Search results for " Map"

One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads.

2020

Mapping of high-throughput sequencing (HTS) reads to a single arbitrary reference genome is a frequently used approach in microbial genomics. However, the choice of a reference may represent a source of errors that may affect subsequent analyses such as the detection of single nucleotide polymorphisms (SNPs) and phylogenetic inference. In this work, we evaluated the effect of reference choice on short-read sequence data from five clinically and epidemiologically relevant bacteria (Klebsiella pneumoniae, Legionella pneumophila, Neisseria gonorrhoeae, Pseudomonas aeruginosa and Serratia marcescens). Publicly available whole-genome assemblies encompassing the genomic diversity of these species…

Emissivity errors in the vegetation cover method caused by the lack of atmospheric correction

2008

The influence of the lack of atmospheric correction of the optical images used to calculate land surface emissivity (LSE) was assessed. When thermal emissivity is determined by the vegetation cover method (VCM), information from the solar spectrum is required to calculate the vegetation cover fraction. The atmospheric correction was obtained in this study by using a combination of the dark dense vegetation (DDV) method and the Second Simulation of the Satellite Signal in the Solar Spectrum (6S) code. The methodology was applied to a Landsat Thematic Mapper (TM) image of Tomelloso, Spain. We determined that the emissivity between 10 and 12 µm only increases by 0.4% (which represents a system…

Analysis of Epitope Spreading over an Eleven-year Period in a Patient with Systemic Lupus Erythematosus: CASE REPORT

1998

During a period of more than eleven years serum samples of a patient with Systemic Lupus Erythematosus were collected and analyzed for anti-nuclear autoantibodies. High titer of anti-La/SS-B were detectable in all serum samples. The La/SS-B epitopes remained constant. Besides anti-La/SS-B antibodies all serum samples contained traces of anti-Ro/SS-A including anti-Ro52 and anti-Ro60 antibodies. During disease flares anti-Ro/SS A antibodies were upregulated and anti-dsDNA antibodies appeared, thus supporting the concept of an antigen driven intermolecular epitope spreading to Ro/SS-A and dsDNA.

Modular organization in the reductive evolution of protein-protein interaction networks

2006

Analysis of the reduction in genome size of Buchnera aphidicola from its common ancestor E. coli shows that the organization of networks into modules is the property that seems to be directly related with the evolutionary process of genome reduction.

Plano euforimétrico del término municipal de Madrid

Orientat amb línies assenyalant el nord. - Llegenda amb els tipus de sòl. - Representat el plànol urbà de Madrid

Mapping and expression pattern analysis of key components of the major histocompatibility complex class I antigen processing and presentation pathway…

2001

Renal cell carcinoma (RCC) represent approximately 5% of all cancer deaths. At the time of presentation, over 50% of the patients have already developed locally advanced or metastatic disease with five-year survival rates of less than 20%. Although relative resistant to conventional regimens, RCC are partially susceptible to T cell-based immunotherapy. To further develop this treatment modality, two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) was applied for both the mapping of the key components of the major histocompatibility complex (MHC) class I antigen processing and presentation machinery (APM) and the characterization of the constitutive and cytokine-regulated protein e…

Identification of T cell epitopes by the use of rapidly generated mRNA fragments.

2004

Abstract Although the number of defined T cell epitopes of clinically relevant antigens is constantly increasing, there is still an enormous need to identify further peptides, processed from new antigens or presented by rare HLA molecules, respectively. Here we introduce a novel two-step approach for the rapid identification of T cell epitopes. It was established in the CMV infection model. From the peripheral blood of healthy donors sharing HLA-A1 according to HLA serotyping we isolated CD8 + T lymphocytes and generated dendritic cells (DCs). DCs were electroporated with CMV pp65 mRNA and tested for recognition by autologous CD8 + T lymphocytes in IFN-γ ELISPOT assays. In all 10 CMV-seropo…

The importance of level stratification for quantitative MR studies of lumbar intervertebral discs : a cross-sectional analysis in 101 healthy adults

2019

Purpose: To investigate whether quantitative T2-times depend on lumbar intervertebral disc (IVD) level. Methods: The lumbar spine (Th12/L1–L5/S1) of 101 participants (53.5% female, 30.0[± 3.6]years, 173.5[± 9.6]cm and 69.9[± 13.4]kg), without history of back pain, was examined on a 3T scanner with sagittal T2-mapping. All IVDs were stratified according to Pfirrmann grade and lumbar level, with mean T2-time determined for the entire IVD volume and in five subregions of interests. Results: Significant level-dependent T2-time differences were detected, both for the entire IVD volume and its subregions. For the entire IVD volume, Pfirrmann grade 2 IVDs displayed 9–18% higher T2-times in Th12/L1…

In silico characterization of an Iroquois family-related homeodomain protein.

2005

Homeobox genes have been demonstrated to play important roles during cancer differentiation and embryonic development. The subset of Iroquois-related homeobox genes (IRXs) have furthermore been. demonstrated to be involved in several embryonic developmental processes such as patterning of the anterior-posterior and dorso-ventral axis, as well as specific regions of the central nervous system, and differentiation of the otic vesicle, branchial epithelium, and limbs. We have characterized a novel homeodomain protein and corresponding gene by means of computational biology. Since the protein sequence displayed high similarity to the human IRX proteins, the newly identified homeodomain protein …

The Mitochondrial Targeting Chaperone 14-3-3ε Regulates a RIG-I Translocon that Mediates Membrane Association and Innate Antiviral Immunity

2012

SummaryRIG-I is a cytosolic pathogen recognition receptor that initiates immune responses against RNA viruses. Upon viral RNA recognition, antiviral signaling requires RIG-I redistribution from the cytosol to membranes where it binds the adaptor protein, MAVS. Here we identify the mitochondrial targeting chaperone protein, 14-3-3ε, as a RIG-I-binding partner and essential component of a translocation complex or “translocon” containing RIG-I, 14-3-3ε, and the TRIM25 ubiquitin ligase. The RIG-I translocon directs RIG-I redistribution from the cytosol to membranes where it mediates MAVS-dependent innate immune signaling during acute RNA virus infection. 14-3-3ε is essential for the stable inte…