Search results for "Genome"
showing 10 items of 1913 documents
DNA methylation episignature testing improves molecular diagnosis of Mendelian chromatinopathies
2021
Abstract Purpose Chromatinopathies include more than 50 disorders caused by disease-causing variants of various components of chromatin structure and function. Many of these disorders exhibit unique genome-wide DNA methylation profiles, known as episignatures. In this study, the methylation profile of a large cohort of individuals with chromatinopathies was analyzed for episignature detection. Methods DNA methylation data was generated on extracted blood samples from 129 affected individuals with the Illumina Infinium EPIC arrays and analyzed using an established bioinformatic pipeline. Results The DNA methylation profiles matched and confirmed the sequence findings in both the discovery an…
Complete decontamination and regeneration of DNA purification silica colum
2008
Silica columns are among the most used DNA purification systems, allowing a good yield of high-quality nucleic acids without organic extractions. Silica column regeneration protocols reported up to now to remove DNA traces are time-consuming, and their effectiveness on genomic DNA has not been demonstrated. Here we report a very rapid regeneration procedure that ensures no DNA carryover, independent of its size, without impairing column efficiency. The method takes advantage of the improved DNA removal by low concentrations of Triton X-100.
GEOBACTER METALLIREDUCENS MUTANTS FOR CHROMIUM BIOREMEDIATION
2011
Geobacter metallireducens is known to use oxidized metals such as Fe(III) and Mn(IV) as terminal extracellular electron acceptors. G. metallireducens can reduce the highly soluble and toxic Cr(VI) to its insoluble form Cr(III), thus enabling chromium removal from contaminated water and soil. This process is limited by the low toxicity resistance of G. metallireducens to Cr(VI). Genome shuffling can generate mutants with improved phenotype. In our work we are carrying out G. metallireducens genome shuffling, in order to increase its resistance to Cr(VI). In Geobacter species, metal toxicity resistance is correlated to the respiration rate, hence to the reduction rate of the metallic electron…
The DrosDel Deletion Collection: A Drosophila Genomewide Chromosomal Deficiency Resource
2007
AbstractWe describe a second-generation deficiency kit for Drosophila melanogaster composed of molecularly mapped deletions on an isogenic background, covering ∼77% of the Release 5.1 genome. Using a previously reported collection of FRT-bearing P-element insertions, we have generated 655 new deletions and verified a set of 209 deletion-bearing fly stocks. In addition to deletions, we demonstrate how the P elements may also be used to generate a set of custom inversions and duplications, particularly useful for balancing difficult regions of the genome carrying haplo-insufficient loci. We describe a simple computational resource that facilitates selection of appropriate elements for generat…
Characteristic Topological Features of Promoter Capture Hi-C Interaction Networks
2020
Current Hi-C technologies for chromosome conformation capture allow to understand a broad spectrum of functional interactions between genome elements. Although significant progress has been made into analysis of Hi-C data to identify the biologically significant features, many questions still remain open. In this paper we describe analysis methods of Hi-C (specifically PCHi-C) interaction networks that are strictly focused on topological properties of these networks. The main questions we are trying to answer are: (1) can topological properties of interaction networks for different cell types alone be sufficient to distinguish between these types, and what the most important of such propert…
Insights into the annotated genome sequence of Methanoculleus bourgensis MS2(T), related to dominant methanogens in biogas-producing plants
2014
The final step of the biogas production process, the methanogenesis, is frequently dominated by members of the genus Methanoculleus. In particular, the species Methanoculleus bourgensis was identified to play a role in different biogas reactor systems. The genome of the type strain M. bourgensis MS2(T), originally isolated from a sewage sludge digestor, was completely sequenced to analyze putative adaptive genome features conferring competitiveness within biogas reactor environments to the strain. Sequencing and assembly of the M. bourgensis MS2(T) genome yielded a chromosome with a size of 2,789,773 bp. Comparative analysis of M. bourgensis MS2(T) and Methanoculleus marisnigri JR1 revealed…
Eight million years of maintained heterozygosity in chromosome homologs of cercopithecine monkeys
2020
In the Cercopithecini ancestor two chromosomes, homologous to human chromosomes 20 and 21, fused to form the Cercopithecini specific 20/21 association. In some individuals from the genus Cercopithecus, this association was shown to be polymorphic for the position of the centromere, suggesting centromere repositioning events. We set out to test this hypothesis by defining the evolutionary history of the 20/21 association in four Cercopithecini species from three different genera. The marker order of the various 20/21 associations was established using molecular cytogenetic techniques, including an array of more than 100 BACs. We discovered that five different forms of the 20/21 association w…
Genome-wide association study of follicular lymphoma identifies a risk locus at 6p21.32
2010
To identify susceptibility loci for non-Hodgkin lymphoma subtypes, we conducted a three-stage genome-wide association study. We identified two variants associated with follicular lymphoma at 6p21.32 (rs10484561, combined P = 1.12 × 10-29 and rs7755224, combined P = 2.00 × 10-19; r2 = 1.0), supporting the idea that major histocompatibility complex genetic variation influences follicular lymphoma susceptibility. We also found confirmatory evidence of a previously reported association between chronic lymphocytic leukemia/small lymphocytic lymphoma and rs735665 (combined P = 4.24 × 10-9). © 2010 Nature America, Inc. All rights reserved.
Actionable Molecular Targets in Cancer Liquid Biopsy
2017
The possibility to detect nucleic acid sequences in the bloodstream deriving from an underlying tumor process has disclosed a unique opportunity in medical oncology. Whether the nucleic acid material is leaked in the blood at any step of cancer development (circulating tumor DNA or ctDNA) or it is obtained from isolated circulating tumor cells (CTCs), the detection and analysis of the meaningful sequence defects harbored in instrumental molecular targets (which we call liquid biopsy) constitutes an invaluable tool toward leading the current oncology practice toward a less invasive and fully personalized diagnostic-therapeutic workflow. In spite of the current technical limitations that liqu…
Variation of haplotype distributions of two genomic regions of Citrus tristeza virus populations from eastern Spain.
2003
Genetic variation in natural populations of Citrus tristeza virus (CTV) was studied using haplotypes detected by single-strand conformation polymorphism (SSCP) analysis of two genomic regions (p20 gene and segment A, located in ORF1a). Analysis of 254 samples from 125 trees, collected at 12 different sites, yielded 8 different haplotypes for p20 and 5 for segment A. The most frequent haplotype of p20 was predominant at all sites, but several sites differed in the predominance of segment A haplotypes. At most sites, the homozygosity observed for the p20 gene tended to be higher than expected in a neutral evolution, whereas the opposite was true for segment A. Comparison of the populations at…