scholarly journals Screening of an E. coli O157:H7 Bacterial Artificial Chromosome Library by Comparative Genomic Hybridization to Identify Genomic Regions Contributing to Growth in Bovine Gastrointestinal Mucus and Epithelial Cell Colonization

2011 ◽  
Vol 2 ◽  
Author(s):  
Jianing Bai ◽  
Sean P. McAteer ◽  
Edith Paxton ◽  
Arvind Mahajan ◽  
David L. Gally ◽  
...  
Keyword(s):  
Epithelial Cell ◽  
Bacterial Artificial Chromosome ◽  
Comparative Genomic Hybridization ◽  
Bacterial Artificial Chromosome Library ◽  
Artificial Chromosome ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
E Coli ◽  
Cell Colonization ◽  
Genomic Regions

scholarly journals aCGH Analysis to Estimate Genetic Variations among Domesticated Chickens

2016 ◽  
Vol 2016 ◽  
pp. 1-8 ◽  
Author(s):  
Tomoyoshi Komiyama ◽  
Mengjie Lin ◽  
Atsushi Ogura
Keyword(s):  
Comparative Genomic Hybridization ◽  
Selection Pressure ◽  
Array Comparative Genomic Hybridization ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Selective Pressures ◽  
Number Of Genes ◽  
Chicken Breeds ◽  
Ancient Times ◽  
Genomic Regions

Chickens have been familiar to humans since ancient times and have been used not only for culinary purposes but also for cultural purposes including ritual ceremonies and traditional entertainment. The various chicken breeds developed for these purposes often display distinct morphological and/or behavioural traits. For example, the JapaneseShamois larger and more aggressive than other domesticated chickens, reflecting its role as a fighting cock breed, whereas JapaneseNaganakidoribreeds, which have long-crowing behaviour, were bred instead for their entertaining and aesthetic qualities. However, the genetic backgrounds of these distinct morphological and behavioural traits remain unclear. Therefore, the question arises as to which genomic regions in these chickens were acted upon by selective pressures through breeding. We compared the entire genomes of six chicken breeds domesticated for various cultural purposes by utilizing array comparative genomic hybridization. From these analyses, we identified 782 regions that underwent insertions, deletions, or mutations, representing man-made selection pressure in these chickens. Furthermore, we found that a number of genes diversified in domesticated chickens bred for cultural or entertainment purposes were different from those diversified in chickens bred for food, such as broilers and layers.

scholarly journals Repetitive genome elements in a European corn borer, Ostrinia nubilalis, bacterial artificial chromosome library were indicated by bacterial artificial chromosome end sequencing and development of sequence tag site markers: implications for lepidopteran genomic research

Genome ◽  
2009 ◽  
Vol 52 (1) ◽  
pp. 57-67 ◽  
Author(s):  
Brad S. Coates ◽  
Douglas V. Sumerford ◽  
Richard L. Hellmich ◽  
Leslie C. Lewis
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Bacterial Artificial Chromosome Library ◽  
Ostrinia Nubilalis ◽  
European Corn Borer ◽  
Artificial Chromosome ◽  
Genomic Research ◽  
Comparative Genomic ◽  
Average Insert Size ◽  
Corn Borer ◽  
Site Markers

The European corn borer, Ostrinia nubilalis , is a serious pest of food, fiber, and biofuel crops in Europe, North America, and Asia and a model system for insect olfaction and speciation. A bacterial artificial chromosome library constructed for O. nubilalis contains 36 864 clones with an estimated average insert size of ≥120 kb and genome coverage of 8.8-fold. Screening OnB1 clones comprising approximately 2.76 genome equivalents determined the physical position of 24 sequence tag site markers, including markers linked to ecologically important and Bacillus thuringiensis toxin resistance traits. OnB1 bacterial artificial chromosome end sequence reads (GenBank dbGSS accessions ET217010 to ET217273) showed homology to annotated genes or expressed sequence tags and identified repetitive genome elements, O. nubilalis miniature subterminal inverted repeat transposable elements (OnMITE01 and OnMITE02), and ezi-like long interspersed nuclear elements. Mobility of OnMITE01 was demonstrated by the presence or absence in O. nubilalis of introns at two different loci. A (GTCT)n tetranucleotide repeat at the 5′ ends of OnMITE01 and OnMITE02 are evidence for transposon-mediated movement of lepidopteran microsatellite loci. The number of repetitive elements in lepidopteran genomes will affect genome assembly and marker development. Single-locus sequence tag site markers described here have downstream application for integration within linkage maps and comparative genomic studies.

Identification of Genomic Imbalances in AML with Complex Karyotype Using Matrix-Based Comparative Genomic Hybridization.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 3382-3382
Author(s):  
Frank G. Rucker ◽  
Carsten Schwanen ◽  
Daniel Lipka ◽  
Swen Wessendorf ◽  
Stefan Frohling ◽  
...  
Keyword(s):  
Comparative Genomic Hybridization ◽  
Fusion Transcript ◽  
Artificial Chromosome ◽  
Hematologic Malignancies ◽  
Physical Distance ◽  
Comparative Genomic ◽  
Complex Karyotype ◽  
Genomic Hybridization ◽  
Genomic Imbalances ◽  
Chromosomal Bands

Abstract Approximately 10 to 15 % of acute myeloid leukemia (AML) cases exhibit complex karyotypes, i.e., three or more chromosome abnormalities without presence of a specific fusion transcript. Using chromosome banding analysis, the majority of such cases cannot be completely described due to the low resolution of this method. Comparative genomic hybridization to microarrays (matrix-CGH) is a novel technique that allows genome-wide screening for genomic imbalances at high resolution and thus may facilitate the identification of novel regions harboring potential disease-related genes. We constructed a microarray consisting of 2799 different human genomic DNA fragments cloned in bacterial artificial chromosome (BAC) or P1-derived artificial chromosome (PAC) vectors. A set of 1502 of these clones covers the whole human genome with a physical distance of approximately 2 Mb. The remaining 1297 clones either contiguously span genomic regions known to be frequently involved in hematologic malignancies (e.g., 1p, 2p, 3q, 7q, 9p, 11q, 12q, 13q, 17p, 18q) (n=610) or contain oncogenes or tumor suppressor genes (n=687). In this study 45 AML cases with complex karyotypes were analyzed. Matrix-CGH detected genomic aberrations in all cases and genomic losses were found more frequently than gains. The most frequent aberration was deletion 5q in 38 of 45 cases. Three consensus regions were delineated mapping to chromosomal bands 5q11 (23 cases), 5q34 (22 cases), and 5q35 (21 cases). Further frequent deletions affected 17p (60%); two consensus regions were identified mapping to chromosomal bands 17p13 (60%), and 17p11-q11 (33%). Other chromosomal losses affected 7q (51%), 16p (31%), 16q, 18q (29% each), 15q (24%), 10p (22%), 14q, 4p (20% each), 11q, 20q (18% each), 3p, and 12p (15% each). The most frequent genomic gain was identified at 8q (40%). Further frequent gains were detected on 11q (38%), 21q (27%), 1p, 2q (24% each), 9p (22%), 6p, 19p (20% each), 3q (18%), 7p, 20p (15% each), 13q, and 20q (13% each). Genomic amplifications were identified on chromosomal band 8q24 including the MYC gene (2 cases), 9p24 (JAK2, 2 cases), 10p15 (PRKCO, 1 case), 11q23 (MLL, 2 cases), 11q23.3 (ETS1 and FLI1, 2 cases each), 12p13 (CCND2 and FGF6, 2 cases), 13q12 (CDX2, 3 cases), 20q11.1 (BCL2L, 1 case), 21p (1 case), 21q (2 cases), and 22q (1 case). These data demonstrate the potential of matrix-CGH with regard to spatial resolution and sensitive detection of genomic imbalances. Analysis of a large series of AML cases with complex karyotype may lead to the identification of novel critical regions and pathogenetically relevant genes.

scholarly journals Extensive Genomic Diversity in Pathogenic Escherichia coli and Shigella Strains Revealed by Comparative Genomic Hybridization Microarray

2004 ◽  
Vol 186 (12) ◽  
pp. 3911-3921 ◽  
Author(s):  
Satoru Fukiya ◽  
Hiroshi Mizoguchi ◽  
Toru Tobe ◽  
Hideo Mori
Keyword(s):  
Escherichia Coli ◽  
Comparative Genomic Hybridization ◽  
Cell Envelope ◽  
Genome Structure ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Phylogenic Tree ◽  
E Coli ◽  
K 12

ABSTRACT Escherichia coli, including the closely related genus Shigella, is a highly diverse species in terms of genome structure. Comparative genomic hybridization (CGH) microarray analysis was used to compare the gene content of E. coli K-12 with the gene contents of pathogenic strains. Missing genes in a pathogen were detected on a microarray slide spotted with 4,071 open reading frames (ORFs) of W3110, a commonly used wild-type K-12 strain. For 22 strains subjected to the CGH microarray analyses 1,424 ORFs were found to be absent in at least one strain. The common backbone of the E. coli genome was estimated to contain about 2,800 ORFs. The mosaic distribution of absent regions indicated that the genomes of pathogenic strains were highly diversified becasue of insertions and deletions. Prophages, cell envelope genes, transporter genes, and regulator genes in the K-12 genome often were not present in pathogens. The gene contents of the strains tested were recognized as a matrix for a neighbor-joining analysis. The phylogenic tree obtained was consistent with the results of previous studies. However, unique relationships between enteroinvasive strains and Shigella, uropathogenic, and some enteropathogenic strains were suggested by the results of this study. The data demonstrated that the CGH microarray technique is useful not only for genomic comparisons but also for phylogenic analysis of E. coli at the strain level.

scholarly journals A New Normalizing Algorithm for BAC CGH Arrays with Quality Control Metrics

2011 ◽  
Vol 2011 ◽  
pp. 1-15 ◽  
Author(s):  
Jeffrey C. Miecznikowski ◽  
Daniel P. Gaile ◽  
Song Liu ◽  
Lori Shepherd ◽  
Norma Nowak
Keyword(s):  
Quality Control ◽  
Comparative Genomic Hybridization ◽  
Random Noise ◽  
Spatial Location ◽  
Artificial Chromosome ◽  
Control Measures ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Cancer Dataset ◽  
Downstream Analysis

The main focus in pin-tip (or print-tip) microarray analysis is determining which probes, genes, or oligonucleotides are differentially expressed. Specifically in array comparative genomic hybridization (aCGH) experiments, researchers search for chromosomal imbalances in the genome. To model this data, scientists apply statistical methods to the structure of the experiment and assume that the data consist of the signal plus random noise. In this paper we propose “SmoothArray”, a new method to preprocess comparative genomic hybridization (CGH) bacterial artificial chromosome (BAC) arrays and we show the effects on a cancer dataset. As part of our R software package “aCGHplus,” this freely available algorithm removes the variation due to the intensity effects, pin/print-tip, the spatial location on the microarray chip, and the relative location from the well plate. removal of this variation improves the downstream analysis and subsequent inferences made on the data. Further, we present measures to evaluate the quality of the dataset according to the arrayer pins, 384-well plates, plate rows, and plate columns. We compare our method against competing methods using several metrics to measure the biological signal. With this novel normalization algorithm and quality control measures, the user can improve their inferences on datasets and pinpoint problems that may arise in their BAC aCGH technology.

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