Search results for " DNA"

Human DNA Telomeres in Presence of Oxidative Lesions: The Crucial Role of Electrostatic Interactions on the Stability of Guanine Quadruplexes

2019

By using all atom molecular dynamics simulations, we studied the behavior of human DNA telomere sequences in guanine quadruplex (G4) conformation and in the presence of oxidative lesions, namely abasic sites. In particular, we evidenced that while removing one guanine base induces a significant alteration and destabilization of the involved leaflet, human telomere oligomers tend, in most cases, to maintain at least a partial quadruplex structure, eventually by replacing the empty site with undamaged guanines of different leaflets. This study shows that (i) the disruption of the quadruplex leaflets induces the release of at least one of the potassium cations embedded in the quadruplex channe…

Liquid Biopsy in Gastrointestinal Stromal Tumor

2017

Over the past 15 years, gastrointestinal stromal tumors (GISTs) have emerged from a poorly understood neoplasm to a well-defined tumor entity. Starting from 2000, the discovery of gain-of-function mutations involving KIT or PDGFRα (platelet-derived growth factor-α) genes and the development of tyrosine kinase inhibitors (TKIs), such as imatinib, revolutionized dramatically the management of GISTs. Due to the almost continual emergence of new data about biological complexity of GISTs and more sophisticated whole-genome technologies, to date, the role of molecular biology is clinically important to drive therapeutic decision making. The possibility of using liquid biopsy in GISTs was reported…

LIQUID BIOPSY AS A DYNAMIC TOOL FOR LUNG CANCER MANAGEMENT: A FEASIBILITY STUDY FOR PLASMA-DERIVED EXOSOMAL miRNAs AND CELL-FREE DNA.

Molecular cloning and characterization of the complementary DNA coding for the B-chain of murine Clq

1989

AbstractcDNA clones coding for the B-chain of murine Clq were isolated from a mouse macrophage library. The characterized clones include the total coding region plus a leader sequence. High homology was found with human Clq B-chain in the coding region (81%). Northern blot analysis of total RNA from different tissues of Balb/c mice showed one band of approximately 1.2 kb. The highest signal was found in RNA preparations of thioglycolate-activated peritoneal macrophages. The probe also hybridized with mRNA from spleen, thymus and heart. Extremely weak signals were found in liver, kidney, lung and intestine tissues.

A new set of DNA macrochips for the yeast Saccharomyces cerevisiae: features and uses

2004

The yeast Saccharomyces cerevisiae has been widely used for the implementation of DNA chip technologies. For this reason and due to the extensive use of this organism for basic and applied studies, yeast DNA chips are being used by many laboratories for expression or genomic analyses. While membrane arrays (macroarrays) offer several advantages, for many laboratories they are not affordable. Here we report that a cluster of four Spanish molecular-biology yeast laboratories, with relatively small budgets, have developed a complete set of probes for the genome of S. cerevisiae. These have been used to produce a new type of macroarray on a nylon surface. The macroarrays have been evaluated and…

Atlas: analysis tools for low-depth and ancient samples

2017

AbstractSummaryPost-mortem damage (PMD) obstructs the proper analysis of ancient DNA samples and can currently only be addressed by removing or down-weighting potentially damaged data. Here we present ATLAS, a suite of methods to accurately genotype and estimate genetic diversity from ancient samples, while accounting for PMD. It works directly from raw BAM files and enables the building of complete and customized pipelines for the analysis of ancient and other low-depth samples in a very user-friendly way. Based on simulations we show that, in the presence of PMD, a dedicated pipeline of ATLAS calls genotypes more accurately than the state-of-the-art pipeline of GATK combined with mapDamag…

Development of Rat DC by in Vitro Culture of Bone Marrow Cells

1995

Dendritic cells (DC) represent a subpopulation of leukocytes of bone marrow (BM) origin, involved in crucial immunological reactions. DC play a fundamental role in the primary immune response by stimulating quiescent T cells. In this study we describe an in vitro culture system to raise DC from unfractionated bone marrow (BM) cells of LEWIS rats in the presence of low doses of mouse recombinant GM-CSF, that was successfully used in previous work to culture mouse DC1,2,3.

Patterns and rates of nucleotide substitution, insertion and deletion in the endosymbiont of antsBlochmannia floridanus

2009

Genome reduction is a general process that has been studied in numerous symbiotic bacteria associated with insects. We investigated the last stages of genome degradation in Blochmannia floridanus, a mutualistic bacterial endosymbiont of the ant Camponotus floridanus. We determined the tempo (rates of insertion and deletion) and mode (size and number of insertion-deletion events) of the process in the last 200,000 years by analysing a total of 16 intergenic regions in several strains of this endosymbiont from different ant populations. We provide the first calculation of the reduction rate for noncoding DNA in this endosymbiont (2.2 x 10(-8) lost nucleotides/site/year) and compare it with th…

Synthesis of nucleoside and nucleotide conjugates of bile acids, and polymerase construction of bile acid-functionalized DNA.

2010

Aqueous Sonogashira cross-coupling reactions of 5-iodopyrimidine or 7-iodo-7-deazaadenine nucleosides with bile acid-derived terminal acetylenes linked via an ester or amide tether gave the corresponding bile acid–nucleoside conjugates. Analogous reactions of halogenated nucleoside triphosphates gave directly bile acid-modified dNTPs. Enzymatic incorporation of these modified nucleotides to DNA was successfully performed using Phusion polymerase for primer extension. One of the dNTPs (dCTP bearing cholic acid) was also efficient for PCR amplification.

Activation of a murine autoreactive B cell by immunization with human recombinant autoantigen La/SS-B: Characterization of the autoepitope

1995

Immunization of Balb/c mice with a homogeneously purified recombinant human La/SS-B protein resulted in activation of an autoreactive B cell secreting a novel monoclonal anti-La antibody termed La4B6. La4B6 reacted with La protein from a variety of sources including human, bovine, rat and mouse. ATP blocked the binding of La4B6 to recombinant La protein. The human epitope was identified as consisting of the amino acid sequence SKGRRFKGKGKGN, which includes the proposed ATP-binding site of the La protein. In the human and bovine La protein, the epitope exists as a continuous amino acid sequence. In rat and mouse the epitope was found to consist of the amino acid sequence SKG interrupted by a…