Relevant bibliographies by topics / Gene Array

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Gene Array'

Author: Grafiati
Published: 4 June 2021
Last updated: 20 February 2023

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Journal articles on the topic "Gene Array"

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Zhang, Xiaoling, Marc E. Lenburg, and Avrum Spira. "Comparison of Nasal Epithelial Smoking-Induced Gene Expression on Affymetrix Exon 1.0 and Gene 1.0 ST Arrays." Scientific World Journal 2013 (2013): 1–7. http://dx.doi.org/10.1155/2013/951416.

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We have previously defined the impact of tobacco smoking on nasal epithelium gene expression using Affymetrix Exon 1.0 ST arrays. In this paper, we compared the performance of the Affymetrix GeneChip Human Gene 1.0 ST array with the Human Exon 1.0 ST array for detecting nasal smoking-related gene expression changes. RNA collected from the nasal epithelium of five current smokers and five never smokers was hybridized to both arrays. While the intersample correlation within each array platform was relatively higher in the Gene array than that in the Exon array, the majority of the genes most changed by smoking were tightly correlated between platforms. Although neither array dataset was powered to detect differentially expressed genes (DEGs) at a false discovery rate (FDR)<0.05, we identified more DEGs than expected by chance using the Gene ST array. These findings suggest that while both platforms show a high degree of correlation for detecting smoking-induced differential gene expression changes, the Gene ST array may be a more cost-effective platform in a clinical setting for gene-level genomewide expression profiling and an effective tool for exploring the host response to cigarette smoking and other inhaled toxins.
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Aschheim, Kathy. "Gene detection by array." Nature Biotechnology 18, no. 11 (November 2000): 1129. http://dx.doi.org/10.1038/81066.

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Thomas, E. V., K. H. Phillippy, B. Brahamsha, D. M. Haaland, J. A. Timlin, L. D. H. Elbourne, B. Palenik, and I. T. Paulsen. "Statistical Analysis of Microarray Data with Replicated Spots: A Case Study withSynechococcusWH8102." Comparative and Functional Genomics 2009 (2009): 1–11. http://dx.doi.org/10.1155/2009/950171.

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Until recently microarray experiments often involved relatively few arrays with only a single representation of each gene on each array. A complete genome microarray with multiple spots per gene (spread out spatially across the array) was developed in order to compare the gene expression of a marine cyanobacterium and a knockout mutant strain in a defined artificial seawater medium. Statistical methods were developed for analysis in the special situation of this case study where there is gene replication within an array and where relatively few arrays are used, which can be the case with current array technology. Due in part to the replication within an array, it was possible to detect very small changes in the levels of expression between the wild type and mutant strains. One interesting biological outcome of this experiment is the indication of the extent to which the phosphorus regulatory system of this cyanobacterium affects the expression of multiple genes beyond those strictly involved in phosphorus acquisition.
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Gellert, Pascal, Mizue Teranishi, Katharina Jenniches, Piera De Gaspari, David John, Karsten grosse Kreymborg, Thomas Braun, and Shizuka Uchida. "Gene Array Analyzer: alternative usage of gene arrays to study alternative splicing events." Nucleic Acids Research 40, no. 6 (November 28, 2011): 2414–25. http://dx.doi.org/10.1093/nar/gkr1110.

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Walsh, James Bruce. "Persistence of Tandem Arrays: Implications for Satellite and Simple-Sequence DNAs." Genetics 115, no. 3 (March 1, 1987): 553–67. http://dx.doi.org/10.1093/genetics/115.3.553.

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ABSTRACT Recombination processes acting on tandem arrays are suggested here to have probable intrinsic biases, producing an expected net decrease in array size following each event, in contrast to previous models which assume no net change in array size. We examine the implications of this by modeling copy number dynamics in a tandem array under the joint interactions of sister-strand unequal crossing over (rate γ per generation per copy) and intrastrand recombination resulting in deletion (rate ∊ per generation per copy). Assuming no gene amplification or selection, the expected mean persistence time of an array starting with z excess copies (i.e., array size z + 1) is z(1 + γ/∊) recombinational events. Nontrivial equilibrium distributions of array sizes exist when gene amplification or certain forms of selection are considered. We characterize the equilibrium distribution for both a simple model of gene amplification and under the assumption that selection imposes a minimal array size, n. For the latter case, n + 1/03B1 is an upper bound for mean array size under fairly general conditions, where α(=2∊/γ) is the scaled deletion rate. Further, the distribution of excess copies over n is bounded above by a geometric distribution with parameter α/(1 + α). Tandem arrays are unlikely to be greatly expanded by unequal crossing over unless α &lt;&lt; 1, implying that other mechanisms, such as gene amplification, are likely important in the evolution of large arrays. Thus unequal crossing over, by itself, is likely insufficient to account for satellite DNA.
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Alkahtani, Mohammed, Yihua Hu, Zuyu Wu, Colin Sokol Kuka, Muflih S. Alhammad, and Chen Zhang. "Gene Evaluation Algorithm for Reconfiguration of Medium and Large Size Photovoltaic Arrays Exhibiting Non-Uniform Aging." Energies 13, no. 8 (April 14, 2020): 1921. http://dx.doi.org/10.3390/en13081921.

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Aging is known to exert various non-uniform effects on photovoltaic (PV) modules within a PV array that consequently can result in non-uniform operational parameters affecting the individual PV modules, leading to a variable power output of the overall PV array. This study presents an algorithm for optimising the configuration of a PV array within which different PV modules are subject to non-uniform aging processes. The PV array reconfiguration approach suggests maximising power generation across non-uniformly aged PV arrays by merely repositioning, rather than replacing, the PV modules, thereby keeping maintenance costs to a minimum. Such a reconfiguration strategy demands data input on the PV module electrical parameters so that optimal reconfiguration arrangements can be selected. The algorithm repetitively sorts the PV modules according to a hierarchical pattern to minimise the impact of module mismatch arising due to non-uniform aging of panels across the array. Computer modelling and analysis have been performed to assess the efficacy of the suggested approach for a variety of dimensions of randomly non-uniformly aged PV arrays (e.g., 5 × 5 and 7 × 20 PV arrays) using MATLAB. The results demonstrate that enhanced power output is possible from a non-uniformly aged PV array and that this can be applied to a PV array of any size.
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Mocellin, Simone, Maurizio Provenzano, Carlo Riccardo Rossi, Pierluigi Pilati, Donato Nitti, and Mario Lise. "DNA Array-Based Gene Profiling." Annals of Surgery 241, no. 1 (January 2005): 16–26. http://dx.doi.org/10.1097/01.sla.0000150157.83537.53.

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O'Neill, Paul. "Gene array breakthrough for glioblastoma." Trends in Molecular Medicine 7, no. 9 (September 2001): 387. http://dx.doi.org/10.1016/s1471-4914(01)02145-1.

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AOKI, Hiroshi, Akiko KITAJIMA, and Hiroaki TAO. "Electrochemical Gene Sensor Arrays Prepared Using Non-contact Nanoliter Array Spotting of Gene Probes." Analytical Sciences 26, no. 3 (2010): 367–70. http://dx.doi.org/10.2116/analsci.26.367.

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Johnston, Mark. "Gene chips: Array of hope for understanding gene regulation." Current Biology 8, no. 5 (February 1998): R171—R174. http://dx.doi.org/10.1016/s0960-9822(98)70103-4.

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Dissertations / Theses on the topic "Gene Array"

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Li, Yan 1978 July 15. "Gene expression array simulator." Thesis, Massachusetts Institute of Technology, 2002. http://hdl.handle.net/1721.1/87263.

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Thesis (M.Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, June 2002.
"May 10, 2002.
Includes bibliographical references (leaf 141).
by Yan Li.
M.Eng.
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Mapiye, Darlington S. "Normalization and statistical methods for crossplatform expression array analysis." University of the Western Cape, 2012. http://hdl.handle.net/11394/4586.

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>Magister Scientiae - MSc
A large volume of gene expression data exists in public repositories like the NCBI’s Gene Expression Omnibus (GEO) and the EBI’s ArrayExpress and a significant opportunity to re-use data in various combinations for novel in-silico analyses that would otherwise be too costly to perform or for which the equivalent sample numbers would be difficult to collects exists. For example, combining and re-analysing large numbers of data sets from the same cancer type would increase statistical power, while the effects of individual study-specific variability is weakened, which would result in more reliable gene expression signatures. Similarly, as the number of normal control samples associated with various cancer datasets are often limiting, datasets can be combined to establish a reliable baseline for accurate differential expression analysis. However, combining different microarray studies is hampered by the fact that different studies use different analysis techniques, microarray platforms and experimental protocols. We have developed and optimised a method which transforms gene expression measurements from continuous to discrete data points by grouping similarly expressed genes into quantiles on a per-sample basis. After cross mapping each probe on each chip to the gene it represents, thereby enabling us to integrate experiments based on genes they have in common across different platforms. We optimised the quantile discretization method on previously published prostate cancer datasets produced on two different array technologies and then applied it to a larger breast cancer dataset of 411 samples from 8 microarray platforms. Statistical analysis of the breast cancer datasets identified 1371 differentially expressed genes. Cluster, gene set enrichment and pathway analysis identified functional groups that were previously described in breast cancer and we also identified a novel module of genes encoding ribosomal proteins that have not been previously reported, but whose overall functions have been implicated in cancer development and progression. The former indicates that our integration method does not destroy the statistical signal in the original data, while the latter is strong evidence that the increased sample size increases the chances of finding novel gene expression signatures. Such signatures are also robust to inter-population variation, and show promise for translational applications like tumour grading, disease subtype classification, informing treatment selection and molecular prognostics.
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Lundén, Karl. "Heterobasidion - conifer pathosystem : heterologous array analysis and transcriptional shift from saprotrophic to necrotrophic growth /." Uppsala : Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, 2010. http://epsilon.slu.se/201019.pdf.

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Norouzi, Masoud. "Development of an RNA array to Protein array (RAPA) platform and its application to gene expression analysis of synthetic riboregulators." Thesis, University of Portsmouth, 2018. https://researchportal.port.ac.uk/portal/en/theses/development-of-an-rna-array-to-protein-array-rapa-platform-and-its-application-to-gene-expression-analysis-of-synthetic-riboregulators(5867a39c-55a4-410a-8e5a-53c347b8a81a).html.

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Bjork, Kathe Elizabeth. "Robust identification of differential gene expression and discrimination /." Connect to full text via ProQuest. Limited to UCD Anschutz Medical Campus, 2006.

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Thesis (Ph.D. in Biostatistics) -- University of Colorado at Denver and Health Sciences Center, 2006.
Typescript. Includes bibliographical references (leaves 237-239). Free to UCDHSC affiliates. Online version available via ProQuest Digital Dissertations;
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Araujo, Tânia Kawasaki de 1985. "Utilização da técnica de Open Array para investigação de genes associados a fendas labiopalatais em amostra da população brasileira." [s.n.], 2015. http://repositorio.unicamp.br/jspui/handle/REPOSIP/313118.

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Orientador: Vera Lúcia Gil da Silva Lopes
Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas
Made available in DSpace on 2018-08-27T00:02:24Z (GMT). No. of bitstreams: 1 Araujo_TaniaKawasakide_D.pdf: 3447671 bytes, checksum: 97911848c6334882843e4b270b9c6771 (MD5) Previous issue date: 2015
Resumo: A fenda de labiopalatal (FLP) isolada é o defeito craniofacial mais comum em humanos. O objetivo deste estudo foi avaliar associações entre 39 genes e a etiologia de FLP isolada em uma amostra da população brasileira. Este estudo de associação do tipo caso-controle foi desenhado com um poder estatístico de 81,29% por meio de regressão logística. O grupo de casos foi composto por 182 pacientes com FLP isolada registrados na Base Brasileira de Dados Clínicos e Familiais de Fendas Orofaciais Típicas. O grupo controle foi formado por 355 indivíduos saudáveis, sem história de fendas orais em três gerações. Toda a amostra foi genotipada por meio do sistema OpenArray®TaqManTM para 253 polimorfismos de nucleotídeo único (SNPs) em 39 genes, incluindo dois genes que, recentemente, haviam sido descritos por este grupo de pesquisa. A seleção de SNPs foi feita com o programa SNPbrowser 4.0 (Applied Biosystems) para verificar o número e a localização dos SNPs apropriados para explorar a associação de cada gene com FLP isolada. A análise de associação foi realizada por meio de regressão logística e regressão stepwise. Os resultados foram corrigidos para múltiplos testes (correção de Bonferroni). Vinte e quatro SNPs em 16 genes foram significativamente associados com a etiologia da FLP isolada, incluindo MSX1, SPRY1, MSX2, PRSS35, TFAP2A, SHH, VAX1, TBX10, WNT11, PAX9, BMP4, JAG2, AXIN2, DVL2, KIF7 e TCBE3. A análise de regressão stepwise revelou que 11 genes contribuiram em 15,5% do fenótipo de FLP isolada nessa amostra. Este é o primeiro estudo a associar os genes KIF7 e TCEB3 à FLP isolada
Abstract: Nonsyndromic cleft lip and palate (NSCLP) is the most common craniofacial birth defect. The aim of this study was to evaluate associations between 39 genes and the etiology of NSCLP in a Brazilian population. This case-control association study was designed with 81.29% statistical power according to logistic regression. The case group was composed of 182 patients with NSCLP enrolled in the Brazilian Database on Orofacial Clefts. The controls included 355 healthy individuals with no history of oral clefting in the past three generations. All samples were genotyped by TaqMan®OpenArrayTM system for 253 single nucleotide polymorphisms (SNPs) in 39 genes, including two that had recently been associated with this process. The SNPs selection was made by SNPbrowser 4.0 (Applied Biosystems) in order to establish the best SNPs to explor the association between each gene and NSCLP. The association analysis was performed using logistic regression and stepwise regression. The results were corrected for multiple testing (Bonferroni correction). Twenty-four SNPs in 16 genes were significantly associated with the etiology of NSCLP, including MSX1, SPRY1, MSX2, PRSS35, TFAP2A, SHH, VAX1, TBX10, WNT11, PAX9, BMP4, JAG2, AXIN2, DVL2, KIF7 and TCBE3. Stepwise regression analysis revealed that 11 genes contributed to 15.5% of the phenotype of NSCLP in the sample. This is the first study to associate KIF7 and TCEB3 with NSCLP
Doutorado
Ciencias Biomedicas
Doutora em Ciências Médicas
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Arlinde, Christina. "Gene expression profiling in animal models of alcoholism /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7140-133-4/.

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Sandgren, Johanna. "Array-based Genomic and Epigenomic Studies in Healthy Individuals and Endocrine Tumours." Doctoral thesis, Uppsala universitet, Institutionen för kirurgiska vetenskaper, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-129533.

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The human genome is a dynamic structure, recently recognized to present with significant large-scale structural variation. DNA-copy number changes represent one common type of such variation and is found both between individuals and within the somatic cells of the same individual, especially in disease states like cancer.  Apart from DNA-rearrangements, epigenomic changes are increasingly acknowledged as important events in the maintenance of genomic integrity. In this thesis, different array-based methods have been applied for global genomic and epigenomic profiling of both normal and cancer cells. In paper I, a genomic microarray was established and used to determine DNA-copy number variants (CNVs) in a cohort of 76 healthy individuals from three ethnic populations. We identified 315 CNV regions that in total encompassed ~3,5% of the genome. In paper II, the array was utilized to discover CNVs within several differentiated tissues from the same subject. Six variants were identified providing evidence for somatic mosaicism. In paper III and IV we studied pheochromocytomas and paragangliomas, rare endocrine tumours that most often present as benign and sporadic with unclear genetic/epigenetic cause. Genome-wide DNA-copy number analysis of 53 benign and malignant samples in paper III revealed numerous common and novel chromosomal regions of losses and gains. High frequencies of relatively small overlapping regions of deletions were detected on chromosome 1p arm, encompassing several candidate tumour suppressor genes. In paper IV, an epigenomic map for two histone modifications associated with silent (H3K27me3) or active (H3K4me3) gene transcription, was generated for one malignant pheochromocytoma. Integrated analysis of global histone methylation, copy number alterations and gene expression data aided in the identification of candidate tumour genes. In conclusion, the performed studies have contributed to gain knowledge of CNVs in healthy individuals, and identified regions and genes which are likely associated with the development and progression of pheochromocytoma/paraganglioma.
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Dumas, Laura Jane. "Gene copy number variation in human and primate evolution /." Connect to full text via ProQuest. Limited to UCD Anschutz Medical Campus, 2008. http://proquest.umi.com/pqdweb?did=1545571861&sid=1&Fmt=6&clientId=18952&RQT=309&VName=PQD.

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Thesis (Ph.D. in Human Medical Genetics) -- University of Colorado Denver, 2008.
Typescript. Includes bibliographical references (leaves 98-112). Free to UCD Anschutz Medical Campus. Online version available via ProQuest Digital Dissertations;
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Tong, Lily. "Probing the function of RNase E family using biochemical techniques and gene array technology." Thesis, University of Leeds, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.414514.

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Books on the topic "Gene Array"

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Muller, Hans-Joachim. Microarrays. Burlington, MA: Elsevier Academic Press, 2005.

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Gene network inference: Verification of methods for systems genetics data. Heidelberg: Springer, 2013.

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1966-, Scherer Andreas, ed. Batch effects and noise in microarray experiments, sources, and solutions. Chichester, West Sussex: J. Wiley, 2009.

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Thomas, Roeder, ed. Microarrays. Burlington, MA: Elsevier Academic Press, 2006.

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T, Kho Alvin, and Butte Atul J, eds. Microarrays for an integrative genomics. Cambridge, Mass: MIT Press, 2003.

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1965-, Blalock Eric M., ed. A beginner's guide to microarrays. Boston: Kluwer Academic Publishers, 2003.

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Formalin-fixed paraffin-embedded tissues: Methods and protocols. New York: Humana Press, 2011.

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1961-, Ye S., and Day Ian N. M, eds. Microarrays & microplates: Applications in biomedical sciences. Oxford: BIOS, 2003.

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Microarray analysis. Hoboken, NJ: Wiley-Liss, 2003.

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Beadchip molecular immunohematology: Toward routine donor and patient antigen profiling by DNA analysis. New York: Springer, 2011.

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Book chapters on the topic "Gene Array"

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Lam, Ching-Wan, and Kin-Chong Lau. "Candidate Screening through High-Density SNP Array." In Gene Discovery for Disease Models, 195–214. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2012. http://dx.doi.org/10.1002/9780470933947.ch10.

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Dorris, David, Chang-gong Liu, Ramesh Ramakrishnan, Richard Shippy, Sangeet Singh-Gasson, Anna Lublinsky, Edward Touma, et al. "Oligonucleotide Array Technologies for Gene Expression Profiling." In Biochips, 1–10. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05092-7_1.

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Jovanovic, Borko D., Raymond C. Bergan, and Warren A. Kibbe. "Some Aspects of Analysis of Gene Array Data." In Biostatistical Applications in Cancer Research, 71–89. Boston, MA: Springer US, 2002. http://dx.doi.org/10.1007/978-1-4757-3571-0_5.

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Dickson, Glenda J., Terence R. Lappin, and Alexander Thompson. "Complete Array of HOX Gene Expression by RQ-PCR." In Leukemia, 369–93. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-59745-418-6_19.

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Lidén, Per, Lars Asker, and Henrik Bostróm. "Rule Induction for Classification of Gene Expression Array Data." In Principles of Data Mining and Knowledge Discovery, 338–47. Berlin, Heidelberg: Springer Berlin Heidelberg, 2002. http://dx.doi.org/10.1007/3-540-45681-3_28.

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González Calabozo, José María, Carmen Peláez-Moreno, and Francisco José Valverde-Albacete. "Gene Expression Array Exploration Using $\mathcal{K}$ -Formal Concept Analysis." In Formal Concept Analysis, 119–34. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-20514-9_11.

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Archer, T. K., M. G. Cordingley, V. Marsaud, H. Richard-Foy, and G. L. Hager. "Steroid Transactivation at a Promoter Organized in a Specifically-Positioned Array of Nucleosomes." In The Steroid/Thyroid Hormone Receptor Family and Gene Regulation, 221–38. Basel: Birkhäuser Basel, 1989. http://dx.doi.org/10.1007/978-3-0348-5466-5_16.

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Aigner, Thomas, Pia M. Gebhard, and Alexander Zien. "Gene expression profiling by the cDNA array technology: Molecular portraying of chondrocytes." In The Many Faces of Osteoarthritis, 293–96. Basel: Birkhäuser Basel, 2002. http://dx.doi.org/10.1007/978-3-0348-8133-3_29.

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Wong, Kwong-Kwok. "Use of Single-Nucleotide Polymorphism Array for Tumor Aberrations in Gene Copy Numbers." In Genomics and Pharmacogenomics in Anticancer Drug Development and Clinical Response, 75–88. Totowa, NJ: Humana Press, 2008. http://dx.doi.org/10.1007/978-1-60327-088-5_6.

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Jovanovic, Borko D., Shuguang Huang, Yuequin Liu, Karen N. Naguib, and Raymond C. Bergan. "An Analysis of Gene Array Data Related to Cell Adhesion and Prostate Cancer." In Biostatistical Applications in Cancer Research, 91–111. Boston, MA: Springer US, 2002. http://dx.doi.org/10.1007/978-1-4757-3571-0_6.

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Conference papers on the topic "Gene Array"

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Neitz, Maureen. "Molecular genetics of red-green color vision." In OSA Annual Meeting. Washington, D.C.: Optica Publishing Group, 1990. http://dx.doi.org/10.1364/oam.1990.fm2.

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Genes encoding cone pigments sensitive to middle-to-long wavelengths lie in a head-to-tail tandem array on the X-chromosome. Although two X-encoded genes, one for long-wavelength-sensitive pigments and one for middle-wavelength-sensitive pigments, are sufficient to serve trichromatic color vision, most people have more than two such genes. The arrangement, location, and degree of homology of the pigment genes promote recombination within the tandem arrays. Such recombination events produce pigment-gene complements that differ in the number and sequences of individual genes and in the interrelationships between genes. The accumulation of recombination-generated changes over the span of evolutionary time has culminated in a large number of X-encoded photopigment gene complements in the human population. It is, thus, not surprising that there are widespread variations in human color vision.
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Caffarena, G., S. Bojanic, J. A. Lopez, C. Pedreira, and O. Nieto-Taladriz. "High-speed systolic array for gene matching." In Proceeding of the 2004 ACM/SIGDA 12th international symposium. New York, New York, USA: ACM Press, 2004. http://dx.doi.org/10.1145/968280.968325.

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Paik, S. J., S. Park, V. Zarnitsyn, M. R. Prausnitz, M. G. Allen, S. Choi, and X. D. Guo. "A HIGHLY DENSE NANONEEDLE ARRAY FOR INTRACELLULAR GENE DELIVERY." In 2012 Solid-State, Actuators, and Microsystems Workshop. San Diego: Transducer Research Foundation, 2012. http://dx.doi.org/10.31438/trf.hh2012.40.

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Venkatesh, E. T., P. Tangaraj, and S. Chitra. "Classification of cancer gene expressions from micro-array analysis." In 2010 International Conference on Innovative Computing Technologies (ICICT). IEEE, 2010. http://dx.doi.org/10.1109/icinnovct.2010.5440095.

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Hu, Jing, Jianbo Gao, Yinhe Cao, and Weijia Zhang. "Detection of gene copy number change in array CGH data." In 2006 IEEE/NLM Life Science Systems and Applications Workshop. IEEE, 2006. http://dx.doi.org/10.1109/lssa.2006.250402.

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Rehna, V. J., and G. Raju. "Signal extraction from microarray images for gene array data analysis." In 2nd International Conference on Computer and Automation Engineering (ICCAE 2010). IEEE, 2010. http://dx.doi.org/10.1109/iccae.2010.5451859.

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Dror, Ron O., Jonathan G. Murnick, Nicola A. Rinaldi, Voichita D. Marinescu, Ryan M. Rifkin, and Richard A. Young. "A bayesian approach to transcript estimation from gene array data." In the sixth annual international conference. New York, New York, USA: ACM Press, 2002. http://dx.doi.org/10.1145/565196.565213.

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Tian, David, and Keith Burley. "Classification of micro-array gene expression data using neural networks." In 2010 International Joint Conference on Neural Networks (IJCNN). IEEE, 2010. http://dx.doi.org/10.1109/ijcnn.2010.5596568.

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Ramalingam, Naveen, Long-Qing Chen, Xin-Hao Yang, Liqun Deng, Qing-Hui Wang, Eric Yap Peng Huat, Chiew Hoon Neo, and Hai-Qing Gong. "A Surface-Directed Microfluidic Scheme for Parallel Nanoliter PCR Array Suitable for Point-of-Care Testing." In ASME 2009 7th International Conference on Nanochannels, Microchannels, and Minichannels. ASMEDC, 2009. http://dx.doi.org/10.1115/icnmm2009-82052.

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In resource-limited settings, it is impractical to get access to a diagnostic laboratory having sophisticated instruments, and it is desirable to use disposable point-of-care diagnostic chips that do not require liquid handling or pumping instruments for sample distribution among an array of reactors. In addition to the pump-less sample loading method, the challenge to seal an array of reactors without the use of microvalves or mechanical parts still persists. Implementation of microvalve array adds complexity to the chip fabrication and operation processes, and also reduces the space on the microchip. In this paper, we report the development of a high-throughput quantitative PCR chip platform for parallel analyses of multiple gene targets. The PCR mixture distribution among an array of 80 microreactors and subsequent isolation of the reactors were solely realized by a two-step surface tension-based microfluidic scheme, which eliminates the use of pumps, valves and liquid handling instruments. Confinement of the PCR mixture inside the micro reactors was achieved by implementing hybrid flow-restriction passive valves. The microreactors were isolated from each other by the flow of a curable liquid sealant delivered through microchannels by capillary action. We also investigated the effect of detergents that are present in most commercial PCR buffers. Presence of detergents makes the PCR buffer much more wetting on the passive capillary valve surface and this imposes another challenge to the design of the conventional hydrophobic patch valves which has been successfully used for deionized water. We demonstrated a successful capillary valve array with a common air venting channel having a hydrophobic surface for restricting the flow of PCR buffer containing surfactant. The interconnected microreactor array was fabricated on a glass chip substrate with approximate volume of 250 nl microreactor volume for PCR. A different set of PCR primers were preloaded into different microreactor on the PCR array chip for simultaneous amplification of multiple genes. Fluorescent signals from all the microreactors were simultaneously detected at every PCR thermal cycle using EvaGreen fluorescent dye on an in-house real-time PCR instrument. The capability of the scalable PCR array chip was demonstrated by amplifying a fragment of uidA gene for beta-glucuronidase of E. coli genome. Key technical issues related to chip operation such as PCR inhibition on the acid-washed glass substrate, and PCR compatibility of the sealant in both the uncured and cured states have been addressed.
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Chretien, Stephane, Christophe Guyeux, Michael Boyer-Guittaut, Regis Delage-Mouroux, and Francoise Descotes. "Investigating gene expression array with outliers and missing data in bladder cancer." In 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2015. http://dx.doi.org/10.1109/bibm.2015.7359819.

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Reports on the topic "Gene Array"

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Fluhr, Robert, and Volker Brendel. Harnessing the genetic diversity engendered by alternative gene splicing. United States Department of Agriculture, December 2005. http://dx.doi.org/10.32747/2005.7696517.bard.

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Our original objectives were to assess the unexplored dimension of alternative splicing as a source of genetic variation. In particular, we sought to initially establish an alternative splicing database for Arabidopsis, the only plant for which a near-complete genome has been assembled. Our goal was to then use the database, in part, to advance plant gene prediction programs that are currently a limiting factor in annotating genomic sequence data and thus will facilitate the exploitation of the ever increasing quantity of raw genomic data accumulating for plants. Additionally, the database was to be used to generate probes for establishing high-throughput alternative transcriptome analysis in the form of a splicing-specific oligonucleotide microarray. We achieved the first goal and established a database and web site termed Alternative Splicing In Plants (ASIP, http://www.plantgdb.org/ASIP/). We also thoroughly reviewed the extent of alternative splicing in plants (Arabidopsis and rice) and proposed mechanisms for transcript processing. We noted that the repertoire of plant alternative splicing differs from that encountered in animals. For example, intron retention turned out to be the major type. This surprising development was proven by direct RNA isolation techniques. We further analyzed EST databases available from many plants and developed a process to assess their alternative splicing rate. Our results show that the lager genome-sized plant species have enhanced rates of alternative splicing. We did advance gene prediction accuracy in plants by incorporating scoring for non-canonical introns. Our data and programs are now being used in the continuing annotation of plant genomes of agronomic importance, including corn, soybean, and tomato. Based on the gene annotation data developed in the early part of the project, it turned out that specific probes for different exons could not be scaled up to a large array because no uniform hybridization conditions could be found. Therefore, we modified our original objective to design and produce an oligonucleotide microarray for probing alternative splicing and realized that it may be reasonable to investigate the extent of alternative splicing using novel commercial whole genome arrays. This possibility was directly examined by establishing algorithms for the analysis of such arrays. The predictive value of the algorithms was then shown by isolation and verification of alternative splicing predictions from the published whole genome array databases. The BARD-funded work provides a significant advance in understanding the extent and possible roles of alternative splicing in plants as well as a foundation for advances in computational gene prediction.
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Tu, Q., Ye Deng, Lu Lin, Chris L. Hemme, Zhili He, and Jizhong Zhou. HuMiChip: Development of a Functional Gene Array for the Study of Human Microbiomes. Office of Scientific and Technical Information (OSTI), May 2010. http://dx.doi.org/10.2172/1008326.

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Xu, Jin-Rong, and Amir Sharon. Comparative studies of fungal pathogeneses in two hemibiotrophs: Magnaporthe grisea and Colletotrichum gloeosporioides. United States Department of Agriculture, May 2008. http://dx.doi.org/10.32747/2008.7695585.bard.

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Plant pathogenic fungi have various life styles and different plant infection strategies. Hemibiotrophs like Magnaporthe grisea and Colletotrichum species develop specialized structures during plant infection. The goal of this study was to identify, characterize, and compare genes required for plant infection in M. grisea and C. gloeosporioides. Specific objectives are to: 1) further characterize genes identified in the preliminary studies of C. gloeosporioides and M. grisea;2) identify and characterize additional fungal genes tagged by GFP; and 3) identify in planta growth and appressorium-specific genes by subtractive hybridization and transcript profiling by the LongSAGE method. In this study, the PI and Co-PI collaborated closely on studies in M. grisea and C. gloeosporioides. In M. grisea, REMI and ATMT were used to transform the wildtype with promoter-less EGFP constructs. A total of 28 mutants defective in different plant infection processes or expressing EGFP during plant infection were identified. Genes disrupted in five selected mutants have been identified, including MG03295 that encodes a putative Rho GTPase. In transformant L1320, the transforming vector was inserted in the MIRI gene that encodes a nuclear protein. The expression of MIRI was highly induced during infection. Deletion and site-directed mutagenesis analyses were used to identify the promoter regions and elements that were essential for induced in planta expression of MIRI. This was the first detailed characterization of the promoter of an in planta gene in M. grisea and the MIRI promoter can be used to monitor infectious growth. In addition, the Agilent whole-genome array of M. grisea was used for microarray analyses with RNA samples from appressoria formed by the wild-type shain and the pmkl and mstl2 mutants. Over 200 genes were downregulated in the mst I 2 and pmkl mutants. Some of them are putative transcription factors that may regulate appressorium formation and infectious hyphal growth. In C. gloeosporioides, various REMI mutants showing different pathogenic behavior were identified and characterized. Mutants N3736 had a single insertion and was hyper-virulent. The gene disrupted in mutant3736 (named CgFMOI) encodes a FAD-dependent monooxygenase. Expression analyses linked the expression of the CgFMOI gene with the necrotrophic phase of fungal infection, and also suggest that expression of CgFMOl is unnecessary for the first stages of infection and for biotrophy establishment. All CgFMOl-silenced mutants had reduced virulence. In REMI mutant N159, the tagged gene encodes a putative copper transporter that is homologue of S. cerevisiae CTR2. In yeast, Ctr2 is a vacuolar transporter for moving copper from the vacuole to the cytoplasm. The gene was therefore termed CgCTR2. In addition to characterization of CgCTR2, we also conducted comparative analyses in M. grisea. The M. grisea CgCTR-2 homolog was isolated, knockout strains were generated and characterized and the M. grisea was used to complement the Nl 59 C. gloeosporioides mutant. Overall, we have accomplished most of proposed experiments and are in the process of organizing and publishing other data generated in this project. For objective 3, we used the microarray analysis approach. Several genes identified in this study are novel fungal virulence factors. They have the potential to be used as targets for developing more specific or effective fungicides. In the long run, comparative studies of fungal genes, such as our CgCTR2 work, may lead to better disease control strategies.
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Steffens, John, Eithan Harel, and Alfred Mayer. Coding, Expression, Targeting, Import and Processing of Distinct Polyphenoloxidases in Tissues of Higher Plants. United States Department of Agriculture, November 1994. http://dx.doi.org/10.32747/1994.7613008.bard.

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Polyphenol oxidase (PPO) catalyzes the oxidation of phenols to quinones at the expense of O2. PPOs are ubiquitous in higer plants, and their role in oxidative browning of plant tissues causes large annual losses to food production. Despite the importance of PPOs to agriculture, the function(s) of PPOs in higher plants are not understood. Among other roles, PPOs have been proposed to participate in aspects of chloroplast metabolism, based on their occurrence in plastids and high Km for O2. Due to the ability of PPO to catalyze formation of highly reactive quinones, PPOs have also been proposed to be involved in a wide array of defensive interactions with insect, bacterial, and fungal pests. Physiological and biochemical studies of PPO have provided few answers to the major problems of PPO function, subcellular localization, and biochemical properties. This proposal achieved the following major objectives: cloning of PPO cDNAs in potato and tomato; characterization of the tomato PPO gene family; antisense downregulation of the tomato PPO gene family; and reduction in post-harvest enzymic browning of potato through expression of antisense PPO genes under the control of tuber-specific promoters. In addition, we established the lumenal localization of PPO, characterized and clarified the means by which PPOs are imported and processed by chloroplasts, and provided insight into the factors which control localization of PPOs. This proposal has thereby provided fundamental advances in the understanding of this enzyme and the control of its expression.
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Levin, Ilan, Avtar K. Handa, Avraham Lalazar, and Autar K. Mattoo. Modulating phytonutrient content in tomatoes combining engineered polyamine metabolism with photomorphogenic mutants. United States Department of Agriculture, December 2006. http://dx.doi.org/10.32747/2006.7587724.bard.

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Fruit constitutes a major component of our diet, providing fiber, vitamins, minerals, and many other phytonutrients that promote good health. Fleshy fruits, such as tomatoes, already contain high levels of several of these ingredients. Nevertheless, efforts have been invested in increasing and diversifying the content of phytonutrients, such as carotenoids and flavonoids, in tomato fruits. Increasing levels of phytonutrients, such as lycopene, is highly justified from the perspective of the lycopene extraction industry due to cost effectiveness reasons. Diversifying phytonutrients, in particular those that contribute to fruit color, could potentially provide an array of attractive colors to our diet. Our major goal was to devise a novel strategy for developing tomato fruits with enhanced levels of phytochemicals known to promote good health with special emphasis on lycopene content. A further important goal was to analyze global gene expression of selected genetic lines produced throughout this study in order is to dissect the molecular mechanisms regulating phytonutrients accumulation in the tomato fruit. To achieve these goals we proposed to: 1. combine, by classical breeding, engineered polyamine metabolism with photomorphogenic high pigment mutants in order generate tomato plant with exceptionally high levels of phytonutrients; 2. use gene transfer technology for genetic introduction of key genes that promote phytonutrient accumulation in the tomato fruit, 3. Analyze accumulation patterns of the phytonutrients in the tomato fruit during ripening; 4. Analyze global gene expression during fruit ripening in selected genotypes identified in objectives 1 and 2, and 5. Identify and analyze regulatory mechanisms of chloroplast disassembly and chromoplast formation. During the 3 years research period we have carried out most of the research activities laid out in the original proposal and our key conclusions are as follows: 1. the engineered polyamine metabolism strategy proposed by the US collaborators can not increase lycopene content either on its own or in combination with an hp mutant (hp-2ᵈᵍ); 2. The hp-2ᵈᵍ affects strongly the transcriptional profile of the tomato fruit showing a strong tendency for up- rather than down-regulation of genes, 3. Ontology assignment of these miss-regulated genes revealed a consistent up-regulation of genes related to chloroplast biogenesis and photosynthesis in hp-2ᵈᵍ mutants throughout fruit development; 4. A tendency for up-regulation was also usually observed in structural genes involved in phytonutrientbiosynthesis; however this up-regulation was not as consistent. 5. Microscopic observations revealed a significantly higher number of chloroplasts in pericarp cells of mature-green hp-2ᵈᵍ/hp-2ᵈᵍ fruits in comparison to their normal fully isogenic counterparts. 6. The relative abundance of chloroplasts could be observed from early stages of fruit development. Cumulatively these results suggest that: 1. the overproduction of secondary metabolites, characterizing hp-2ᵈᵍ/hp-2ᵈᵍ fruits, is more due to chloroplast number rather then to transcriptional activation of structural genes of the relevant metabolic pathways, and 2. The molecular trigger increasing metabolite levels in hp-2ᵈᵍ mutant fruits should be traced at early stage of fruit development.
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Seroussi, Eyal, and George Liu. Genome-Wide Association Study of Copy Number Variation and QTL for Economic Traits in Holstein Cattle. United States Department of Agriculture, September 2010. http://dx.doi.org/10.32747/2010.7593397.bard.

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Copy number variation (CNV) has been recently identified in human and other mammalian genomes and increasing awareness that CNV might be a major source for heritable variation in complex traits has emerged. Despite this, little has been published on CNVs in Holsteins. In order to fill this knowledge-gap, we proposed a genome-wide association study between quantitative trait loci (QTL) for economic traits and CNV in the Holstein cattle. The approved feasibility study was aimed at the genome-wide characterization of CNVs in Holstein cattle and at the demonstrating of their possible association with economic traits by performing the activities of preparation of DNA samples, Comparative Genomic Hybridization (CGH), initial association study between CNVs and production traits and characterization of CNVSNP associations. For both countries, 40 genomic DNA samples of bulls representing the extreme sub-populations for economically important traits were CGH analyzed using the same reference genome on a NimbleGen tiling array. We designed this array based on the latest build of the bovine genome (UMD3) with average probe spacing of 1150 bases (total number of probes was 2,166,672). Two CNV gene clusters, PLA2G2D on BTA2 and KIAA1683 on BTA7 revealed significant association with milk percentage and cow fertility, respectively, and were chosen for further characterization and verification in a larger sample using other methodologies including sequencing, tag SNPs and real time PCR (qPCR). Comparison between these four methods indicated that there is under estimation of the number of CNV loci in Holstein cattle and their complexity. The variation in sequence between different copies seemed to affect their functionality and thus the hybridization based methods were less informative than the methods that are based on sequencing. We thus conclude that large scale sequencing effort complemented by array CGH should be considered to better detect and characterize CNVs in order to effectively employ them in marker-assisted selection.
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Abbo, Shahal, Hongbin Zhang, Clarice Coyne, Amir Sherman, Dan Shtienberg, and George J. Vandemark. Winter chickpea; towards a new winter pulse for the semiarid Pacific Northwest and wider adaptation in the Mediterranean basin. United States Department of Agriculture, January 2011. http://dx.doi.org/10.32747/2011.7597909.bard.

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Original objectives: [a] Screen an array of chickpea and wild annual Cicer germplasm for winter survival. [b] Genetic analysis of winter hardiness in domesticated x wild chickpea crosses. [c] Genetic analysis of vernalization response in domesticated x wild chickpea crosses. [d] Digital expression analysis of a core selection of breeding and germplasm lines of chickpea that differ in winter hardiness and vernalization. [e] Identification of the genes involved in the chickpea winter hardiness and vernalization and construction of gene network controlling these traits. [f] Assessing the phenotypic and genetic correlations between winter hardiness, vernalization response and Ascochyta blight response in chickpea. The complexity of the vernalization response and the inefficiency of our selection experiments (below) required quitting the work on ascochyta response in the framework of this project. Background to the subject: Since its introduction to the Palouse region of WA and Idaho, and the northern Great Plains, chickpea has been a spring rotation legume due to lack of winter hardiness. The short growing season of spring chickpea limits its grain yield and leaves relatively little stubble residue for combating soil erosion. In Israel, chilling temperatures limit pod setting in early springs and narrow the effective reproductive time window of the crop. Winter hardiness and vernalization response of chickpea alleles were lost due to a series of evolutionary bottlenecks; however, such alleles are prevalent in its wild progenitor’s genepool. Major conclusions, solutions, achievements: It appears that both vernalization response and winter hardiness are polygenic traits in the wild-domesticated chickpea genepool. The main conclusion from the fieldwork in Israel is that selection of domesticated winter hardy and vernalization responsive types should be conducted in late flowering and late maturity backgrounds to minimize interference by daylength and temperature response alleles (see our Plant Breeding paper on the subject). The main conclusion from the US winter-hardiness studies is that excellent lines have been identified for germplasm release and continued genetic study. Several of the lines have good seed size and growth habit that will be useful for introgressing winter-hardiness into current chickpea cultivars to develop releases for autumn sowing. We sequenced the transcriptomes and profiled the expression of genes in 87 samples. Differential expression analysis identified a total of 2,452 differentially expressed genes (DEGs) between vernalized plants and control plants, of which 287 were shared between two or more Cicer species studied. We cloned 498 genes controlling vernalization, named CVRN genes. Each of the CVRN genes contributes to flowering date advance (FDA) by 3.85% - 10.71%, but 413 (83%) other genes had negative effects on FDA, while only 83 (17%) had positive effects on FDA, when the plant is exposed to cold temperature. The cloned CVRN genes provide new toolkits and knowledge to develop chickpea cultivars that are suitable for autumn-sowing. Scientific & agricultural implications: Unlike the winter cereals (barley, wheat) or pea, in which a single allelic change may induce a switch from winter to spring habit, we were unable to find any evidence for such major gene action in chickpea. In agricultural terms this means that an alternative strategy must be employed in order to isolate late flowering – ascochyta resistant (winter types) domesticated forms to enable autumn sowing of chickpea in the US Great Plains. An environment was identified in U.S. (eastern Washington) where autumn-sown chickpea production is possible using the levels of winter-hardiness discovered once backcrossed into advanced cultivated material with acceptable agronomic traits. The cloned CVRN genes and identified gene networks significantly advance our understanding of molecular mechanisms underlying plant vernalization in general, and chickpea in particular, and provide a new toolkit for switching chickpea from a spring-sowing to autumn-sowing crop.
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Bercovier, Herve, and Ronald P. Hedrick. Diagnostic, eco-epidemiology and control of KHV, a new viral pathogen of koi and common carp. United States Department of Agriculture, December 2007. http://dx.doi.org/10.32747/2007.7695593.bard.

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Original objectives and revisions-The proposed research included these original objectives: field validation of diagnostic tests (PCR), the development and evaluation of new sensitive tools (LC-PCR/TaqManPCR, antibody detection by ELISA) including their use to study the ecology and the epidemiology of KHV (virus distribution in the environment and native cyprinids) and the carrier status of fish exposed experimentally or naturally to KHV (sites of virus replication and potential persistence or latency). In the course of the study we completed the genome sequence of KHV and developed a DNA array to study the expression of KHV genes in different conditions. Background to the topics-Mass mortality of koi or common carp has been observed in Israel, USA, Europe and Asia. These outbreaks have reduced exports of koi from Israel and have created fear about production, import, and movements of koi and have raised concerns about potential impacts on native cyprinid populations in the U.S.A. Major conclusions-A suite of new diagnostic tools was developed that included 3 PCR assays for detection of KHV DNA in cell culture and fish tissues and an ELISA assay capable of detecting anti-KHV antibodies in the serum of koi and common carp. The TKPCR assay developed during the grant has become an internationally accepted gold standard for detection of viral DNA. Additionally, the ELISA developed for detecting serum anti-KHV antibodies is now in wide use as a major nonlethal screening tool for evaluating virus status of koi and common carp populations. Real time PCR assays have been able to detect viral DNA in the internal organs of survivors of natural and wild type vaccine exposures at 1 and 10³ genome equivalents at 7 months after exposure. In addition, vaccinated fish were able to transmit the virus to naive fish. Potential control utilizing hybrids of goldfish and common carp for production demonstrated they were considerably more resistant than pure common carp or koi to both KHV (CyHV-3). There was no evidence that goldfish or other tested endemic cyprinids species were susceptible to KHV. The complete genomic sequencing of 3 strains from Japan, the USA, and Israel revealed a 295 kbp genome containing a 22 kbp terminal direct repeat encoding clear gene homologs to other fish herpesviruses in the family Herpesviridae. The genome encodes156 unique protein-coding genes, eight of which are duplicated in the terminal repeat. Four to seven genes are fragmented and the loss of these genes may be associated with the high virulence of the virus. Viral gene expression was studies by a newly developed chip which has allowed verification of transcription of most all hypothetical genes (ORFs) as well as their kinetics. Implications, both scientific and agricultural- The results from this study have immediate application for the control and management of KHV. The proposal provides elements key to disease management with improved diagnostic tools. Studies on the ecology of the virus also provide insights into management of the virus at the farms that farmers will be able to apply immediately to reduce risks of infections. Lastly, critical issues that surround present procedures used to create “resistant fish” must be be resolved (e.g. carriers, risks, etc.). Currently stamping out may be effective in eradicating the disease. The emerging disease caused by KHV continues to spread. With the economic importance of koi and carp and the vast international movements of koi for the hobby, this disease has the potential for even further spread. The results from our studies form a critical component of a comprehensive program to curtail this emerging pathogen at the local, regional and international levels.
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Porat, Ron, Gregory T. McCollum, Amnon Lers, and Charles L. Guy. Identification and characterization of genes involved in the acquisition of chilling tolerance in citrus fruit. United States Department of Agriculture, December 2007. http://dx.doi.org/10.32747/2007.7587727.bard.

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Citrus, like many other tropical and subtropical fruit are sensitive to chilling temperatures. However, application of a pre-storage temperature conditioning (CD) treatment at 16°C for 7 d or of a hot water brushing (HWB) treatment at 60°C for 20 sec remarkably enhances chilling tolerance and reduces the development of chilling injuries (CI) upon storage at 5°C. In the current research, we proposed to identify and characterize grapefruit genes that are induced by CD, and may contribute to the acquisition of fruit chilling tolerance, by two different molecular approaches: cDNA array analysis and PCR cDNA subtraction. In addition, following the recent development and commercialization of the new Affymetrix Citrus Genome Array, we further performed genome-wide transcript profiling analysis following exposure to CD and chilling treatments. To conduct the cDNA array analysis, we constructed cDNA libraries from the peel tissue of CD- and HWB-treated grapefruit, and performed an EST sequencing project including sequencing of 3,456 cDNAs from each library. Based on the obtained sequence information, we chose 70 stress-responsive and chilling-related genes and spotted them on nylon membranes. Following hybridization the constructed cDNA arrays with RNA probes from control and CD-treated fruit and detailed confirmations by RT-PCR analysis, we found that six genes: lipid-transfer protein, metallothionein-like protein, catalase, GTP-binding protein, Lea5, and stress-responsive zinc finger protein, showed higher transcript levels in flavedo of conditioned than in non-conditioned fruit stored at 5 ᵒC. The transcript levels of another four genes: galactinol synthase, ACC oxidase, temperature-induced lipocalin, and chilling-inducible oxygenase, increased only in control untreated fruit but not in chilling-tolerant CD-treated fruit. By PCR cDNA subtraction analysis we identified 17 new chilling-responsive and HWB- and CD-induced genes. Overall, characterization of the expression patterns of these genes as well as of 11 more stress-related genes by RNA gel blot hybridizations revealed that the HWB treatment activated mainly the expression of stress-related genes(HSP19-I, HSP19-II, dehydrin, universal stress protein, EIN2, 1,3;4-β-D-glucanase, and SOD), whereas the CD treatment activated mainly the expression of lipid modification enzymes, including fatty acid disaturase2 (FAD2) and lipid transfer protein (LTP). Genome wide transcriptional profiling analysis using the newly developed Affymetrix Citrus GeneChip® microarray (including 30,171 citrus probe sets) revealed the identification of three different chilling-related regulons: 1,345 probe sets were significantly affected by chilling in both control and CD-treated fruits (chilling-response regulon), 509 probe sets were unique to the CD-treated fruits (chilling tolerance regulon), and 417 probe sets were unique to the chilling-sensitive control fruits (chilling stress regulon). Overall, exposure to chilling led to expression governed arrest of general cellular metabolic activity, including concretive down-regulation of cell wall, pathogen defense, photosynthesis, respiration, and protein, nucleic acid and secondary metabolism. On the other hand, chilling enhanced various adaptation processes, such as changes in the expression levels of transcripts related to membranes, lipid, sterol and carbohydrate metabolism, stress stimuli, hormone biosynthesis, and modifications in DNA binding and transcription factors.
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Horwitz, Benjamin, and Barbara Gillian Turgeon. Secondary Metabolites, Stress, and Signaling: Roles and Regulation of Peptides Produced by Non-ribosomal Peptide Synthetases. United States Department of Agriculture, 2005. http://dx.doi.org/10.32747/2005.7696522.bard.

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Fungal pathogens of plants produce a diverse array of small molecules. Often referred to as secondary metabolites because they were thought to be dispensable for basic functions, they may indeed have central roles as signals for the fungal cell, and in interactions with the host. We have identified more than a dozen genes encoding nonribosomal peptide synthetases (NPS) in Cochliobolusheterostrophus, the agent of southern corn leaf blight. The aim of this project was to identify roles of these genes in stress responses and signaling. The first objective was to test a complete collection of C. heterostrophus nonribosomal peptide synthetase (NRPS)-encoding gene deletion mutant and wildtype (WT) strains for sensitivity to various agents of oxidative (ROS) and nitrosative (RNOS) stress, in vitro. The second objective and next step in this part of the project was to study the relevance of sensitivity to ROS and RNOS in the host pathogen interaction, by measuring the production of ROS and RNOS in planta, when plants are inoculated with wild type and mutant strains. A third objective was to study expression of any genes shown to be involved in sensitivity to ROS or RNOS, in vitro and in planta. Another objective was to determine if any of the genes involved in oxidative or nitrosative stress responses are regulated by components of signal transduction pathways (STP) that we have identified and to determine where mechanisms overlap. Study of the collection of nps mutants identified phenotypes relevant for virulence, development and oxidative stress resistance for two of the genes, NPS2 and NPS6. Mutants in genes related to RNOS stress have no virulence phenotypes, while some of those related to ROS stress have reduced virulence as well as developmental phenotypes, so we focused primarily on ROS stress pathways. Furthermore, the identification of NPS2 and NPS6 as encoding for NRPS responsible for siderophore biosynthesis lent a new focus to the project, regulation by Fe. We have not yet developed good methods to image ROS in planta and work in this direction is continuing. We found that NPS6 expression is repressed by Fe, responding over the physiological Fe concentration range. Studying our collection of mutants, we found that conserved MAPK and G protein signal transduction pathways are dispensable for Fe regulation of NPS6, and initiated work to identify other pathways. The transcription factor SreA is one candidate, and is responsible for part, but not all, of the control of NPS6 expression. The results of this project show that the pathogen contends with oxidative stress through several signaling pathways. Loss of the siderophore produced by Nps6 makes the fungus sensitive to oxidative stress, and decreases virulence, suggesting a central role of the ability to sequester and take up extracellular iron in the host-pathogen interaction. Siderophores, and manipulation of Fe levels, could be targets for new strategies to deal with fungal pathogens of maize and other plants.
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