies were performed on normal mucosa, adenoma, and carcinoma samples obtained during surgery or colonoscopy. Collections of cryostat sections prepared from the tissue samples were evaluated by a pathologist to control the relative cell type content. The measurements were done using Affymetrix GeneChip HG-U133plus2, and probe set data was generated using two normalization algorithms: MAS5.0 and GCRMA with least-variant set (LVS). The data was evaluated using pair-wise comparisons and data decomposition into singular value decomposition (SVD) modes. The method selected for the functional analysis used the Kolmogorov-Smirnov test. Expressional profiles obtained in 105 samples of whole tissue sections were used to establish oncogenic signaling alterations in progression of CRC, while those representing 40 microdissected specimens were used to select differences in KEGG pathways between epithelium and mucosa. Based on a consensus of the results obtained by two normalization algorithms, and two probe set sorting criteria, we identified 14 and 17 KEGG signaling and metabolic pathways that are significantly altered between normal and tumor samples and between benign and malignant tumors, respectively. Several of them were also selected from the raw microarray data of 2 recently published studies (GSE4183 and GSE8671). Conclusion/Significance Although the proposed strategy is computationally complex and labor–intensive, it may reduce the number of false results. PMID:20957034

  8. Microarray analysis of mediastinal lymph node of pigs naturally affected by postweaning multisystemic wasting syndrome.

    PubMed

    Fernandes, L T; Tomás, A; Bensaid, A; Sibila, M; Sánchez, A; Segalés, J

    2012-05-01

    Postweaning multisystemic wasting syndrome (PMWS) is one of the pig diseases with major economic impact worldwide. Clinical, pathologic and some immunologic aspects of this disease are relatively well-known, but the molecular mechanisms underlying the pathogenic mechanisms of the disease are still poorly understood. The objective of the present study was to investigate the global transcriptome changes in the mediastinal lymph nodes from pigs naturally affected by PMWS, as well as healthy counterparts, using the Affymetrix Porcine Genechip(®). From 366 transcripts showing significant differential abundance in the PMWS group of pigs relative to healthy animals, 229 showed higher and 137 lower abundance. A relative increased abundance of mRNAs coded by a large set of genes involved in the inflammatory responses (e.g. cytokines, acute phase proteins, and respiratory burst) was observed in PMWS affected pigs. The Gpnmb and Lgals3 genes, which have antagonistic functions in regulation of inflammatory processes, showed high mRNA levels in diseased pigs. The complement system was altered by PMWS, notably by the lower levels of Cr1 mRNA, which might favour both complement deposition and secondary infections by impairing phagocytosis. Decreased mRNA abundance of several genes involved in lymphocyte activation/differentiation, such as Cd79b, Cd19, Cd21 and MybL1, and the high level of Vsig4 mRNA, which can compromise the activation of residing T-cells, pointed towards a defective adaptive immunity. This is the first study on gene expression in pigs naturally affected by PMWS. The present results allowed identifying potential mechanisms underlying the inflammation and lymphocyte depletion in lymphoid tissues by complement mediated damage and immunosuppression, which are key features of PMWS. PMID:22366492

  9. The innate immune system is activated by stimulation of vaginal epithelial cells with Staphylococcus aureus and toxic shock syndrome toxin 1.

    PubMed

    Peterson, Marnie L; Ault, Kevin; Kremer, Mary J; Klingelhutz, Aloysius J; Davis, Catherine C; Squier, Christopher A; Schlievert, Patrick M

    2005-04-01

    Despite knowledge of the effects of toxic shock syndrome (TSS) toxin 1 (TSST-1) on the adaptive immune system, little is known about stimulation of the innate immune system, particularly epithelial cells. This study investigated the interactions of TSS Staphylococcus aureus and TSST-1 with human vaginal epithelial cells (HVECs) and porcine mucosal surfaces. When cocultured with HVECs for 6 h, TSS S. aureus MN8 proliferated, formed aggregates on the HVEC surfaces, and produced exotoxins. Receptor binding studies showed that 35S-TSST-1 bound to 5 x 10(4) receptors per HVEC, with saturation at 15 min. Affymetrix Human GeneChip U133A microarray analysis determined S. aureus MNSM (100 bacteria/HVEC) caused at least twofold up- or down-regulation of 410 HVEC genes by 6 h; these data were also confirmed with S. aureus MN8. TSST-1 (100 microg/ml) caused up- or down-regulation of 2,386 HVEC genes by 6 h. In response to S. aureus, the HVEC genes most up-regulated compared to those in controls were those coding for chemokines or cytokines--MIP-3alpha, 478-fold; GRO-alpha, 26-fold; GRO-beta, 14-fold; and GRO-gamma, 30-fold--suggesting activation of innate immunity. TSST-1 also caused up-regulation of chemokine/cytokine genes. Chemokine/cytokine gene up-regulation was confirmed by enzyme-linked immunosorbent assays measuring the corresponding proteins induced by S. aureus and TSST-1. S. aureus MN8, when incubated with porcine vaginal tissue, increased the flux of 35S-TSST-1 across the mucosal surface. This was accompanied by influx of lymphocytes into the upper layers of the tissue. These data suggest innate immune system activation through epithelial cells, reflected in chemokine/cytokine production and influx of lymphocytes, may cause changes in vaginal mucosa permeability, facilitating TSST-1 penetration. PMID:15784559

  10. Endometrial gene expression in high- and low-fertility heifers in the late luteal phase of the estrous cycle and a comparison with midluteal gene expression.

    PubMed

    Killeen, Aideen P; Diskin, Michael G; Morris, Dermot G; Kenny, David A; Waters, Sinéad M

    2016-04-01

    Embryonic mortality is a major constraint to improving reproductive efficiency and profitability in livestock enterprises. We previously reported differential expression of genes with identified roles in cellular growth and proliferation, lipid metabolism, endometrial remodeling, inflammation, angiogenesis, and metabolic exchange in endometrial tissue on day 7 of the estrous cycle (D7), between heifers ranked as either high (HF) or low (LF) for fertility. The aim of the current study was to further elucidate the underlying molecular mechanisms contributing to early embryo loss by examining differential endometrial gene expression in HF or LF heifers at a later stage of the estrous cycle;day 14(D14). A second objective was to compare these expression profiles with those from midluteal HF and LF endometrium. Using the same animal model as employed in the previous study, we slaughtered HF and LF animals on D14, harvested endometrial tissue, and carried out global gene expression analysis using the Affymetrix Bovine GeneChip. Microarray analysis detected 430 differentially expressed genes (DEG) between HF and LF animals. Ingenuity Pathway Analysis revealed enrichment for a host of biological pathways including lipid metabolism, molecular transport, immune response, cell morphology and development, and cell growth and proliferation. Important DEG includedALB, BMPR2, CCL28, COL4A3/4, FADS1, ITGA6, LDLR, PLCB3, PPARG, PTGS2, and SLC27A4 Furthermore, DEG expressed on both D7 and D14 included:PCCB,SLC25A24,DAP, and COL4A4 This study highlights some of the pathways and mechanisms underpinning late luteal bovine endometrial physiology and endometrial-related conception rate variance. PMID:26850042

  11. Molecular Dissection of Variation in Carbohydrate Metabolism Related to Water-Soluble Carbohydrate Accumulation in Stems of Wheat1[W

    PubMed Central

    Xue, Gang-Ping; McIntyre, C. Lynne; Jenkins, Colin L.D.; Glassop, Donna; van Herwaarden, Anthony F.; Shorter, Ray

    2008-01-01

    Water-soluble carbohydrates (WSCs; composed of mainly fructans, sucrose [Suc], glucose [Glc], and fructose) deposited in wheat (Triticum aestivum) stems are important carbon sources for grain filling. Variation in stem WSC concentrations among wheat genotypes is one of the genetic factors influencing grain weight and yield under water-limited environments. Here, we describe the molecular dissection of carbohydrate metabolism in stems, at the WSC accumulation phase, of recombinant inbred Seri/Babax lines of wheat differing in stem WSC concentrations. Affymetrix GeneChip analysis of carbohydrate metabolic enzymes revealed that the mRNA levels of two fructan synthetic enzyme families (Suc:Suc 1-fructosyltransferase and Suc:fructan 6-fructosyltransferase) in the stem were positively correlated with stem WSC and fructan concentrations, whereas the mRNA levels of enzyme families involved in Suc hydrolysis (Suc synthase and soluble acid invertase) were inversely correlated with WSC concentrations. Differential regulation of the mRNA levels of these Suc hydrolytic enzymes in Seri/Babax lines resulted in genotypic differences in these enzyme activities. Down-regulation of Suc synthase and soluble acid invertase in high WSC lines was accompanied by significant decreases in the mRNA levels of enzyme families related to sugar catabolic pathways (fructokinase and mitochondrion pyruvate dehydrogenase complex) and enzyme families involved in diverting UDP-Glc to cell wall synthesis (UDP-Glc 6-dehydrogenase, UDP-glucuronate decarboxylase, and cellulose synthase), resulting in a reduction in cell wall polysaccharide contents (mainly hemicellulose) in the stem of high WSC lines. These data suggest that differential carbon partitioning in the wheat stem is one mechanism that contributes to genotypic variation in WSC accumulation. PMID:18083795

  12. Molecular characterization of Neisseria meningitidis isolates using a resequencing DNA microarray.

    PubMed

    Corless, Caroline E; Kaczmarski, Edward; Borrow, Ray; Guiver, Malcolm

    2008-05-01

    Neisseria meningitidis is a major cause of both meningitis and septicemia. Typically, isolates are characterized by using a combination of immunological phenotyping, using monoclonal and polyclonal antisera, and Sanger nucleotide sequencing of epitope-encoding variable regions, although these methods can be both time-consuming and limited by reagent availability. Herein, we describe and evaluate a novel microarray to define the porB and porA serotypes of N. meningitidis by the resequencing of variable regions in a single hybridization reaction. PCR products for each gene were amplified, pooled in equimolar concentrations, hybridized to the microarray, and analyzed using Affymetrix GeneChip DNA Analysis Software. Resequencing of the microarray data was then validated by comparison with sequencing data. Molecular profiles were generated for 50 isolates that were combinations of phenotypically typeable (ie, PorA and PorB) and non-typeable (PorB only) isolates. Microarray-generated profiles from isolates with a PorB phenotype were concordant with predicted profiles compared with a previously described typing scheme. In addition, 42% (8 of 19) of previously non-typeable samples were assigned a PorB type when tested using the microarray. The remaining isolates were novel types for which no typing antisera are currently available. The porA data were 97% concordant with Sanger nucleotide sequencing. These results suggest that that microarray resequencing may be a useful tool for the characterization of meningococci, particularly for those isolates that cannot be phenotyped, offering an alternative to conventional sequencing methods. PMID:18372424

  13. Transcriptomic analysis of tomato carpel development reveals alterations in ethylene and gibberellin synthesis during pat3/pat4 parthenocarpic fruit set

    PubMed Central

    Pascual, Laura; Blanca, Jose M; Cañizares, Joaquin; Nuez, Fernado

    2009-01-01

    Background Tomato fruit set is a key process that has a great economic impact on crop production. We employed the Affymetrix GeneChip Tomato Genome Array to compare the transcriptome of a non-parthenocarpic line, UC82, with that of the parthenocarpic line RP75/59 (pat3/pat4 mutant). We analyzed the transcriptome under normal conditions as well as with forced parthenocarpic development in RP75/59, emasculating the flowers 2 days before anthesis. This analysis helps to understand the fruit set in tomato. Results Differentially expressed genes were extracted with maSigPro, which is designed for the analysis of single and multiseries time course microarray experiments. 2842 genes showed changes throughout normal carpel development and fruit set. Most of them showed a change of expression at or after anthesis. The main differences between lines were concentrated at the anthesis stage. We found 758 genes differentially expressed in parthenocarpic fruit set. Among these genes we detected cell cycle-related genes that were still activated at anthesis in the parthenocarpic line, which shows the lack of arrest in the parthenocarpic line at anthesis. Key genes for the synthesis of gibberellins and ethylene, which were up-regulated in the parthenocarpic line were also detected. Conclusion Comparisons between array experiments determined that anthesis was the most different stage and the key point at which most of the genes were modulated. In the parthenocarpic line, anthesis seemed to be a short transitional stage to fruit set. In this line, the high GAs contends leads to the development of a parthenocarpic fruit, and ethylene may mimic pollination signals, inducing auxin synthesis in the ovary and the development of a jelly fruit. PMID:19480705

  14. Global analysis of the root hair morphogenesis transcriptome reveals new candidate genes involved in root hair formation in barley.

    PubMed

    Kwasniewski, Miroslaw; Janiak, Agnieszka; Mueller-Roeber, Bernd; Szarejko, Iwona

    2010-09-01

    Root hairs are long tubular outgrowths of specialized root epidermal cells that play an important role in plant nutrition and water uptake. They are also an important model in studies of higher plant cell differentiation. In contrast to the model dicot Arabidopsis thaliana, currently very little is known about the genetic and molecular basis of root hair formation in monocots, including major cereals. To elucidate candidate genes controlling this developmental process in barley, we took advantage of the recently established Affymetrix GeneChip Barley1 Genome Array to carry out global transcriptome analyses of hairless and root hair primordia-forming roots of two barely mutant lines. Expression profiling of the root-hairless mutant rhl1.a and its wild type parent variety 'Karat' revealed 10 genes potentially involved in the early step of root hair formation in barley. Differential expression of all identified genes was confirmed by quantitative reverse transcription-polymerase chain reaction. The genes identified encode proteins associated with the cell wall and membranes, including one gene for xyloglucan endotransglycosylase, three for peroxidase enzymes and five for arabinogalactan protein, extensin, leucine-rich-repeat protein, phosphatidylinositol phosphatidylcholine transfer protein and a RhoGTPase GDP dissociation inhibitor, respectively. The molecular function of one gene is unknown at present. The expression levels of these genes were strongly reduced in roots of the root-hairless mutant rhl1.a compared to the parent variety, while expression of all 10 genes was similar in another mutant, i.e. rhp1.b, that has lost its ability to develop full root hairs but still forms hairs blocked at the primordium stage, and its wild type relative. This clearly indicates that the new genes identified are involved in the initiation of root hair morphogenesis in barley. PMID:20388575

  15. Transcriptome Signature of Virulent and Attenuated Pseudorabies Virus-Infected Rodent Brain

    PubMed Central

    Paulus, Christina; Sollars, Patricia J.; Pickard, Gary E.; Enquist, Lynn W.

    2006-01-01

    Mammalian alphaherpesviruses normally establish latent infections in ganglia of the peripheral nervous system in their natural hosts. Occasionally, however, these viruses spread to the central nervous system (CNS), where they cause damaging, often fatal, infections. Attenuated alphaherpesvirus derivatives have been used extensively as neuronal circuit tracers in a variety of animal models. Their circuit-specific spread provides a unique paradigm to study the local and global CNS response to infection. Thus, we systematically analyzed the host gene expression profile after acute pseudorabies virus (PRV) infection of the CNS using Affymetrix GeneChip technology. Rats were injected intraocularly with one of three selected virulent and attenuated PRV strains. Relative levels of cellular transcripts were quantified from hypothalamic and cerebellar tissues at various times postinfection. The number of cellular genes responding to infection correlated with the extent of virus dissemination and relative virulence of the PRV strains. A total of 245 out of 8,799 probe sets, corresponding to 182 unique cellular genes, displayed increased expression ranging from 2- to more than 100-fold higher than in uninfected tissue. Over 60% thereof were categorized as immune, proinflammatory, and other cellular defense genes. Additionally, a large fraction of infection-induced transcripts represented cellular stress responses, including glucocorticoid- and redox-related pathways. This is the first comprehensive in vivo analysis of the global transcriptional response of the mammalian CNS to acute alphaherpesvirus infection. The differentially regulated genes reported here are likely to include potential diagnostic and therapeutic targets for viral encephalitides and other neurodegenerative or neuroinflammatory diseases. PMID:16439534

  16. Genetically Determined Susceptibility to Tuberculosis in Mice Causally Involves Accelerated and Enhanced Recruitment of Granulocytes

    PubMed Central

    Keller, Christine; Hoffmann, Reinhard; Lang, Roland; Brandau, Sven; Hermann, Corinna; Ehlers, Stefan

    2006-01-01

    Classical twin studies and recent linkage analyses of African populations have revealed a potential involvement of host genetic factors in susceptibility or resistance to Mycobacterium tuberculosis infection. In order to identify the candidate genes involved and test their causal implication, we capitalized on the mouse model of tuberculosis, since inbred mouse strains also differ substantially in their susceptibility to infection. Two susceptible and two resistant mouse strains were aerogenically infected with 1,000 CFU of M. tuberculosis, and the regulation of gene expression was examined by Affymetrix GeneChip U74A array with total lung RNA 2 and 4 weeks postinfection. Four weeks after infection, 96 genes, many of which are involved in inflammatory cell recruitment and activation, were regulated in common. One hundred seven genes were differentially regulated in susceptible mouse strains, whereas 43 genes were differentially expressed only in resistant mice. Data mining revealed a bias towards the expression of genes involved in granulocyte pathophysiology in susceptible mice, such as an upregulation of those for the neutrophil chemoattractant LIX (CXCL5), interleukin 17 receptor, phosphoinositide kinase 3 delta, or gamma interferon-inducible protein 10. Following M. tuberculosis challenge in both airways or peritoneum, granulocytes were recruited significantly faster and at higher numbers in susceptible than in resistant mice. When granulocytes were efficiently depleted by either of two regimens at the onset of infection, only susceptible mice survived aerosol challenge with M. tuberculosis significantly longer than control mice. We conclude that initially enhanced recruitment of granulocytes contributes to susceptibility to tuberculosis. PMID:16790804

  17. Global gene expression profiles of ischemic preconditioning in deceased donor liver transplantation.

    PubMed

    Raza, Ali; Dikdan, George; Desai, Kunj K; Shareef, Asif; Fernandes, Helen; Aris, Virginie; de la Torre, Andrew N; Wilson, Dorian; Fisher, Adrian; Soteropoulos, Patricia; Koneru, Baburao

    2010-05-01

    The benefits of ischemic preconditioning (IPC) in reducing ischemia/reperfusion injury (IRI) remain indistinct in human liver transplantation (LT). To further understand mechanistic aspects of IPC, we performed microarray analyses as a nested substudy in a randomized trial of 10-minute IPC in 101 deceased donor LTs. Liver biopsies were performed after cold storage and at 90 minutes postreperfusion in 40 of 101 subjects. Global gene expression profiles in 6 biopsy pairs in IPC and work standard organ recovery groups at both time points were compared using the Affymetrix GeneChip Human Gene 1.0 ST array. Transcripts with >1.5-fold change and P < 0.05 were considered significant. IPC altered expression of 82 transcripts in antioxidant, immunological, lipid biosynthesis, cell development and growth, and other groups. Real-time polymerase chain reaction and immunoblotting validated our microarray data. IPC-induced overexpression of glutathione S-transferase mu transcripts (GSTM1, GSTM3, GSTM4, and GSTM5) was accompanied by increased protein expression and may contribute to a decrease in oxidative stress. However, the increased expression of fatty acid synthase may increase oxidative stress, and tumor necrosis factor ligand superfamily member 10 may promote apoptosis. These changes, in combination with decreased expression of heparin-binding epidermal growth factor-like growth factor and insulin-like growth factor binding protein-1, both of which inhibit apoptosis, may increase IRI. In our study of deceased donor LT, IPC induces changes in gene expression, some of which are potentially beneficial but some which are potentially injurious. Thus, our findings of changes in gene expression mirror the outcomes in our clinical trial. PMID:20440768

  18. Global Gene Expression in Staphylococcus aureus Biofilms

    PubMed Central

    Beenken, Karen E.; Dunman, Paul M.; McAleese, Fionnuala; Macapagal, Daphne; Murphy, Ellen; Projan, Steven J.; Blevins, Jon S.; Smeltzer, Mark S.

    2004-01-01

    We previously demonstrated that mutation of the staphylococcal accessory regulator (sarA) in a clinical isolate of Staphylococcus aureus (UAMS-1) results in an impaired capacity to form a biofilm in vitro (K. E. Beenken, J. S. Blevins, and M. S. Smeltzer, Infect. Immun. 71:4206-4211, 2003). In this report, we used a murine model of catheter-based biofilm formation to demonstrate that a UAMS-1 sarA mutant also has a reduced capacity to form a biofilm in vivo. Surprisingly, mutation of the UAMS-1 ica locus had little impact on biofilm formation in vitro or in vivo. In an effort to identify additional loci that might be relevant to biofilm formation and/or the adaptive response required for persistence of S. aureus within a biofilm, we isolated total cellular RNA from UAMS-1 harvested from a biofilm grown in a flow cell and compared the transcriptional profile of this RNA to RNA isolated from both exponential- and stationary-phase planktonic cultures. Comparisons were done using a custom-made Affymetrix GeneChip representing the genomic complement of six strains of S. aureus (COL, N315, Mu50, NCTC 8325, EMRSA-16 [strain 252], and MSSA-476). The results confirm that the sessile lifestyle associated with persistence within a biofilm is distinct by comparison to the lifestyles of both the exponential and postexponential phases of planktonic culture. Indeed, we identified 48 genes in which expression was induced at least twofold in biofilms over expression under both planktonic conditions. Similarly, we identified 84 genes in which expression was repressed by a factor of at least 2 compared to expression under both planktonic conditions. A primary theme that emerged from the analysis of these genes is that persistence within a biofilm requires an adaptive response that limits the deleterious effects of the reduced pH associated with anaerobic growth conditions. PMID:15231800

  19. High-throughput transcriptomic analysis nominates proteasomal genes as age-specific biomarkers and therapeutic targets in prostate cancer

    PubMed Central

    Zhao, S G; Jackson, W C; Kothari, V; Schipper, M J; Erho, N; Evans, J R; Speers, C; Hamstra, D A; Niknafs, Y S; Nguyen, P L; Schaeffer, E M; Ross, A E; Den, R B; Klein, E A; Jenkins, R B; Davicioni, E; Feng, F Y

    2015-01-01

    Background: Although prostate cancer (PCa) is hypothesized to differ in nature between younger versus older patients, the underlying molecular distinctions are poorly understood. We hypothesized that high-throughput transcriptomic analysis would elucidate biological differences in PCas arising in younger versus older men, and would nominate potential age-specific biomarkers and therapeutic targets. Methods: The high-density Affymetrix GeneChip platform, encompassing >1 million genomic loci, was utilized to assess gene expression in 1090 radical prostatectomy samples from patients with long-term follow-up. We identified genes associated with metastatic progression by 10 years post-treatment in younger (age<65) versus older (age⩾65) patients, and ranked these genes by their prognostic value. We performed Gene Set Enrichment Analysis (GSEA) to nominate biological concepts that demonstrated age-specific effects, and validated a target by treating with a clinically available drug in three PCa cell lines derived from younger men. Results: Over 80% of the top 1000 prognostic genes in younger and older men were specific to that age group. GSEA nominated the proteasome pathway as the most differentially prognostic in younger versus older patients. High expression of proteasomal genes conferred worse prognosis in younger but not older men on univariate and multivariate analysis. Bortezomib, a Food and Drug Administration approved proteasome inhibitor, decreased proliferation in three PCa cell lines derived from younger patients. Conclusions: Our data show significant global differences in prognostic genes between older versus younger men. We nominate proteasomeal gene expression as an age-specific biomarker and potential therapeutic target specifically in younger men. Limitations of our study include clinical differences between cohorts, and increased comorbidities and lower survival in older patients. These intriguing findings suggest that current models of PCa biology do

  20. Hypoxia-Induced Alternative Splicing in Endothelial Cells

    PubMed Central

    Weigand, Julia E.; Boeckel, Jes-Niels; Gellert, Pascal; Dimmeler, Stefanie

    2012-01-01

    Background Adaptation to low oxygen by changing gene expression is vitally important for cell survival and tissue development. The sprouting of new blood vessels, initiated from endothelial cells, restores the oxygen supply of ischemic tissues. In contrast to the transcriptional response induced by hypoxia, which is mainly mediated by members of the HIF family, there are only few studies investigating alternative splicing events. Therefore, we performed an exon array for the genome-wide analysis of hypoxia-related changes of alternative splicing in endothelial cells. Methodology/Principal findings Human umbilical vein endothelial cells (HUVECs) were incubated under hypoxic conditions (1% O2) for 48 h. Genome-wide transcript and exon expression levels were assessed using the Affymetrix GeneChip Human Exon 1.0 ST Array. We found altered expression of 294 genes after hypoxia treatment. Upregulated genes are highly enriched in glucose metabolism and angiogenesis related processes, whereas downregulated genes are mainly connected to cell cycle and DNA repair. Thus, gene expression patterns recapitulate known adaptations to low oxygen supply. Alternative splicing events, until now not related to hypoxia, are shown for nine genes: six which are implicated in angiogenesis-mediated cytoskeleton remodeling (cask, itsn1, larp6, sptan1, tpm1 and robo1); one, which is involved in the synthesis of membrane-anchors (pign) and two universal regulators of gene expression (cugbp1 and max). Conclusions/Significance For the first time, this study investigates changes in splicing in the physiological response to hypoxia on a genome-wide scale. Nine alternative splicing events, until now not related to hypoxia, are reported, considerably expanding the information on splicing changes due to low oxygen supply. Therefore, this study provides further knowledge on hypoxia induced gene expression changes and presents new starting points to study the hypoxia adaptation of endothelial cells

  1. CSR1, the sole target of imidazolinone herbicide in Arabidopsis thaliana.

    PubMed

    Manabe, Yuzuki; Tinker, Nicholas; Colville, Adam; Miki, Brian

    2007-09-01

    The imidazolinone-tolerant mutant of Arabidopsis thaliana, csr1-2(D), carries a mutation equivalent to that found in commercially available Clearfield crops. Despite their widespread usage, the mechanism by which Clearfield crops gain imidazolinone herbicide tolerance has not yet been fully characterized. Transcription profiling of imazapyr (an imidazolinone herbicide)-treated wild-type and csr1-2(D) mutant plants using Affymetrix ATH1 GeneChip microarrays was performed to elucidate further the biochemical and genetic mechanisms of imidazolinone resistance. In wild-type shoots, the genes which responded earliest to imazapyr treatment were detoxification-related genes which have also been shown to be induced by other abiotic stresses. Early-response genes included steroid sulfotransferase (ST) and 1-aminocyclopropane-1-carboxylic acid oxidase (ACO), as well as members of the glycosyltransferase, glutathione transferase (GST), cytochrome P450, ATP-binding cassette (ABC) transporter, multidrug and toxin extrusion (MATE) and alternative oxidase (AOX) protein families. Later stages of the imazapyr response involved regulation of genes participating in biosynthesis of amino acids, secondary metabolites and tRNA. In contrast to the dynamic changes in the transcriptome profile observed in imazapyr-treated wild-type plants, the transcriptome of csr1-2(D) did not exhibit significant changes following imazapyr treatment, compared with mock-treated csr1-2(D). Further, no substantial difference was observed between wild-type and csr1-2(D) transcriptomes in the absence of imazapyr treatment. These results indicate that CSR1 is the sole target of imidazolinone and that the csr1-2(D) mutation has little or no detrimental effect on whole-plant fitness. PMID:17693453

  2. Analysis of Changes in Hepatic Gene Expression in a Murine Model of Tolerance to Acetaminophen Hepatotoxicity (Autoprotection)

    PubMed Central

    O’Connor, Meeghan A; Koza-Taylor, Petra; Campion, Sarah N; Aleksunes, Lauren M; Gu, Xinsheng; Enayetallah, Ahmed E.; Lawton, Michael P; Manautou, José E

    2013-01-01

    Pretreatment of mice with a low hepatotoxic dose of acetaminophen (APAP) results in resistance to a subsequent, higher dose of APAP. This mouse model, termed APAP autoprotection was used here to identify differentially expressed genes and cellular pathways that could contribute to this development of resistance to hepatotoxicity. Male C57BL/6J mice were pretreated with APAP (400 mg/kg) and then challenged 48 hr later with 600 mg APAP/kg. Livers were obtained 4 or 24 hr later and total hepatic RNA was isolated and hybridized to Affymetrix Mouse Genome MU430_2 GeneChip. Statistically significant genes were determined and gene expression changes were also interrogated using the Causal Reasoning Engine (CRE). Extensive literature review narrowed our focus to methionine adenosyl transferase-1 alpha (MAT1A), nuclear factor (erythroid-derived 2)-like 2 (Nrf2), flavin-containing monooxygenase 3 (Fmo3) and galectin-3 (Lgals3). Down-regulation of MAT1A could lead to decreases in S-adenosylmethionine (SAMe), which is known to protect against APAP toxicity. Nrf2 activation is expected to play a role in protective adaptation. Up-regulation of Lgals3, one of the genes supporting the Nrf2 hypothesis, can lead to suppression of apoptosis and reduced mitochondrial dysfunction. Fmo3 induction suggests the involvement of an enzyme not known to metabolize APAP in the development of tolerance to APAP toxicity. Subsequent quantitative RT-PCR and immunochemical analysis confirmed the differential expression of some of these genes in the APAP autoprotection model. In conclusion, our genomics strategy identified cellular pathways that might further explain the molecular basis for APAP autoprotection. PMID:24126418

  3. NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases.

    PubMed

    Bagewadi, Shweta; Adhikari, Subash; Dhrangadhariya, Anjani; Irin, Afroza Khanam; Ebeling, Christian; Namasivayam, Aishwarya Alex; Page, Matthew; Hofmann-Apitius, Martin; Senger, Philipp

    2015-01-01

    Neurodegenerative diseases are chronic debilitating conditions, characterized by progressive loss of neurons that represent a significant health care burden as the global elderly population continues to grow. Over the past decade, high-throughput technologies such as the Affymetrix GeneChip microarrays have provided new perspectives into the pathomechanisms underlying neurodegeneration. Public transcriptomic data repositories, namely Gene Expression Omnibus and curated ArrayExpress, enable researchers to conduct integrative meta-analysis; increasing the power to detect differentially regulated genes in disease and explore patterns of gene dysregulation across biologically related studies. The reliability of retrospective, large-scale integrative analyses depends on an appropriate combination of related datasets, in turn requiring detailed meta-annotations capturing the experimental setup. In most cases, we observe huge variation in compliance to defined standards for submitted metadata in public databases. Much of the information to complete, or refine meta-annotations are distributed in the associated publications. For example, tissue preparation or comorbidity information is frequently described in an article's supplementary tables. Several value-added databases have employed additional manual efforts to overcome this limitation. However, none of these databases explicate annotations that distinguish human and animal models in neurodegeneration context. Therefore, adopting a more specific disease focus, in combination with dedicated disease ontologies, will better empower the selection of comparable studies with refined annotations to address the research question at hand. In this article, we describe the detailed development of NeuroTransDB, a manually curated database containing metadata annotations for neurodegenerative studies. The database contains more than 20 dimensions of metadata annotations within 31 mouse, 5 rat and 45 human studies, defined in

  4. Molecular cloning and characterization of an up-regulated UDP-glucosyltransferase gene induced by DON from Triticum aestivum L. cv. Wangshuibai.

    PubMed

    Lulin, Ma; Yi, Shang; Aizhong, Cao; Zengjun, Qi; Liping, Xing; Peidu, Chen; Dajun, Liu; Xiu-E, Wang

    2010-02-01

    Fusarium head blight, also called scab, is a serious disease of small grain cereals and maize. Scab can not only cause yield loss, more seriously is that it can also deteriorate seed quality by contaminating the infected grains with trichothecenes toxins harmful to human and animal health. Deoxynivalenol (DON) is one of the most important toxin members. It was proposed that DON acted first as a virulence factor during fungal pathogenesis and then accumulated in grain to levels posing a threat to human and animal health. In the present research, by expression analysis of DON-induced samples using GeneChip Wheat Genome Array ( http://www.affymetrix.com/products/arrays/specific/wheat.affx ), a DON-resistance related gene TaUGT3 (GenBank accession FJ236328) was cloned and characterized from a scab resistant wheat (Triticum aestivum L.) variety Wangshuibai. The full-length cDNA of TaUGT3 was 1,755 bp and contained a putative open reading frame (ORF) with 496 amino acids encoding a UDP-glucosyltransferase (UGT). TaUGT3 showed high similarity in amino acid level with DOGT1 gene in Arabidopsis, which is able to detoxify DON. TaUGT3 was located on the group 3 chromosomes of wheat using nulli-tetrasomic lines and deletion lines of Chinese Spring. Co-transformed of TaUGT3 with GFP genes to onion epidermis cells using transient transformation technique by microprojectile bombardment indicated the subcellular location of the protein encoded by TaUGT3 was in the plasma membrane and nuclear. Transformation and overexpression of the TaUGT3 gene in Arabidopsis could enhance tolerance against DON. PMID:19585272

  5. Experimental heart transplantation: effect of cyclosporine on expression and activity of metzincins.

    PubMed

    Berthier, C C; Pally, C; Weckbecker, G; Raulf, F; Rehrauer, H; Wagner, U; Le Hir, M; Marti, H P

    2009-04-18

    Metzincins, such as matrix metalloproteases (MMP), and extracellular matrix (ECM) proteins are differentially regulated in inflammation. We hypothesised that metzincins are also dysregulated in experimental acute cardiac allograft rejection. We investigated the Dark Agouti-to-Lewis (DA-to-Lew) rat model of acute cardiac allograft rejection. Cyclosporine (CsA) (7.5 mg/kg/d) was given from transplantation to sacrifice (day +5). At that time, mRNA levels were analysed by Affymetrix genechip and quantitative reverse transcription polymerase chain reaction (qRTPCR). MMP protein and activities were analysed by immunohistology, fluorometry, zymography and Western blots. In untreated rejected DA allografts, mRNA levels of MMP-2/-7/-9/-/12-/14, a disintegrin and metalloprotease (ADAM)-17, tissue inhibitor of metalloprotease (TIMP)-1/-3 were increased, whereas MMP-11/-16/-24 and TIMP-2/-4 were lowered compared to native DA hearts. With respect to these untreated allografts, CsA lowered mRNA levels of MMP-7, TIMP-1/-3 (TIMP-2/-4 remained relatively low) and ADAM17, but augmented mRNA levels of MMP-11/-16/-23 and of many ECM genes. Immunohistology showed increased staining of MMP-2 in acute rejection (AR). Overall MMP activity was augmented in both transplanted groups, but CsA reduced MMP-9 activity and MMP-14 production. Taken together, MMP and TIMP were upregulated during acute AR. CsA ameliorated histology of rejection but showed potential pro-fibrotic effects. Thus, MMP and TIMP may play a role in acute cardiac allograft rejection, and beneficial modification of the MMP-ECM balance requires interventions beyond CsA. PMID:19418307

  6. Detection of differentially expressed genes between Erhualian and Large White placentas on day 75 and 90 of gestation

    PubMed Central

    Zhou, Quan-Yong; Fang, Ming-Di; Huang, Ting-Hua; Li, Chang-Chun; Yu, Mei; Zhao, Shu-Hong

    2009-01-01

    Background Placental efficiency is strongly associated with litter size, fetal weight and prenatal mortality. Together with its rapid growth during late gestation, the Large White pig breed shows a significant increase in placental size and weight, but this does not occur in the highly prolific Chinese pig breeds. To understand the molecular basis of placental development during late gestation in Chinese indigenous and Western breeds with different placental efficiency, female placental samples were collected from six pregnant Erhualian gilts at gestation day 75 (E75) and day 90 (E90) and from six pregnant Large White gilts at gestation day 75 (L75) and day 90 (L90). Two female placentas from one sow were used to extract RNA and then pooled in equal volumes. Twelve pooled samples were hybridized to the porcine Affymetrix GeneChip. Results A total of 226 and 577 transcripts were detected that were differentially expressed between E75 and L75 and between E90 and L90 (p < 0.01, q < 0.2), respectively. Gene Ontology (GO) analysis revealed that these genes belong to the class of genes that participate in angiogenesis and development. Real-time RT-PCR confirmed the differential expression of eight selected genes. Significant differential expression of five genes in the VEGF pathway was also detected between the breeds. A search of chromosomal location revealed that 44 differentially expressed genes located to QTL regions related to reproduction. Differential expression of six candidate imprinted genes was also confirmed. Three of the six genes (PLAGL1, DIRAS3, and SLC38A4) showed monoallelic expression in the porcine placenta. Conclusion Our study detected many genes that showed differential expression between placentas of two divergent breed of pigs, and confirmed the imprinting of three genes. These findings help to elucidate the genetic control of placental efficiency and improve the understanding of placental development. PMID:19630995

  7. CD4+ T-Cell Decline after the Interruption of Antiretroviral Therapy in ACTG A5170 Is Predicted by Differential Expression of Genes in the Ras Signaling Pathway*

    PubMed Central

    Wang, Zhining; Su, Zhaohui; Nau, Martin E.; Krambrink, Amy; Skiest, Daniel J.; Margolis, David M.

    2008-01-01

    Abstract Patterns of expressed genes examined in cryopreserved peripheral blood mononuclear cells (PBMCs) of seropositive persons electing to stop antiretroviral therapy in the AIDS Clinical Trials Group Study A5170 were scrutinized to identify markers capable of predicting the likelihood of CD4+ T-cell depletion after cessation of antiretroviral therapy (ART). A5170 was a multicenter, 96-week, prospective study of HIV-infected patients with immunological preservation on ART who elected to interrupt therapy. Study entry required that the CD4 count was greater than 350 cells/mm3 within 6 months of ART initiation. Median nadir CD4 count of enrollees was 436 cells/mm3. Two cohorts, matched for clinical characteristics, were selected from A5170. Twenty-four patients with an absolute CD4 cell decline of less that 20% at week 24 (good outcome group) and 24 with a CD4 cell decline of >20% (poor outcome group) were studied. The good outcome group had a decline in CD4+ T-cell count that was 50% less than the poor outcome group. Significance analysis of microarrays identified differential gene expression (DE) in the two groups in data obtained from Affymetrix Human FOCUS GeneChips. DE was significantly higher in the poor outcome group than in the good outcome group. Prediction analysis of microarrays (PAM-R) identified genes that classified persons as to progression with greater than 80% accuracy at therapy interruption (TI) as well as at 24 weeks after TI. Gene set enrichment analysis (GSEA) identified a set of genes in the Ras signaling pathway, associated with the downregulation of apoptosis, as significantly upregulated in the good outcome group at cessation of ART. These observations identify specific host cell processes associated with differential outcome in this cohort after TI. PMID:18724805

  8. Antagonist effect of Interleukin 1 receptor on normal thymopoiesis and thymus toxicity of 5-azacytidine in mouse.

    PubMed

    Yu, Hongjing; Wu, Mingyuan; Wen, Bin; Sun, Ningyun; Xiang, Di; Zhang, Jing; Zhu, Shunying; Weng, Shunyan; Yu, Yan; Han, Wei

    2016-01-01

    Thymopoiesis is essential and significant for development and maintenance of the robust and healthy immune system. The acute suppression of thymopoiesis induced by 5-Azacytidine (5-Aza) is an intractable clinical problem complicating chemotherapy. Interleukin 1 receptor antagonist (IL-1Ra) is a cytokine that competitively blocks binding of interleukin 1 (IL-1) to its receptor. This study aims to investigate the effects of the IL-1Ra on the thymus toxicity of 5-Aza in mouse. In this study, we treated the mice with the 5-Aza (100 mg/kg per mouse). The GeneChip methodology developed by Affymetrix was used to monitor global gene expression during mouse thymus regeneration induced by a single injection of 5-Aza. The total thymocytes were counted using a hemocytometer. Cell cycle of samples were analyzed on a Becton Dickinson FACScan. Cells surfaces were labeled with anti-CD4, anti-CD8 and anti-CD45RA antibodies, and detected by flow cytometry. BrdU incorporation was detected by flow cytometry. The results indicated that administering exogenous IL-1Ra to normal mice inhibited cell cycle progress of thymocytes in a dosage-dependent manner. Proliferation of immature CD4(-)CD8(-) double negative (DN) and CD4(+)CD8(+) double positive (DP) thymocytes were both inhibited. The pretreatment of normal mice with exogenous IL-1Ra reduced acute toxicity on thymus and immune suppression induced by 5-Aza. Furthermore, thymus reconstitution after 5-Aza treatment was accelerated by IL-1Ra. In conclusion, interleukin 1 receptor antagonist could inhibit normal thymopoiesis and reduce thymus toxicity of 5-azacytidine in mouse. Pretreatment with IL-1Ra would offer a new and promising strategy to alleviate immunotoxicity of chemotherapy in clinical. PMID:27158410

  9. Antagonist effect of Interleukin 1 receptor on normal thymopoiesis and thymus toxicity of 5-azacytidine in mouse

    PubMed Central

    Yu, Hongjing; Wu, Mingyuan; Wen, Bin; Sun, Ningyun; Xiang, Di; Zhang, Jing; Zhu, Shunying; Weng, Shunyan; Yu, Yan; Han, Wei

    2016-01-01

    Thymopoiesis is essential and significant for development and maintenance of the robust and healthy immune system. The acute suppression of thymopoiesis induced by 5-Azacytidine (5-Aza) is an intractable clinical problem complicating chemotherapy. Interleukin 1 receptor antagonist (IL-1Ra) is a cytokine that competitively blocks binding of interleukin 1 (IL-1) to its receptor. This study aims to investigate the effects of the IL-1Ra on the thymus toxicity of 5-Aza in mouse. In this study, we treated the mice with the 5-Aza (100 mg/kg per mouse). The GeneChip methodology developed by Affymetrix was used to monitor global gene expression during mouse thymus regeneration induced by a single injection of 5-Aza. The total thymocytes were counted using a hemocytometer. Cell cycle of samples were analyzed on a Becton Dickinson FACScan. Cells surfaces were labeled with anti-CD4, anti-CD8 and anti-CD45RA antibodies, and detected by flow cytometry. BrdU incorporation was detected by flow cytometry. The results indicated that administering exogenous IL-1Ra to normal mice inhibited cell cycle progress of thymocytes in a dosage-dependent manner. Proliferation of immature CD4-CD8- double negative (DN) and CD4+CD8+ double positive (DP) thymocytes were both inhibited. The pretreatment of normal mice with exogenous IL-1Ra reduced acute toxicity on thymus and immune suppression induced by 5-Aza. Furthermore, thymus reconstitution after 5-Aza treatment was accelerated by IL-1Ra. In conclusion, interleukin 1 receptor antagonist could inhibit normal thymopoiesis and reduce thymus toxicity of 5-azacytidine in mouse. Pretreatment with IL-1Ra would offer a new and promising strategy to alleviate immunotoxicity of chemotherapy in clinical. PMID:27158410

  10. The Innate Immune System Is Activated by Stimulation of Vaginal Epithelial Cells with Staphylococcus aureus and Toxic Shock Syndrome Toxin 1

    PubMed Central

    Peterson, Marnie L.; Ault, Kevin; Kremer, Mary J.; Klingelhutz, Aloysius J.; Davis, Catherine C.; Squier, Christopher A.; Schlievert, Patrick M.

    2005-01-01

    Despite knowledge of the effects of toxic shock syndrome (TSS) toxin 1 (TSST-1) on the adaptive immune system, little is known about stimulation of the innate immune system, particularly epithelial cells. This study investigated the interactions of TSS Staphylococcus aureus and TSST-1 with human vaginal epithelial cells (HVECs) and porcine mucosal surfaces. When cocultured with HVECs for 6 h, TSS S. aureus MN8 proliferated, formed aggregates on the HVEC surfaces, and produced exotoxins. Receptor binding studies showed that 35S-TSST-1 bound to 5 × 104 receptors per HVEC, with saturation at 15 min. Affymetrix Human GeneChip U133A microarray analysis determined S. aureus MNSM (100 bacteria/HVEC) caused at least twofold up- or down-regulation of 410 HVEC genes by 6 h; these data were also confirmed with S. aureus MN8. TSST-1 (100 μg/ml) caused up- or down-regulation of 2,386 HVEC genes by 6 h. In response to S. aureus, the HVEC genes most up-regulated compared to those in controls were those coding for chemokines or cytokines—MIP-3α, 478-fold; GRO-α, 26-fold; GRO-β, 14-fold; and GRO-γ, 30-fold—suggesting activation of innate immunity. TSST-1 also caused up-regulation of chemokine/cytokine genes. Chemokine/cytokine gene up-regulation was confirmed by enzyme-linked immunosorbent assays measuring the corresponding proteins induced by S. aureus and TSST-1. S. aureus MN8, when incubated with porcine vaginal tissue, increased the flux of 35S-TSST-1 across the mucosal surface. This was accompanied by influx of lymphocytes into the upper layers of the tissue. These data suggest innate immune system activation through epithelial cells, reflected in chemokine/cytokine production and influx of lymphocytes, may cause changes in vaginal mucosa permeability, facilitating TSST-1 penetration. PMID:15784559

  11. Transcriptome Analysis of Epithelial and Stromal Contributions to Mammogenesis in Three Week Prepartum Cows

    PubMed Central

    Casey, Theresa; Dover, Heather; Liesman, James; DeVries, Lindsey; Kiupel, Matti; VandeHaar, Michael; Plaut, Karen

    2011-01-01

    Transcriptome analysis of bovine mammary development has provided insight into regulation of mammogenesis. However, previous studies primarily examined expression of epithelial and stromal tissues combined, and consequently did not account for tissue specific contribution to mammary development. Our objective was to identify differences in gene expression in epithelial and intralobular stromal compartments. Tissue was biopsied from non-lactating dairy cows 3 weeks prepartum, cut into explants and incubated for 2 hr with insulin and hydrocortisone. Epithelial and intralobular stromal tissues were isolated with laser capture microdissection. Global gene expression was measured with Bovine Affymetrix GeneChips, and data were preprocessed using RMA method. Moderated t-tests from gene-specific linear model analysis with cell type as a fixed effect showed more than 3,000 genes were differentially expressed between tissues (P<0.05; FDR<0.17). Analysis of epithelial and stromal transcriptomes using Database for Annotation, Visualization and Integrated Discovery (DAVID) and Ingenuity Pathways Analysis (IPA) showed that epithelial and stromal cells contributed distinct molecular signatures. Epithelial signatures were enriched with gene sets for protein synthesis, metabolism and secretion. Stromal signatures were enriched with genes that encoded molecules important to signaling, extracellular matrix composition and remodeling. Transcriptome differences also showed evidence for paracrine interactions between tissues in stimulation of IGF1 signaling pathway, stromal reaction, angiogenesis, neurogenesis, and immune response. Molecular signatures point to the dynamic role the stroma plays in prepartum mammogenesis and highlight the importance of examining the roles of cell types within the mammary gland when targeting therapies and studying mechanisms that affect milk production. PMID:21829467

  12. Genetic Diversity of the Q Fever Agent, Coxiella burnetii, Assessed by Microarray-Based Whole-Genome Comparisons†

    PubMed Central

    Beare, Paul A.; Samuel, James E.; Howe, Dale; Virtaneva, Kimmo; Porcella, Stephen F.; Heinzen, Robert A.

    2006-01-01

    Coxiella burnetii, a gram-negative obligate intracellular bacterium, causes human Q fever and is considered a potential agent of bioterrorism. Distinct genomic groups of C. burnetii are revealed by restriction fragment-length polymorphisms (RFLP). Here we comprehensively define the genetic diversity of C. burnetii by hybridizing the genomes of 20 RFLP-grouped and four ungrouped isolates from disparate sources to a high-density custom Affymetrix GeneChip containing all open reading frames (ORFs) of the Nine Mile phase I (NMI) reference isolate. We confirmed the relatedness of RFLP-grouped isolates and showed that two ungrouped isolates represent distinct genomic groups. Isolates contained up to 20 genomic polymorphisms consisting of 1 to 18 ORFs each. These were mostly complete ORF deletions, although partial deletions, point mutations, and insertions were also identified. A total of 139 chromosomal and plasmid ORFs were polymorphic among all C. burnetii isolates, representing ca. 7% of the NMI coding capacity. Approximately 67% of all deleted ORFs were hypothetical, while 9% were annotated in NMI as nonfunctional (e.g., frameshifted). The remaining deleted ORFs were associated with diverse cellular functions. The only deletions associated with isogenic NMI variants of attenuated virulence were previously described large deletions containing genes involved in lipopolysaccharide (LPS) biosynthesis, suggesting that these polymorphisms alone are responsible for the lower virulence of these variants. Interestingly, a variant of the Australia QD isolate producing truncated LPS had no detectable deletions, indicating LPS truncation can occur via small genetic changes. Our results provide new insight into the genetic diversity and virulence potential of Coxiella species. PMID:16547017

  13. Genomic Analysis of Reactive Astrogliosis

    PubMed Central

    Zamanian, JL; Xu, L; Foo, LC; Nouri, N; Zhou, L; Giffard, RG; Barres, BA

    2012-01-01

    Reactive astrogliosis is characterized by a profound change in astrocyte phenotype in response to all CNS injuries and diseases. To better understand the reactive astrocyte state, we used Affymetrix GeneChip arrays to profile gene expression in populations of reactive astrocytes isolated at various time points after induction using two mouse injury models, ischemic stroke and neuroinflammation. We find reactive gliosis consists of a rapid, but quickly attenuated induction of gene expression after insult and identify two induced genes, Lcn2 and Serpina3n, as strong markers of reactive astrocytes. Strikingly, reactive astrocyte phenotype strongly depended on the type of inducing injury. Although there is a core set of genes that is up-regulated in reactive astrocytes from both injury models, at least 50% of the altered gene expression is specific to a given injury type. Reactive astrocytes in ischemia exhibited a molecular phenotype that suggests that they may be beneficial or protective, whereas reactive astrocytes induced by LPS exhibited a phenotype that suggests that they may be detrimental. These findings demonstrate that, despite well established commonalities, astrocyte reactive gliosis is a highly heterogeneous state in which astrocyte activities are altered to respond to the specific injury. This raises the question of how many subtypes of reactive astrocytes exist. Our findings provide transcriptome databases for two subtypes of reactive astrocytes that will be highly useful in generating new and testable hypotheses of their function, as well as for providing new markers to detect different types of reactive astrocytes in human neurological diseases. PMID:22553043

  14. Sex Differences in Global mRNA Content of Human Skeletal Muscle

    PubMed Central

    Maher, Amy C.; Fu, Minghua H.; Isfort, Robert J.; Varbanov, Alex R.; Qu, Xiaoyan A.; Tarnopolsky, Mark A.

    2009-01-01

    Women oxidize more fat as compared to men during endurance exercise and several groups have shown that the mRNA content of selected genes related to fat oxidation are higher in women (e.g. hormone sensitive lipase, β-hydroxyacyl-CoA dehydrogenase, CD36). One of the possible mechanisms is that women tend to have a higher area percentage of type I skeletal muscle fibers as compared with men. Consequently, we hypothesized that sex would influence the basal mRNA and protein content for genes involved in metabolism and the determination of muscle fiber type. Muscle biopsies from the vastus lateralis were collected from healthy men and women. We examined mRNA content globally using Affymetrix GeneChips, and selected genes were examined and/or confirmed by RT-PCR. Furthermore, we examined protein content by Western blot analysis. Stringent gene array analysis revealed 66 differentially expressed genes representing metabolism, mitochondrial function, transport, protein biosynthesis, cell proliferation, signal transduction pathways, transcription and translation. Stringent gene array analysis and RT-PCR confirmed that mRNA for; acyl-coenzyme A acyltransferase 2 (ACAA2), trifunctional protein β (HADHB), catalase, lipoprotein lipase (LPL), and uncoupling protein-2 (UCP-2) were higher in women. Targeted gene analysis revealed that myosin heavy chain I (MHCI), peroxisome proliferator-activated receptor (PPAR)δ were higher in women compared with men. Surprisingly, there were no significant sex based differences in protein content for HADHB, ACAA2, catalase, PPARδ, and MHC1. In conclusion, the differences in the basal mRNA content in resting skeletal muscle suggest that men and women are transcriptionally “primed” for known physiological differences in metabolism however the mechanism behind sex differences in fiber type remains to be determined. PMID:19623254

  15. A MiRNA Signature for Defining Aggressive Phenotype and Prognosis in Gliomas

    PubMed Central

    Pasculli, Barbara; Galasso, Marco; Volinia, Stefano; D'Angelo, Vincenzo; Icolaro, Nadia; Coco, Michelina; Dimitri, Lucia; Graziano, Paolo; Copetti, Massimiliano; Valori, Vanna Maria; Maiello, Evaristo; Carella, Massimo; Fazio, Vito Michele; Parrella, Paola

    2014-01-01

    Gliomas represent a disparate group of tumours for which there are to date no cure. Thus, there is a recognized need for new diagnostic and therapeutic approaches based on increased understanding of their molecular nature. We performed the comparison of the microRNA (miRNA) profile of 8 WHO grade II gliomas and 24 higher grade tumours (2 WHO grade III and 22 glioblastomas) by using the Affymetrix GeneChip miRNA Array v. 1.0. A relative quantification method (RT-qPCR) with standard curve was used to confirm the 22 miRNA signature resulted by array analysis. The prognostic performances of the confirmed miRNAs were estimated on the Tumor Cancer Genome Atlas (TCGA) datasets. We identified 22 miRNAs distinguishing grade II gliomas from higher grade tumours. RT-qPCR confirmed the differential expression in the two patients' groups for 13 out of the 22 miRNAs. The analysis of the Glioblastoma Multiforme (GBM) and Lower Grade Glioma (LGG) datasets from TCGA demonstrated the association with prognosis for 6 of those miRNAs. Moreover, in the GBM dataset miR-21 and miR-210 were predictors of worse prognosis in both univariable and multivariable Cox regression analyses (HR 1.19, p = 0.04, and HR 1.18, p = 0.029 respectively). Our results support a direct contribution of miRNAs to glioma cancerogenesis and suggest that miR-21 and miR-210 may play a role in the aggressive clinical behaviour of glioblastomas. PMID:25279461

  16. Maternal age effects on myometrial expression of contractile proteins, uterine gene expression, and contractile activity during labor in the rat

    PubMed Central

    Elmes, Matthew; Szyszka, Alexandra; Pauliat, Caroline; Clifford, Bethan; Daniel, Zoe; Cheng, Zhangrui; Wathes, Claire; McMullen, Sarah

    2015-01-01

    Advanced maternal age of first time pregnant mothers is associated with prolonged and dysfunctional labor and significant risk of emergency cesarean section. We investigated the influence of maternal age on myometrial contractility, expression of contractile associated proteins (CAPs), and global gene expression in the parturient uterus. Female Wistar rats either 8 (YOUNG n = 10) or 24 (OLDER n = 10) weeks old were fed laboratory chow, mated, and killed during parturition. Myometrial strips were dissected to determine contractile activity, cholesterol (CHOL) and triglycerides (TAG) content, protein expression of connexin-43 (GJA1), prostaglandin-endoperoxide synthase 2 (PTGS2), and caveolin 1 (CAV-1). Maternal plasma concentrations of prostaglandins PGE2, PGF2α, and progesterone were determined by RIA. Global gene expression in uterine samples was compared using Affymetrix Genechip Gene 2.0 ST arrays and Ingenuity Pathway analysis (IPA). Spontaneous contractility in myometrium exhibited by YOUNG rats was threefold greater than OLDER animals (P < 0.027) but maternal age had no significant effect on myometrial CAP expression, lipid profiles, or pregnancy-related hormones. OLDER myometrium increased contractile activity in response to PGF2α, phenylephrine, and carbachol, a response absent in YOUNG rats (all P < 0.002). Microarray analysis identified that maternal age affected expression of genes related to immune and inflammatory responses, lipid transport and metabolism, steroid metabolism, tissue remodeling, and smooth muscle contraction. In conclusion YOUNG laboring rat myometrium seems primed to contract maximally, whereas activity is blunted in OLDER animals and requires stimulation to meet contractile potential. Further work investigating maternal age effects on myometrial function is required with focus on lipid metabolism and inflammatory pathways. PMID:25876907

  17. Identification of molecular pathways affected by pterostilbene, a natural dimethylether analog of resveratrol

    PubMed Central

    Pan, Zhiqiang; Agarwal, Ameeta K; Xu, Tao; Feng, Qin; Baerson, Scott R; Duke, Stephen O; Rimando, Agnes M

    2008-01-01

    Background Pterostilbene, a naturally occurring phenolic compound produced by agronomically important plant genera such as Vitis and Vacciunium, is a phytoalexin exhibiting potent antifungal activity. Additionally, recent studies have demonstrated several important pharmacological properties associated with pterostilbene. Despite this, a systematic study of the effects of pterostilbene on eukaryotic cells at the molecular level has not been previously reported. Thus, the aim of the present study was to identify the cellular pathways affected by pterostilbene by performing transcript profiling studies, employing the model yeast Saccharomyces cerevisiae. Methods S. cerevisiae strain S288C was exposed to pterostilbene at the IC50 concentration (70 μM) for one generation (3 h). Transcript profiling experiments were performed on three biological replicate samples using the Affymetrix GeneChip Yeast Genome S98 Array. The data were analyzed using the statistical methods available in the GeneSifter microarray data analysis system. To validate the results, eleven differentially expressed genes were further examined by quantitative real-time RT-PCR, and S. cerevisiae mutant strains with deletions in these genes were analyzed for altered sensitivity to pterostilbene. Results Transcript profiling studies revealed that pterostilbene exposure significantly down-regulated the expression of genes involved in methionine metabolism, while the expression of genes involved in mitochondrial functions, drug detoxification, and transcription factor activity were significantly up-regulated. Additional analyses revealed that a large number of genes involved in lipid metabolism were also affected by pterostilbene treatment. Conclusion Using transcript profiling, we have identified the cellular pathways targeted by pterostilbene, an analog of resveratrol. The observed response in lipid metabolism genes is consistent with its known hypolipidemic properties, and the induction of mitochondrial

  18. Genome-wide expression analysis upon constitutive activation of the HacA bZIP transcription factor in Aspergillus niger reveals a coordinated cellular response to counteract ER stress

    PubMed Central

    2012-01-01

    Background HacA/Xbp1 is a conserved bZIP transcription factor in eukaryotic cells which regulates gene expression in response to various forms of secretion stress and as part of secretory cell differentiation. In the present study, we replaced the endogenous hacA gene of an Aspergillus niger strain with a gene encoding a constitutively active form of the HacA transcription factor (HacACA). The impact of constitutive HacA activity during exponential growth was explored in bioreactor controlled cultures using transcriptomic analysis to identify affected genes and processes. Results Transcription profiles for the wild-type strain (HacAWT) and the HacACA strain were obtained using Affymetrix GeneChip analysis of three replicate batch cultures of each strain. In addition to the well known HacA targets such as the ER resident foldases and chaperones, GO enrichment analysis revealed up-regulation of genes involved in protein glycosylation, phospholipid biosynthesis, intracellular protein transport, exocytosis and protein complex assembly in the HacACA mutant. Biological processes over-represented in the down-regulated genes include those belonging to central metabolic pathways, translation and transcription. A remarkable transcriptional response in the HacACA strain was the down-regulation of the AmyR transcription factor and its target genes. Conclusions The results indicate that the constitutive activation of the HacA leads to a coordinated regulation of the folding and secretion capacity of the cell, but with consequences on growth and fungal physiology to reduce secretion stress. PMID:22846479

  19. Developmental pathways during in vitro progression of human islet neogenesis

    PubMed Central

    Dodge, Rikke; Loomans, Cindy; Sharma, Arun; Bonner-Weir, Susan

    2009-01-01

    Islet neogenesis, or the differentiation of islet cells from precursor cells, is seen in vitro and in vivo both embryonically and after birth. However, little is known about the differentiation pathways during embryonic development for human pancreas. Our previously reported in vitro generation of islets from human pancreatic tissue provides a unique system to identify potential markers of neogenesis and to determine the molecular mechanisms underlying this process. To this end, we analyzed the gene expression profiles of three different stages during in vitro islet generation: the Initial Adherent-, Expanded-, and Differentiated- stages. Samples from four human pancreases were hybridized to Affymetrix U95A GeneChips, and data analyzed using GeneSpring 7.0/9.0 software. Using Scatter plots we selected genes with a 2-fold or greater differential expression.. Of the 12,000 genes/ESTs present on these arrays, 295 genes including 38 acinar–enriched genes were selectively lost during the progression from the Initially Adherent stage to the Expanded stage; 468 genes were increased in this progression to Expanded tissue; and 529 genes had a two-fold greater expression in the Differentiated-stage than in the Expanded tissue. Besides the expected increases in insulin, glucagon and duct markers (mucin 6, aquaporin 1 and 5), the beta cell auto-antigen IA-2/phogrin was increased 5-fold in Differentiated. In addition developmentally important pathways, including Notch/jagged, Wnt/Frizzled, TGFβ superfamily (follistatin, BMPs and SMADs), retinoic acid (COUP-TFI, CRABP1, 2 and RAIG1) were differentially regulated during the expansion/differentiation. Two putative markers for islet precursor cells, UCHL1/PGP9.5 and DMBT1, were enhanced during the progression to differentiated cells, but only the latter could be a marker of islet precursor cells. We suggest that appropriate manipulation of these differentiation-associated pathways will enhance the efficiency of differentiation

  20. Molecular Signatures Reveal Circadian Clocks May Orchestrate the Homeorhetic Response to Lactation

    PubMed Central

    Casey, Theresa; Patel, Osman; Dykema, Karl; Dover, Heather; Furge, Kyle; Plaut, Karen

    2009-01-01

    Genes associated with lactation evolved more slowly than other genes in the mammalian genome. Higher conservation of milk and mammary genes suggest that species variation in milk composition is due in part to the environment and that we must look deeper into the genome for regulation of lactation. At the onset of lactation, metabolic changes are coordinated among multiple tissues through the endocrine system to accommodate the increased demand for nutrients and energy while allowing the animal to remain in homeostasis. This process is known as homeorhesis. Homeorhetic adaptation to lactation has been extensively described; however how these adaptations are orchestrated among multiple tissues remains elusive. To develop a clearer picture of how gene expression is coordinated across multiple tissues during the pregnancy to lactation transition, total RNA was isolated from mammary, liver and adipose tissues collected from rat dams (n = 5) on day 20 of pregnancy and day 1 of lactation, and gene expression was measured using Affymetrix GeneChips. Two types of gene expression analysis were performed. Genes that were differentially expressed between days within a tissue were identified with linear regression, and univariate regression was used to identify genes commonly up-regulated and down-regulated across all tissues. Gene set enrichment analysis showed genes commonly up regulated among the three tissues enriched gene ontologies primary metabolic processes, macromolecular complex assembly and negative regulation of apoptosis ontologies. Genes enriched in transcription regulator activity showed the common up regulation of 2 core molecular clock genes, ARNTL and CLOCK. Commonly down regulated genes enriched Rhythmic process and included: NR1D1, DBP, BHLHB2, OPN4, and HTR7, which regulate intracellular circadian rhythms. Changes in mammary, liver and adipose transcriptomes at the onset of lactation illustrate the complexity of homeorhetic adaptations and suggest that

  1. NTM and NR3C2 polymorphisms influencing intelligence: family-based association studies.

    PubMed

    Pan, Yue; Wang, Ke-Sheng; Aragam, Nagesh

    2011-01-15

    Family, twin, and adoption studies have indicated that human intelligence quotient (IQ) has significant genetic components. We performed a low-density genome-wide association analysis with a family-based association test to identify genetic variants influencing IQ, as measured by Wechsler Adult Intelligence Scale full-score IQ (FSIQ). We examined 11,120 single-nucleotide polymorphisms (SNPs) from the Affymetrix GeneChips 10K mapping array genotyped in 292 nuclear families from Genetic Analysis Workshop 14, a subset from the Collaborative Study on the Genetics of Alcoholism (COGA). A replication analysis was performed using part of International Multi-Center ADHD Genetics Project (IMAGE) dataset. Twenty-two SNPs were identified as having suggestive associations with IQ (p<10(-3)) in the COGA sample and eleven of the SNPs were located within known genes. In particular, NTM at 11q25 (rs411280, p = 0.000764) and NR3C2 at 4q31.1 (rs3846329, p = 0.000675) were two novel genes which have not been associated with IQ in other studies. It has been reported that NTM might play a role in late-onset Alzheimer disease while NR3C2 may be associated with cognitive function and major depression. The associations of these two genes were well-replicated by single-marker and haplotype analyses in the IMAGE sample. In conclusion, our findings provide evidence that chromosome regions of 11q25 and 4q31.1 contain genes affecting IQ. This study will serve as a resource for replication in other populations. PMID:21036197

  2. Cellularity and Adipogenic Profile of the Abdominal Subcutaneous Adipose Tissue From Obese Adolescents: Association With Insulin Resistance and Hepatic Steatosis

    PubMed Central

    Kursawe, Romy; Eszlinger, Markus; Narayan, Deepak; Liu, Teresa; Bazuine, Merlijn; Cali, Anna M.G.; D'Adamo, Ebe; Shaw, Melissa; Pierpont, Bridget; Shulman, Gerald I.; Cushman, Samuel W.; Sherman, Arthur; Caprio, Sonia

    2010-01-01

    OBJECTIVE We explored whether the distribution of adipose cell size, the estimated total number of adipose cells, and the expression of adipogenic genes in subcutaneous adipose tissue are linked to the phenotype of high visceral and low subcutaneous fat depots in obese adolescents. RESEARCH DESIGN AND METHODS A total of 38 adolescents with similar degrees of obesity agreed to have a subcutaneous periumbilical adipose tissue biopsy, in addition to metabolic (oral glucose tolerance test and hyperinsulinemic euglycemic clamp) and imaging studies (MRI, DEXA, 1H-NMR). Subcutaneous periumbilical adipose cell-size distribution and the estimated total number of subcutaneous adipose cells were obtained from tissue biopsy samples fixed in osmium tetroxide and analyzed by Beckman Coulter Multisizer. The adipogenic capacity was measured by Affymetrix GeneChip and quantitative RT-PCR. RESULTS Subjects were divided into two groups: high versus low ratio of visceral to visceral + subcutaneous fat (VAT/[VAT+SAT]). The cell-size distribution curves were significantly different between the high and low VAT/(VAT+SAT) groups, even after adjusting for age, sex, and ethnicity (MANOVA P = 0.035). Surprisingly, the fraction of large adipocytes was significantly lower (P < 0.01) in the group with high VAT/(VAT+SAT), along with the estimated total number of large adipose cells (P < 0.05), while the mean diameter was increased (P < 0.01). From the microarray analyses emerged a lower expression of lipogenesis/adipogenesis markers (sterol regulatory element binding protein-1, acetyl-CoA carboxylase, fatty acid synthase) in the group with high VAT/(VAT+SAT), which was confirmed by RT-PCR. CONCLUSIONS A reduced lipo-/adipogenic capacity, fraction, and estimated number of large subcutaneous adipocytes may contribute to the abnormal distribution of abdominal fat and hepatic steatosis, as well as to insulin resistance in obese adolescents. PMID:20805387

  3. Early changes in gene expression induced by blue light irradiation of A2E-laden retinal pigment epithelial cells

    PubMed Central

    van der Burght, Barbro W.; Hansen, Morten; Olsen, Jørgen; Zhou, Jilin; Wu, Yalin; Nissen, Mogens H.; Sparrow, Janet R.

    2016-01-01

    Purpose Accumulation of bisretinoids as lipofuscin in retinal pigment epithelial (RPE) cells is implicated in the pathogenesis of some blinding diseases including age-related macular degeneration (AMD). To identify genes whose expression may change under conditions of bisretinoid accumulation, we investigated the differential gene expression in RPE cells that had accumulated the lipofuscin fluorophore A2E and were exposed to blue light (430 nm). Methods A2E-laden RPE cells were exposed to blue light (A2E/430 nm) at various time intervals. Cell death was quantified using Dead Red staining, and RNA levels for the entire genome was determined using DNA microarrays (Affymetrix GeneChip Human Genome 2.0 Plus). Array results for selected genes were confirmed by real-time reverse-transcriptase polymerase chain reaction. Results Principal component analysis revealed that the A2E-laden RPE cells irradiated with blue light were clearly distinguishable from the control samples. We found differential regulation of genes belonging to the following functional groups: transcription factors, stress response, apoptosis and immune response. Among the last mentioned were downregulation of four genes that coded for proteins that have an inhibitory effect on the complement cascade: (complement factor H, complement factor H-related 1, complement factor I and vitronectin) and of two belonging to the classical pathway (complement component 1, s subcomponent and complement component 1, r subcomponent). Conclusion This study demonstrates that blue light irradiation of A2E-laden RPE cells can alter the transcription of genes belonging to different functional pathways including stress response, apoptosis and the immune response. We suggest that these molecules may be associated to the pathogenesis of AMD and can potentially serve as future therapeutic targets. PMID:23742627

  4. Uncovering the Arabidopsis thaliana nectary transcriptome: investigation of differential gene expression in floral nectariferous tissues

    PubMed Central

    Kram, Brian W; Xu, Wayne W; Carter, Clay J

    2009-01-01

    Background Many flowering plants attract pollinators by offering a reward of floral nectar. Remarkably, the molecular events involved in the development of nectaries, the organs that produce nectar, as well as the synthesis and secretion of nectar itself, are poorly understood. Indeed, to date, no genes have been shown to directly affect the de novo production or quality of floral nectar. To address this gap in knowledge, the ATH1 Affymetrix® GeneChip array was used to systematically investigate the Arabidopsis nectary transcriptome to identify genes and pathways potentially involved in nectar production. Results In this study, we identified a large number of genes differentially expressed between secretory lateral nectaries and non-secretory median nectary tissues, as well as between mature lateral nectaries (post-anthesis) and immature lateral nectaries (pre-anthesis). Expression within nectaries was also compared to thirteen non-nectary reference tissues, from which 270 genes were identified as being significantly upregulated in nectaries. The expression patterns of 14 nectary-enriched genes were also confirmed via RT PCR. Upon looking into functional groups of upregulated genes, pathways involved in gene regulation, carbohydrate metabolism, and lipid metabolism were particularly enriched in nectaries versus reference tissues. Conclusion A large number of genes preferentially expressed in nectaries, as well as between nectary types and developmental stages, were identified. Several hypotheses relating to mechanisms of nectar production and regulation thereof are proposed, and provide a starting point for reverse genetics approaches to determine molecular mechanisms underlying nectar synthesis and secretion. PMID:19604393

  5. Computational identification of conserved transcription factor binding sites upstream of genes induced in rat brain by transient focal ischemic stroke.

    PubMed

    Pulliam, John V K; Xu, Zhenfeng; Ford, Gregory D; Liu, Cuimei; Li, Yonggang; Stovall, Kyndra C; Cannon, Virginetta S; Tewolde, Teclemichael; Moreno, Carlos S; Ford, Byron D

    2013-02-01

    Microarray analysis has been used to understand how gene regulation plays a critical role in neuronal injury, survival and repair following ischemic stroke. To identify the transcriptional regulatory elements responsible for ischemia-induced gene expression, we examined gene expression profiles of rat brains following focal ischemia and performed computational analysis of consensus transcription factor binding sites (TFBS) in the genes of the dataset. In this study, rats were sacrificed 24 h after middle cerebral artery occlusion (MCAO) stroke and gene transcription in brain tissues following ischemia/reperfusion was examined using Affymetrix GeneChip technology. The CONserved transcription FACtor binding site (CONFAC) software package was used to identify over-represented TFBS in the upstream promoter regions of ischemia-induced genes compared to control datasets. CONFAC identified 12 TFBS that were statistically over-represented from our dataset of ischemia-induced genes, including three members of the Ets-1 family of transcription factors (TFs). Microarray results showed that mRNA for Ets-1 was increased following tMCAO but not pMCAO. Immunohistochemical analysis of Ets-1 protein in rat brains following MCAO showed that Ets-1 was highly expressed in neurons in the brain of sham control animals. Ets-1 protein expression was virtually abolished in injured neurons of the ischemic brain but was unchanged in peri-infarct brain areas. These data indicate that TFs, including Ets-1, may influence neuronal injury following ischemia. These findings could provide important insights into the mechanisms that lead to brain injury and could provide avenues for the development of novel therapies. PMID:23246490

  6. Over-expression of the miRNA cluster at chromosome 14q32 in the alcoholic brain correlates with suppression of predicted target mRNA required for oligodendrocyte proliferation.

    PubMed

    Manzardo, A M; Gunewardena, S; Butler, M G

    2013-09-10

    We examined miRNA expression from RNA isolated from the frontal cortex (Broadman area 9) of 9 alcoholics (6 males, 3 females, mean age 48 years) and 9 matched controls using both the Affymetrix GeneChip miRNA 2.0 and Human Exon 1.0 ST Arrays to further characterize genetic influences in alcoholism and the effects of alcohol consumption on predicted target mRNA expression. A total of 12 human miRNAs were significantly up-regulated in alcohol dependent subjects (fold change≥1.5, false discovery rate (FDR)≤0.3; p<0.05) compared with controls including a cluster of 4 miRNAs (e.g., miR-377, miR-379) from the maternally expressed 14q32 chromosome region. The status of the up-regulated miRNAs was supported using the high-throughput method of exon microarrays showing decreased predicted mRNA gene target expression as anticipated from the same RNA aliquot. Predicted mRNA targets were involved in cellular adhesion (e.g., THBS2), tissue differentiation (e.g., CHN2), neuronal migration (e.g., NDE1), myelination (e.g., UGT8, CNP) and oligodendrocyte proliferation (e.g., ENPP2, SEMA4D1). Our data support an association of alcoholism with up-regulation of a cluster of miRNAs located in the genomic imprinted domain on chromosome 14q32 with their predicted gene targets involved with oligodendrocyte growth, differentiation and signaling. PMID:23747354

  7. Two new behavioral QTLs, Emo4 and Reb1, map to mouse Chromosome 1: Congenic strains and candidate gene identification studies.

    PubMed

    de Ledesma, Ana Maria Rodriguez; Desai, Aarti N; Bolivar, Valerie J; Symula, Derek J; Flaherty, Lorraine

    2006-02-01

    By use of newly developed subcongenic strains of mice from a parental B6.129-Il10-/- knockout/congenic strain, we have narrowed the critical region for a new behavioral QTL, called Emo4, for open-field activity to a segment of Chromosome 1 between Erbb4 (68.4Mb) and B3gnt7 (86.2 Mb). We have also uncovered an additional QTL governing repetitive beam breaks in the open field. This QTL, called Reb1, maps to the interval between Asb1 (91.4 Mb) and NM_172851 (100.0 Mb) and is one of the first QTLs mapped for this type of behavior. Genome-wide microarray expression analyses were then undertaken to help to identify candidate genes that may be the cause of these genetic differences in open-field performance. In this effort, we analyzed global gene expression differences in the amygdalae by use of Affymetrix GeneChips between B6, B6.129-Il10-/-, and B6.129R4. Several probe sets representing target Chr 1 genes were found that showed significantly differential expression in the subcongenic and congenic strains. Several candidate genes have been identified. One of these regions coincides with an homologous region in humans that has been associated with autism, a disease whose symptoms include repetitive actions. This study illustrates that the use of congenic strains combined with global gene expression analyses can produce a list of viable candidates. It further shows that caution should be observed when analyzing the effects of knockout/congenic strains because many of the gene expression differences in these comparisons could not be attributable to the ablated Il10 gene but rather to passenger gene effects. PMID:16465591

  8. Microarray Analysis of the Abscission-Related Transcriptome in the Tomato Flower Abscission Zone in Response to Auxin Depletion1[C][W][OA

    PubMed Central

    Meir, Shimon; Philosoph-Hadas, Sonia; Sundaresan, Srivignesh; Selvaraj, K.S. Vijay; Burd, Shaul; Ophir, Ron; Kochanek, Bettina; Reid, Michael S.; Jiang, Cai-Zhong; Lers, Amnon

    2010-01-01

    The abscission process is initiated by changes in the auxin gradient across the abscission zone (AZ) and is triggered by ethylene. Although changes in gene expression have been correlated with the ethylene-mediated execution of abscission, there is almost no information on the molecular and biochemical basis of the increased AZ sensitivity to ethylene. We examined transcriptome changes in the tomato (Solanum lycopersicum ‘Shiran 1335’) flower AZ during the rapid acquisition of ethylene sensitivity following flower removal, which depletes the AZ from auxin, with or without preexposure to 1-methylcyclopropene or application of indole-3-acetic acid after flower removal. Microarray analysis using the Affymetrix Tomato GeneChip revealed changes in expression, occurring prior to and during pedicel abscission, of many genes with possible regulatory functions. They included a range of auxin- and ethylene-related transcription factors, other transcription factors and regulatory genes that are transiently induced early, 2 h after flower removal, and a set of novel AZ-specific genes. All gene expressions initiated by flower removal and leading to pedicel abscission were inhibited by indole-3-acetic acid application, while 1-methylcyclopropene pretreatment inhibited only the ethylene-induced expressions, including those induced by wound-associated ethylene signals. These results confirm our hypothesis that acquisition of ethylene sensitivity in the AZ is associated with altered expression of auxin-regulated genes resulting from auxin depletion. Our results shed light on the regulatory control of abscission at the molecular level and further expand our knowledge of auxin-ethylene cross talk during the initial controlling stages of the process. PMID:20947671

  9. Transcriptome Adaptation of Group B Streptococcus to Growth in Human Amniotic Fluid

    PubMed Central

    Sitkiewicz, Izabela; Green, Nicole M.; Guo, Nina; Bongiovanni, Ann Marie; Witkin, Steven S.; Musser, James M.

    2009-01-01

    Background Streptococcus agalactiae (group B Streptococcus) is a bacterial pathogen that causes severe intrauterine infections leading to fetal morbidity and mortality. The pathogenesis of GBS infection in this environment is poorly understood, in part because we lack a detailed understanding of the adaptation of this pathogen to growth in amniotic fluid. To address this knowledge deficit, we characterized the transcriptome of GBS grown in human amniotic fluid (AF) and compared it with the transcriptome in rich laboratory medium. Methods GBS was grown in Todd Hewitt-yeast extract medium and human AF. Bacteria were collected at mid-logarithmic, late-logarithmic and stationary growth phase. We performed global expression microarray analysis using a custom-made Affymetrix GeneChip. The normalized hybridization values derived from three biological replicates at each growth point were obtained. AF/THY transcript ratios representing greater than a 2-fold change and P-value exceeding 0.05 were considered to be statistically significant. Principal Findings We have discovered that GBS significantly remodels its transcriptome in response to exposure to human amniotic fluid. GBS grew rapidly in human AF and did not exhibit a global stress response. The majority of changes in GBS transcripts in AF compared to THY medium were related to genes mediating metabolism of amino acids, carbohydrates, and nucleotides. The majority of the observed changes in transcripts affects genes involved in basic bacterial metabolism and is connected to AF composition and nutritional requirements of the bacterium. Importantly, the response to growth in human AF included significant changes in transcripts of multiple virulence genes such as adhesins, capsule, and hemolysin and IL-8 proteinase what might have consequences for the outcome of host-pathogen interactions. Conclusions/Significance Our work provides extensive new information about how the transcriptome of GBS responds to growth in AF, and

  10. Responses of the mammary transcriptome of dairy cows to altered photoperiod during late gestation.

    PubMed

    Bentley, P A; Wall, E H; Dahl, G E; McFadden, T B

    2015-10-01

    Cows exposed to short day photoperiod (SD, 8L:16D) during the 60-day nonlactating period prior to parturition produce more milk in their subsequent lactation compared with cows exposed to long day photoperiod (LD, 16L:8D). Although this response is well established in dairy cows, the underlying mechanisms are not understood. We hypothesized that differential gene expression in cows exposed to SD or LD photoperiods during the dry period could be used to identify the functional basis for the subsequent increase in milk production during lactation. Pregnant, multiparous cows were maintained on an SD or LD photoperiod for 60 days prior to parturition. Mammary biopsies were obtained on days -24 and -9 relative to parturition and Affymetrix GeneChip Bovine Genome Arrays were used to quantify gene expression. Sixty-four genes were differentially expressed (P ≤ 0.05 and fold-change ≥ |1.5|) between SD and LD treatments. Many of these genes were associated with cell growth and proliferation, or immune function. Ingenuity Pathway Analysis predicted upstream regulators to include TNF, TGF-β1, interferon-γ, and several interleukins. In addition, expression of 125 genes was significantly different between day -24 and day -9; those genes were associated with milk component metabolism and immune function. The interaction of photoperiod and time affected 32 genes associated with insulin-like growth factor I signaling. Genes differentially expressed in response to photoperiod were associated with mammary development and immune function consistent with the enhancement of milk yield in the ensuing lactation. Our results provide insight into the mechanisms by which photoperiod affects the mammary gland and subsequently lactation. PMID:26175502

  11. Acetaminophen-NAPQI Hepatotoxicity: A Cell Line Model System Genome-Wide Association Study

    PubMed Central

    Moyer, Ann M.; Fridley, Brooke L.; Jenkins, Gregory D.; Batzler, Anthony J.; Pelleymounter, Linda L.; Kalari, Krishna R.; Ji, Yuan; Chai, Yubo; Nordgren, Kendra K. S.; Weinshilboum, Richard M.

    2011-01-01

    Acetaminophen is the leading cause of acute hepatic failure in many developed nations. Acetaminophen hepatotoxicity is mediated by the reactive metabolite N-acetyl-p-benzoquinonimine (NAPQI). We performed a “discovery” genome-wide association study using a cell line–based model system to study the possible contribution of genomics to NAPQI-induced cytotoxicity. A total of 176 lymphoblastoid cell lines from healthy subjects were treated with increasing concentrations of NAPQI. Inhibiting concentration 50 values were determined and were associated with “glutathione pathway” gene single nucleotide polymorphisms (SNPs) and genome-wide basal messenger RNA expression, as well as with 1.3 million genome-wide SNPs. A group of SNPs in linkage disequilibrium on chromosome 3 was highly associated with NAPQI toxicity. The p value for rs2880961, the SNP with the lowest p value, was 1.88 × 10−7. This group of SNPs mapped to a “gene desert,” but chromatin immunoprecipitation assays demonstrated binding of several transcription factor proteins including heat shock factor 1 (HSF1) and HSF2, at or near rs2880961. These chromosome 3 SNPs were not significantly associated with variation in basal expression for any of the genome-wide genes represented on the Affymetrix U133 Plus 2.0 GeneChip. We have used a cell line–based model system to identify a SNP signal associated with NAPQI cytotoxicity. If these observations are validated in future clinical studies, this SNP signal might represent a potential biomarker for risk of acetaminophen hepatotoxicity. The mechanisms responsible for this association remain unclear. PMID:21177773

  12. The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: Evolution during disease progression

    PubMed Central

    Oh, Jung D.; Kling-Bäckhed, Helene; Giannakis, Marios; Xu, Jian; Fulton, Robert S.; Fulton, Lucinda A.; Cordum, Holland S.; Wang, Chunyan; Elliott, Glendoria; Edwards, Jennifer; Mardis, Elaine R.; Engstrand, Lars G.; Gordon, Jeffrey I.

    2006-01-01

    Helicobacter pylori produces acute superficial gastritis in nearly all of its human hosts. However, a subset of individuals develops chronic atrophic gastritis (ChAG), a condition characterized in part by diminished numbers of acid-producing parietal cells and increased risk for development of gastric adenocarcinoma. Previously, we used a gnotobiotic transgenic mouse model with an engineered ablation of parietal cells to show that loss of parietal cells provides an opportunity for a H. pylori isolate from a patient with ChAG (HPAG1) to bind to, enter, and persist within gastric stem cells. This finding raises the question of how ChAG influences H. pylori genome evolution, physiology, and tumorigenesis. Here we describe the 1,596,366-bp HPAG1 genome. Custom HPAG1 Affymetrix GeneChips, representing 99.6% of its predicted ORFs, were used for whole-genome genotyping of additional H. pylori ChAG isolates obtained from Swedish patients enrolled in a case-control study of gastric cancer, as well as ChAG- and cancer-associated isolates from an individual who progressed from ChAG to gastric adenocarcinoma. The results reveal a shared gene signature among ChAG strains, as well as genes that may have been lost or gained during progression to adenocarcinoma. Whole-genome transcriptional profiling of HPAG1’s response to acid during in vitro growth indicates that genes encoding components of metal uptake and utilization pathways, outer membrane proteins, and virulence factors are among those associated with H. pylori’s adaptation to ChAG. PMID:16788065

  13. Effects of aging on apoptosis gene expression in oral mucosal tissues.

    PubMed

    Gonzalez, Octavio A; Novak, M John; Kirakodu, Sreenatha; Stromberg, Arnold J; Shen, Shu; Orraca, Luis; Gonzalez-Martinez, Janis; Ebersole, Jeffrey L

    2013-03-01

    Apoptotic processes are important for physiologic renewal of an intact epithelial barrier and contribute some antimicrobial resistance for bacteria and viruses, as well as anti-inflammatory effects that benefits the mucosa. The oral cavity presents a model of host-bacterial interactions at mucosal surfaces, in which a panoply of microorganisms colonizes various niches in the oral cavity and creates complex multispecies biofilms that challenge the gingival tissues. This report details gene expression in apoptotic pathways that occur in oral mucosal tissues across the lifespan, using a nonhuman primate model. Macaca mulatta primates from 2 to 23 years of age (n = 23) were used in a cross-sectional study to obtain clinical healthy gingival tissues specimens. Further, mRNA was prepared and evaluated using the Affymetrix Rhesus GeneChip and 88 apoptotic pathway genes were evaluated. The results identified significant positive correlations with age in 12 genes and negative correlations with an additional five genes. The gene effects were predicted to alter apoptosis receptor levels, extrinsic apoptotic pathways through caspases, cytokine effects on apoptotic events, Ca(+2)-induced death signaling, cell cycle checkpoints, and potential effects of survival factors. Both the positively and negatively correlated genes within the apoptotic pathways provided evidence that healthy tissues in aging animals exhibit decreased apoptotic potential compared to younger animals. The results suggested that decreased physiologic apoptotic process in the dynamic septic environment of the oral mucosal tissues could increase the risk of aging tissues to undergo destructive disease processes through dysregulated inflammatory responses to the oral microbial burden. PMID:23334583

  14. Glomerulonephritis-induced changes in kidney gene expression in rats

    PubMed Central

    Pavkovic, Mira; Riefke, Björn; Frisk, Anna-Lena; Gröticke, Ina; Ellinger-Ziegelbauer, Heidrun

    2015-01-01

    We investigated a glomerulonephritis (GN) model in rats induced by nephrotoxic serum (NTS) which contains antibodies against the glomerular basement membrane (GBM). The anti-GBM GN model in rats is widely used since its biochemical and histopathological characteristics are similar to crescentic nephritis and Goodpasture's disease in humans (Pusey, 2003[2]). Male Wistar Kyoto (WKY) and Sprague–Dawley (SD) rats were dosed once with 1, 2.5 and 5 ml/kg nephrotoxic serum (NTS) or 1.5 and 5 ml/kg NTS, respectively. GN and tubular damage were observed histopathologically in all treated rats after 14 days. To obtain insight into molecular processes during GN pathogenesis, mRNA expression was investigated in WKY and SD kidneys using Affymetrix's GeneChip Rat genome 230_2.0 arrays (GSE64265). The immunopathological processes during GN are still not fully understood and likely involve both innate and adaptive immunity. In the present study, several hundred mRNAs were found deregulated, which functionally were mostly associated with inflammation and regeneration. The β-chain of the major histocompatibility complex class II RT1.B (Rt1-Bb) and complement component 6 (C6) were identified as two mRNAs differentially expressed between WKY and SD rat strains which could be related to known different susceptibilities to NTS of different rat strains; both were increased in WKY and decreased in SD rats (Pavkovic et al., 2015 [1]). Increased Rt1-Bb expression in WKY rats could indicate a stronger and more persistent cellular reaction of the adaptive immune system in this strain, in line with findings indicating adaptive immune reactions during GN. The complement cascade is also known to be essential for GN development, especially terminal cascade products like C6. PMID:26697341

  15. Phycocyanobilin promotes PC12 cell survival and modulates immune and inflammatory genes and oxidative stress markers in acute cerebral hypoperfusion in rats

    SciTech Connect

    Marín-Prida, Javier; Riva, Federica; Pentón-Arias, Eduardo

    2013-10-01

    Since the inflammatory response and oxidative stress are involved in the stroke cascade, we evaluated here the effects of Phycocyanobilin (PCB, the C-Phycocyanin linked tetrapyrrole) on PC12 cell survival, the gene expression and the oxidative status of hypoperfused rat brain. After the permanent bilateral common carotid arteries occlusion (BCCAo), the animals were treated with saline or PCB, taking samples 24 h post-surgery. Global gene expression was analyzed with GeneChip Rat Gene ST 1.1 from Affymetrix; the expression of particular genes was assessed by the Fast SYBR Green RT-PCR Master Mix and Bioplex methods; and redox markers (MDA, PP, CAT, SOD) were evaluated spectrophotometrically. The PCB treatment prevented the H{sub 2}O{sub 2} and glutamate induced PC12 cell injury assessed by the MTT assay, and modulated 190 genes (93 up- and 97 down-regulated) associated to several immunological and inflammatory processes in BCCAo rats. Furthermore, PCB positively modulated 19 genes mostly related to a detrimental pro-inflammatory environment and counteracted the oxidative imbalance in the treated BCCAo animals. Our results support the view of an effective influence of PCB on major inflammatory mediators in acute cerebral hypoperfusion. These results suggest that PCB has a potential to be a treatment for ischemic stroke for which further studies are needed. - Highlights: • Phycocyanobilin (PCB) prevents H{sub 2}O{sub 2} and glutamate induced PC12 cell viability loss. • Anterior cortex and striatum are highly vulnerable to cerebral hypoperfusion (CH). • PCB modulates 190 genes associated to inflammation in acute CH. • PCB regulates 19 genes mostly related to a detrimental pro-inflammatory environment. • PCB restores redox and immune balances showing promise as potential stroke therapy.

  16. Toxicogenomics of subchronic hexachlorobenzene exposure in Brown Norway rats.

    PubMed Central

    Ezendam, Janine; Staedtler, Frank; Pennings, Jeroen; Vandebriel, Rob J; Pieters, Raymond; Boffetta, Paolo; Harleman, Johannes H; Vos, Joseph G

    2004-01-01

    Hexachlorobenzene (HCB) is a persistent environmental pollutant with toxic effects in man and rat. Reported adverse effects are hepatic porphyria, neurotoxicity, and adverse effects on the reproductive and immune system. To obtain more insight into HCB-induced mechanisms of toxicity, we studied gene expression levels using DNA microarrays. For 4 weeks, Brown Norway rats were fed a diet supplemented with 0, 150, or 450 mg HCB/kg. Spleen, mesenteric lymph nodes (MLN), thymus, blood, liver, and kidney were collected and analyzed using the Affymetrix rat RGU-34A GeneChip microarray. Most significant (p < 0.001) changes, compared to the control group, occurred in spleen, followed by liver, kidney, blood, and MLN, but only a few genes were affected in thymus. This was to be expected, as the thymus is not a target organ of HCB. Transcriptome profiles confirmed known effects of HCB such as stimulatory effects on the immune system and induction of enzymes involved in drug metabolism, porphyria, and the reproductive system. In line with previous histopathological findings were increased transcript levels of markers for granulocytes and macrophages. New findings include the upregulation of genes encoding proinflammatory cytokines, antioxidants, acute phase proteins, mast cell markers, complements, chemokines, and cell adhesion molecules. Generally, gene expression data provide evidence that HCB induces a systemic inflammatory response, accompanied by oxidative stress and an acute phase response. In conclusion, this study confirms previously observed (immuno)toxicological effects of HCB but also reveals several new and mechanistically relevant gene products. Thus, transcriptome profiles can be used as markers for several of the processes that occur after HCB exposure. PMID:15159207

  17. The Regulation of Cytokine Networks in Hippocampal CA1 Differentiates Extinction from Those Required for the Maintenance of Contextual Fear Memory after Recall

    PubMed Central

    Scholz, Birger; Doidge, Amie N.; Barnes, Philip; Hall, Jeremy; Wilkinson, Lawrence S.; Thomas, Kerrie L.

    2016-01-01

    We investigated the distinctiveness of gene regulatory networks in CA1 associated with the extinction of contextual fear memory (CFM) after recall using Affymetrix GeneChip Rat Genome 230 2.0 Arrays. These data were compared to previously published retrieval and reconsolidation-attributed, and consolidation datasets. A stringent dual normalization and pareto-scaled orthogonal partial least-square discriminant multivariate analysis together with a jack-knifing-based cross-validation approach was used on all datasets to reduce false positives. Consolidation, retrieval and extinction were correlated with distinct patterns of gene expression 2 hours later. Extinction-related gene expression was most distinct from the profile accompanying consolidation. A highly specific feature was the discrete regulation of neuroimmunological gene expression associated with retrieval and extinction. Immunity–associated genes of the tyrosine kinase receptor TGFβ and PDGF, and TNF families’ characterized extinction. Cytokines and proinflammatory interleukins of the IL-1 and IL-6 families were enriched with the no-extinction retrieval condition. We used comparative genomics to predict transcription factor binding sites in proximal promoter regions of the retrieval-regulated genes. Retrieval that does not lead to extinction was associated with NF-κB-mediated gene expression. We confirmed differential NF-κBp65 expression, and activity in all of a representative sample of our candidate genes in the no-extinction condition. The differential regulation of cytokine networks after the acquisition and retrieval of CFM identifies the important contribution that neuroimmune signalling plays in normal hippocampal function. Further, targeting cytokine signalling upon retrieval offers a therapeutic strategy to promote extinction mechanisms in human disorders characterised by dysregulation of associative memory. PMID:27224427

  18. IL-17/Th17 Pathway Is Activated in Acne Lesions

    PubMed Central

    Kelhälä, Hanna-Leena; Palatsi, Riitta; Fyhrquist, Nanna; Lehtimäki, Sari; Väyrynen, Juha P.; Kallioinen, Matti; Kubin, Minna E.; Greco, Dario; Tasanen, Kaisa; Alenius, Harri; Bertino, Beatrice; Carlavan, Isabelle; Mehul, Bruno; Déret, Sophie; Reiniche, Pascale; Martel, Philippe; Marty, Carine; Blume-Peytavi, Ulrike; Voegel, Johannes J.; Lauerma, Antti

    2014-01-01

    The mechanisms of inflammation in acne are currently subject of intense investigation. This study focused on the activation of adaptive and innate immunity in clinically early visible inflamed acne lesions and was performed in two independent patient populations. Biopsies were collected from lesional and non-lesional skin of acne patients. Using Affymetrix Genechips, we observed significant elevation of the signature cytokines of the Th17 lineage in acne lesions compared to non-lesional skin. The increased expression of IL-17 was confirmed at the RNA and also protein level with real-time PCR (RT-PCR) and Luminex technology. Cytokines involved in Th17 lineage differentiation (IL-1β, IL-6, TGF-β, IL23p19) were remarkably induced at the RNA level. In addition, proinflammatory cytokines and chemokines (TNF-α, IL-8, CSF2 and CCL20), Th1 markers (IL12p40, CXCR3, T-bet, IFN-γ), T regulatory cell markers (Foxp3, IL-10, TGF-β) and IL-17 related antimicrobial peptides (S100A7, S100A9, lipocalin, hBD2, hBD3, hCAP18) were induced. Importantly, immunohistochemistry revealed significantly increased numbers of IL-17A positive T cells and CD83 dendritic cells in the acne lesions. In summary our results demonstrate the presence of IL-17A positive T cells and the activation of Th17-related cytokines in acne lesions, indicating that the Th17 pathway is activated and may play a pivotal role in the disease process, possibly offering new targets of therapy. PMID:25153527

  19. Clinical Impact of a Novel MicroRNA Chemo-Sensitivity Predictor in Gastrooesophageal Cancer

    PubMed Central

    Winther, Mette; Knudsen, Steen; Dahlgaard, Jesper; Jensen, Thomas; Hansen, Anker; Jensen, Peter Buhl; Tramm, Trine; Alsner, Jan; Nordsmark, Marianne

    2016-01-01

    Background miRNAs might be potentially useful biomarkers for prediction of response to chemotherapeutic agents, radiotherapy and survival. The aim of this retrospective study was to validate miRNA response predictors in a cohort of patients with gastrooesophageal cancer in order to predict overall survival (OS) and disease-specific survival (DSS). Material and Methods The study population encompassed 53 patients treated with curative intend for loco-regional gastrooesophageal cancer. miRNA expression was quantified from pre-therapeutic and diagnostic, formalin-fixed, paraffin embedded tumour specimens using Affymetrix GeneChip miRNA 1.0 Array. Based on growth inhibition of the NCI60 panel in the presence of cisplatin, epirubicine and capecitabine, a miRNA based response predictor was developed. The Cox proportional hazards model was applied to assess the correlations of the response predictor with OS and DSS. Results A univariate analysis demonstrated a statistical significant improvement of OS for patients who had undergone surgical resection with prediction scores above the median prediction score (HR: 0.41 (95% CI: 0.17–0.96). Adjusting for surgery and stage, this predictor was identified to be independently associated with both OS (HR: 0.37 (95% CI: 0.16–0.87)) and DSS (HR: 0.32 (0.12–0.87)). Conclusion The miRNA profile predictive for sensitivity to cisplatin, epirubicine and capecitabine was shown to be independently associated with OS and DSS in patients with gastrooesophageal cancer. PMID:26885979

  20. Changes in transcriptional output of human peripheral blood mononuclear cells following resistance exercise.

    PubMed

    Carlson, Lara A; Tighe, S W; Kenefick, R W; Dragon, J; Westcott, N W; Leclair, R J

    2011-12-01

    Various types of exercise alter the population of circulating peripheral blood mononuclear cells (PBMCs) and change their transcriptional output. This work examines changes in PBMC populations and transcription in response to resistance exercise training (RET), and identify key transcriptional changes in PBMCs that may play a role in altering peripheral tissues in response to RET. Ten resistance-trained men (20-24 years), performed an acute bout of RET for ~30 min following a 12 h fast. Venous blood was sampled at rest, immediately following exercise, and at 2 h post-exercise and analyzed for total and differential leukocytes and global gene expression using Affymetrix Genechips. Results showed elevated leukocytes, monocytes, lymphocytes, and lactate values immediately post-exercise (P < 0.05) over baseline. At 2 h post-exercise, leukocytes, and granulocytes remained elevated (P < 0.05), whereas lymphocytes were lower than (P < 0.05) baseline values. Initial microarray results showed the greatest transcriptional changes in pathways related to immune response, inflammation, and cellular communication. The change in PBMC population (2 h time point) correlated with a dramatic decrease in the expression of CD160, and XCL1, markers of lymphocyte populations. At the 2 h recovery time point upregulation of matrix metalloproteinase 9, orosomucoid 1, dishevelled-associated activator of morphogenesis 2, and arginase 1 suggest an induction in muscle damage and repair during this time frame. These results demonstrate that an acute bout of RET disrupts cellular homeostasis, induces a transient redistribution of certain leukocytes, and results in transcriptional changes in PBMCs translating into systemic changes in response to RET. PMID:21437602

  1. Investigation of Radiosensitivity Gene Signatures in Cancer Cell Lines

    PubMed Central

    Hall, John S.; Iype, Rohan; Senra, Joana; Taylor, Janet; Armenoult, Lucile; Oguejiofor, Kenneth; Li, Yaoyong; Stratford, Ian; Stern, Peter L.; O’Connor, Mark J.; Miller, Crispin J.; West, Catharine M. L.

    2014-01-01

    Intrinsic radiosensitivity is an important factor underlying radiotherapy response, but there is no method for its routine assessment in human tumours. Gene signatures are currently being derived and some were previously generated by expression profiling the NCI-60 cell line panel. It was hypothesised that focusing on more homogeneous tumour types would be a better approach. Two cell line cohorts were used derived from cervix [n = 16] and head and neck [n = 11] cancers. Radiosensitivity was measured as surviving fraction following irradiation with 2 Gy (SF2) by clonogenic assay. Differential gene expression between radiosensitive and radioresistant cell lines (SF2 median) was investigated using Affymetrix GeneChip Exon 1.0ST (cervix) or U133A Plus2 (head and neck) arrays. There were differences within cell line cohorts relating to tissue of origin reflected by expression of the stratified epithelial marker p63. Of 138 genes identified as being associated with SF2, only 2 (1.4%) were congruent between the cervix and head and neck carcinoma cell lines (MGST1 and TFPI), and these did not partition the published NCI-60 cell lines based on SF2. There was variable success in applying three published radiosensitivity signatures to our cohorts. One gene signature, originally trained on the NCI-60 cell lines, did partially separate sensitive and resistant cell lines in all three cell line datasets. The findings do not confirm our hypothesis but suggest that a common transcriptional signature can reflect the radiosensitivity of tumours of heterogeneous origins. PMID:24466029

  2. Molecular Classification of Gastric Cancer: A new paradigm

    PubMed Central

    Shah, Manish A.; Khanin, Raya; Tang, Laura; Janjigian, Yelena Y.; Klimstra, David S.; Gerdes, Hans; Kelsen, David P.

    2011-01-01

    Purpose Gastric cancer may be subdivided into three distinct subtypes –proximal, diffuse, and distal gastric cancer– based on histopathologic and anatomic criteria. Each subtype is associated with unique epidemiology. Our aim is to test the hypothesis that these distinct gastric cancer subtypes may also be distinguished by gene expression analysis. Experimental Design Patients with localized gastric adenocarcinoma being screened for a phase II preoperative clinical trial (NCI 5917) underwent endoscopic biopsy for fresh tumor procurement. 4–6 targeted biopsies of the primary tumor were obtained. Macrodissection was performed to ensure >80% carcinoma in the sample. HG-U133A GeneChip (Affymetrix) was used for cDNA expression analysis, and all arrays were processed and analyzed using the Bioconductor R-package. Results Between November 2003 and January 2006, 57 patients were screened to identify 36 patients with localized gastric cancer who had adequate RNA for expression analysis. Using supervised analysis, we built a classifier to distinguish the three gastric cancer subtypes, successfully classifying each into tightly grouped clusters. Leave-one-out cross validation error was 0.14, suggesting that >85% of samples were classified correctly. Gene set analysis with the False Discovery Rate set at 0.25 identified several pathways that were differentially regulated when comparing each gastric cancer subtype to adjacent normal stomach. Conclusions Subtypes of gastric cancer that have epidemiologic and histologic distinction are also distinguished by gene expression data. These preliminary data suggest a new classification of gastric cancer with implications for improving our understanding of disease biology and identification of unique molecular drivers for each gastric cancer subtype. PMID:21430069

  3. Evaluation of power of the Illumina HumanOmni5M-4v1 BeadChip to detect risk variants for human complex diseases.

    PubMed

    Xing, Chuanhua; Huang, Jie; Hsu, Yi-Hsiang; DeStefano, Anita L; Heard-Costa, Nancy L; Wolf, Philip A; Seshadri, Sudha; Kiel, Douglas P; Cupples, L Adrienne; Dupuis, Josée

    2016-07-01

    Although emerging sequencing technologies can characterize all genetic variants, the cost is still high. Illumina released the HumanOmni5M-4v1 (Omni5) genotype array with ~4.3M assayed SNPs, a much denser array compared with other available arrays. The Omni5 balances both cost and array density. In this article, we illustrate the power of Omni5 to detect genetic associations. The Omni5 includes variants with a wide range of minor allele frequencies down to <1%. The theoretical power calculation examples indicate the increased power of the Omni5 array compared with other arrays with lower density when evaluating associations with some known loci, although there are exceptions. We further evaluate the genetic associations between known loci and several quantitative traits in the Framingham Heart Study: femoral neck bone mineral density, lumbar spine bone mineral density and hippocampal volume. Finally, we search genome wide for novel associations using the Omni5 genotypes. We compare our association results from Affymetrix 500K+MIPS 50K arrays and two imputed data sets: (1) HapMap Phase II and (2) 1000 Genomes reference panel. We observed increased evidence for genotype-phenotype associations with smaller P-values for selected known loci using the Omni5 genotypes. With limited sample sizes, we identify novel variants with genome-wide significant P-values. Our observations support the notion that dense genotyping using the Omni5 can be powerful in detecting novel associated variants. Comparison with imputed data with higher density also suggests that imputation helps but cannot replace genotyping, especially when imputation quality is low. PMID:26577045

  4. DNA-PK – a candidate driver of hepatocarcinogenesis and tissue biomarker that predicts response to treatment and survival

    PubMed Central

    Cornell, Liam; Munck, Joanne; Alsinet, Clara; Villanueva, Augusto; Ogle, Laura; Willoughby, Catherine; Televantou, Despina; Thomas, Huw; Jackson, Jennifer; Burt, Alastair; Newell, David; Rose, John; Manas, Derek M; Shapiro, Geoffrey; Curtin, Nicola; Reeves, Helen L

    2014-01-01

    Purpose Therapy resistance and associated liver disease make hepatocellular cancers (HCC) difficult to treat with traditional cytotoxic therapies, while newer targeted approaches offer only modest survival benefit. We focused on DNA-dependent protein kinase, DNA-PKcs, encoded by PRKDC and central to DNA damage repair by non-homologous end joining. Our aim was to explore its roles in hepatocarcinogenesis and as a novel therapeutic candidate. Experimental Design PRKDC was characterised in liver tissues from of 132 patients (normal liver (n=10), cirrhotic liver (n=13), dysplastic nodules (n=18), HCC (n=91)) using Affymetrix U133 Plus 2.0 and 500K Human Mapping SNP arrays (cohort 1). In addition, we studied a case series of 45 patients with HCC undergoing diagnostic biopsy (cohort 2). Histological grading, response to treatment and survival were correlated with DNA-PKcs quantified immunohistochemically. Parallel in vitro studies determined the impact of DNA-PK on DNA repair and response to cytotoxic therapy. Results Increased PRKDC expression in HCC was associated with amplification of its genetic locus in cohort 1. In cohort 2, elevated DNA-PKcs identified patients with treatment-resistant HCC, progressing at a median of 4.5 months compared to 16.9 months, while elevation of activated pDNA-PK independently predicted poorer survival. DNA-PKcs was high in HCC cell lines, where its inhibition with NU7441 potentiated irradiation and doxorubicin-induced cytoxicity, while the combination suppressed HCC growth in vitro and in vivo. Conclusions These data identify PRKDC/DNA-PKcs as a candidate driver of hepatocarcinogenesis, whose biopsy characterisation at diagnosis may impact stratification of current therapies, and whose specific future targeting may overcome resistance. PMID:25480831

  5. Support for the involvement of large copy number variants in the pathogenesis of schizophrenia

    PubMed Central

    Kirov, George; Grozeva, Detelina; Norton, Nadine; Ivanov, Dobril; Mantripragada, Kiran K.; Holmans, Peter; Craddock, Nick; Owen, Michael J.; O'Donovan, Michael C.

    2009-01-01

    We investigated the involvement of rare (<1%) copy number variants (CNVs) in 471 cases of schizophrenia and 2792 controls that had been genotyped using the Affymetrix GeneChip® 500K Mapping Array. Large CNVs >1 Mb were 2.26 times more common in cases (P = 0.00027), with the effect coming mostly from deletions (odds ratio, OR = 4.53, P = 0.00013) although duplications were also more common (OR = 1.71, P = 0.04). Two large deletions were found in two cases each, but in no controls: a deletion at 22q11.2 known to be a susceptibility factor for schizophrenia and a deletion on 17p12, at 14.0–15.4 Mb. The latter is known to cause hereditary neuropathy with liability to pressure palsies. The same deletion was found in 6 of 4618 (0.13%) cases and 6 of 36 092 (0.017%) controls in the re-analysed data of two recent large CNV studies of schizophrenia (OR = 7.82, P = 0.001), with the combined significance level for all three studies achieving P = 5 × 10−5. One large duplication on 16p13.1, which has been previously implicated as a susceptibility factor for autism, was found in three cases and six controls (0.6% versus 0.2%, OR = 2.98, P = 0.13). We also provide the first support for a recently reported association between deletions at 15q11.2 and schizophrenia (P = 0.026). This study confirms the involvement of rare CNVs in the pathogenesis of schizophrenia and contributes to the growing list of specific CNVs that are implicated. PMID:19181681

  6. Novel loci for major depression identified by genome-wide association study of STAR*D and meta-analysis of three studies

    PubMed Central

    Shyn, SI; Shi, J; Kraft, JB; Potash, JB; Knowles, JA; Weissman, MM; Garriock, HA; Yokoyama, JS; McGrath, PJ; Peters, EJ; Scheftner, WA; Coryell, W; Lawson, WB; Jancic, D; Gejman, PV; Sanders, AR; Holmans, P; Slager, SL; Levinson, DF; Hamilton, SP

    2009-01-01

    We report a genome-wide association study (GWAS) of major depressive disorder (MDD) in 1,221 cases from the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study and 1,636 screened controls. No genome-wide evidence for association was detected. We also carried out a meta-analysis of three European-ancestry MDD GWAS datasets: STAR*D, Genetics of Recurrent Early-Onset Depression (GenRED) and the publicly-available Genetic Association Information Network MDD dataset (GAIN-MDD). These datasets, totaling 3,957 cases and 3,428 controls, were genotyped using four different platforms (Affymetrix 6.0, 5.0 and 500K, and Perlegen). For each of 2.4 million HapMap II SNPs, using genotyped data where available and imputed data otherwise, single-SNP association tests were carried out in each sample with correction for ancestry-informative principal components. The strongest evidence for association in the meta-analysis was observed for intronic SNPs in ATP6V1B2 (P = 6.78 × 10−7), SP4 (P = 7.68 × 10−7) and GRM7 (P = 1.11 × 10−6). Additional exploratory analyses were carried out for a narrower phenotype (recurrent MDD with onset before age 31, N = 2,191 cases), and separately for males and females. Several of the best findings were supported primarily by evidence from narrow cases or from either males or females. Based on previous biological evidence, we consider GRM7 a strong MDD candidate gene. Larger samples will be required to determine whether any common SNPs are significantly associated with MDD. PMID:20038947

  7. Association of SNPs on Chromosome 9p21.3 with Platelet Reactivity: A Potential Mechanism for Increased Vascular Disease

    PubMed Central

    Musunuru, Kiran; Post, Wendy S.; Herzog, William; Shen, Haiqing; O’Connell, Jeffrey R.; McArdle, Patrick F.; Ryan, Kathleen A.; Gibson, Quince; Cheng, Yu-Ching; Clearfield, Elizabeth; Johnson, Andrew D.; Tofler, Geoffrey; Yang, Qiong; O’Donnell, Christopher J.; Becker, Diane M.; Yanek, Lisa R.; Becker, Lewis C.; Faraday, Nauder; Bielak, Lawrence F.; Peyser, Patricia A.; Shuldiner, Alan R.; Mitchell, Braxton D.

    2010-01-01

    Background Genome-wide association studies have identified a locus on chromosome 9p21.3 to be strongly associated with myocardial infarction/coronary artery disease (MI/CAD) and ischemic stroke. To gain insights into the mechanisms underlying these associations, we hypothesized that single nucleotide polymorphisms (SNPs) in this region would be associated with platelet reactivity across multiple populations. Methods and Results Subjects in the initial population included 1,402 asymptomatic Amish adults in whom we measured platelet reactivity (n=788) and/or coronary artery calcification (CAC) (n=939). Platelet reactivity on agonist stimulation was measured by impedence aggregometry, and CAC by electron beam computed tomography. Twenty-nine SNPs at the 9p21.3 locus were genotyped using the Affymetrix 500K array. Twelve correlated SNPs in the locus were significantly associated with platelet reactivity (all p ≤ 0.001). The SNP most strongly associated with platelet reactivity, rs10965219 (p = 0.0002) was also associated with CAC (p = 0.002), along with 9 other SNPs (all p < 0.004). Association of rs10965219 with platelet reactivity persisted after adjustment for CAC, a measure of underlying atherosclerotic burden known to affect platelet reactivity. We then tested rs10965219 for association with platelet function in 2,364 subjects from the Framingham Heart Study (FHS) and 1,169 subjects from the GeneSTAR Study. The rs10965219 G allele (frequency ~ 51% across all three populations) was significantly associated with higher platelet reactivity in FHS (p = 0.001) and trended toward higher reactivity in GeneSTAR (p = 0.087); the combined p-value for meta-analysis was 0.0002. Conclusions These results suggest that risk alleles at 9p21.3 locus may have pleiotropic effects on MI/CAD and stroke risk, possibly through their influence on platelet reactivity. PMID:20858905

  8. Effects of Metformin on Tissue Oxidative and Dicarbonyl Stress in Transgenic Spontaneously Hypertensive Rats Expressing Human C-Reactive Protein.

    PubMed

    Malínská, Hana; Oliyarnyk, Olena; Škop, Vojtěch; Šilhavý, Jan; Landa, Vladimír; Zídek, Václav; Mlejnek, Petr; Šimáková, Miroslava; Strnad, Hynek; Kazdová, Ludmila; Pravenec, Michal

    2016-01-01

    Inflammation and oxidative and dicarbonyl stress play important roles in the pathogenesis of type 2 diabetes. Metformin is the first-line drug of choice for the treatment of type 2 diabetes because it effectively suppresses gluconeogenesis in the liver. However, its "pleiotropic" effects remain controversial. In the current study, we tested the effects of metformin on inflammation, oxidative and dicarbonyl stress in an animal model of inflammation and metabolic syndrome, using spontaneously hypertensive rats that transgenically express human C-reactive protein (SHR-CRP). We treated 8-month-old male transgenic SHR-CRP rats with metformin (5 mg/kg/day) mixed as part of a standard diet for 4 weeks. A corresponding untreated control group of male transgenic SHR-CRP rats were fed a standard diet without metformin. In a similar fashion, we studied a group of nontransgenic SHR treated with metformin and an untreated group of nontransgenic SHR controls. In each group, we studied 6 animals. Parameters of glucose and lipid metabolism and oxidative and dicarbonyl stress were measured using standard methods. Gene expression profiles were determined using Affymetrix GeneChip Arrays. Statistical significance was evaluated by two-way ANOVA. In the SHR-CRP transgenic strain, we found that metformin treatment decreased circulating levels of inflammatory response marker IL-6, TNFα and MCP-1 while levels of human CRP remained unchanged. Metformin significantly reduced oxidative stress (levels of conjugated dienes and TBARS) and dicarbonyl stress (levels of methylglyoxal) in left ventricles, but not in kidneys. No significant effects of metformin on oxidative and dicarbonyl stress were observed in SHR controls. In addition, metformin treatment reduced adipose tissue lipolysis associated with human CRP. Possible molecular mechanisms of metformin action-studied by gene expression profiling in the liver-revealed deregulated genes from inflammatory and insulin signaling, AMP

  9. Identity-by-descent approaches identify regions of importance for genetic susceptibility to hereditary esophageal squamous cell carcinoma.

    PubMed

    Ko, Josephine My; Zhang, Peng; Law, Simon; Fan, Yanhui; Song, You-Qiang; Zhao, Xue Ke; Wong, Elibe H W; Tang, Sa; Song, Xin; Lung, Maria Li; Wang, Li Dong

    2014-08-01

    Worldwide, the highest prevalence of esophageal cancer (EC) occurs in Northern China. High-density SNP arrays allow identification of identity-by-descent (IBD) segments in genomic DNAs representative of shared common ancestral regions. We utilized IBD approaches to map susceptibility loci associated with low-penetrance SNPs in high-risk Henan hereditary esophageal squamous cell carcinoma (ESCC) patients. Affymetrix GeneChip Human mapping SNP array IBD analysis was performed in 32 Henan family history-positive (FH+) ESCC patients, 18 Henan healthy unrelated individuals, and 45 Chinese individuals from a CHB HapMap dataset using PLink (scoring IBD segments individually) and Beagle (scoring of shared IBD segments among case/case vs. control/control pairs) software. Both analyses identified longer IBD segment lengths associated with FH+ ESCC compared to controls. However, there was no strong evidence for a genetic founder effect. Pairing IBD analysis with BEAGLE identified 8 critical IBD segments residing at 2q32.1-q32.2, 3p22.3-p22.2, 4q21.1-q21.21, 7p22.2, 8q23.2-q23.3, 10q23.33-q24.1, 14q24.3 and 16q11.2-q12.1, which were more significantly shared among case/case compared to control/control. The shared IBD segments in FH+ ESCC samples with no overlap with control/CHB Hapmap may encompass potential cancer susceptibility loci. Selected targeted genes, PLCE1, GPT2, SIAH1 and CYP2C-18, residing within the IBD segments at 10q23.33-q24.1 and 16q11.2-q12.1, had statistically significant differential expression in primary ESCC tissues and are likely involved in ESCC carcinogenesis. The importance of these IBD segments to the etiology and development of ESCC in high-risk areas requires further study with expanded sample sizes. This is the first report employing the pairing IBD approach for elucidation of the genetic basis of hereditary ESCC in Henan by applying high throughput SNP array analysis. PMID:24890309

  10. Characterization of Sugar Insensitive (sis) Mutants of Arabidopsis

    SciTech Connect

    Gibson, Susan I.

    2009-06-08

    . Characterization of mutant and wild-type plants has revealed that sugars inhibit breakdown of seed storage lipids. In addition, high concentrations of exogenous sugars largely eliminate the development of mature chloroplasts by developing seedlings. Affymetrix GeneChip experiments have revealed that expression of many plant genes is partially regulated by sugar levels, with approximately two percent of genes exhibiting alterations in steady-state mRNA levels in response to changing sugar concentrations. Ultimately, a better understanding of plant sugar responses may allow improvements in rates of carbon fixation and manipulation of carbon partitioning. These improvements will be needed to help make production of energy from biomass more economically attractive.

  11. Extremely Low-Frequency Electromagnetic Fields Affect the miRNA-Mediated Regulation of Signaling Pathways in the GC-2 Cell Line

    PubMed Central

    Liu, Kai-jun; Ao, Lin; Cao, Jia; Zhong, Julia Li; Liu, Jin-yi

    2015-01-01

    Extremely low-frequency electromagnetic fields (ELF-EMFs) can affect male reproductive function, but the underlying mechanism of this effect remains unknown. miRNA-mediated regulation has been implicated as an important epigenetic mechanism for regulatory pathways. Herein, we profiled miRNA expression in response to ELF-EMFs in vitro. Mouse spermatocyte-derived GC–2 cells were intermittently exposed to a 50 Hz ELF-EMF for 72 h (5 min on/10 min off) at magnetic field intensities of 1 mT, 2 mT and 3 mT. Cell viability was assessed using the CCK–8 assay. Apoptosis and the cell cycle were analyzed with flow cytometry. miRNA expression was profiled using Affymetrix Mouse Genechip miRNA 3.0 arrays. Our data showed that the growth, apoptosis or cell cycle arrest of GC–2 cells exposed to the 50 Hz ELF-EMF did not significantly change. However, we identified a total of 55 miRNAs whose expression significantly changed compared with the sham group, including 19 differentially expressed miRNAs (7 miRNAs were upregulated, and 12 were downregulated) in the 1 mT exposure group and 36 (9 miRNAs were upregulated, and 27 were downregulated) in the 3 mT exposure group. The changes in the expression of 15 selected miRNAs measured by real-time PCR were consistent with the microarray results. A network analysis was used to predict core miRNAs and target genes, including miR-30e-5p, miR-210-5p, miR-196b-5p, miR-504-3p, miR-669c-5p and miR-455-3p. We found that these miRNAs were differentially expressed in response to different magnetic field intensities of ELF-EMFs. GO term and KEGG pathway annotation based on the miRNA expression profiling results showed that miRNAs may regulate circadian rhythms, cytokine-cytokine receptor interactions and the p53 signaling pathway. These results suggested that miRNAs could serve as potential biomarkers, and the miRNA-mediated regulation of signaling pathways might play significant roles in the biological effects of ELF-EMFs. PMID:26439850

  12. Genome-wide association with select biomarker traits in the Framingham Heart Study

    PubMed Central

    Benjamin, Emelia J; Dupuis, Josée; Larson, Martin G; Lunetta, Kathryn L; Booth, Sarah L; Govindaraju, Diddahally R; Kathiresan, Sekar; Keaney, John F; Keyes, Michelle J; Lin, Jing-Ping; Meigs, James B; Robins, Sander J; Rong, Jian; Schnabel, Renate; Vita, Joseph A; Wang, Thomas J; Wilson, Peter WF; Wolf, Philip A; Vasan, Ramachandran S

    2007-01-01

    Background Systemic biomarkers provide insights into disease pathogenesis, diagnosis, and risk stratification. Many systemic biomarker concentrations are heritable phenotypes. Genome-wide association studies (GWAS) provide mechanisms to investigate the genetic contributions to biomarker variability unconstrained by current knowledge of physiological relations. Methods We examined the association of Affymetrix 100K GeneChip single nucleotide polymorphisms (SNPs) to 22 systemic biomarker concentrations in 4 biological domains: inflammation/oxidative stress; natriuretic peptides; liver function; and vitamins. Related members of the Framingham Offspring cohort (n = 1012; mean age 59 ± 10 years, 51% women) had both phenotype and genotype data (minimum-maximum per phenotype n = 507–1008). We used Generalized Estimating Equations (GEE), Family Based Association Tests (FBAT) and variance components linkage to relate SNPs to multivariable-adjusted biomarker residuals. Autosomal SNPs (n = 70,987) meeting the following criteria were studied: minor allele frequency ≥ 10%, call rate ≥ 80% and Hardy-Weinberg equilibrium p ≥ 0.001. Results With GEE, 58 SNPs had p < 10-6: the top SNPs were rs2494250 (p = 1.00*10-14) and rs4128725 (p = 3.68*10-12) for monocyte chemoattractant protein-1 (MCP1), and rs2794520 (p = 2.83*10-8) and rs2808629 (p = 3.19*10-8) for C-reactive protein (CRP) averaged from 3 examinations (over about 20 years). With FBAT, 11 SNPs had p < 10-6: the top SNPs were the same for MCP1 (rs4128725, p = 3.28*10-8, and rs2494250, p = 3.55*10-8), and also included B-type natriuretic peptide (rs437021, p = 1.01*10-6) and Vitamin K percent undercarboxylated osteocalcin (rs2052028, p = 1.07*10-6). The peak LOD (logarithm of the odds) scores were for MCP1 (4.38, chromosome 1) and CRP (3.28, chromosome 1; previously described) concentrations; of note the 1.5 support interval included the MCP1 and CRP SNPs reported above (GEE model). Previous candidate SNP associations

  13. Upregulation of Gingival Tissue miR-200b in Obese Periodontitis Subjects

    PubMed Central

    Kalea, A.Z.; Hoteit, R.; Suvan, J.; Lovering, R.C.; Palmen, J.; Cooper, J.A.; Khodiyar, V.K.; Harrington, Z.; Humphries, S.E.; D’Aiuto, F.

    2015-01-01

    Increased local immune and inflammatory responses in obese individuals with periodontitis may explain the aggressive clinical presentation and altered treatment response when compared to that of normal weight subjects. Our goal was to identify any differences in microRNA (miRNA) expression profiles of gingival tissue in periodontitis when obesity is present, which may suggest novel molecular pathways that this miRNA network may affect. Total RNA was extracted from gingival tissue biopsies collected from normal weight and obese individuals with periodontitis; miRNA expression profiling was performed with Affymetrix GeneChip miRNA 3.0 arrays; and results were validated with quantitative reverse transcription polymerase chain reaction (qRT-PCR). In silico identification of previously confirmed miRNA gene targets was conducted through miRTarBase and miRWalk databases, and pathway enrichment analysis identified enriched miRNA gene sets. Expression of selected genes in the same biopsy samples was tested with qRT-PCR. The gingival tissue miRNA profile of obese patients, compared to that of normal weight patients, showed 13 upregulated and 22 downregulated miRNAs, among which miR-200b was validated by qRT-PCR to be significantly increased in obesity. Functional analysis of 51 experimentally validated miR-200b gene targets identified enrichment of genes involved in cell motility, differentiation, DNA binding, response to stimulus, and vasculature development pathways not previously identified in the obesity-specific disease profile. Furthermore, the expression of the miR-200b gene targets ZEB1/2, GATA2, and KDR was confirmed by qRT-PCR as being lower in obese patients with periodontitis versus normal weight patients, suggesting a role of miR-200b in regulation of a set of gene targets and biological pathways relevant to wound healing and angiogenesis. Functional studies to explore the role of miR-200b in the above processes may offer new insights on putative therapeutic

  14. Gene expression of transporters and phase I/II metabolic enzymes in murine small intestine during fasting

    PubMed Central

    van den Bosch, Heleen M; Bünger, Meike; de Groot, Philip J; van der Meijde, Jolanda; Hooiveld, Guido JEJ; Müller, Michael

    2007-01-01

    Background Fasting has dramatic effects on small intestinal transport function. However, little is known on expression of intestinal transport and phase I/II metabolism genes during fasting and the role the fatty acid-activated transcription factor PPARα may play herein. We therefore investigated the effects of fasting on expression of these genes using Affymetrix GeneChip MOE430A arrays and quantitative RT-PCR. Results After 24 hours of fasting, expression levels of 33 of the 253 analyzed transporter and phase I/II metabolism genes were changed. Upregulated genes were involved in transport of energy-yielding molecules in processes such as glycogenolysis (G6pt1) and mitochondrial and peroxisomal oxidation of fatty acids (Cact, Mrs3/4, Fatp2, Cyp4a10, Cyp4b1). Other induced genes were responsible for the inactivation of the neurotransmitter serotonin (Sert, Sult1d1, Dtd, Papst2), formation of eicosanoids (Cyp2j6, Cyp4a10, Cyp4b1), or for secretion of cholesterol (Abca1 and Abcg8). Cyp3a11, typically known because of its drug metabolizing capacity, was also increased. Fasting had no pronounced effect on expression of phase II metabolic enzymes, except for glutathione S-transferases which were down-regulated. Time course studies revealed that some genes were acutely regulated, whereas expression of other genes was only affected after prolonged fasting. Finally, we identified 8 genes that were PPARα-dependently upregulated upon fasting. Conclusion We have characterized the response to fasting on expression of transporters and phase I/II metabolic enzymes in murine small intestine. Differentially expressed genes are involved in a variety of processes, which functionally can be summarized as a) increased oxidation of fat and xenobiotics, b) increased cholesterol secretion, c) increased susceptibility to electrophilic stressors, and d) reduced intestinal motility. This knowledge increases our understanding of gut physiology, and may be of relevance for e.g. pre

  15. Effects of Metformin on Tissue Oxidative and Dicarbonyl Stress in Transgenic Spontaneously Hypertensive Rats Expressing Human C-Reactive Protein

    PubMed Central

    Malínská, Hana; Oliyarnyk, Olena; Škop, Vojtěch; Šilhavý, Jan; Landa, Vladimír; Zídek, Václav; Mlejnek, Petr; Šimáková, Miroslava; Strnad, Hynek; Kazdová, Ludmila; Pravenec, Michal

    2016-01-01

    Inflammation and oxidative and dicarbonyl stress play important roles in the pathogenesis of type 2 diabetes. Metformin is the first-line drug of choice for the treatment of type 2 diabetes because it effectively suppresses gluconeogenesis in the liver. However, its “pleiotropic” effects remain controversial. In the current study, we tested the effects of metformin on inflammation, oxidative and dicarbonyl stress in an animal model of inflammation and metabolic syndrome, using spontaneously hypertensive rats that transgenically express human C-reactive protein (SHR-CRP). We treated 8-month-old male transgenic SHR-CRP rats with metformin (5 mg/kg/day) mixed as part of a standard diet for 4 weeks. A corresponding untreated control group of male transgenic SHR-CRP rats were fed a standard diet without metformin. In a similar fashion, we studied a group of nontransgenic SHR treated with metformin and an untreated group of nontransgenic SHR controls. In each group, we studied 6 animals. Parameters of glucose and lipid metabolism and oxidative and dicarbonyl stress were measured using standard methods. Gene expression profiles were determined using Affymetrix GeneChip Arrays. Statistical significance was evaluated by two-way ANOVA. In the SHR-CRP transgenic strain, we found that metformin treatment decreased circulating levels of inflammatory response marker IL-6, TNFα and MCP-1 while levels of human CRP remained unchanged. Metformin significantly reduced oxidative stress (levels of conjugated dienes and TBARS) and dicarbonyl stress (levels of methylglyoxal) in left ventricles, but not in kidneys. No significant effects of metformin on oxidative and dicarbonyl stress were observed in SHR controls. In addition, metformin treatment reduced adipose tissue lipolysis associated with human CRP. Possible molecular mechanisms of metformin action–studied by gene expression profiling in the liver–revealed deregulated genes from inflammatory and insulin signaling, AMP

  16. Sequential analysis of global gene expression profiles in immature and in vitro matured bovine oocytes: potential molecular markers of oocyte maturation

    PubMed Central

    2011-01-01

    Background Without intensive selection, the majority of bovine oocytes submitted to in vitro embryo production (IVP) fail to develop to the blastocyst stage. This is attributed partly to their maturation status and competences. Using the Affymetrix GeneChip Bovine Genome Array, global mRNA expression analysis of immature (GV) and in vitro matured (IVM) bovine oocytes was carried out to characterize the transcriptome of bovine oocytes and then use a variety of approaches to determine whether the observed transcriptional changes during IVM was real or an artifact of the techniques used during analysis. Results 8489 transcripts were detected across the two oocyte groups, of which ~25.0% (2117 transcripts) were differentially expressed (p < 0.001); corresponding to 589 over-expressed and 1528 under-expressed transcripts in the IVM oocytes compared to their immature counterparts. Over expression of transcripts by IVM oocytes is particularly interesting, therefore, a variety of approaches were employed to determine whether the observed transcriptional changes during IVM were real or an artifact of the techniques used during analysis, including the analysis of transcript abundance in oocytes in vitro matured in the presence of α-amanitin. Subsets of the differentially expressed genes were also validated by quantitative real-time PCR (qPCR) and the gene expression data was classified according to gene ontology and pathway enrichment. Numerous cell cycle linked (CDC2, CDK5, CDK8, HSPA2, MAPK14, TXNL4B), molecular transport (STX5, STX17, SEC22A, SEC22B), and differentiation (NACA) related genes were found to be among the several over-expressed transcripts in GV oocytes compared to the matured counterparts, while ANXA1, PLAU, STC1and LUM were among the over-expressed genes after oocyte maturation. Conclusion Using sequential experiments, we have shown and confirmed transcriptional changes during oocyte maturation. This dataset provides a unique reference resource for studies

  17. Transcriptome analysis of heat stress response in switchgrass (Panicum virgatum L.)

    PubMed Central

    2013-01-01

    Background Global warming predictions indicate that temperatures will increase by another 2-6°C by the end of this century. High temperature is a major abiotic stress limiting plant growth and productivity in many areas of the world. Switchgrass (Panicum virgatum L.) is a model herbaceous bioenergy crop, due to its rapid growth rate, reliable biomass yield, minimal requirements of water and nutrients, adaptability to grow on marginal lands and widespread distribution throughout North America. The effect of high temperature on switchgrass physiology, cell wall composition and biomass yields has been reported. However, there is void in the knowledge of the molecular responses to heat stress in switchgrass. Results We conducted long-term heat stress treatment (38°/30°C, day/night, for 50 days) in the switchgrass cultivar Alamo. A significant decrease in the plant height and total biomass was evident in the heat stressed plants compared to controls. Total RNA from control and heat stress samples were used for transcriptome analysis with switchgrass Affymetrix genechips. Following normalization and pre-processing, 5365 probesets were identified as differentially expressed using a 2-fold cutoff. Of these, 2233 probesets (2000 switchgrass unigenes) were up-regulated, and 3132 probesets (2809 unigenes) were down-regulated. Differential expression of 42 randomly selected genes from this list was validated using RT-PCR. Rice orthologs were retrieved for 78.7% of the heat stress responsive switchgrass probesets. Gene ontology (GOs) enrichment analysis using AgriGO program showed that genes related to ATPase regulator, chaperone binding, and protein folding was significantly up-regulated. GOs associated with protein modification, transcription, phosphorus and nitrogen metabolic processes, were significantly down-regulated by heat stress. Conclusions Plausible connections were identified between the identified GOs, physiological responses and heat response phenotype

  18. dsRNA-induced changes in gene expression profiles of primary nasal and bronchial epithelial cells from patients with asthma, rhinitis and controls

    PubMed Central

    2014-01-01

    Background Rhinovirus infections are the most common cause of asthma exacerbations. The complex responses by airway epithelium to rhinovirus can be captured by gene expression profiling. We hypothesized that: a) upper and lower airway epithelium exhibit differential responses to double-stranded RNA (dsRNA), and b) that this is modulated by the presence of asthma and allergic rhinitis. Objectives Identification of dsRNA-induced gene expression profiles of primary nasal and bronchial epithelial cells from the same individuals and examining the impact of allergic rhinitis with and without concomitant allergic asthma on expression profiles. Methods This study had a cross-sectional design including 18 subjects: 6 patients with allergic asthma with concomitant rhinitis, 6 patients with allergic rhinitis, and 6 healthy controls. Comparing 6 subjects per group, the estimated false discovery rate was approximately 5%. RNA was extracted from isolated and cultured primary epithelial cells from nasal biopsies and bronchial brushings stimulated with dsRNA (poly(I:C)), and analyzed by microarray (Affymetrix U133+ PM Genechip Array). Data were analysed using R and the Bioconductor Limma package. Overrepresentation of gene ontology groups were captured by GeneSpring GX12. Results In total, 17 subjects completed the study successfully (6 allergic asthma with rhinitis, 5 allergic rhinitis, 6 healthy controls). dsRNA-stimulated upper and lower airway epithelium from asthma patients demonstrated significantly fewer induced genes, exhibiting reduced down-regulation of mitochondrial genes. The majority of genes related to viral responses appeared to be similarly induced in upper and lower airways in all groups. However, the induction of several interferon-related genes (IRF3, IFNAR1, IFNB1, IFNGR1, IL28B) was impaired in patients with asthma. Conclusions dsRNA differentially changes transcriptional profiles of primary nasal and bronchial epithelial cells from patients with allergic

  19. Potential candidate genomic biomarkers of drug induced vascular injury in the rat

    SciTech Connect

    Dalmas, Deidre A.; Scicchitano, Marshall S.; Mullins, David; Hughes-Earle, Angela; Tatsuoka, Kay; Magid-Slav, Michal; Frazier, Kendall S.; Thomas, Heath C.

    2011-12-15

    Drug-induced vascular injury is frequently observed in rats but the relevance and translation to humans present a hurdle for drug development. Numerous structurally diverse pharmacologic agents have been shown to induce mesenteric arterial medial necrosis in rats, but no consistent biomarkers have been identified. To address this need, a novel strategy was developed in rats to identify genes associated with the development of drug-induced mesenteric arterial medial necrosis. Separate groups (n = 6/group) of male rats were given 28 different toxicants (30 different treatments) for 1 or 4 days with each toxicant given at 3 different doses (low, mid and high) plus corresponding vehicle (912 total rats). Mesentery was collected, frozen and endothelial and vascular smooth muscle cells were microdissected from each artery. RNA was isolated, amplified and Affymetrix GeneChip Registered-Sign analysis was performed on selectively enriched samples and a novel panel of genes representing those which showed a dose responsive pattern for all treatments in which mesenteric arterial medial necrosis was histologically observed, was developed and verified in individual endothelial cell- and vascular smooth muscle cell-enriched samples. Data were confirmed in samples containing mesentery using quantitative real-time RT-PCR (TaqMan Trade-Mark-Sign ) gene expression profiling. In addition, the performance of the panel was also confirmed using similarly collected samples obtained from a timecourse study in rats given a well established vascular toxicant (Fenoldopam). Although further validation is still required, a novel gene panel has been developed that represents a strategic opportunity that can potentially be used to help predict the occurrence of drug-induced mesenteric arterial medial necrosis in rats at an early stage in drug development. -- Highlights: Black-Right-Pointing-Pointer A gene panel was developed to help predict rat drug-induced mesenteric MAN. Black

  20. Epidermal differentiation complex (locus 1q21) gene expression in head and neck cancer and normal mucosa.

    PubMed

    Tyszkiewicz, Tomasz; Jarzab, Michal; Szymczyk, Cezary; Kowal, Monika; Krajewska, Jolanta; Jaworska, Magdalena; Fraczek, Marcin; Krajewska, Anna; Hadas, Ewa; Swierniak, Michal; Markowski, Jaroslaw; Lange, Dariusz; Poltorak, Stanislaw; Wiench, Malgorzata; Krecicki, Tomasz; Jarzab, Jerzy; Maciejewski, Adam

    2014-01-01

    Epidermal differentiation complex (EDC) comprises a number of genes associated with human skin diseases including psoriasis, atopic dermatitis and hyperkeratosis. These genes have also been linked to numerous cancers, among them skin, gastric, colorectal, lung, ovarian and renal carcinomas. The involvement of EDC components encoding S100 proteins, small proline-rich proteins (SPRRs) and other genes in the tumorigenesis of head and neck squamous cell cancer (HNSCC) has been previously suggested. The aim of the study was to systematically analyze the expression of EDC components on the transcript level in HNSCC. Tissue specimens from 93 patients with HNC of oral cavity and 87 samples from adjacent or distant grossly normal oral mucosawere analyzed. 48 samples (24 tumor and 24 corresponding surrounding tissue) were hybridized to Affymetrix GeneChip Human 1.0 ST Arrays. For validation by quantitative real-time PCR (QPCR) the total RNA from all180 samples collected in the study was analyzed with Real-Time PCR system and fluorescent amplicon specific-probes. Additional set of samples from 14 patients with laryngeal carcinoma previously obtained by HG-U133 Plus 2.0 microarray was also included in the analyses. The expression of analyzed EDC genes was heterogeneous. Two transcripts (S100A1 and S100A4) were significantly down-regulated in oral cancer when compared to normal mucosa (0.69 and 0.36-fold change, respectively), showing an opposite pattern of expression to the remaining S100 genes. Significant up-regulation in tumors was found for S100A11, S100A7, LCE3D, S100A3 and S100A2 genes. The increased expression of S100A7 was subsequently validated by QPCR, confirming significant differences. The remaining EDC genes, including all encoding SPRR molecules, did not show any differences between oral cancer and normal mucosa. The observed differences were also assessed in the independent set of laryngeal cancer samples, confirming the role of S100A3 and LCE3D transcripts in

  1. Overexpression of miR-9 in mast cells is associated with invasive behavior and spontaneous metastasis

    PubMed Central

    2014-01-01

    Background While microRNA (miRNA) expression is known to be altered in a variety of human malignancies contributing to cancer development and progression, the potential role of miRNA dysregulation in malignant mast cell disease has not been previously explored. The purpose of this study was to investigate the potential contribution of miRNA dysregulation to the biology of canine mast cell tumors (MCTs), a well-established spontaneous model of malignant mast cell disease. Methods We evaluated the miRNA expression profiles from biologically low-grade and biologically high-grade primary canine MCTs using real-time PCR-based TaqMan Low Density miRNA Arrays and performed real-time PCR to evaluate miR-9 expression in primary canine MCTs, malignant mast cell lines, and normal bone marrow-derived mast cells (BMMCs). Mouse mast cell lines and BMMCs were transduced with empty or pre-miR-9 expressing lentiviral constructs and cell proliferation, caspase 3/7 activity, and invasion were assessed. Transcriptional profiling of cells overexpressing miR-9 was performed using Affymetrix GeneChip Mouse Gene 2.0 ST arrays and real-time PCR was performed to validate changes in mRNA expression. Results Our data demonstrate that unique miRNA expression profiles correlate with the biological behavior of primary canine MCTs and that miR-9 expression is increased in biologically high grade canine MCTs and malignant cell lines compared to biologically low grade tumors and normal canine BMMCs. In transformed mouse malignant mast cell lines expressing either wild-type (C57) or activating (P815) KIT mutations and mouse BMMCs, miR-9 overexpression significantly enhanced invasion but had no effect on cell proliferation or apoptosis. Transcriptional profiling of normal mouse BMMCs and P815 cells possessing enforced miR-9 expression demonstrated dysregulation of several genes, including upregulation of CMA1, a protease involved in activation of matrix metalloproteases and extracellular matrix

  2. Unique genome-wide transcriptome profiles of chicken macrophages exposed to Salmonella-derived endotoxin

    PubMed Central

    2010-01-01

    Background Macrophages play essential roles in both innate and adaptive immune responses. Bacteria require endotoxin, a complex lipopolysaccharide, for outer membrane permeability and the host interprets endotoxin as a signal to initiate an innate immune response. The focus of this study is kinetic and global transcriptional analysis of the chicken macrophage response to in vitro stimulation with endotoxin from Salmonella typhimurium-798. Results The 38535-probeset Affymetrix GeneChip Chicken Genome array was used to profile transcriptional response to endotoxin 1, 2, 4, and 8 hours post stimulation (hps). Using a maximum FDR (False Discovery Rate) of 0.05 to declare genes as differentially expressed (DE), we found 13, 33, 1761 and 61 DE genes between endotoxin-stimulated versus non-stimulated cells at 1, 2, 4 and 8 hps, respectively. QPCR demonstrated that endotoxin exposure significantly affected the mRNA expression of IL1B, IL6, IL8, and TLR15, but not IL10 and IFNG in HD 11 cells. Ingenuity Pathway Analysis showed that 10% of the total DE genes were involved in inflammatory response. Three, 9.7, 96.8, and 11.8% of the total DE inflammatory response genes were significantly differentially expressed with endotoxin stimulation at 1, 2, 4 and 8 hps, respectively. The NFKBIA, IL1B, IL8 and CCL4 genes were consistently induced at all times after endotoxin treatment. NLRC5 (CARD domain containing, NOD-like receptor family, RCJMB04_18i2), an intracellular receptor, was induced in HD11 cells treated with endotoxin. Conclusions As above using an in vitro model of chicken response to endotoxin, our data revealed the kinetics of gene networks involved in host response to endotoxin and extend the known complexity of networks in chicken immune response to Gram-negative bacteria such as Salmonella. The induction of NFKBIA, IL1B, IL8, CCL4 genes is a consistent signature of host response to endotoxin over time. We make the first report of induction of a NOD-like receptor

  3. Prenatal stress-induced programming of genome-wide promoter DNA methylation in 5-HTT-deficient mice

    PubMed Central

    Schraut, K G; Jakob, S B; Weidner, M T; Schmitt, A G; Scholz, C J; Strekalova, T; El Hajj, N; Eijssen, L M T; Domschke, K; Reif, A; Haaf, T; Ortega, G; Steinbusch, H W M; Lesch, K P; Van den Hove, D L

    2014-01-01

    The serotonin transporter gene (5-HTT/SLC6A4)-linked polymorphic region has been suggested to have a modulatory role in mediating effects of early-life stress exposure on psychopathology rendering carriers of the low-expression short (s)-variant more vulnerable to environmental adversity in later life. The underlying molecular mechanisms of this gene-by-environment interaction are not well understood, but epigenetic regulation including differential DNA methylation has been postulated to have a critical role. Recently, we used a maternal restraint stress paradigm of prenatal stress (PS) in 5-HTT-deficient mice and showed that the effects on behavior and gene expression were particularly marked in the hippocampus of female 5-Htt+/− offspring. Here, we examined to which extent these effects are mediated by differential methylation of DNA. For this purpose, we performed a genome-wide hippocampal DNA methylation screening using methylated-DNA immunoprecipitation (MeDIP) on Affymetrix GeneChip Mouse Promoter 1.0 R arrays. Using hippocampal DNA from the same mice as assessed before enabled us to correlate gene-specific DNA methylation, mRNA expression and behavior. We found that 5-Htt genotype, PS and their interaction differentially affected the DNA methylation signature of numerous genes, a subset of which showed overlap with the expression profiles of the corresponding transcripts. For example, a differentially methylated region in the gene encoding myelin basic protein (Mbp) was associated with its expression in a 5-Htt-, PS- and 5-Htt × PS-dependent manner. Subsequent fine-mapping of this Mbp locus linked the methylation status of two specific CpG sites to Mbp expression and anxiety-related behavior. In conclusion, hippocampal DNA methylation patterns and expression profiles of female prenatally stressed 5-Htt+/− mice suggest that distinct molecular mechanisms, some of which are promoter methylation-dependent, contribute to the behavioral effects of the 5-Htt

  4. Habituation to thaxtomin A in hybrid poplar cell suspensions provides enhanced and durable resistance to inhibitors of cellulose synthesis

    PubMed Central

    2010-01-01

    Background Thaxtomin A (TA), a phytotoxin produced by the phytopathogen Streptomyces scabies, is essential for the development of potato common scab disease. TA inhibits cellulose synthesis but its actual mode of action is unknown. Addition of TA to hybrid poplar (Populus trichocarpa x Populus deltoides) cell suspensions can activate a cellular program leading to cell death. In contrast, it is possible to habituate hybrid poplar cell cultures to grow in the presence of TA levels that would normally induce cell death. The purpose of this study is to characterize TA-habituated cells and the mechanisms that may be involved in enhancing resistance to TA. Results Habituation to TA was performed by adding increasing levels of TA to cell cultures at the time of subculture over a period of 12 months. TA-habituated cells were then cultured in the absence of TA for more than three years. These cells displayed a reduced size and growth compared to control cells and had fragmented vacuoles filled with electron-dense material. Habituation to TA was associated with changes in the cell wall composition, with a reduction in cellulose and an increase in pectin levels. Remarkably, high level of resistance to TA was maintained in TA-habituated cells even after being cultured in the absence of TA. Moreover, these cells exhibited enhanced resistance to two other inhibitors of cellulose biosynthesis, dichlobenil and isoxaben. Analysis of gene expression in TA-habituated cells using an Affymetrix GeneChip Poplar Genome Array revealed that durable resistance to TA is associated with a major and complex reprogramming of gene expression implicating processes such as cell wall synthesis and modification, lignin and flavonoid synthesis, as well as DNA and chromatin modifications. Conclusions We have shown that habituation to TA induced durable resistance to the bacterial toxin in poplar cells. TA-habituation also enhanced resistance to two other structurally different inhibitors of cellulose

  5. Cystatin A, a Potential Common Link for Mutant Myocilin Causative Glaucoma

    PubMed Central

    Kennedy, K. David; AnithaChristy, S. A.; Buie, LaKisha K.; Borrás, Teresa

    2012-01-01

    Myocilin (MYOC) is a 504 aa secreted glycoprotein induced by stress factors in the trabecular meshwork tissue of the eye, where it was discovered. Mutations in MYOC are linked to glaucoma. The glaucoma phenotype of each of the different MYOC mutation varies, but all of them cause elevated intraocular pressure (IOP). In cells, forty percent of wild-type MYOC is cleaved by calpain II, a cysteine protease. This proteolytic process is inhibited by MYOC mutants. In this study, we investigated the molecular mechanisms by which MYOC mutants cause glaucoma. We constructed adenoviral vectors with variants Q368X, R342K, D380N, K423E, and overexpressed them in human trabecular meshwork cells. We analyzed expression profiles with Affymetrix U133Plus2 GeneChips using wild-type and null viruses as controls. Analysis of trabecular meshwork relevant mechanisms showed that the unfolded protein response (UPR) was the most affected. Search for individual candidate genes revealed that genes that have been historically connected to trabecular meshwork physiology and pathology were altered by the MYOC mutants. Some of those had known MYOC associations (MMP1, PDIA4, CALR, SFPR1) while others did not (EDN1, MGP, IGF1, TAC1). Some, were top-changed in only one mutant (LOXL1, CYP1B1, FBN1), others followed a mutant group pattern. Some of the genes were new (RAB39B, STC1, CXCL12, CSTA). In particular, one selected gene, the cysteine protease inhibitor cystatin A (CSTA), was commonly induced by all mutants and not by the wild-type. Subsequent functional analysis of the selected gene showed that CSTA was able to reduce wild-type MYOC cleavage in primary trabecular meshwork cells while an inactive mutated CSTA was not. These findings provide a new molecular understanding of the mechanisms of MYOC-causative glaucoma and reveal CSTA, a serum biomarker for cancer, as a potential biomarker and drug for the treatment of MYOC-induced glaucoma. PMID:22615763

  6. Gene Expression Profile and Toxic Effects in Human Bronchial Epithelial Cells Exposed to Zearalenone

    PubMed Central

    So, Mei Yu; Tian, ZhiPeng; Phoon, Yong Shian; Sha, Sha; Antoniou, Michael N.; Zhang, JiangWen; Wu, Rudolf S. S.; Tan-Un, Kian C

    2014-01-01

    Zearalenone (ZEA), a mycoestrogen produced by Fusarium fungal species, is mainly found in cereal crops such as maize, wheat and barley. Although ZEA has been reported to be present in air, little is known about the health risk or the molecular basis of action when lung cells are exposed to ZEA. As ZEA has a similar structure to estrogen, its potential risk as an endocrine disrupting chemical (EDC) has thus aroused both environmental and public health concerns. The purpose of this study is to identify the responses and underlying molecular changes that occur when human bronchial epithelial BEAS-2B cells are exposed to ZEA. Differential gene expression profiles were identified in cells that were treated with 40 µM ZEA for 6 h and 24 h by high-throughput microarray analysis using Affymetrix Human Gene 2.0 GeneChip. The array results showed that after ZEA treatment, 262 genes at 6 h and 1073 genes at 24 h were invovled in the differential regulation. Pathway analysis revealed that diverse cellular processes were affected when lung cells were exposed to ZEA resulting in impaired response to DNA damage, cell cycle arrest, down-regulation of inflammatory responses and alterations of epigenetic marks. Results of further experiments indicated that 40 µM ZEA decreased cell viability, induced apoptosis and promoted reactive oxygen species (ROS) generation in a time-dependent manner. Immuno-suppressive effects of ZEA were further revealed through the suppression of lipopolysaccharide (LPS)-induced expression of pro-inflammatory cytokines (IL-6, IL-8 and IL-1β). Interestingly, the level of global DNA methylation was markedly decreased after 24 h exposure to ZEA. Collectively, these observations suggested that a broad range of toxic effects are elicited by ZEA. Particularly, ROS may play a pivotal role in ZEA-induced cell death. These adverse effects observed in lung cells suggest that exposure to ZEA may increase susceptibility of lung cells to diseases and required further

  7. Estrogen Receptor Alpha (ESR1)-Dependent Regulation of the Mouse Oviductal Transcriptome

    PubMed Central

    Cerny, Katheryn L.; Ribeiro, Rosanne A. C.; Jeoung, Myoungkun; Ko, CheMyong; Bridges, Phillip J.

    2016-01-01

    Estrogen receptor-α (ESR1) is an important transcriptional regulator in the mammalian oviduct, however ESR1-dependent regulation of the transcriptome of this organ is not well defined, especially at the genomic level. The objective of this study was therefore to investigate estradiol- and ESR1-dependent regulation of the transcriptome of the oviduct using transgenic mice, both with (ESR1KO) and without (wild-type, WT) a global deletion of ESR1. Oviducts were collected from ESR1KO and WT littermates at 23 days of age, or ESR1KO and WT mice were treated with 5 IU PMSG to stimulate follicular development and the production of ovarian estradiol, and the oviducts collected 48 h later. RNA extracted from whole oviducts was hybridized to Affymetrix Genechip Mouse Genome 430–2.0 arrays (n = 3 arrays per genotype and treatment) or reverse transcribed to cDNA for analysis of the expression of selected mRNAs by real-time PCR. Following microarray analysis, a statistical two-way ANOVA and pairwise comparison (LSD test) revealed 2428 differentially expressed transcripts (DEG’s, P < 0.01). Genotype affected the expression of 2215 genes, treatment (PMSG) affected the expression of 465 genes, and genotype x treatment affected the expression of 438 genes. With the goal of determining estradiol/ESR1-regulated function, gene ontology (GO) and bioinformatic pathway analyses were performed on DEG’s in the oviducts of PMSG-treated ESR1KO versus PMSG-treated WT mice. Significantly enriched GO molecular function categories included binding and catalytic activity. Significantly enriched GO cellular component categories indicated the extracellular region. Significantly enriched GO biological process categories involved a single organism, modulation of a measurable attribute and developmental processes. Bioinformatic analysis revealed ESR1-regulation of the immune response within the oviduct as the primary canonical pathway. In summary, a transcriptomal profile of estradiol- and ESR1

  8. The effect of enterotoxigenic Escherichia coli F4ab,ac on early-weaned piglets: a gene expression study.

    PubMed

    Schroyen, M; Goddeeris, B M; Stinckens, A; Verhelst, R; Janssens, S; Cox, E; Georges, M; Niewold, T; Buys, N

    2013-03-15

    Diarrhoea in neonatal and early-weaned piglets due to enterotoxigenic Escherichia coli-F4 (ETEC-F4) is an important problem in the pig farming industry. There is substantial evidence for a genetic basis for susceptibility to ETEC-F4 since not all pigs suffer from diarrhoea after an ETEC-F4 infection. A region on SSC13 has been found to be in close linkage to the susceptibility of piglets for ETEC-F4ab,ac. Potential candidate genes on SSC13 have been examined and although some polymorphisms were found to be in linkage disequilibrium with the phenotype, the causative mutation has not yet been found. In this study we are looking at the expression of porcine genes in relation to ETEC-F4ab,ac. With the aid of the Affymetrix GeneChip Porcine Genome Array we were able to find differentially expressed genes between ETEC-F4ab,ac receptor positive (Fab,acR(+)) piglets without diarrhoea and F4ab,acR(+) piglets with diarrhoea or F4ab,acR(-) animals. Since the susceptibility to ETEC-F4ab,ac was described as a Mendelian trait, it is not so surprisingly that only two differentially expressed genes, transferrin receptor (TFRC) and trefoil factor 1 (TFF1), came out of the analysis. Although both genes could pass for functional candidate genes only TFRC also mapped to the region on SSC13 associated with susceptibility for ETEC-F4, which makes TFRC a positional functional candidate gene. Validation by qRT-PCR confirmed the differential expression of TFRC and TFF1. In piglets without diarrhoea, the expression of both genes was higher in F4ab,acR(+) than in F4ab,acR(-) piglets. Similarly, TFRC and TFF1 expression in F4ab,acR(+) piglets without diarrhoea was also higher than in F4ab,acR(+) piglets with diarrhoea. Consequently, although both genes might not play a role as receptor for F4 fimbriae, they could be of great importance during an ETEC-F4 outbreak. An upregulation of TFRC can be a consequence of the piglets ability to raise an effective immune response. An elevation of TFF1, a

  9. Comparison of TCDD-elicited genome-wide hepatic gene expression in Sprague–Dawley rats and C57BL/6 mice

    SciTech Connect

    Nault, Rance; Kim, Suntae; Zacharewski, Timothy R.

    2013-03-01

    Although the structure and function of the AhR are conserved, emerging evidence suggests that downstream effects are species-specific. In this study, rat hepatic gene expression data from the DrugMatrix database (National Toxicology Program) were compared to mouse hepatic whole-genome gene expression data following treatment with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). For the DrugMatrix study, male Sprague–Dawley rats were gavaged daily with 20 μg/kg TCDD for 1, 3 and 5 days, while female C57BL/6 ovariectomized mice were examined 1, 3 and 7 days after a single oral gavage of 30 μg/kg TCDD. A total of 649 rat and 1386 mouse genes (|fold change| ≥ 1.5, P1(t) ≥ 0.99) were differentially expressed following treatment. HomoloGene identified 11,708 orthologs represented across the rat Affymetrix 230 2.0 GeneChip (12,310 total orthologs), and the mouse 4 × 44K v.1 Agilent oligonucleotide array (17,578 total orthologs). Comparative analysis found 563 and 922 orthologs differentially expressed in response to TCDD in the rat and mouse, respectively, with 70 responses associated with immune function and lipid metabolism in common to both. Moreover, QRTPCR analysis of Ceacam1, showed divergent expression (induced in rat; repressed in mouse) functionally consistent with TCDD-elicited hepatic steatosis in the mouse but not the rat. Functional analysis identified orthologs involved in nucleotide binding and acetyltransferase activity in rat, while mouse-specific responses were associated with steroid, phospholipid, fatty acid, and carbohydrate metabolism. These results provide further evidence that TCDD elicits species-specific regulation of distinct gene networks, and outlines considerations for future comparisons of publicly available microarray datasets. - Highlights: ► We performed a whole-genome comparison of TCDD-regulated genes in mice and rats. ► Previous species comparisons were extended using data from the DrugMatrix database. ► Less than 15% of TCDD

  10. Expression profiling and Ingenuity biological function analyses of interleukin-6- versus nerve growth factor-stimulated PC12 cells

    PubMed Central

    Kunz, Dieter; Walker, Gaby; Bedoucha, Marc; Certa, Ulrich; März-Weiss, Pia; Dimitriades-Schmutz, Beatrice; Otten, Uwe

    2009-01-01

    Background The major goal of the study was to compare the genetic programs utilized by the neuropoietic cytokine Interleukin-6 (IL-6) and the neurotrophin (NT) Nerve Growth Factor (NGF) for neuronal differentiation. Results The designer cytokine Hyper-IL-6 in which IL-6 is covalently linked to its soluble receptor s-IL-6R as well as NGF were used to stimulate PC12 cells for 24 hours. Changes in gene expression levels were monitored using Affymetrix GeneChip technology. We found different expression for 130 genes in IL-6- and 102 genes in NGF-treated PC12 cells as compared to unstimulated controls. The gene set shared by both stimuli comprises only 16 genes. A key step is upregulation of growth factors and functionally related external molecules known to play important roles in neuronal differentiation. In particular, IL-6 enhances gene expression of regenerating islet-derived 3 alpha (REG3A; 1084-fold), regenerating islet-derived 3 beta (REG3B/PAPI; 672-fold), growth differentiation factor 15 (GDF15; 80-fold), platelet-derived growth factor alpha (PDGFA; 69-fold), growth hormone releasing hormone (GHRH; 30-fold), adenylate cyclase activating polypeptide (PACAP; 20-fold) and hepatocyte growth factor (HGF; 5-fold). NGF recruits GDF15 (131-fold), transforming growth factor beta 1 (TGFB1; 101-fold) and brain-derived neurotrophic factor (BDNF; 89-fold). Both stimuli activate growth-associated protein 43 (GAP-43) indicating that PC12 cells undergo substantial neuronal differentiation. Moreover, IL-6 activates the transcription factors retinoic acid receptor alpha (RARA; 20-fold) and early growth response 1 (Egr1/Zif268; 3-fold) known to play key roles in neuronal differentiation. Ingenuity biological function analysis revealed that completely different repertoires of molecules are recruited to exert the same biological functions in neuronal differentiation. Major sub-categories include cellular growth and differentiation, cell migration, chemotaxis, cell adhesion, small

  11. Gene expression profiling of Gram-negative bacteria-induced inflammation in human whole blood: The role of complement and CD14-mediated innate immune response.

    PubMed

    Lau, Corinna; Olstad, Ole Kristoffer; Holden, Marit; Nygård, Ståle; Fure, Hilde; Lappegård, Knut Tore; Brekke, Ole-Lars; Espevik, Terje; Hovig, Eivind; Mollnes, Tom Eirik

    2015-09-01

    Non-sterile pathogen-induced sepsis and sterile inflammation like in trauma or ischemia-reperfusion injury may both coincide with the life threatening systemic inflammatory response syndrome and multi-organ failure. Consequently, there is an urgent need for specific biomarkers in order to distinguish sepsis from sterile conditions. The overall aim of this study was to uncover putative sepsis biomarkers and biomarker pathways, as well as to test the efficacy of combined inhibition of innate immunity key players complement and Toll-like receptor co-receptor CD14 as a possible therapeutic regimen for sepsis. We performed whole blood gene expression analyses using microarray in order to profile Gram-negative bacteria-induced inflammatory responses in an ex vivo human whole blood model. The experiments were performed in the presence or absence of inhibitors of complement proteins (C3 and CD88 (C5a receptor 1)) and CD14, alone or in combination. In addition, we used blood from a C5-deficient donor. Anti-coagulated whole blood was challenged with heat-inactivated Escherichia coli for 2 h, total RNA was isolated and microarray analyses were performed on the Affymetrix GeneChip Gene 1.0 ST Array platform. The initial experiments were performed in duplicates using blood from two healthy donors. C5-deficiency is very rare, and only one donor could be recruited. In order to increase statistical power, a technical replicate of the C5-deficient samples was run. Subsequently, log2-transformed intensities were processed by robust multichip analysis and filtered using a threshold of four. In total, 73 microarray chips were run and analyzed. The normalized and filtered raw data have been deposited in NCBI's Gene Expression Omnibus (GEO) and are accessible with GEO Series accession number GSE55537. Linear models for microarray data were applied to estimate fold changes between data sets and the respective multiple testing adjusted p-values (FDR q-values). The interpretation of the

  12. Estrogen Receptor Alpha (ESR1)-Dependent Regulation of the Mouse Oviductal Transcriptome.

    PubMed

    Cerny, Katheryn L; Ribeiro, Rosanne A C; Jeoung, Myoungkun; Ko, CheMyong; Bridges, Phillip J

    2016-01-01

    Estrogen receptor-α (ESR1) is an important transcriptional regulator in the mammalian oviduct, however ESR1-dependent regulation of the transcriptome of this organ is not well defined, especially at the genomic level. The objective of this study was therefore to investigate estradiol- and ESR1-dependent regulation of the transcriptome of the oviduct using transgenic mice, both with (ESR1KO) and without (wild-type, WT) a global deletion of ESR1. Oviducts were collected from ESR1KO and WT littermates at 23 days of age, or ESR1KO and WT mice were treated with 5 IU PMSG to stimulate follicular development and the production of ovarian estradiol, and the oviducts collected 48 h later. RNA extracted from whole oviducts was hybridized to Affymetrix Genechip Mouse Genome 430-2.0 arrays (n = 3 arrays per genotype and treatment) or reverse transcribed to cDNA for analysis of the expression of selected mRNAs by real-time PCR. Following microarray analysis, a statistical two-way ANOVA and pairwise comparison (LSD test) revealed 2428 differentially expressed transcripts (DEG's, P < 0.01). Genotype affected the expression of 2215 genes, treatment (PMSG) affected the expression of 465 genes, and genotype x treatment affected the expression of 438 genes. With the goal of determining estradiol/ESR1-regulated function, gene ontology (GO) and bioinformatic pathway analyses were performed on DEG's in the oviducts of PMSG-treated ESR1KO versus PMSG-treated WT mice. Significantly enriched GO molecular function categories included binding and catalytic activity. Significantly enriched GO cellular component categories indicated the extracellular region. Significantly enriched GO biological process categories involved a single organism, modulation of a measurable attribute and developmental processes. Bioinformatic analysis revealed ESR1-regulation of the immune response within the oviduct as the primary canonical pathway. In summary, a transcriptomal profile of estradiol- and ESR1

  13. Sequence mining and transcript profiling to explore cyst nematode parasitism

    PubMed Central

    Elling, Axel A; Mitreva, Makedonka; Gai, Xiaowu; Martin, John; Recknor, Justin; Davis, Eric L; Hussey, Richard S; Nettleton, Dan; McCarter, James P; Baum, Thomas J

    2009-01-01

    Background Cyst nematodes are devastating plant parasites that become sedentary within plant roots and induce the transformation of normal plant cells into elaborate feeding cells with the help of secreted effectors, the parasitism proteins. These proteins are the translation products of parasitism genes and are secreted molecular tools that allow cyst nematodes to infect plants. Results We present here the expression patterns of all previously described parasitism genes of the soybean cyst nematode, Heterodera glycines, in all major life stages except the adult male. These insights were gained by analyzing our gene expression dataset from experiments using the Affymetrix Soybean Genome Array GeneChip, which contains probeset sequences for 6,860 genes derived from preparasitic and parasitic H. glycines life stages. Targeting the identification of additional H. glycines parasitism-associated genes, we isolated 633 genes encoding secretory proteins using algorithms to predict secretory signal peptides. Furthermore, because some of the known H. glycines parasitism proteins have strongest similarity to proteins of plants and microbes, we searched for predicted protein sequences that showed their highest similarities to plant or microbial proteins and identified 156 H. glycines genes, some of which also contained a signal peptide. Analyses of the expression profiles of these genes allowed the formulation of hypotheses about potential roles in parasitism. This is the first study combining sequence analyses of a substantial EST dataset with microarray expression data of all major life stages (except adult males) for the identification and characterization of putative parasitism-associated proteins in any parasitic nematode. Conclusion We have established an expression atlas for all known H. glycines parasitism genes. Furthermore, in an effort to identify additional H. glycines genes with putative functions in parasitism, we have reduced the currently known 6,860 H

  14. NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases

    PubMed Central

    Bagewadi, Shweta; Adhikari, Subash; Dhrangadhariya, Anjani; Irin, Afroza Khanam; Ebeling, Christian; Namasivayam, Aishwarya Alex; Page, Matthew; Hofmann-Apitius, Martin

    2015-01-01

    Neurodegenerative diseases are chronic debilitating conditions, characterized by progressive loss of neurons that represent a significant health care burden as the global elderly population continues to grow. Over the past decade, high-throughput technologies such as the Affymetrix GeneChip microarrays have provided new perspectives into the pathomechanisms underlying neurodegeneration. Public transcriptomic data repositories, namely Gene Expression Omnibus and curated ArrayExpress, enable researchers to conduct integrative meta-analysis; increasing the power to detect differentially regulated genes in disease and explore patterns of gene dysregulation across biologically related studies. The reliability of retrospective, large-scale integrative analyses depends on an appropriate combination of related datasets, in turn requiring detailed meta-annotations capturing the experimental setup. In most cases, we observe huge variation in compliance to defined standards for submitted metadata in public databases. Much of the information to complete, or refine meta-annotations are distributed in the associated publications. For example, tissue preparation or comorbidity information is frequently described in an article’s supplementary tables. Several value-added databases have employed additional manual efforts to overcome this limitation. However, none of these databases explicate annotations that distinguish human and animal models in neurodegeneration context. Therefore, adopting a more specific disease focus, in combination with dedicated disease ontologies, will better empower the selection of comparable studies with refined annotations to address the research question at hand. In this article, we describe the detailed development of NeuroTransDB, a manually curated database containing metadata annotations for neurodegenerative studies. The database contains more than 20 dimensions of metadata annotations within 31 mouse, 5 rat and 45 human studies, defined in

  15. Transcriptional responses in thyroid tissues from rats treated with a tumorigenic and a non-tumorigenic triazole conazole fungicide

    SciTech Connect

    Hester, Susan D. Nesnow, Stephen

    2008-03-15

    Conazoles are azole-containing fungicides that are used in agriculture and medicine. Conazoles can induce follicular cell adenomas of the thyroid in rats after chronic bioassay. The goal of this study was to identify pathways and networks of genes that were associated with thyroid tumorigenesis through transcriptional analyses. To this end, we compared transcriptional profiles from tissues of rats treated with a tumorigenic and a non-tumorigenic conazole. Triadimefon, a rat thyroid tumorigen, and myclobutanil, which was not tumorigenic in rats after a 2-year bioassay, were administered in the feed to male Wistar/Han rats for 30 or 90 days similar to the treatment conditions previously used in their chronic bioassays. Thyroid gene expression was determined using high density Affymetrix GeneChips (Rat 230{sub 2}). Gene expression was analyzed by the Gene Set Expression Analyses method which clearly separated the tumorigenic treatments (tumorigenic response group (TRG)) from the non-tumorigenic treatments (non-tumorigenic response group (NRG)). Core genes from these gene sets were mapped to canonical, metabolic, and GeneGo processes and these processes compared across group and treatment time. Extensive analyses were performed on the 30-day gene sets as they represented the major perturbations. Gene sets in the 30-day TRG group had over representation of fatty acid metabolism, oxidation, and degradation processes (including PPAR{gamma} and CYP involvement), and of cell proliferation responses. Core genes from these gene sets were combined into networks and found to possess signaling interactions. In addition, the core genes in each gene set were compared with genes known to be associated with human thyroid cancer. Among the genes that appeared in both rat and human data sets were: Acaca, Asns, Cebpg, Crem, Ddit3, Gja1, Grn, Jun, Junb, and Vegf. These genes were major contributors in the previously developed network from triadimefon-treated rat thyroids. It is

  16. Comprehensive Genome-Wide Transcriptomic Analysis of Immature Articular Cartilage following Ischemic Osteonecrosis of the Femoral Head in Piglets

    PubMed Central

    Adapala, Naga Suresh; Kim, Harry K. W.

    2016-01-01

    Objective Ischemic osteonecrosis of the femoral head (ONFH) in piglets results in an ischemic injury to the immature articular cartilage. The molecular changes in the articular cartilage in response to ONFH have not been investigated using a transcriptomic approach. The purpose of this study was to perform a genome-wide transcriptomic analysis to identify genes that are upregulated in the immature articular cartilage following ONFH. Methods ONFH was induced in the right femoral head of 6-week old piglets. The unoperated femoral head was used as the normal control. At 24 hours (acute ischemic-hypoxic injury), 2 weeks (avascular necrosis in the femoral head) and 4 weeks (early repair) after surgery (n = 4 piglets/time point), RNA was isolated from the articular cartilage of the femoral head. A microarray analysis was performed using Affymetrix Porcine GeneChip Array. An enrichment analysis and functional clustering of the genes upregulated due to ONFH were performed using DAVID and STRING software, respectively. The increased expression of selected genes was confirmed by a real-time qRTPCR analysis. Results Induction of ONFH resulted in the upregulation of 383 genes at 24 hours, 122 genes at 2 weeks and 124 genes at 4 weeks compared to the normal controls. At 24 hours, the genes involved in oxidoreductive, cell-survival, and angiogenic responses were significantly enriched among the upregulated genes. These genes were involved in HIF-1, PI3K-Akt, and MAPK signaling pathways. At 2 weeks, secretory and signaling proteins involved in angiogenic and inflammatory responses, PI3K-Akt and matrix-remodeling pathways were significantly enriched. At 4 weeks, genes that represent inflammatory cytokines and chemokine signaling pathways were significantly enriched. Several index genes (genes that are upregulated at more than one time point following ONFH and are known to be important in various biological processes) including HIF-1A, VEGFA, IL-6, IL6R, IL-8, CCL2, FGF2, TGFB2

  17. Differential gene expression and a functional analysis of PCB-exposed children: understanding disease and disorder development.

    PubMed

    Dutta, Sisir K; Mitra, Partha S; Ghosh, Somiranjan; Zang, Shizhu; Sonneborn, Dean; Hertz-Picciotto, Irva; Trnovec, Tomas; Palkovicova, Lubica; Sovcikova, Eva; Ghimbovschi, Svetlana; Hoffman, Eric P

    2012-04-01

    The goal of the present study is to understand the probable molecular mechanism of toxicities and the associated pathways related to observed pathophysiology in high PCB-exposed populations. We have performed a microarray-based differential gene expression analysis of children (mean age 46.1 months) of Central European descent from Slovak Republic in a well-defined study cohort. The subset of children having high blood PCB concentrations (>75 percentile) were compared against their low PCB counterparts (<25 percentile), with mean lipid-adjusted PCB values of 3.02±1.3 and 0.06±0.03 ng/mg of serum lipid, for the two groups, respectively (18.1±4.4 and 0.3±0.1 ng/ml of serum). The microarray was conducted with the total RNA from the peripheral blood mononuclear cells of the children using an Affymetrix platform (GeneChip Human genome U133 Plus 2.0 Array) and was analyzed by Gene Spring (GX 10.0). A highly significant set of 162 differentially expressed genes between high and low PCB groups (p value <0.00001) were identified and subsequently analyzed using the Ingenuity Pathway Analysis tool. The results indicate that Cell-To-Cell Signaling and Interaction, Cellular Movement, Cell Signaling, Molecular Transport, and Vitamin and Mineral Metabolism were the major molecular and cellular functions associated with the differentially altered gene set in high PCB-exposed children. The differential gene expressions appeared to play a pivotal role in the development of probable diseases and disorders, including cardiovascular disease and cancer, in the PCB-exposed population. The analyses also pointed out possible organ-specific effects, e.g., cardiotoxicity, hepatotoxicity and nephrotoxicity, in high PCB-exposed subjects. A few notable genes, such as BCL2, PON1, and ITGB1, were significantly altered in our study, and the related pathway analysis explained their plausible involvement in the respective disease processes, as mentioned. Our results provided insight into

  18. Early inflammatory response to the saponin adjuvant Matrix-M in the pig.

    PubMed

    Fossum, Caroline; Hjertner, Bernt; Ahlberg, Viktor; Charerntantanakul, Wasin; McIntosh, Kathy; Fuxler, Lisbeth; Balagunaseelan, Navisraj; Wallgren, Per; Lövgren Bengtsson, Karin

    2014-03-15

    The early inflammatory response to Matrix-M was evaluated in pigs. Adverse reactions measured as body temperature, appetite, activity level and reaction at the site of injection were not observed after s.c. injection with three doses of the adjuvant (75, 100 or 150μg) into one week old piglets. Analyses of the immediate cytokine response of PBMC after in vitro exposure to Matrix-M (AbISCO-100(®)) revealed only a low expression of mRNA for tumour necrosis factor-α (p<0.05) after 6h incubation. Histological examination revealed an infiltration of leukocytes, haemorrhage and necrosis in muscle 24h after i.m. injection of 150μg Matrix-M in pigs aged eleven weeks. At this time, different grades of reactive lymphoid hyperplasia were recorded in the draining lymph node that was enlarged in three of these six pigs injected with Matrix-M. The global transcriptional response at the site of injection and in the draining lymph node was analyzed using Affymetrix GeneChip Porcine Genome Array. A significant enrichment of gene signatures for the cell types described as "myeloid cells" and "plasmacytoid dendritic cells" was observed at the site of injection in Matrix-M injected pigs compared with pigs injected with saline. A number of genes encoding cytokines/chemokines or their receptors were upregulated at the injection site as well as in the draining lymph node. In the draining lymph node, a majority of the upregulated genes were interferon-regulated genes (IRGs). The expression of IFN-β, but not IFN-α, was increased in the draining lymph nodes of a majority of the pigs exposed to Matrix-M. These IFN-β expressing pigs also expressed increased levels of osteopontin (OPN) or stimulator of interferon genes (STING), two factors known to facilitate the expression of type I IFNs in response to viral infection. Thus, Matrix-M does not appear to induce any harmful inflammatory response in piglets whilst contributing to the innate immunity by activating the type I IFN system

  19. Peripheral inflammation is associated with remote global gene expression changes in the brain

    PubMed Central

    2014-01-01

    Background Although the central nervous system (CNS) was once considered an immunologically privileged site, in recent years it has become increasingly evident that cross talk between the immune system and the CNS does occur. As a result, patients with chronic inflammatory diseases, such as rheumatoid arthritis, inflammatory bowel disease or psoriasis, are often further burdened with neuropsychiatric symptoms, such as depression, anxiety and fatigue. Despite the recent advances in our understanding of neuroimmune communication pathways, the precise effect of peripheral immune activation on neural circuitry remains unclear. Utilizing transcriptomics in a well-characterized murine model of systemic inflammation, we have started to investigate the molecular mechanisms by which inflammation originating in the periphery can induce transcriptional modulation in the brain. Methods Several different systemic and tissue-specific models of peripheral toll-like-receptor-(TLR)-driven (lipopolysaccharide (LPS), lipoteichoic acid and Imiquimod) and sterile (tumour necrosis factor (TNF) and 12-O-tetradecanoylphorbol-13-acetate (TPA)) inflammation were induced in C57BL/6 mice. Whole brain transcriptional profiles were assessed and compared 48 hours after intraperitoneal injection of lipopolysaccharide or vehicle, using Affymetrix GeneChip microarrays. Target gene induction, identified by microarray analysis, was validated independently using qPCR. Expression of the same panel of target genes was then investigated in a number of sterile and other TLR-dependent models of peripheral inflammation. Results Microarray analysis of whole brains collected 48 hr after LPS challenge revealed increased transcription of a range of interferon-stimulated genes (ISGs) in the brain. In addition to acute LPS challenge, ISGs were induced in the brain following both chronic LPS-induced systemic inflammation and Imiquimod-induced skin inflammation. Unique to the brain, this transcriptional response is

  20. Annotation of gene function in citrus using gene expression information and co-expression networks

    PubMed Central

    2014-01-01

    Background The genus Citrus encompasses major cultivated plants such as sweet orange, mandarin, lemon and grapefruit, among the world’s most economically important fruit crops. With increasing volumes of transcriptomics data available for these species, Gene Co-expression Network (GCN) analysis is a viable option for predicting gene function at a genome-wide scale. GCN analysis is based on a “guilt-by-association” principle whereby genes encoding proteins involved in similar and/or related biological processes may exhibit similar expression patterns across diverse sets of experimental conditions. While bioinformatics resources such as GCN analysis are widely available for efficient gene function prediction in model plant species including Arabidopsis, soybean and rice, in citrus these tools are not yet developed. Results We have constructed a comprehensive GCN for citrus inferred from 297 publicly available Affymetrix Genechip Citrus Genome microarray datasets, providing gene co-expression relationships at a genome-wide scale (33,000 transcripts). The comprehensive citrus GCN consists of a global GCN (condition-independent) and four condition-dependent GCNs that survey the sweet orange species only, all citrus fruit tissues, all citrus leaf tissues, or stress-exposed plants. All of these GCNs are clustered using genome-wide, gene-centric (guide) and graph clustering algorithms for flexibility of gene function prediction. For each putative cluster, gene ontology (GO) enrichment and gene expression specificity analyses were performed to enhance gene function, expression and regulation pattern prediction. The guide-gene approach was used to infer novel roles of genes involved in disease susceptibility and vitamin C metabolism, and graph-clustering approaches were used to investigate isoprenoid/phenylpropanoid metabolism in citrus peel, and citric acid catabolism via the GABA shunt in citrus fruit. Conclusions Integration of citrus gene co-expression networks

  1. Transcriptomic comparison of Aspergillus niger growing on two different sugars reveals coordinated regulation of the secretory pathway

    PubMed Central

    Jørgensen, Thomas R; Goosen, Theo; van den Hondel, Cees AMJJ; Ram, Arthur FJ; Iversen, Jens JL

    2009-01-01

    Background The filamentous fungus, Aspergillus niger, responds to nutrient availability by modulating secretion of various substrate degrading hydrolases. This ability has made it an important organism in industrial production of secreted glycoproteins. The recent publication of the A. niger genome sequence and availability of microarrays allow high resolution studies of transcriptional regulation of basal cellular processes, like those of glycoprotein synthesis and secretion. It is known that the activities of certain secretory pathway enzymes involved N-glycosylation are elevated in response to carbon source induced secretion of the glycoprotein glucoamylase. We have investigated whether carbon source dependent enhancement of protein secretion can lead to upregulation of secretory pathway elements extending beyond those involved in N-glycosylation. Results This study compares the physiology and transcriptome of A. niger growing at the same specific growth rate (0.16 h-1) on xylose or maltose in carbon-limited chemostat cultures. Transcription profiles were obtained using Affymetrix GeneChip analysis of six replicate cultures for each of the two growth-limiting carbon sources. The production rate of extracellular proteins per gram dry mycelium was about three times higher on maltose compared to xylose. The defined culture conditions resulted in high reproducibility, discriminating even low-fold differences in transcription, which is characteristic of genes encoding basal cellular functions. This included elements in the secretory pathway and central metabolic pathways. Increased protein secretion on maltose was accompanied by induced transcription of > 90 genes related to protein secretion. The upregulated genes encode key elements in protein translocation to the endoplasmic reticulum (ER), folding, N-glycosylation, quality control, and vesicle packaging and transport between ER and Golgi. The induction effect of maltose resembles the unfolded protein response

  2. Analysis of changes in hepatic gene expression in a murine model of tolerance to acetaminophen hepatotoxicity (autoprotection)

    SciTech Connect

    O'Connor, Meeghan A.; Koza-Taylor, Petra; Campion, Sarah N.; Aleksunes, Lauren M.; Gu, Xinsheng; Enayetallah, Ahmed E.; Lawton, Michael P.; Manautou, José E.

    2014-01-01

    Pretreatment of mice with a low hepatotoxic dose of acetaminophen (APAP) results in resistance to a subsequent, higher dose of APAP. This mouse model, termed APAP autoprotection was used here to identify differentially expressed genes and cellular pathways that could contribute to this development of resistance to hepatotoxicity. Male C57BL/6J mice were pretreated with APAP (400 mg/kg) and then challenged 48 h later with 600 mg APAP/kg. Livers were obtained 4 or 24 h later and total hepatic RNA was isolated and hybridized to Affymetrix Mouse Genome MU430{sub 2} GeneChip. Statistically significant genes were determined and gene expression changes were also interrogated using the Causal Reasoning Engine (CRE). Extensive literature review narrowed our focus to methionine adenosyl transferase-1 alpha (MAT1A), nuclear factor (erythroid-derived 2)-like 2 (Nrf2), flavin-containing monooxygenase 3 (Fmo3) and galectin-3 (Lgals3). Down-regulation of MAT1A could lead to decreases in S-adenosylmethionine (SAMe), which is known to protect against APAP toxicity. Nrf2 activation is expected to play a role in protective adaptation. Up-regulation of Lgals3, one of the genes supporting the Nrf2 hypothesis, can lead to suppression of apoptosis and reduced mitochondrial dysfunction. Fmo3 induction suggests the involvement of an enzyme not known to metabolize APAP in the development of tolerance to APAP toxicity. Subsequent quantitative RT-PCR and immunochemical analysis confirmed the differential expression of some of these genes in the APAP autoprotection model. In conclusion, our genomics strategy identified cellular pathways that might further explain the molecular basis for APAP autoprotection. - Highlights: • Differential expression of genes in mice resistant to acetaminophen hepatotoxicity. • Increased gene expression of Flavin-containing monooxygenase 3 and Galectin-3. • Decrease in MAT1A expression and compensatory hepatocellular regeneration. • Two distinct gene

  3. Identification and characterization of genes that control fat deposition in chickens

    PubMed Central

    2013-01-01

    Background Fat deposits in chickens contribute significantly to meat quality attributes such as juiciness, flavor, taste and other organoleptic properties. The quantity of fat deposited increases faster and earlier in the fast-growing chickens than in slow-growing chickens. In this study, Affymetrix Genechip® Chicken Genome Arrays 32773 transcripts were used to compare gene expression profiles in liver and hypothalamus tissues of fast-growing and slow-growing chicken at 8 wk of age. Real-time RT-PCR was used to validate the differential expression of genes selected from the microarray analysis. The mRNA expression of the genes was further examined in fat tissues. The association of single nucleotide polymorphisms of four lipid-related genes with fat traits was examined in a F2 resource population. Results Four hundred genes in the liver tissues and 220 genes hypothalamus tissues, respectively, were identified to be differentially expressed in fast-growing chickens and slow-growing chickens. Expression levels of genes for lipid metabolism (SULT1B1, ACSBG2, PNPLA3, LPL, AOAH) carbohydrate metabolism (MGAT4B, XYLB, GBE1, PGM1, HKDC1)cholesttrol biosynthesis (FDPS, LSS, HMGCR, NSDHL, DHCR24, IDI1, ME1) HSD17B7 and other reaction or processes (CYP1A4, CYP1A1, AKR1B1, CYP4V2, DDO) were higher in the fast-growing White Recessive Rock chickens than in the slow-growing Xinghua chickens. On the other hand, expression levels of genes associated with multicellular organism development, immune response, DNA integration, melanin biosynthetic process, muscle organ development and oxidation-reduction (FRZB, DMD, FUT8, CYP2C45, DHRSX, and CYP2C18) and with glycol-metabolism (GCNT2, ELOVL 6, and FASN), were higher in the XH chickens than in the fast-growing chickens. RT-PCR validated high expression levels of nine out of 12 genes in fat tissues. The G1257069A and T1247123C of the ACSBG2 gene were significantly associated with abdominal fat weight. The G4928024A of the FASN gene

  4. Molecular fingerprinting reflects different histotypes and brain region in low grade gliomas

    PubMed Central

    2013-01-01

    Background Paediatric low-grade gliomas (LGGs) encompass a heterogeneous set of tumours of different histologies, site of lesion, age and gender distribution, growth potential, morphological features, tendency to progression and clinical course. Among LGGs, Pilocytic astrocytomas (PAs) are the most common central nervous system (CNS) tumours in children. They are typically well-circumscribed, classified as grade I by the World Health Organization (WHO), but recurrence or progressive disease occurs in about 10-20% of cases. Despite radiological and neuropathological features deemed as classic are acknowledged, PA may present a bewildering variety of microscopic features. Indeed, tumours containing both neoplastic ganglion and astrocytic cells occur at a lower frequency. Methods Gene expression profiling on 40 primary LGGs including PAs and mixed glial-neuronal tumours comprising gangliogliomas (GG) and desmoplastic infantile gangliogliomas (DIG) using Affymetrix array platform was performed. A biologically validated machine learning workflow for the identification of microarray-based gene signatures was devised. The method is based on a sparsity inducing regularization algorithm l1l2 that selects relevant variables and takes into account their correlation. The most significant genetic signatures emerging from gene-chip analysis were confirmed and validated by qPCR. Results We identified an expression signature composed by a biologically validated list of 15 genes, able to distinguish infratentorial from supratentorial LGGs. In addition, a specific molecular fingerprinting distinguishes the supratentorial PAs from those originating in the posterior fossa. Lastly, within supratentorial tumours, we also identified a gene expression pattern composed by neurogenesis, cell motility and cell growth genes which dichotomize mixed glial-neuronal tumours versus PAs. Our results reinforce previous observations about aberrant activation of the mitogen-activated protein kinase

  5. Chronic Lunar Dust Exposure on Rat Cornea: Evaluation by Gene Expression Profiling

    NASA Technical Reports Server (NTRS)

    Theriot, C. A.; Glass, A.; Lam, C-W.; James, J.; Zanello, S. B.

    2014-01-01

    Lunar dust is capable of entering habitats and vehicle compartments by sticking to spacesuits or other objects that are transferred into the spacecraft from the lunar surface and has been reported to cause irritation upon exposure. During the Apollo missions, crewmembers reported irritation specifically to the skin and eyes after contamination of the lunar and service modules. It has since been hypothesized that ocular irritation and abrasion might occur as a result of such exposure, impairing crew vision. Recent work has shown that both ultrafine and unground lunar dust exhibited minimal irritancy of the ocular surface (i.e., cornea); however, the assessment of the severity of ocular damage resulting from contact of lunar dust particles to the cornea has focused only on macroscopic signs of mechanical irritancy and cytotoxicity. Given the chemical reactive properties of lunar dust, exposure of the cornea may contribute to detrimental effects at the molecular level including but not limited to oxidative damage. Additionally, low level chronic exposures may confound any results obtained in previous acute studies. We report here preliminary results from a tissue sharing effort using 10-week-old Fischer 344 male rats chronically exposed to filtered air or jet milled lunar dust collected during Apollo 14 using a Jaeger-NYU nose-only chamber for a total of 120 hours (6 hours daily, 5 days a week) over a 4-week period. RNA was isolated from corneas collected from rats at 1 day and 7 days after being exposed to concentrations of 0, 20, and 60 mg/m3 of lunar dust. Microarray analysis was performed using the Affymetrix GeneChip Rat Genome 230 2.0 Array with Affymetrix Expression Console and Transcriptome Analysis Console used for normalization and secondary analysis. An Ingenuity iReport"TM" was then generated for canonical pathway identification. The number of differentially expressed genes identified increases with dose compared to controls suggesting a more severe

  6. Genome-Wide Association Study Identifies GPC5 as a Novel Genetic Locus Protective against Sudden Cardiac Arrest

    PubMed Central

    Post, Wendy; Jui, Jonathan; Hilton, Gina; O'Connor, Ashley; Prineas, Ronald J.; Boerwinkle, Eric; Psaty, Bruce M.; Tomaselli, Gordon F.; Rea, Thomas; Sotoodehnia, Nona; Siscovick, David S.; Burke, Gregory L.; Marban, Eduardo; Spooner, Peter M.

    2010-01-01

    Background Existing studies indicate a significant genetic component for sudden cardiac arrest (SCA) and genome-wide association studies (GWAS) provide an unbiased approach for identification of novel genes. We performed a GWAS to identify genetic determinants of SCA. Methodology/Principal Findings We used a case-control design within the ongoing Oregon Sudden Unexpected Death Study (Oregon-SUDS). Cases (n = 424) were SCAs with coronary artery disease (CAD) among residents of Portland, OR (2002–07, population ∼1,000,000) and controls (n = 226) were residents with CAD, but no history of SCA. All subjects were of White-European ancestry and GWAS was performed using Affymetrix 500K/5.0 and 6.0 arrays. High signal markers were genotyped in SCA cases (n = 521) identified from the Atherosclerosis Risk in Communities Study (ARIC) and the Cardiovascular Health Study (CHS) (combined n = 19,611). No SNPs reached genome-wide significance (p<5×10−8). SNPs at 6 loci were prioritized for follow-up primarily based on significance of p<10−4 and proximity to a known gene (CSMD2, GPR37L1, LIN9, B4GALNT3, GPC5, and ZNF592). The minor allele of GPC5 (GLYPICAN 5, rs3864180) was associated with a lower risk of SCA in Oregon-SUDS, an effect that was also observed in ARIC/CHS whites (p<0.05) and blacks (p<0.04). In a combined Cox proportional hazards model analysis that adjusted for race, the minor allele exhibited a hazard ratio of 0.85 (95% CI 0.74 to 0.98; p<0.01). Conclusions/Significance A novel genetic locus for SCA, GPC5, was identified from Oregon-SUDS and successfully validated in the ARIC and CHS cohorts. Three other members of the Glypican family have been previously implicated in human disease, including cardiac conditions. The mechanism of this specific association requires further study. PMID:20360844

  7. Detection of transcriptional difference of porcine imprinted genes using different microarray platforms

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Presently, multiple options exist for conducting gene expression profiling studies in swine. In order to determine the performance of some of the existing platforms, Affymetrix Porcine, Affymetrix Human U133+2.0, and the U.S. Pig Genome Coordination Program spotted glass oligonucleotide microarray p...

  8. Gene Expression Quantitative Trait Locus Analysis of 16,000 Barley Genes Reveals a Complex Pattern of Genome-wide Transcriptional Regulation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Transcript abundance data from cRNA hybridizations to Affymetrix microarrays can be used for simultaneous marker development and genome-wide eQTL (expression Quantitative Trait Loci) analysis of crops. We have shown that it is easily possible to use the information from Affymetrix expression arrays ...

  9. Expression profiling of endometrium from women with endometriosis reveals candidate genes for disease-based implantation failure and infertility.

    PubMed

    Kao, L C; Germeyer, A; Tulac, S; Lobo, S; Yang, J P; Taylor, R N; Osteen, K; Lessey, B A; Giudice, L C

    2003-07-01

    Endometriosis is clinically associated with pelvic pain and infertility, with implantation failure strongly suggested as an underlying cause for the observed infertility. Eutopic endometrium of women with endometriosis provides a unique experimental paradigm for investigation into molecular mechanisms of reproductive dysfunction and an opportunity to identify specific markers for this disease. We applied paralleled gene expression profiling using high-density oligonucleotide microarrays to investigate differentially regulated genes in endometrium from women with vs. without endometriosis. Fifteen endometrial biopsy samples (obtained during the window of implantation from eight subjects with and seven subjects without endometriosis) were processed for expression profiling on Affymetrix Hu95A microarrays. Data analysis was conducted with GeneChip Analysis Suite, version 4.01, and GeneSpring version 4.0.4. Nonparametric testing was applied, using a P value of 0.05, to assess statistical significance. Of the 12,686 genes analyzed, 91 genes were significantly increased more than 2-fold in their expression, and 115 genes were decreased more than 2-fold. Unsupervised clustering demonstrated down-regulation of several known cell adhesion molecules, endometrial epithelial secreted proteins, and proteins not previously known to be involved in the pathogenesis of endometriosis, as well as up-regulated genes. Selected dysregulated genes were randomly chosen and validated with RT-PCR and/or Northern/dot-blot analyses, and confirmed up-regulation of collagen alpha2 type I, 2.6-fold; bile salt export pump, 2.0-fold; and down-regulation of N-acetylglucosamine-6-O-sulfotransferase (important in synthesis of L-selectin ligands), 1.7-fold; glycodelin, 51.5-fold; integrin alpha2, 1.8-fold; and B61 (Ephrin A1), 4.5-fold. Two-way overlapping layer analysis used to compare endometrial genes in the window of implantation from women with and without endometriosis further identified three

  10. Diagnostic microRNA markers to screen for sporadic human colon cancer in stool: I. Proof of principle.

    PubMed

    Ahmed, Farid E; Ahmed, Nancy C; Vos, Paul W; Bonnerup, Chris; Atkins, James N; Casey, Michelle; Nuovo, Gerard J; Naziri, Wade; Wiley, John E; Mota, Helvecio; Allison, Ron R

    2013-01-01

    To present proof-of-principle application for employing micro(mi)RNAs as diagnostic markers for colon cancer, we carried out global microarray expression studies on stool samples obtained from fifteen individuals (three controls, and three each with TNM stage 0-1, stage 2, stage 3, and stage 4 colon cancer), using Affymetrix GeneChip miRNA 3.0 Array, to select for a panel of miRNA genes for subsequent focused semi-quantitative polymerase chain reaction (PCR) analysis studies. Microarray results showed 202 preferentially expressed miRNA genes that were either increased (141 miRNAs), or reduced (61 miRNAs) in expression. We then conducted a stem-loop reverse transcriptase (RT)-TaqMan® minor groove binding (MGB) probes, followed by a modified qPCR expression study on 20 selected miRNAs. Twelve of the miRNAs exhibited increased and 8 decreased expression in stool from 60 individuals (20 controls, 20 with tumor-lymph node-metastatic (TNM) stage 0-1, 10 with stage 2, five with stage 3, and 5 with stage 4 colon cancer) to quantitatively monitor miRNA changes at various TNM stages of colon cancer progression. We also used laser-capture microdissection (LCM) of colon mucosal epithelial tissue samples (three control samples, and three samples from each of the four stages of colon cancer, for a total of 15 samples) to find concordance or lack thereof with stool findings. The reference housekeeping pseudogene-free ribosomal gene (18S rRNA), which shows little variation in expression, was employed as a normalization standard for relative PCR quantification. Results of the PCR analyses confirmed that twelve miRNAs (miR-7, miR-17, miR-20a, miR-21, miR-92a, miR-96, miR-106a, miR-134, miR-183, miR-196a, miR-199a-3p and miR214) had an increased expression in the stool of patients with colon cancer, and that later TNM carcinoma stages exhibited a more pronounced expression than did adenomas. On the other hand, eight miRNAs (miR-9, miR-29b, miR-127-5p, miR-138, miR-143, miR-146a, mi

  11. Gravitropism of cut shoots is mediated by oxidative processes: A physiological and molecular study

    NASA Astrophysics Data System (ADS)

    Philosoph-Hadas, Sonia; Friedman, Haya; Meir, Shimon

    2012-07-01

    in favor of the lower shoot side was completely eliminated in the NAC-treated shoots, in which the bending response was inhibited. These results suggest that the gravitropic-induced asymmetric auxin redistribution precedes shoot bending, and NAC inhibits this response by abolishing the auxin gradient across the shoot. Our microarray analysis of tomato shoots, using the Affymetrix Tomato GeneChip, revealed differential changes in expression of 266 genes, occurring during the initial 0.5-5 h of shoot reorientation prior to bending. The differential changes in expression of auxin-related genes in favor of the lower shoot side occurred already following 0.5 h of reorientation, while those of cell wall-related genes, associated with shoot bending, occurred only 3 h following shoot reorientation. Among the identified genes, 11 genes were related to auxin, and 36 genes were associated with oxidative processes, demonstrating the involvement of ROS in early events of shoot gravitropism. Taken together, our results suggest that ROS mediate the early gravity-induced amyloplast sedimentation required for signal perception, as well as the lateral auxin movement across the shoot, which is necessary for the auxin asymmetric distribution leading to shoot upward bending.

  12. Transcriptome dynamics and molecular cross-talk between bovine oocyte and its companion cumulus cells

    PubMed Central

    2011-01-01

    Background The bi-directional communication between the oocyte and its companion cumulus cells (CCs) is crucial for development and functions of both cell types. Transcripts that are exclusively expressed either in oocytes or CCs and molecular mechanisms affected due to removal of the communication axis between the two cell types is not investigated at a larger scale. The main objectives of this study were: 1. To identify transcripts exclusively expressed either in oocyte or CCs and 2. To identify those which are differentially expressed when the oocyte is cultured with or without its companion CCs and vice versa. Results We analyzed transcriptome profile of different oocyte and CC samples using Affymetrix GeneChip Bovine Genome array containing 23000 transcripts. Out of 13162 genes detected in germinal vesicle (GV) oocytes and their companion CCs, 1516 and 2727 are exclusively expressed in oocytes and CCs, respectively, while 8919 are expressed in both. Similarly, of 13602 genes detected in metaphase II (MII) oocytes and CCs, 1423 and 3100 are exclusively expressed in oocytes and CCs, respectively, while 9079 are expressed in both. A total of 265 transcripts are differentially expressed between oocytes cultured with (OO + CCs) and without (OO - CCs) CCs, of which 217 and 48 are over expressed in the former and the later groups, respectively. Similarly, 566 transcripts are differentially expressed when CCs mature with (CCs + OO) or without (CCs - OO) their enclosed oocytes. Of these, 320 and 246 are over expressed in CCs + OO and CCs - OO, respectively. While oocyte specific transcripts include those involved in transcription (IRF6, POU5F1, MYF5, MED18), translation (EIF2AK1, EIF4ENIF1) and CCs specific ones include those involved in carbohydrate metabolism (HYAL1, PFKL, PYGL, MPI), protein metabolic processes (IHH, APOA1, PLOD1), steroid biosynthetic process (APOA1, CYP11A1, HSD3B1, HSD3B7). Similarly, while transcripts over expressed in OO + CCs are involved in

  13. DNA microarray gene expression analysis technology and its application to neurological disorders.

    PubMed

    Greenberg, S A

    2001-09-11

    DNA microarray technology is currently an area of great interest. Also called "genechip" technology, it incorporates molecular genetics and computer science on a massive scale. This technology can rapidly provide a detailed view of the simultaneous expression of entire genomes and provide new insights into gene function, disease pathophysiology, disease classification, and drug development. In this review, the author discusses the basic theory behind genechip and the other biologic chip technologies, their limitations given the current state of biologic knowledge and computational abilities, and their potential applications to the understanding of neurologic disorders. PMID:11575306

  14. HvWRKY10, HvWRKY19, and HvWRKY28 positively regulate Mla-triggered immunity and basal defense to barley powdery mildew

    Technology Transfer Automated Retrieval System (TEKTRAN)

    WRKY proteins represent a large family of transcription factors (TFs), involved in plant development and defense responses. So far, fifty-five unique barley TFs have been annotated that contain the WRKY domain; twenty-six of these are present on the Barley1 GeneChip. We analyzed time-course expres...

  15. On the Difference between Designing Children and Raising Them: Ethics and the Use of Educationally Oriented Biotechnology

    ERIC Educational Resources Information Center

    Stein, Zachary

    2010-01-01

    The use of educationally oriented biotechnology has grown drastically in recent decades and is likely to continue to grow. Advances in both the neurosciences and genetics have opened up important areas of application and industry, from psychopharmacology to gene-chip technologies. This article reviews the current state of educationally oriented…

  16. Microarray analysis identified Puccinia striiformis f. sp. tritici genes involved in infection and sporulation.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Puccinia striiformis f. sp. tritici (Pst) causes stripe rust, one of the most important diseases of wheat worldwide. To identify Pst genes involved in infection and sporulation, a custom oligonucleotide Genechip was made using sequences of 442 genes selected from Pst cDNA libraries. Microarray analy...

  17. Transcript Profiling of Common Bean (Phaseolus vulgaris L.) Using the GeneChip(R) Soybean Genome Array: Optimizing Analysis by Masking Biased Probes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Common bean (Phaseolus vulgaris) and soybean (Glycine max) both belong to the Phaseoleae tribe and share significant coding sequence homology. This suggests that the GeneChip(R) Soybean Genome Array (soybean GeneChip) may be used for gene expression studies using common bean. To evaluate the utility...

  18. Expression Analysis of Ethylene Biosynthesis and Receptor Genes From Barley Embryo and Tissue Culture

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ethylene affects regeneration of green plants from barley tissue culture. With the availability of the HarvEST barley database and barley GeneChip, genome-wide expression studies have focused on differential development between Morex and Golden Promise at various stages of plant growth. The data f...

  19. Transcript-based Cloning of RRP46, a Regulator of rRNA Processing and R-Gene-Independent Cell Death in Barley–Powdery Mildew Interactions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Programmed cell death (PCD) plays a pivotal role in plant development and defense. To investigate the degree of interaction between PCD and R-gene mediated defense, we used the 22K Barley1 GeneChip to compare and contrast time-course expression profiles of Blumeria graminis f. sp. hordei (Bgh) chal...

  20. 75 FR 57005 - Notice of Availability of Draft Environmental Impact Statement and Public Hearings for the...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-17

    ... construction, operation, maintenance, and connection of either a double-circuit 230-kilovolt (kV) or a single-circuit 500-kV electric transmission line that would cross the U.S.-Mexico border in the vicinity...

  1. Protection of semiconductor converters for controlled bypass reactors

    SciTech Connect

    Dolgopolov, A. G.; Akhmetzhanov, N. G.; Karmanov, V. F.

    2010-05-15

    Possible ways of protecting thyristor converters in systems for magnetizing 110 - 500 kV controlled bypass reactors during switching and automatic reclosing are examined based on experience with the development of equipment, line tests, and mathematical modelling.

  2. Advanced, High Power, Next Scale, Wave Energy Conversion Device

    SciTech Connect

    Hart, Philip R.

    2011-09-27

    This presentation from the Water Peer Review highlights one of the program's marine and hyrokinetics device design projects to scale up the current Ocean Power Technology PowerBuoy from 150kW to 500kW.

  3. Mechanical Unloading of Mouse Bone in Microgravity Significantly Alters Cell Cycle Gene Set Expression

    NASA Astrophysics Data System (ADS)

    Blaber, Elizabeth; Dvorochkin, Natalya; Almeida, Eduardo; Kaplan, Warren; Burns, Brnedan

    2012-07-01

    unloading in spaceflight, we conducted genome wide microarray analysis of total RNA isolated from the mouse pelvis. Specifically, 16 week old mice were subjected to 15 days spaceflight onboard NASA's STS-131 space shuttle mission. The pelvis of the mice was dissected, the bone marrow was flushed and the bones were briefly stored in RNAlater. The pelvii were then homogenized, and RNA was isolated using TRIzol. RNA concentration and quality was measured using a Nanodrop spectrometer, and 0.8% agarose gel electrophoresis. Samples of cDNA were analyzed using an Affymetrix GeneChip\\S Gene 1.0 ST (Sense Target) Array System for Mouse and GenePattern Software. We normalized the ST gene arrays using Robust Multichip Average (RMA) normalization, which summarizes perfectly matched spots on the array through the median polish algorithm, rather than normalizing according to mismatched spots. We also used Limma for statistical analysis, using the BioConductor Limma Library by Gordon Smyth, and differential expression analysis to identify genes with significant changes in expression between the two experimental conditions. Finally we used GSEApreRanked for Gene Set Enrichment Analysis (GSEA), with Kolmogorov-Smirnov style statistics to identify groups of genes that are regulated together using the t-statistics derived from Limma. Preliminary results show that 6,603 genes expressed in pelvic bone had statistically significant alterations in spaceflight compared to ground controls. These prominently included cell cycle arrest molecules p21, and p18, cell survival molecule Crbp1, and cell cycle molecules cyclin D1, and Cdk1. Additionally, GSEA results indicated alterations in molecular targets of cyclin D1 and Cdk4, senescence pathways resulting from abnormal laminin maturation, cell-cell contacts via E-cadherin, and several pathways relating to protein translation and metabolism. In total 111 gene sets out of 2,488, about 4%, showed statistically significant set alterations. These

  4. Hippocampal gene expression in a rat model of depression after electroacupuncture at the Baihui and Yintang acupoints

    PubMed Central

    Duan, Dongmei; Yang, Xiuyan; Ya, Tu; Chen, Liping

    2014-01-01

    Preliminary basic research and clinical findings have demonstrated that electroacupuncture therapy exhibits positive effects in ameliorating depression. However, most studies of the underlying mechanism are at the single gene level; there are few reports regarding the mechanism at the whole-genome level. Using a rat genomic gene-chip, we profiled hippocampal gene expression changes in rats after electroacupuncture therapy. Electroacupuncture therapy alleviated depression-related manifestations in the model rats. Using gene-chip analysis, we demonstrated that electroacupuncture at Baihui (DU20) and Yintang (EX-HN3) regulates the expression of 21 genes. Real-time PCR showed that the genes Vgf, Igf2, Tmp32, Loc500373, Hif1a, Folr1, Nmb, and Rtn were upregulated or downregulated in depression and that their expression tended to normalize after electroacupuncture therapy. These results indicate that electroacupuncture at Baihui and Yintang modulates depression by regulating the expression of particular genes. PMID:25206746

  5. Friction and friction-generated temperature at a polymer-metal interface

    NASA Technical Reports Server (NTRS)

    Price, H. L.; Burks, H. D.

    1974-01-01

    Results of friction and thermal tests of molded polyimide and pyrrone polymers are presented. The coefficient of sliding friction up to surface velocities of 2 m/sec and the coefficient of thermal expansion from 300 to 500 K were measured. An apparatus was constructed to measure simultaneously the coefficient of sliding friction and the friction-generated temperature. Measurements were made at a nominal pressure-velocity product of 0.25 MN/msec and at temperatures between 300 and 500 K.

  6. Tiling Microarray Analysis Tools

    SciTech Connect

    Nix, Davis Austin

    2005-05-04

    TiMAT is a package of 23 command line Java applications for use in the analysis of Affymetrix tiled genomic microarray data. TiMAT enables: 1) Rebuilding the genome annotation for entire tiled arrays (repeat filtering, chromosomal coordinate assignment). 2) Post processing of oligo intensity values (quantile normalization, median scaling, PMMM transformation), 3) Significance testing (Wilcoxon rank sum and signed rank tests, intensity difference and ratio tests) and Interval refinement (filtering based on multiple statistics, overlap comparisons), 4) Data visualization (detailed thumbnail/zoomed view with Interval Plots and data export to Affymetrix's Integrated Genome Browser) and Data reports (spreadsheet summaries and detailed profiles)

  7. Conversion of Seven Completed Maps into ArcGIS for Publication

    NASA Astrophysics Data System (ADS)

    Anderson, R. C.; Parker, T. J.; Schroeder, J. F.

    2016-06-01

    We plan to convert seven 1:500K maps of East Acidalia and Argyre Planitia as two 1:1M scale maps of these regions, begun in the early and mid 90s, in two years. We will start with East Acidalia the first year and conclude with Argyre during year two.

  8. European Union bulk tank SCC standards and proposed US standards: Compliance based on data from four Federal Milk Marketing Orders

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study was to evaluate compliance of US producers with the proposed BTSCC limits. Four different SCC levels of compliance were evaluated: 750K; 600K; 500K; 400K. For the 12 month period ending October 2010, 1.0% of producers and 0.2% of milk exceeded the current US limit of 750K...

  9. Eurpoean Union bulk tank SCC standards and proposed US standards: Compliance based on data from four Federal Milk Marketing Orders

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study was to evaluate the percentage of US producers and milk not currently meeting the proposed bulk tank somatic cell counts (BTSCC) limits. Five different limits of BTSCC were evaluated for compliance: 750K, 600K, 500K, and 400K using the current US methods and 400K using th...

  10. Equation of state and thermmodynamic properties of 1,1,1,2-tetrafluoroethane (refrigerant R134a)

    SciTech Connect

    Vas`kov, E.T.

    1995-08-01

    An equation of state and tables of thermodynamic properties of R134a in the saturation state and in the one-phase region are obtained in the temperature interval 320-500 K at pressures ranging from 0.01 to 7.5 MPa.

  11. WWC Quick Review of the Report "Evaluation of the DC Opportunity Scholarship Program: Impacts After Three Years"

    ERIC Educational Resources Information Center

    What Works Clearinghouse, 2010

    2010-01-01

    "Evaluation of the DC Opportunity Scholarship Program: Impacts After Three Years" examined whether the "Opportunity Scholarship Program," which offers vouchers to students to attend private schools, improved the reading and math achievement of low-income students. The study analyzed data on about 1,500 K-12 students in the District of Columbia who…

  12. ENVIRONMENTAL ASSESSMENT OF A RECIPROCATING ENGINE RETROFITTED WITH SELECTIVE CATALYTIC REDUCTION. VOLUME 2. DATA SUPPLEMENT

    EPA Science Inventory

    The report gives results of comprehensive emission measurements and 15-day continuous emission monitoring for a 1,500 kW (2000 hp) gas-fired, four-stroke turbocharged reciprocating engine equipped with an ammonia-based selective catalytic reduction system for NOx control.

  13. ENVIRONMENTAL ASSESSMENT OF A RECIPROCATING ENGINE RETROFITTED WITH SELECTIVE CATALYTIC REDUCTION. VOLUME 1. TECHNICAL RESULTS

    EPA Science Inventory

    The report gives results of comprehensive emission measurements and 15-day continuous emission monitoring for a 1,500 kW (2000 hp) gas-fired, four-stroke turbocharged reciprocating engine equipped with an ammonia-based selective catalytic reduction system for NOx control.

  14. The design of a gamma-ray irradiation plant—shanghai irradiation center

    NASA Astrophysics Data System (ADS)

    Fugen, Chen; Xiangrong, Xue; Zewu, Yao

    Shanghai Irradiation Center, situated in western suburb of Shanghai, was completed in March, 1986. The intensity of Co 60 is 177 KCuries at present, and untimate loading will be 500 K Curies. The Center is designed mainly for food radiation preservation and sterilization of medical devices and tools. Its processing ability is 10 T/hr for potatoes.

  15. To future generations....

    SciTech Connect

    Drees, H.M.

    1997-12-31

    One of the world`s first 500 kW turbines was installed in the Netherlands in 1989. This forerunner of the current NedWind 500 kW range also represents the earliest predesign of the NedWind megawatt turbine. After the first turbines several design modifications followed, e.g. rotor diameter was increased and a tip brake was added. After that polyester blades were introduced and rotor diameter was further increased. The drive train was also redesigned. Improvements on the 500 kW turbine concept resulted in decreased cost and increased annual energy output. The 500 kW turbines serve in the first Dutch off-shore wind farm installed in 1994. This pilot project established proof that off-shore implementation is a promising option for the Dutch energy supply. Installation of megawatt turbines off-shore is currently being studied. Wind energy can substantially contribute to electricity supply. Maximum output in kilowatt-hours is the target.

  16. From medium-sized to megawatt turbines...

    SciTech Connect

    Dongen, W. van

    1996-12-31

    One of the world`s first 500 kW turbines was installed in 1989 in the Netherlands. This forerunner of the current NedWind 500 kW range also represents the earliest predesign of the NedWind megawatt turbine. After the first 500 kW turbines with steel rotor blades and rotor diameter of 34 m, several design modifications followed, e.g. the rotor diameter was increased to 35 m and a tip brake was added. Later polyester blades were introduced and the rotor diameter was increased with 5 in. The drive train was also redesigned. Improvements on the 500 kW turbine concept has resulted in decreased cost, whereas annual energy output has increased to approx. 1.3 million kWh. Wind energy can substantially contribute to electricity supply. Maximum output in kiloWatthours is the target. Further improvement of the existing technology and implementation of flexible components may well prove to be a way to increase energy output, not only in medium or large sized wind turbines. 7 figs.

  17. Neutron radiography and neutron-induced autoradiography for the classroom

    SciTech Connect

    Aderhold, H.C. )

    1992-01-01

    The Cornell 500-kW MARK II TRIGA reactor at the Ward Laboratory of Nuclear Engineering has been used to illustrate the application of neutron radiography (NR) and neutron-induced autoradiography (NIAR) for solving problems in engineering as well as problems in art history. The applications are described in the paper.

  18. IMES-Ural: the system of the computer programs for operational analysis of power flow distribution using telemetric data

    SciTech Connect

    Bogdanov, V.A.; Bol'shchikov, A.A.; Zifferman, E.O.

    1981-02-01

    A system of computer programs was described which enabled the user to perform real-time calculation and analysis of the current flow in the 500 kV network of the Ural Regional Electric Power Plant for all possible variations of the network, based on teleinformation and correctable equivalent parameters of the 220 to 110 kV network.

  19. Lateral growth rates in laser CVD of microstructures

    NASA Astrophysics Data System (ADS)

    Petzoldt, F.; Piglmayer, K.; Kräuter, W.; Bäuerle, D.

    1984-11-01

    Lateral growth rates of Ni spots deposited on absorbing substrates by decomposition of Ni(CO)4 with visible Kr+ laser light have been measured. The experimental data are consistent with the calculated temperature distributions. The mechanism of decomposition is thermal with an apparent chemical activation energy of 22±3 kcal/mole for the temperature range 350 K≦ T≦500 K.

  20. Standby Generators for North Portal Electrical Loads (SCPB:N/A)

    SciTech Connect

    Y.D. Shane

    1995-03-31

    The purpose and objective of this design analysis is to establish the best and most economical way to provide standby power generation required for the North Portal loads. This analysis calculates the size and number of the new standby generators that will supplement the already-specified four 500 kW diesel generator units (7007-GN-401, -402, -403, and -404).

  1. Solubility of hydrogen and deuterium in bcc-uranium-titanium alloys

    SciTech Connect

    Powell, G.L.; Kirkpatrick, J.R.

    1996-08-05

    For the bcc-U-Ti alloy system, H and D solubility measurements have been made on 12 alloy specimens ranging in composition from pure U to pure Ti and temperature range bounded by 900 K to 1,500 K. The results are described by a model within a standard error of 3%.

  2. 47 CFR 15.247 - Operation within the bands 902-928 MHz, 2400-2483.5 MHz, and 5725-5850 MHz.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ..., whichever is greater. Alternatively, frequency hopping systems operating in the 2400-2483.5 MHz band may... synchronization with the transmitted signals. (i) For frequency hopping systems operating in the 902-928 MHz band... bandwidth of the hopping channel is 500 kHz. (ii) Frequency hopping systems operating in the 5725-5850...

  3. Initial detailed designs for intermediate photovoltaic systems: Branch bank

    NASA Astrophysics Data System (ADS)

    Obrien, G.; Herz, J.

    1981-12-01

    The first of four detailed PV system designs for intermediate applications with a peak electrical load of 20 to 500 kW is presented. The initial design for a 6 kW direct roof mount, fixed tilt, flat plate array is analyzed for performance and economics. A drawing set, specifications, and installation details are included for procurement and construction bids.

  4. Analysis of small commercial photovoltaic applications

    NASA Astrophysics Data System (ADS)

    Herz, J.; Allred, R.; McCarthy, R.

    1982-07-01

    The objective was to determine promising small commercial (to 500 kW) grid connected photovoltaic applications. Twelve applications were evaluated, including detailed performance and economic analyses covering different collector types, utility rate structures and geographic locations. The attractiveness of battery storage was also examined.

  5. 78 FR 19700 - Pacific Northwest-Pacific Southwest Intertie Project-Rate Order No. WAPA-157

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-02

    ... No. WAPA-159 was approved by the Deputy Secretary of Energy on August 27, 2012 (77 FR 54575... rate process were: 1. A FRN was published on June 11, 2012, (77 FR 34381) announcing the proposed rates... Substation (Arizona); a 202-mile, 500-kV transmission line from Mead Substation to Adelanto...

  6. Differential Transcriptional Response to Nonassociative and Associative Components of Classical Fear Conditioning in the Amygdala and Hippocampus

    ERIC Educational Resources Information Center

    Isiegas, Carolina; Stein, Joel; Hellman, Kevin; Hannenhalli, Sridhar; Abel, Ted; Keeley, Michael B.; Wood, Marcelo A.

    2006-01-01

    Classical fear conditioning requires the recognition of conditioned stimuli (CS) and the association of the CS with an aversive stimulus. We used Affymetrix oligonucleotide microarrays to characterize changes in gene expression compared to naive mice in both the amygdala and the hippocampus 30 min after classical fear conditioning and 30 min after…

  7. Gene expression profiling of soybean near-isogenic lines contrasting in seed protein and oil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soybean profitability is affected by protein and oil content. Thus, an understanding of the genetic controls on protein and oil yield is important for future soybean improvement. In this study, we used Affymetrix soybean genome arrays with >37,500 Glycine max probe sets to compare gene expression pr...

  8. transcriptional response of pigs to Salmonella infection: Comparison of responses to infection with Salmonella eimerica serotype Typhimurium as that observed in S. choleraesuis infection.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Swine responses to, and control of, Salmonella enterica serotype Typhimurium (ST) infection have been compared to S. enterica serotype Choleraesuis (SC) infection. Using subtractive suppression hybridization (SSH), long oligonucleotide Qiagen and Affymetrix porcine GeneChip® arrays, and real time ge...

  9. GLOBAL TRANSCRIPTIONAL RESPONSE OF PORCINE MESENTERIC LYMPH NODES TO SALMONELLA ENTERICA SEROVAR TYPHIMURIUM

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Salmonellosis is prevalent worldwide and is both a food safety and animal production problem. To understand the host transcriptional response to Salmonella enterica serovar Typhimurium, the Affymetrix GeneChip® porcine genome array was used to identify differentially expressed (DE) genes in mesente...

  10. Gene expression in bovine mammary gland in response to increased milking frequency as determined by microarray and SAGE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Transcript profiling was performed by Affymetrix microarray analysis and SAGE to characterize changes in gene expression in the bovine mammary gland in response to 4× versus 2× daily milking during the first week of lactation. These changes in gene expression may contribute to the increased milk pro...

  11. Characterization of a novel RING-type ubiquitin E3 ligase GhRING2 differentially expressed in cotton fiber

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The ubiquitin-proteasome proteolysis pathway is responsible for the degradation of abnormal and short-lived proteins to regulate many important biochemical activities in eukaryotes. By employing affymetrix microarray analysis, we have identified a novel ubiquitin ligase E3 gene GhRING2 that is diffe...

  12. Comparative immune responses of pigs to infection with Salmonella enterica serovars of food safety (Typhimurium) and animal health (Choleraesuis) importance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Salmonella infections cause food safety concerns for humans as well as production problems for swine. Our team has used suppression hybridization (SSH), long oligonucleotide Qiagen and Affymetrix porcine GeneChip® arrays, and real time gene expression (Q-PCR) to understand the host response to, and ...

  13. Linkage Disequilibrium And Genome-Wide Association Studies In O. sativa

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There is increasing evidence that genome-wide association studies provide a powerful approach to find the genetic basis of complex phenotypic variation in all kinds of species. For this purpose, we developed the first generation 44K Affymetrix SNP array in rice (see Tung et al. poster). We genotyped...

  14. MOLECULAR METHODS (E.G., MICROARRAYS) APPLIED TO PLANT GENOMES FOR ASSESSING GENETIC CHANGE AND ENVIRONMENTAL STRESS

    EPA Science Inventory

    This is a technical document that presents a detailed sample standard operating procedure (S.O.P.) for preparing plant nucleic acid samples for microarray analyses using commercial ¿chips¿ such as those sold by Affymetrix. It also presents the application of a commercially availa...

  15. Exploiting Regulatory Variation to Identify Genes Underlying Quantitative Resistance to the Wheat Stem Rust Pathogen Puccinia graminis f. sp. tritici in Barley

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We previously mapped mRNA transcript abundance traits 1 eQTL (expression- quantitative trait loci) using the Barley1 Affymetrix array and "whole plant" tissue from 139 progeny of the Steptoe x Morex (St/Mx) reference barley mapping population. Of the 22,840 probesets (genes) on the array, 15,987 rep...

  16. ANALYSIS OF PORCINE TRANSCRIPTIONAL RESPONSE TO SALMONELLA ENTERICA SEROVAR CHOLERAESUIS SUGGESTS NOVEL TARGETS OF NFKAPPAB ARE ACTIVATED IN THE MESENTERIC LYMPH NODE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Affymetrix GeneChip® porcine genome array was used to identify differentially expressed genes in pig mesenteric lymph nodes (MLN) responding to infection with Salmonella enterica serovar Choleraesuis (S. Choleraesuis) at acute (8 hours (h), 24h and 48h post-inoculation (pi)) and chronic stages (...

  17. PLEXdb: Plant and Pathogen Expression Database and Tools for Comparative and Functional Genomics Analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    PLEXdb is a plant expression database that supports all Affymetrix microarray designs for plants and plant pathogens. PLEXdb provides annotation and hand-curated microarray data. Experiments deposited in PLEXdb are checked for MIAME/Plant compliance and completeness, then processed by normalizing th...

  18. Association of "ADAM10" and "CAMK2A" Polymorphisms with Conduct Disorder: Evidence from Family-Based Studies

    ERIC Educational Resources Information Center

    Jian, Xue-Qiu; Wang, Ke-Sheng; Wu, Tie-Jian; Hillhouse, Joel J.; Mullersman, Jerald E.

    2011-01-01

    Twin and family studies have shown that genetic factors play a role in the development of conduct disorder (CD). The purpose of this study was to identify genetic variants associated with CD using a family-based association study. We used 4,720 single nucleotide polymorphisms (SNPs) from the Illumina Panel and 11,120 SNPs from the Affymetrix 10K…

  19. A Microarray Analysis for Differential Gene Expression in the Soybean Genome Using Bioconductor and R

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This paper describes specific procedures for conducting quality assessment of Affymetrix GeneChip® soybean genome data and performing analyses to determine differential gene expression using the open-source R language and environment in conjunction with the open-source Bioconductor package. Procedu...

  20. Design And Performance Of 44,100 SNP Genotyping Array For Rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To document genome-wide allelic variation within and between the different subpopulations of both O. sativa and O. rufipogon, we developed an Affymetrix custom genotyping array containing 44,100 SNPs well distributed across the 400Mb rice genome. The SNPs on this array were selected from the MBML-in...

  1. Transcriptome profiling and expression analyses of genes critical to wheat adaptation to low temperature

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: To identify the genes involved in the development of low temperature (LT) tolerance in hexaploid wheat, we examined the global changes in expression in response to cold of the 55,052 potentially unique genes represented in the Affymetrix Wheat Genome microarray. We compared the expressi...

  2. FULL-GENOME ANALYSIS OF ALTERNATIVE SPLICING IN MOUSE LIVER AFTER HEPATOTOXICANT EXPOSURE

    EPA Science Inventory

    Alternative splicing plays a role in determining gene function and protein diversity. We have employed whole genome exon profiling using Affymetrix Mouse Exon 1.0 ST arrays to understand the significance of alternative splicing on a genome-wide scale in response to multiple toxic...

  3. 75 FR 19558 - Cancellation of Rule of Practice 41.200(b) Before the Board of Patent Appeals and Interferences...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-15

    ... for the Federal Circuit issued a decision in Agilent Technologies, Inc. v. Affymetrix, Inc., 567 F.3d....3d at 1375. The Court also noted that `` hen a party challenges a claim's validity under 35 U.S.C.... Cardiac Science Operating Co., 590 F.3d 1326, 1335 (Fed. Cir. 2010), the Court stated that `` ny...

  4. Axiom turkey genotyping array

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Axiom®Turkey Genotyping Array interrogates 643,845 probesets on the array, covering 643,845 SNPs. The array development was led by Dr. Julie Long of the USDA-ARS Beltsville Agricultural Research Center under a public-private partnership with Hendrix Genetics, Aviagen, and Affymetrix. The Turk...

  5. Identification of SNPs and INDELS in swine transcribed sequences using short oligonucleotide microarrays

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genome-wide detection of single feature polymorphisms (SFP) in swine using transcriptome profiling of day 25 placental RNA by contrasting probe intensities from either Meishan or an occidental composite breed with Affymetrix porcine microarrays is presented. A linear mixed model analysis was used to...

  6. IDENTIFICATION OF INTERSPECIES CONCORDANCE OF MECHANISMS OF ARSENIC-INDUCED BLADDER CANCER

    EPA Science Inventory

    Exposure to arsenic causes cancer by inducing a variety of responses that affect the expression of genes associated with numerous biological pathways leading to altered cell growth and proliferation, signaling, apoptosis and oxidative stress response. Affymetrix GeneChip® arrays ...

  7. Laser capture microdissection (LCM) and comparative microarray expression analysis of syncytial cells isolated from incompatible and compatible soybean roots infected by soybean cyst nematode (Heterodera glycines)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Syncytial cells in soybean (Glycine max cultivar [cv.] Peking) roots infected by incompatible (I) and compatible (C) populations of soybean cyst nematode [SCN] (Heterodera glycines) were collected using laser capture microdissection. Gene transcript abundance was assayed using an Affymetrix® soybean...

  8. Cross comparing gene expression profiles of nodulation and pathogen infection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Symbiotic microbes must evade the host defense response as they penetrate plant tissue and establish symbiosis. Bradyrhizobium japonicum successfully penetrates soybean root hairs and cortical cells to establish nitrogen fixing nodules. We have been using Affymetrix and cDNA soybean microarrays to o...

  9. A composite transcriptional signature differentiates responses towards closely related herbicides in Arabidopsis thaliana and brassica napus

    EPA Science Inventory

    In this study, genome-wide expression profiling based on Affymetrix ATH1 arrays was used to identify discriminating responses of Arabidopsis thaliana to five herbicides, which contain active ingredients targeting two different branches of amino acid biosynthesis. One herbicide co...

  10. An orthologous transcriptional signature differentiates responses towards closely related chemicals in Arabidopsis thaliana and brassica napus

    EPA Science Inventory

    Herbicides are structurally diverse chemicals that inhibit plant-specific targets, however their off-target and potentially differentiating side-effects are less well defined. In this study, genome-wide expression profiling based on Affymetrix AtH1 arrays was used to identify dis...

  11. High temperature structural and magnetic properties of cobalt nanorods

    SciTech Connect

    Ait Atmane, Kahina; Zighem, Fatih; Soumare, Yaghoub; Ibrahim, Mona; Boubekri, Rym; Maurer, Thomas; Margueritat, Jeremie; Piquemal, Jean-Yves; Ott, Frederic; Chaboussant, Gregory; Schoenstein, Frederic; Jouini, Noureddine; Viau, Guillaume

    2013-01-15

    We present in this paper the structural and magnetic properties of high aspect ratio Co nanoparticles ({approx}10) at high temperatures (up to 623 K) using in-situ X ray diffraction (XRD) and SQUID characterizations. We show that the anisotropic shapes, the structural and texture properties are preserved up to 500 K. The coercivity can be modelled by {mu}{sub 0}H{sub C}=2(K{sub MC}+K{sub shape})/M{sub S} with K{sub MC} the magnetocrystalline anisotropy constant, K{sub shape} the shape anisotropy constant and M{sub S} the saturation magnetization. H{sub C} decreases linearly when the temperature is increased due to the loss of the Co magnetocrystalline anisotropy contribution. At 500 K, 50% of the room temperature coercivity is preserved corresponding to the shape anisotropy contribution only. We show that the coercivity drop is reversible in the range 300-500 K in good agreement with the absence of particle alteration. Above 525 K, the magnetic properties are irreversibly altered either by sintering or by oxidation. - Graphical abstract: We present in this paper the structural and magnetic properties of high aspect ratio Co nanorods ({approx}10) at high temperatures (up to 623 K) using in-situ X-ray diffraction and SQUID characterizations. We show that the anisotropic shapes, the structural and texture properties are preserved up to 500 K. Above 525 K, the magnetic properties are irreversibly altered either by sintering or by oxidation. Highlights: Black-Right-Pointing-Pointer Ferromagnetic Co nanorods are prepared using the polyol process. Black-Right-Pointing-Pointer The structural and texture properties of the Co nanorods are preserved up to 500 K. Black-Right-Pointing-Pointer The magnetic properties of the Co nanorods are irreversibly altered above 525 K.

  12. Light modulation of human sleep depends on a polymorphism in the clock gene Period3.

    PubMed

    Chellappa, Sarah L; Viola, Antoine U; Schmidt, Christina; Bachmann, Valérie; Gabel, Virginie; Maire, Micheline; Reichert, Carolin F; Valomon, Amandine; Landolt, Hans-Peter; Cajochen, Christian

    2014-09-01

    Non-image-forming (NIF) responses to light powerfully modulate human physiology. However, it remains scarcely understood how NIF responses to light modulate human sleep and its EEG hallmarks, and if there are differences across individuals. Here we investigated NIF responses to light on sleep in individuals genotyped for the PERIOD3 (PER3) variable-number tandem-repeat (VNTR) polymorphism. Eighteen healthy young men (20-28 years; mean ± SEM: 25.9 ± 1.2) homozygous for the PER3 polymorphism were matched by age, body-mass index, and ethnicity. The study protocol comprised a balanced cross-over design during the winter, during which participants were exposed to either light of 40 lx at 6,500 K (blue-enriched) or light at 2,500 K (non-blue enriched), during 2h in the evening. Compared to light at 2,500 K, light at 6,500 K induced a significant increase in all-night NREM sleep slow-wave activity (SWA: 1.0-4.5 Hz) in the occipital cortex for PER3(5/5) individuals, but not for PER3(4/4) volunteers. Dynamics of SWA across sleep cycles revealed increased occipital NREM sleep SWA for virtually all sleep episode only for PER3(5/5) individuals. Furthermore, they experienced light at 6,500 K as significantly brighter. Intriguingly, this subjective perception of brightness significantly predicted their increased occipital SWA throughout the sleep episode. Our data indicate that humans homozygous for the PER3(5/5) allele are more sensitive to NIF light effects, as indexed by specific changes in sleep EEG activity. Ultimately, individual differences in NIF light responses on sleep may depend on a clock gene polymorphism involved in sleep-wake regulation. PMID:24893318

  13. Use of heat stress responsive gene expression levels for early selection of heat tolerant cabbage (Brassica oleracea L.).

    PubMed

    Park, Hyun Ji; Jung, Won Yong; Lee, Sang Sook; Song, Jun Ho; Kwon, Suk-Yoon; Kim, Hyeran; Kim, Chulwook; Ahn, Jun Cheul; Cho, Hye Sun

    2013-01-01

    Cabbage is a relatively robust vegetable at low temperatures. However, at high temperatures, cabbage has disadvantages, such as reduced disease tolerance and lower yields. Thus, selection of heat-tolerant cabbage is an important goal in cabbage breeding. Easier or faster selection of superior varieties of cabbage, which are tolerant to heat and disease and have improved taste and quality, can be achieved with molecular and biological methods. We compared heat-responsive gene expression between a heat-tolerant cabbage line (HTCL), "HO", and a heat-sensitive cabbage line (HSCL), "JK", by Genechip assay. Expression levels of specific heat stress-related genes were increased in response to high-temperature stress, according to Genechip assays. We performed quantitative RT-PCR (qRT-PCR) to compare expression levels of these heat stress-related genes in four HTCLs and four HSCLs. Transcript levels for heat shock protein BoHsp70 and transcription factor BoGRAS (SCL13) were more strongly expressed only in all HTCLs compared to all HSCLs, showing much lower level expressions at the young plant stage under heat stress (HS). Thus, we suggest that expression levels of these genes may be early selection markers for HTCLs in cabbage breeding. In addition, several genes that are involved in the secondary metabolite pathway were differentially regulated in HTCL and HSCL exposed to heat stress. PMID:23736694

  14. GeneChip{sup {trademark}} screening assay for cystic fibrosis mutations

    SciTech Connect

    Cronn, M.T.; Miyada, C.G.; Fucini, R.V.

    1994-09-01

    GeneChip{sup {trademark}} assays are based on high density, carefully designed arrays of short oligonucleotide probes (13-16 bases) built directly on derivatized silica substrates. DNA target sequence analysis is achieved by hybridizing fluorescently labeled amplification products to these arrays. Fluorescent hybridization signals located within the probe array are translated into target sequence information using the known probe sequence at each array feature. The mutation screening assay for cystic fibrosis includes sets of oligonucleotide probes designed to detect numerous different mutations that have been described in 14 exons and one intron of the CFTR gene. Each mutation site is addressed by a sub-array of at least 40 probe sequences, half designed to detect the wild type gene sequence and half designed to detect the reported mutant sequence. Hybridization with homozygous mutant, homozygous wild type or heterozygous targets results in distinctive hybridization patterns within a sub-array, permitting specific discrimination of each mutation. The GeneChip probe arrays are very small (approximately 1 cm{sup 2}). There miniature size coupled with their high information content make GeneChip probe arrays a useful and practical means for providing CF mutation analysis in a clinical setting.

  15. Array-based genotyping and expression analysis of barley cv. Maythorpe and Golden Promise

    PubMed Central

    Walia, Harkamal; Wilson, Clyde; Condamine, Pascal; Ismail, Abdelbagi M; Xu, Jin; Cui, Xinping; Close, Timothy J

    2007-01-01

    Background Golden Promise is a salt-tolerant spring barley closely related to Maythorpe. Salt tolerance in Golden Promise has been attributed to a single mutation at the Ari-e locus (on 5H) resulting from irradiation of Maythorpe. Golden Promise accumulates lower shoot Na+ compared to Maythorpe when growing under saline conditions. This study focused on elucidating the genetic basis and mechanisms involved in this difference. Results The level of polymorphism between the two genotypes was explored using the Barley1 GeneChip for single feature polymorphisms (SFPs) and an oligonucleotide pool assay for single nucleotide polymorphisms (SNPs). Polymorphism analyses revealed three haplotype blocks spanning 6.4 cM on chromosome 1H, 23.7 cM on chromosome 4H and 3.0 cM on 5H. The Barley1 GeneChip was used to examine transcript abundance in different tissues and stages during development. Several genes within the polymorphic haplotype blocks were differentially regulated. Additionally, a more global difference in the jasmonic acid pathway regulation was detected between the two genotypes. Conclusion The results confirm that Golden Promise and Maythorpe are genetically very closely related but establish that they are not isogenic, as previously reported, due to three polymorphic haplotype blocks. Transcriptome analysis indicates that the response of the two genotypes to salinity stress is quite different. Additionally, the response to salinity stress in the roots and shoot tissue is strikingly different. PMID:17394671

  16. Thermal Performance of High Temperature Titanium -- Water Heat Pipes by Multiple Heat Pipe Manufacturers

    NASA Technical Reports Server (NTRS)

    Sanzi, James L.

    2007-01-01

    Titanium - water heat pipes are being investigated for use in heat rejection systems for lunar and Mars fission surface power systems. Heat pipes provide an efficient and reliable means to transfer heat to a radiator heat rejection system. NASA Glenn Research Center requisitioned nine titanium water heat pipes from three vendors. Each vendor supplied three heat pipes 1.25 cm diameter by 1.1 meter long with each vendor selecting a different wick design. Each of the three heat pipes is slightly different in construction. Additional specifications for the heat pipes included 500 K nominal operating temperature, light weight, and freeze tolerance. The heat pipes were performance tested gravity-aided, in the horizontal position and at elevations against gravity at 450 K and 500 K. Performance of the three heat pipes is compared. The heat pipe data will be used to verify models of heat pipe radiators that will be used in future space exploration missions.

  17. Variations of thermal electron energy distribution associated with field-aligned currents

    SciTech Connect

    Oyama, Kohichiro ); Fukunishi, Hiroshi ); Abe, Takumi; Okuzawa, Takashi; Fujii, Ryoichi

    1991-02-01

    Relationships between thermal electrons and field aligned currents (FACs) in the auroral region have been investigated using data simultaneously obtained from the Thermal Electron Detector (TED) and the fluxgate magnetometer both onboard the EXOS-D satellite. Several features resulted from the observations are summarized as; (1) At altitudes from 300 to 1,800km, electron temperature in the upward FAC region is higher than that of the neighboring no FAC region by the increment {Delta}T=1,100-9,500K, while the temperature is lower in the downward FAC region by the decrement {minus}{Delta}T=500-1,500K. (2) The electron temperature increase in the upward-current region grows with an increase of the FAC density. (3) The thermal electrons do not have Maxwell distribution in the upward-current region at altitudes higher than about 2,000km.

  18. Detection of a white dwarf in a visual binary system

    NASA Technical Reports Server (NTRS)

    Boehm-Vitense, Erika

    1992-01-01

    The F6 giant HD 160365 was detected to have a white dwarf companion about 8 arcsec south of the star. The UV energy distribution observed with IUE shows that the white dwarf has an effective temperature of 23,000 +/- 2000 K. If log g = 8 the Lya profile indicates an effective temperature around 24,500 K. Using the theoretical models by Wesemael et al. (1980) one finds a visual magnitude of m(V) about 16.5. For T(eff) = 24,500 K one expects for a white dwarf a luminosity of log L/L(solar) about 1.3 and M(V) about 10.67. This gives a distance modulus for the system of m(V) - M(V) = 5.83 and an absolute magnitude M(V)= 0.3 for the giant.

  19. Detection of a white dwarf in a visual binary system

    NASA Technical Reports Server (NTRS)

    Boehm-Vitense, Erika

    1980-01-01

    The F6 giant HD 160365 was detected to have a white dwarf companion about 8 arcsec south of the star. The UV energy distribution observed with International Ultraviolet Explorer (IUE) shows that the white dwarf has an effective temperature of 23,000 +/- 2,000 K. If log g = 8 the Ly(alpha) profile indicates an effective temperature around 24,500 K. Using the theoretical models, one finds a visual magnitude of m(sub v) is approximately 16.5. For T(sub eff) = 24,500 K one expects for a white dwarf a luminosity of log L/solar luminosity is approximately -1.3 and M(sub V) is approximately 10.67. This gives a distance modulus for the system of m(sub v) - M(sub V) = 5.83 and an absolute magnitude M(sub v) = 0.3 for the giant.

  20. Electrical transport in carbon black-epoxy resin composites at different temperatures

    NASA Astrophysics Data System (ADS)

    Macutkevic, J.; Kuzhir, P.; Paddubskaya, A.; Maksimenko, S.; Banys, J.; Celzard, A.; Fierro, V.; Bistarelli, S.; Cataldo, A.; Micciulla, F.; Bellucci, S.

    2013-07-01

    Results of broadband electric/dielectric properties of different surface area—carbon black/epoxy resin composites above the percolation threshold are reported in a wide temperature range (25-500 K). At higher temperatures (above 400 K), the electrical conductivity of composites is governed by electrical transport in polymer matrix and current carriers tunneling from carbon black clusters to polymer matrix. The activation energy of such processes decreases when the carrier concentration increases, i.e., with the increase of carbon black concentration. At lower temperatures, the electrical conductivity is governed by electron tunneling and hopping. The electrical conductivity and dielectric permittivity of composites strongly decrease after annealing composites at high temperatures (500 K); at the same time potential barrier for carriers tunneling strongly increases. All the observed peculiarities can be used for producing effective low-cost materials on the basis of epoxy resin working at different temperatures for electrical applications.

  1. Test Results of a Compact Conventional Modulator for Two-Klystron Operation

    SciTech Connect

    Gold, S

    2004-05-04

    Modulator technology has not advanced greatly over the last 30 years. Today, with the advent of the High Voltage, High Power IGBT there are several approaches for a solid state ON/OFF switched modulator. Klystron and accelerator technology is forcing voltages and peak powers higher such as the demand for 500 kV and 500 amperes peak to power two X-Band klystrons. Conventional technology (line-type modulators) were never overly concerned about rise time and efficiency. A few years ago, the klystron department at Stanford Linear Accelerator Center (SLAC) undertook an investigation into what could be done in a conventional modulator at 500 kV. We have reported on test bed measurements and shown both conceptual and hardware pictures during design and construction. We have now completed the modulator tank.

  2. Reactivity and reaction intermediates for acetic acid adsorbed on CeO2(111)

    DOE PAGESBeta

    Calaza, Florencia C.; Chen, Tsung -Liang; Mullins, David R.; Xu, Ye; Steven H. Overbury

    2015-05-02

    Adsorption and reaction of acetic acid on a CeO2(1 1 1) surface was studied by a combination of ultra-highvacuum based methods including temperature desorption spectroscopy (TPD), soft X-ray photoelectronspectroscopy (sXPS), near edge X-ray absorption spectroscopy (NEXAFS) and reflection absorption IRspectroscopy (RAIRS), together with density functional theory (DFT) calculations. TPD shows that thedesorption products are strongly dependent upon the initial oxidation state of the CeO2 surface, includingselectivity between acetone and acetaldehyde products. The combination of sXPS and NEXAFS demon-strate that acetate forms upon adsorption at low temperature and is stable to above 500 K, above whichpoint ketene, acetone and acetic acidmore » desorb. Furthermore, DFT and RAIRS show that below 500 K, bridge bondedacetate coexists with a moiety formed by adsorption of an acetate at an oxygen vacancy, formed bywater desorption.« less

  3. Thermal Performance of High Temperature Titanium-Water Heat Pipes by Multiple Heat Pipe Manufacturers

    NASA Technical Reports Server (NTRS)

    Sanzi, James L.

    2007-01-01

    Titanium-water heat pipes are being investigated for use in heat rejection systems for lunar and Mars fission surface power systems. Heat pipes provide an efficient and reliable means to transfer heat to a radiator heat rejection system. NASA Glenn Research Center requisitioned nine titanium water heat pipes from three vendors. Each vendor supplied three heat pipes 1.25 cm diameter by 1.1 meter long with each vendor selecting a different wick design. Each of the three heat pipes is slightly different in construction. Additional specifications for the heat pipes included 500 K nominal operating temperature, light weight, and freeze tolerance. The heat pipes were performance tested gravity-aided, in the horizontal position and at elevations against gravity at 450 and 500 K. Performance of the three heat pipes is compared. The heat pipe data will be used to verify models of heat pipe radiators that will be used in future space exploration missions.

  4. Reactivity and reaction intermediates for acetic acid adsorbed on CeO2(111)

    SciTech Connect

    Calaza, Florencia C.; Chen, Tsung -Liang; Mullins, David R.; Xu, Ye; Steven H. Overbury

    2015-05-02

    Adsorption and reaction of acetic acid on a CeO2(1 1 1) surface was studied by a combination of ultra-highvacuum based methods including temperature desorption spectroscopy (TPD), soft X-ray photoelectronspectroscopy (sXPS), near edge X-ray absorption spectroscopy (NEXAFS) and reflection absorption IRspectroscopy (RAIRS), together with density functional theory (DFT) calculations. TPD shows that thedesorption products are strongly dependent upon the initial oxidation state of the CeO2 surface, includingselectivity between acetone and acetaldehyde products. The combination of sXPS and NEXAFS demon-strate that acetate forms upon adsorption at low temperature and is stable to above 500 K, above whichpoint ketene, acetone and acetic acid desorb. Furthermore, DFT and RAIRS show that below 500 K, bridge bondedacetate coexists with a moiety formed by adsorption of an acetate at an oxygen vacancy, formed bywater desorption.

  5. Energetics of charge order transition in Bi{sub 1-x}Sr{sub x}MnO{sub 3}

    SciTech Connect

    Sedmidubsky, D. . E-mail: sedmidub@vscht.cz; Strejc, A.; Benes, O.; Ruzicka, K.; Hejtmanek, J.; Javorsky, P.; Nevriva, M.; Martin, C.

    2006-12-15

    The transition from the high-temperature pseudocubic form of the perovskite manganites Bi{sub 1-x}Sr{sub x}MnO{sub 3}, x=0.3,0.5,0.8, to their orthorhombically distorted charge-ordered state is examined. As the experimental probe the measuring of the heat capacity by heat flux DSC incremental method above 300K and by relaxation method below 300K is used. While a broad symmetrical transition spanning the temperature interval {delta}T{approx}500K with a maximum at the apparent T{sub CO}{approx}500K is observed for x=0.5, the other two compositions reveal typical {lambda}-shaped peaks often considered as typical for the second order transitions. The total entropy release on heating is interpreted in terms of a simultaneous change of charge, orbital and spin degree of freedom.

  6. Analysis of power loss in Ni-Zn ferrites

    NASA Astrophysics Data System (ADS)

    Kondo, K.; Chiba, T.; Yamada, S.; Otsuki, E.

    2000-05-01

    The power loss (Pcv) was analyzed by combining two methods. The first, Pcv, is divided into hysteresis loss (Ph) and residual loss (Pr) from the frequency dependence of the power loss according to the method of Otsuki et al., and, second, the loss factors are attributed to domain wall motion (Pw) and the rotation magnetization (Prot) by adapting the method proposed by Visser et al. It was found that Pw coincides with Ph in the lower frequency range, but the difference between them becomes significant as frequency goes up. The higher value of Pw, in comparison with Ph in the higher frequency range, can be attributed to the enhancement of loss due to the dynamic motion of the domain wall (Pwd) by raising the frequency. The hysteresis loss dominates Pcv in the frequency range below 500 kHz, while Pwd becomes predominant factor in the higher frequency range more than 500 kHz.

  7. Microstructure and thermo-electrical transport properties of Cd-Sn alloys

    SciTech Connect

    Ari, M. Saatci, B.; Guenduez, M.; Meydaneri, F.; Bozoklu, M.

    2008-05-15

    The thermophysical transport properties of Cd-Sn alloys have been investigated for six samples. The electrical resistivity measurements were obtained by using a standard dc four-point probe technique in the temperature range of 300 K-550 K. The resistivity of samples increases linearly with temperature and the electrical current mainly flows through the Sn phase channel. The electrical conductivity of samples is inversely proportional to temperature. Also, thermal conductivity of the Cd-Sn alloys was determined. The phonon component contribution of thermal conductivity dominates the thermal conduction processes at T < 500 K. The electronic component contribution of thermal conductivity affects the thermal transport process at T > 500 K. The thermal conductivity of the Cd-Sn alloys also depends on the grain size and grain boundary of the pure Cd and the pure Sn phases in the matrix. The temperature coefficient of resistivity was also determined, which is independent with the alloying elements.

  8. Conformations of Low-Molecular-Weight Lignin Polymers in Water.

    PubMed

    Petridis, Loukas; Smith, Jeremy C

    2016-02-01

    Low-molecular-weight lignin binds to cellulose during the thermochemical pretreatment of biomass for biofuel production, which prevents the efficient hydrolysis of the cellulose to sugars. The binding properties of lignin are influenced strongly by the conformations it adopts. Here, we use molecular dynamics simulations in aqueous solution to investigate the dependence of the shape of lignin polymers on chain length and temperature. Lignin is found to adopt collapsed conformations in water at 300 and 500 K. However, at 300 K, a discontinuous transition is found in the shape of the polymer as a function of the chain length. Below a critical degree of polymerization, Nc =15, the polymer adopts less spherical conformations than above Nc. The transition disappears at high temperatures (500 K) at which only spherical shapes are adopted. An implication relevant to cellulosic biofuel production is that lignin will self-aggregate even at high pretreatment temperatures. PMID:26763657

  9. Study of tip loss corrections using CFD rotor computations

    NASA Astrophysics Data System (ADS)

    Shen, W. Z.; Zhu, W. J.; Sørensen, J. N.

    2014-12-01

    Tip loss correction is known to play an important role for engineering prediction of wind turbine performance. There are two different types of tip loss corrections: tip corrections on momentum theory and tip corrections on airfoil data. In this paper, we study the latter using detailed CFD computations for wind turbines with sharp tip. Using the technique of determination of angle of attack and the CFD results for a NordTank 500 kW rotor, airfoil data are extracted and a new tip loss function on airfoil data is derived. To validate, BEM computations with the new tip loss function are carried out and compared with CFD results for the NordTank 500 kW turbine and the NREL 5 MW turbine. Comparisons show that BEM with the new tip loss function can predict correctly the loading near the blade tip.

  10. Kinetic Isotope Effects for the Reactions of Muonic Helium and Muonium with H2

    SciTech Connect

    Fleming, Donald G.; Arseneau, Donald J.; Sukhorukov, Oleksandr; Brewer, Jess H.; Mielke, Steven L.; Schatz, George C.; Garrett, Bruce C.; Peterson, Kirk A.; Truhlar, Donald G.

    2011-01-28

    The neutral muonic helium atom may be regarded as the heaviest isotope of the hydrogen atom, with a mass of ~4.1 amu (4.1H), because the negative muon screens one proton charge. We report the reaction rate of 4.1H with 1H2 to produce 4.1H1H + 1H at 295 to 500 K. The experimental rate constants are compared with the predictions of accurate quantum mechanical dynamics calculations carried out on an accurate Born-Huang potential energy surface and with previously measured rate constants of 0.11H (where 0.11H is shorthand for muonium). Kinetic isotope effects can be compared for the unprecedentedly large mass ratio of 36. The agreement with accurate quantum dynamics is quantitative at 500 K, and variational transition state theory is used to interpret the extremely low (large inverse) kinetic isotope effects in the 10-4 to 10-2 range.

  11. Magnetic Bearing Amplifier Output Power Filters for Flywheel Systems

    NASA Technical Reports Server (NTRS)

    Lebron-Velilla, Ramon C.; Jansen, Ralph H.; Palazzolo, Alan; Thomas, Erwin; Kascak, Peter E.; Birchenough, Arthur G.; Dever, Timothy P.

    2003-01-01

    Five power filters and two types of power amplifiers were tested for use with active magnetic bearings for flywheel applications. Filter topologies included low pass filters and low pass filters combined with trap filters at the PWM switching frequency. Two state and three state PWM amplifiers were compared. Each system was evaluated based on current magnitude at the switching frequency, voltage magnitude at 500 kHz, and power consumption. The base line system was a two state amplifier without a power filter. The recommended system is a three state power amplifier with a 50 kHz low pass filter and a 27 kHz trap filter. This system uses 5.57 W. It reduces the switching current by an order of magnitude and the 500 kHz voltage by two orders of magnitude. The relative power consumption varied depending on the test condition between 60 to 130 percent of the baseline.

  12. PVUSA construction and safety: Experience, lessons learned and costs

    SciTech Connect

    Shipman, D.

    1994-09-01

    This report is the first of a series of PVUSA reports on PVUSA experiences and lessons learned at the demonstration sites in Davis and Kerman, California. During the course of approximately 6 years (1988--1993), nine PV systems have been installed ranging from 20 kW to 500 kW. Five 20-kW emerging module technology arrays were installed on universal project-provided structures, and four utility-scale systems (200 to 500 kW) were installed as turnkey (vendor designed and integrated) systems. The report emphasizes PVUSA construction and safety experience from the installation of these systems and is intended for use by utility personnel engaged in the construction of a photovoltaic (PV) power plant (e.g., engineers, construction supervisors, etc.).

  13. Composite rod insulators for ac power lines; Electrical performance of various designs at a coastal testing station

    SciTech Connect

    Houlgate, R.G.; Swift, D.A. )

    1990-10-01

    The electrical performance of thirty-six composite insulators - of four commercial types for each AC system level of 34.5 kV, 230 kV and 500 kV - has been determined at the CEGB insulator testing station, Brighton, England. The weathershed materials were epoxy-resin, ethylene propylene rubber and silicone rubber; half of the 230 kV insulators had no stress rings. Surface leakage current was recorded for surge levels of 25 mA, 150 mA and 500 mA; a special technique was developed to obtain the flashover statistics of the 500 kV insulators, thereby enabling performance of the composite insulator to be quantified relative to that of a string of cap and pin porcelain insulators of anti-fog design, the deterioration of the insulators was observed by making regular visual inspections. The practical consequences of the findings and the causes of the degradation are discussed.

  14. Catalytic gasification: Isotopic labeling and transient reaction

    SciTech Connect

    Saber, J.M.; Falconer, J.L.; Brown, L.F.

    1985-01-01

    Temperature-programmed reaction was used with labeled isotopes (/sup 13/C and /sup 18/O) to study interactions between carbon black and potassium carbonate in pure He and 10% CO/sub 2//90% He atmospheres. Catalytic gasification precursor complexes were observed. Carbon and oxygen-bearing carbon surface groups interacted with the carbonate above 500 K to form surface complexes. Between 500 K and 950 K, and in the presence of gaseous carbon dioxide, the complexes promoted carbon and oxygen exchange between the gas-phase CO/sub 2/ and the surface. Oxygen exchanged between the surface complexes; but carbon did not exchange between the carbonate and the carbon black. As the temperature rose, the complexes decomposed to produce carbon dioxide, and catalytic gasification then began. Elemental potassium formed, and the active catalyst appears to alternate between potassium metal and a potassium-oxygen-carbon complex.

  15. Design study of wind turbines 50 kW to 3000 kW for electric utility applications. Volume 2: Analysis and design

    NASA Technical Reports Server (NTRS)

    1976-01-01

    All possible overall system configurations, operating modes, and subsystem concepts for a wind turbine configuration for cost effective generation of electrical power were evaluated for both technical feasibility and compatibility with utility networks, as well as for economic attractiveness. A design optimization computer code was developed to determine the cost sensitivity of the various design features, and thus establish the configuration and design conditions that would minimize the generated energy costs. The preliminary designs of both a 500 kW unit and a 1500 kW unit operating in a 12 mph and 18 mph median wind speed respectively, were developed. The various design features and components evaluated are described, and the rationale employed to select the final design configuration is given. All pertinent technical performance data and component cost data is included. The costs of all major subassemblies are estimated and the resultant energy costs for both the 500 kW and 1500 kW units are calculated.

  16. Mid-infrared point sensor for in situ monitoring of CO2 emissions from large-scale engines.

    PubMed

    Dooly, Gerard; Clifford, John; Leen, Gabriel; Lewis, Elfed

    2012-11-01

    This paper describes an optical fiber based system that has been developed for the monitoring of carbon dioxide emissions in situ within engines above 500 kW. Conventional sensors, reviewed here, fail to meet monitoring requirements, such as lifespan, accuracy, and robustness. This paper describes a sensor designed as a single point reflective probe configuration using low cost, compact mid-infrared optical components, making it suitable for insertion in large-scale engines including automotive tailpipes. The response of the sensor to carbon dioxide supplied from a cylinder in the laboratory environment is presented, as well as a number of experimental results taken in situ in an exhaust of an automotive diesel engine (smaller than 500 kW). The sensor is shown to have a long term stable operation over a wide range of concentrations (2%-15% CO(2)) with a lower detection limit smaller than the lowest value encountered in modern day engines. PMID:23128714

  17. Quality Visualization of Microarray Datasets Using Circos

    PubMed Central

    Koch, Martin; Wiese, Michael

    2012-01-01

    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.

  18. Tiling Microarray Analysis Tools

    2005-05-04

    TiMAT is a package of 23 command line Java applications for use in the analysis of Affymetrix tiled genomic microarray data. TiMAT enables: 1) Rebuilding the genome annotation for entire tiled arrays (repeat filtering, chromosomal coordinate assignment). 2) Post processing of oligo intensity values (quantile normalization, median scaling, PMMM transformation), 3) Significance testing (Wilcoxon rank sum and signed rank tests, intensity difference and ratio tests) and Interval refinement (filtering based on multiple statistics, overlap comparisons),more » 4) Data visualization (detailed thumbnail/zoomed view with Interval Plots and data export to Affymetrix's Integrated Genome Browser) and Data reports (spreadsheet summaries and detailed profiles)« less

  19. Remnants of Tropical Storm Allison over Southeast United States

    NASA Technical Reports Server (NTRS)

    2002-01-01

    On June 13, 2001 MODIS acquired this true-color image of Tropical Storm Allison over the Southeastern United States. Also pictured are a few wildfires burning in the stat of Florida. MODIS has thermal detectors uniquely designed to detect fires as hot as 500K without saturating, and it is being used by land managers throughout the U.S. to monitor and manage wildfires. Credit: Jacques Descloitres, MODIS Land Rapid Response Team

  20. Detection and some properties of a high molecular weight toxin in the hypobranchial gland of strawberry conch Strombus luhuanus.

    PubMed

    Abiko, Keisuke; Iwayama, Ayane; Shiomi, Kazuo

    2015-10-01

    The extract from the hypobranchial gland of strawberry conch Strombus luhuanus was found to be lethal to mice. There were no marked regional and seasonal variations in toxicity although a considerable individual variation was recognized. The toxin was thermostable and extractable with aqueous solvents but not with organic solvents. Behaviors in dialysis, ultrafiltration and column chromatography on various adsorbents suggested that the toxin is a high molecular weight acidic substance of 400-500 k. PMID:26299337

  1. Long-term monitoring of local stress changes in 67km installed OPGW cable using BOTDA

    NASA Astrophysics Data System (ADS)

    Zou, L.; Sezerman, O.

    2015-09-01

    The initial results from continuing long-term monitoring of a 67 km of an aerial fiber optic cable installed on a 500 kV power line cable (total fiber length of 134km) using BOTDA are presented. The effects of thunderstorms and rime ice on the cable were identified by monitoring strain on OPGW fibers. Variations of strain between day and night on the OPGW cable were observed and can potentially be exploited.

  2. Collisional Induced Absorption (CIA) bands of CO2 and H2 measured in the IR spectral range

    NASA Astrophysics Data System (ADS)

    Stefani, S.; Piccioni, G.; Snels, M.; Adriani, A.; Grassi, D.

    2015-10-01

    In this paper we present the results on the Collisional Induced Absorption (CIA) bands of CO2 and H2 measured employing two different experimental setup. Each of them allows us to reproduce typical planetary conditions, at a pressure and temperature from 1 up to 50 bar and from 298 up to 500 K respectively. A detailed study on the temperature dependence of the CO2 CIA absorption bands will be presented.

  3. Tungsten dust nanoparticles generation from blistering bursts under hydrogen environment in microwave ECR discharge

    NASA Astrophysics Data System (ADS)

    Ouaras, K.; Hassouni, K.; Delacqua, L. Colina; Lombardi, G.; Vrel, D.; Bonnin, X.

    2015-11-01

    Blistering burst induced tungsten dust nanoparticles were observed for the first time when a tungsten sample is submitted to a hydrogen low-temperature discharge under low flux and low incident energy values (20, 120 and 220 eV) at a surface temperature of 500 K. Tungsten nanoparticles (˜50 nm) were organized in 2D domains with diameter that is well correlated to the blister volume losses by burst. These observations suggest that dust nanoparticles were generated from blistering burst.

  4. Design comparison of single-anode and double-anode 300-MW magnetron injection gun

    SciTech Connect

    Lawson, W.; Specht, V. )

    1993-07-01

    Analytic tradeoff equations based on adiabatic assumptions are used to explore feasible design regions for single-anode Magnetron Injection Guns (MIG's). Particle simulations are then used to optimize a single-anode and a double-anode design for a 1-[mu]s, 500-kV, 600-A MIG which is required for a second-harmonic gyroklystron. The advantages and disadvantages of each configuration are critically examined.

  5. Initial operation of an x-band 100 MW gryoklystron

    SciTech Connect

    Lawson, W.; Cheng, J.; Calame, J.P.; Hogan, B.; Castle, M.; Saraph, G.P.; Granatstein, V.L.

    1995-12-31

    In this paper the authors describe the experimental test bed and preliminary cold-testing of the coaxial gyrotron experiment which is designed to produce over 100 MW at 8.57 GHz. Theoretical efficiency estimates exceed 40%. The nominal beam voltage is 500 kV and the single-anode Magnetron Injection Gun can operate with a beam current up to 720 A. Construction of the new facility is nearing completion.

  6. Controllability of Large SEP for Earth Orbit Raising

    NASA Technical Reports Server (NTRS)

    Woodcock, Gordon

    2004-01-01

    A six-degree-of-freedom (6DOF) simulation was constructed and exercised for a large solar electric propulsion (SEP) vehicle operating in low Earth orbit Nominal power was 500 kWe, with the large array sizes implied. Controllability issues, including gravity gradient, roll maneuvering for Sun tracking, and flexible arrays, and flight control methods, were investigated. Initial findings are that a SEP vehicle of this size is controllable and could be used for orbit raising of heavy payloads.

  7. Materials characterization of phosphoric acid fuel cell system

    NASA Technical Reports Server (NTRS)

    Venkatesh, Srinivasan

    1986-01-01

    The component materials used in the fabrication of phosphoric acid fuel cells (PAFC) must have mechanical, chemical, and electrochemical stability to withstand the moderately high temperature (200 C) and pressure (500 kPa) and highly oxidizing nature of phosphoric acid. This study discusses the chemical and structural stability, performance and corrosion data on certain catalysts, catalyst supports, and electrode support materials used in PAFC applications.

  8. IUE spectra of Feige 4, a suspected source of extreme-ultraviolet radiation

    NASA Astrophysics Data System (ADS)

    Holm, A. V.; Boggess, A.

    1982-06-01

    IUE spectra are presented for Feige 4, a DB-type white dwarf. The observed energy distribution is in good agreement with that predicted by a model atmosphere with an effective temperature of 15,500 K and having extremely low hydrogen and metal abundances. These results are evidence against Feige 4 being the source of the apparent extreme-ultraviolet signal detected by Prognoz 6.

  9. The varistor protected series capacitors at the 500 KV broadview substation

    SciTech Connect

    Barcus, J.M. ); Miske, S.A. Jr. ); Vitols, A.P. ); Maynard, H.M. ); Peterson, W.G. )

    1988-10-01

    Two 235 Mvar series capacitors have been successfully applied at the 500 kV Broadview substation of the Colstrip Transmission Project. The series capacitors have an overvoltage protection system based on metal oxide varistors. The system provides instantaneous bypass and reinsertion of the capacitors following external line section faults. The excellent performance of the equipment was demonstrated during staged fault tests performed in October, 1985. The banks have been in successful operation since January, 1986.

  10. Energy saver prototype accelerating resonator

    SciTech Connect

    Kerns, Q.; May, M.; Miller, H.W.; Reid, J.; Turkot, F.; Webber, R.; Wildman, D.

    1981-06-01

    A fixed frequency rf accelerating resonator has been built and tested for the Fermilab Energy Saver. The design parameters and prototype resonator test results are given. The resonator features a high permeability nickel alloy resistor which damps unwanted modes and corona rolls designed with the aid of the computer code SUPERFISH. In bench measurements, the prototype resonator has achieved peak accelerating voltages of 500 kV for a 1% duty cycle and cw operation at 360 kV. 4 refs.

  11. System and method for investigating sub-surface features of a rock formation with acoustic sources generating conical broadcast signals

    DOEpatents

    Vu, Cung Khac; Skelt, Christopher; Nihei, Kurt; Johnson, Paul A.; Guyer, Robert; Ten Cate, James A.; Le Bas, Pierre -Yves; Larmat, Carene S.

    2015-08-18

    A method of interrogating a formation includes generating a conical acoustic signal, at a first frequency--a second conical acoustic signal at a second frequency each in the between approximately 500 Hz and 500 kHz such that the signals intersect in a desired intersection volume outside the borehole. The method further includes receiving, a difference signal returning to the borehole resulting from a non-linear mixing of the signals in a mixing zone within the intersection volume.

  12. Specific features of the electronic properties of Ti50Ni50- x Cu x alloys with the shape memory effect

    NASA Astrophysics Data System (ADS)

    Kourov, N. I.; Korolev, A. V.; Kuranova, N. N.; Pushin, V. G.

    2016-06-01

    The magnetic susceptibility, electrical resistivity, and thermoelectric power of Ti50Ni50‒ x Cu x alloys with copper concentrations x ⩽ 25 at % have been measured in the temperature range of 2-500 K. The change in the electronic band structure near the Fermi level upon thermoelastic martensitic transformations, such as B2 ↔ B19', B2 ↔ B19 ↔ B19', and B2 ↔ B19, has been considered.

  13. An Analysis of Wind Power Development in the Town of Hull, MA_Appendix 4_Geophysical Survey Report

    SciTech Connect

    Adams, Christopher

    2013-06-30

    CR Environmental, Inc. (CR) was contracted by GZA GeoEnvironmental, Inc. (GZA) to perform hydrographic and geophysical surveys of an approximately 3.35 square mile area off the eastern shore of Hull, Massachusetts. Survey components included: • Single-beam bathymetry; • 100-kHz and 500-kHz side scan sonar; • Magnetometry; and • Low to mid-frequency sub-bottom profiling.

  14. Synthesis and characterization of Nb/sub 2/Se/sub 9/ single crystals grown in molten solution

    SciTech Connect

    Sanjines, R.; Berger, H.; Levy, F.

    1988-04-01

    Nb/sub 2/Se/sub 9/ single crystals were grown from the liquid solution of niobium in selenium. The crystals have been characterized by X-ray diffraction. Resistivity measurements in the temperature range 200 < T < 500 K revealed a semiconducting behaviour with an activation energy of 0.72 eV. The resistivity at room temperature is about 3 . 10/sup 5/ ..cap omega..cm.

  15. Intermediate Temperature Water Heat Pipe Tests

    NASA Technical Reports Server (NTRS)

    Devarakonda, Angirasa; Xiong, Da-Xi; Beach, Duane E.

    2005-01-01

    Heat pipes are among the most promising technologies for space radiator systems. Water heat pipes are explored in the intermediate temperature range of 400 to above 500 K. The thermodynamic and thermo-physical properties of water are reviewed in this temperature range. Test data are reported for a copper-water heat pipe. The heat pipe was tested under different orientations. Water heat pipes show promise in this temperature range. Fabrication and testing issues are being addressed.

  16. Materials Technology Support for Radioisotope Power Systems Final Report

    SciTech Connect

    Daniel P. Kramer; Chadwick D. Barklay

    2008-10-07

    Over the period of this sponsored research, UDRI performed a number of materials related tasks that helped to facilitate increased understanding of the properties and applications of a number of candidate program related materials including; effects of neutron irradiation on tantalum alloys using a 500kW reactor, thermodynamic based modeling of the chemical species in weld pools, and the application of candidate coatings for increased oxidation resistance of FWPF (Fine Weave Pierced Fabric) modules.

  17. 45. 800 H.P. WATER WHEEL UNIT (LEFT HAND) DIRECT CONNECTED ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    45. 800 H.P. WATER WHEEL UNIT (LEFT HAND) DIRECT CONNECTED TO A 500 K.W. G.E. CO. GENERATOR, SPEED 176 R.P.M., HEAD OF WATER 305 FT EFF., FOR SANTA ANA RIVER NO. 2 PLANT. ABNER DOBLE CO., ENGINEERS, SAN FRANCISCO, AUG. 29, 1904. TRACED FROM DOBLE BLUE PRINT, SEPT. 9, 1911. SCE drawing no. 5698. - Santa Ana River Hydroelectric System, SAR-2 Powerhouse, Redlands, San Bernardino County, CA

  18. IUE spectra of Feige 4, a suspected source of extreme-ultraviolet radiation

    NASA Technical Reports Server (NTRS)

    Holm, A. V.; Boggess, A.

    1982-01-01

    IUE spectra are presented for Feige 4, a DB-type white dwarf. The observed energy distribution is in good agreement with that predicted by a model atmosphere with an effective temperature of 15,500 K and having extremely low hydrogen and metal abundances. These results are evidence against Feige 4 being the source of the apparent extreme-ultraviolet signal detected by Prognoz 6.

  19. 50 MW, 35 GHz Gyroklystron Design for Advanced Accelerators

    NASA Astrophysics Data System (ADS)

    Arjona, Melany; Lawson, Wes

    1999-11-01

    We present the design results for a 50 MW, 35 GHz, 4-cavity gyroklystron system. We present both the design of the double-anode magnetron injection gun and the microwave circuit. The gun produces a 500 kV, 300 A beam with a velocity ratio of 1.5 and an axial spread of about 5The interaction efficiency is near 4050 dB. Details of the simulations, including sensitivity studies, will be given in the talk.

  20. Simultaneous density and magnetic field fluctuation measurements by far-infrared interferometry and polarimetry in MST

    SciTech Connect

    Yates, T. F.; Ding, W. X.; Carter, T. A.; Brower, D. L.

    2008-10-15

    Fluctuations are expected to play an important role in anomalous particle, momentum, and energy transport for magnetic confinement devices. Magnetic and density fluctuations are simultaneously measured using a high-speed laser-based Faraday rotation-interferometry system with a bandwidth of 500 kHz and 8 cm chord spacing. Density fluctuation and magnetic fluctuation profiles are obtained by using a newly developed fitting procedure.