Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays

<p>Abstract</p> <p>Background</p> <p>Array-based comparative genomic hybridization (aCGH) is a high-throughput method for measuring genome-wide DNA copy number changes. Current aCGH methods have limited resolution, sensitivity and reproducibility. Microarrays for aCGH are available only for a few organisms and combination of aCGH data with expression data is cumbersome.</p> <p>Results</p> <p>We present a novel method of using commercial oligonucleotide expression microarrays for aCGH, enabling DNA copy number measurements and expression profiles to be combined using the same platform. This method yields aCGH data from genomic DNA without complexity reduction at a median resolution of approximately 17,500 base pairs. Due to the well-defined nature of oligonucleotide probes, DNA amplification and deletion can be defined at the level of individual genes and can easily be combined with gene expression data.</p> <p>Conclusion</p> <p>A novel method of gene resolution analysis of copy number variation (graCNV) yields high-resolution maps of DNA copy number changes and is applicable to a broad range of organisms for which commercial oligonucleotide expression microarrays are available. Due to the standardization of oligonucleotide microarrays, graCNV results can reliably be compared between laboratories and can easily be combined with gene expression data using the same platform.</p

Discutindo a educação ambiental no cotidiano escolar: desenvolvimento de projetos na escola formação inicial e continuada de professores

A presente pesquisa buscou discutir como a Educação Ambiental (EA) vem sendo trabalhada, no Ensino Fundamental e como os docentes desta escola compreendem e vem inserindo a EA no cotidiano escolar., em uma escola estadual do município de Tangará da Serra/MT, Brasil. Para tanto, realizou-se entrevistas com os professores que fazem parte de um projeto interdisciplinar de EA na escola pesquisada. Verificou-se que o projeto da escola não vem conseguindo alcançar os objetivos propostos por: desconhecimento do mesmo, pelos professores; formação deficiente dos professores, não entendimento da EA como processo de ensino-aprendizagem, falta de recursos didáticos, planejamento inadequado das atividades. A partir dessa constatação, procurou-se debater a impossibilidade de tratar do tema fora do trabalho interdisciplinar, bem como, e principalmente, a importância de um estudo mais aprofundado de EA, vinculando teoria e prática, tanto na formação docente, como em projetos escolares, a fim de fugir do tradicional vínculo “EA e ecologia, lixo e horta”.Facultad de Humanidades y Ciencias de la Educació

Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays-4

<p><b>Copyright information:</b></p><p>Taken from "Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays"</p><p>http://www.biomedcentral.com/1471-2164/8/111</p><p>BMC Genomics 2007;8():111-111.</p><p>Published online 30 Apr 2007</p><p>PMCID:PMC1868757.</p><p></p>re shown by asterisks; the bracket shows the region of variable copy numbers (A). Pulsed field electrophoresis analysis of the C4/CYP21A2 region of four individuals showing two copies (C2), four copies (C4), five copies (C5) and six copies (C6) of the region. The ruler to the left shows fragment size in kb; observed long and short alleles are indicated by L and S respectively (B). graCNV analysis of chromosome 6 at 32,045 kb to 32,194 kb; log2 copy number differences are shown relative to individual C2 (two copies) for individuals C4 (light gray, four copies), C5 (dark gray, five copies) C6 (black, 6 copies)

Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays-0

<p><b>Copyright information:</b></p><p>Taken from "Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays"</p><p>http://www.biomedcentral.com/1471-2164/8/111</p><p>BMC Genomics 2007;8():111-111.</p><p>Published online 30 Apr 2007</p><p>PMCID:PMC1868757.</p><p></p> genomic DNAs (C2, C4, C5 and C6) and neuroblastoma cell lines (SK-N-SH/G, SK-N-SH/L, SK-N-AS and IMR-32). log2 copy number estimates calculated by WPP (left) and RMA (right) were analyzed for relative distance by PCA (top) and by hierarchical clustering (bottom). RMA separates two closely related cell lines (SK-N-SH/G and SK-N-SH/L) in PCA (Fig. 1B) and clustering (Fig. 1D), while WPP groups them together (Fig. 1A and C), clearly separated from normal genomic DNAs

Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays-2

<p><b>Copyright information:</b></p><p>Taken from "Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays"</p><p>http://www.biomedcentral.com/1471-2164/8/111</p><p>BMC Genomics 2007;8():111-111.</p><p>Published online 30 Apr 2007</p><p>PMCID:PMC1868757.</p><p></p>r differences at 140 to 228 Mb of chromosome 1, where SK-N-SH/L shows gain while SK-N-SH/G shows normal DNA content. Segmentation analysis of BAC aCGH (A) and graCNV (B) highlight the same region as amplified. log2 copy numbers inferred from CBS are shown as red (SK-N-SH/G) and blue (SK-N-SH/L) lines

Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays-5

<p><b>Copyright information:</b></p><p>Taken from "Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays"</p><p>http://www.biomedcentral.com/1471-2164/8/111</p><p>BMC Genomics 2007;8():111-111.</p><p>Published online 30 Apr 2007</p><p>PMCID:PMC1868757.</p><p></p>ese genes in homozygous mutants of the megabladder mouse was observed by graCNV (A) and confirmed by quantitative PCR (B). Differential gene expression between homozygous mutants and wild type shows overexpression of four of the amplified genes in whole embryos (C) and overexpression of three genes in the target organ, the embryonic bladder (D). (E) Interphase FISH analysis of a homozygous megabladder mutant shows two copies of chromosome 11 (green) and four copies of the duplicated region of chromosome 16 at 27.0 Mb (red)

Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays-1

<p><b>Copyright information:</b></p><p>Taken from "Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays"</p><p>http://www.biomedcentral.com/1471-2164/8/111</p><p>BMC Genomics 2007;8():111-111.</p><p>Published online 30 Apr 2007</p><p>PMCID:PMC1868757.</p><p></p>ept for chromosome 2 (-2 to +8). log2 copy numbers inferred from CBS are shown as red lines for segments > 1 Mb. Measurements are plotted along the physical map of chromosomes

Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays-3

<p><b>Copyright information:</b></p><p>Taken from "Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays"</p><p>http://www.biomedcentral.com/1471-2164/8/111</p><p>BMC Genomics 2007;8():111-111.</p><p>Published online 30 Apr 2007</p><p>PMCID:PMC1868757.</p><p></p>is from graCNV data (C), but only the amplicon at 67 Mb from BAC aCGH data (A). In SK-N-SH/G cells, a deletion on chromosome 8 at 39.5 Mb was inferred from graCNV data (D), but not from BAC aCGH data (B). Physical positions are shown at the x-axis in units of 1000