Search results for "Profilin"
showing 10 items of 900 documents
A web application for the unspecific detection of differentially expressed DNA regions in strand-specific expression data
2015
Abstract Genomic technologies allow laboratories to produce large-scale data sets, either through the use of next-generation sequencing or microarray platforms. To explore these data sets and obtain maximum value from the data, researchers view their results alongside all the known features of a given reference genome. To study transcriptional changes that occur under a given condition, researchers search for regions of the genome that are differentially expressed between different experimental conditions. In order to identify these regions several algorithms have been developed over the years, along with some bioinformatic platforms that enable their use. However, currently available appli…
RNA-Seq Atlas—a reference database for gene expression profiling in normal tissue by next-generation sequencing
2012
Abstract Motivation: Next-generation sequencing technology enables an entirely new perspective for clinical research and will speed up personalized medicine. In contrast to microarray-based approaches, RNA-Seq analysis provides a much more comprehensive and unbiased view of gene expression. Although the perspective is clear and the long-term success of this new technology obvious, bioinformatics resources making these data easily available especially to the biomedical research community are still evolving. Results: We have generated RNA-Seq Atlas, a web-based repository of RNA-Seq gene expression profiles and query tools. The website offers open and easy access to RNA-Seq gene expression pr…
Structure Learning in Nested Effects Models
2007
Nested Effects Models (NEMs) are a class of graphical models introduced to analyze the results of gene perturbation screens. NEMs explore noisy subset relations between the high-dimensional outputs of phenotyping studies, e.g., the effects showing in gene expression profiles or as morphological features of the perturbed cell. In this paper we expand the statistical basis of NEMs in four directions. First, we derive a new formula for the likelihood function of a NEM, which generalizes previous results for binary data. Second, we prove model identifiability under mild assumptions. Third, we show that the new formulation of the likelihood allows efficiency in traversing model space. Fourth, we…
Approaches for a Sustainable Use of the Bioactive Potential in Sponges: Analysis of Gene Clusters, Differential Display of mRNA and DNA Chips
2003
In recent years, analyses of the genome organization of marine sponges have begun that have led to the elucidation of selected genes and gene arrangements that exist in gene clusters (e.g. the receptor tyrosine kinase cluster and the allograft inflammatory factor cluster). Most of these studies were performed with the demosponge Suberites domuncula; but Geodia cydonium (Demospongiae), Aphrocallistes vastus (Hexactinellida) and Sycon raphanus (Calcarea) were also investigated. Both S. domuncula and G. cydonium possess a surprisingly large genome of approximately 1.7 pg DNA per haploid set. Taking the high gene density in these sponges into account and considering that predominantly single-co…
Profiling deaf and hard-of-hearing users of subtitles for the deaf and hard-of-hearing in Italy: a questionnaire-based study
2012
The aim of this article is to present the results of a questionnaire-based study carried out as part of the author’s Master’s Degree dissertation about Subtitles for the Deaf and Hard-of-hearing (SDH). In particular, the need to gather specific information regarding audience design will be highlighted in the paper, since this research field has long been neglected in Italy. The questions were aimed at shedding light on the needs, cultural environment and world-view of Italian SDH users, by eliciting personal data as well as subtitlerelated information. Moreover, the 232 respondents were asked to suggest improvements to SDH services in Italy. Although these first results cannot allow definit…
Near-surface defect profiling with slow positrons: Argon-sputtered Al(110).
1985
We report on slow-positron measurements of atomic defect distribution near a solid surface. Defects are produced by argon-ion bombardment of an Al(110) surface in ultrahigh vacuum. Defect profiles have a typical width of 15–25 Å and contain a broader tail extending to 50–100 Å. The defect density at the outermost atomic layers saturates at high argon fluences to a few atomic percent, depending on sputtering conditions. Defect production rate at >1 keV Ar+ energies is typically 1–5 vacancy-interstitial pairs per incident ion. Molecular-dynamics simulations of the collision cascade predict similar defect distributions. Peer reviewed
Inactivation of the ftsH gene of Lactobacillus plantarum WCFS1: Effects on growth, stress tolerance, cell surface properties and biofilm formation
2012
FtsH proteins are ubiquitous membrane-bound, ATP-dependent metalloproteases of the AAA family. In eubacteria, FtsH is involved in protein quality control under stress conditions. Lactobacillus plantarum is a widespread lactic acid bacterium that is encountered in several fermented food, including dairy products, vegetables and meat. In the present work the expression of the ftsH gene of L. plantarum was studied by quantitative real time RT-PCR in bacterial cultures subjected to various abiotic stresses. Both oxidative stress and addition of a membrane-fluidizing agent induced ftsH transcription, while a depletion of carbon-source repressed its mRNA level. Mutants deprived of the FtsH protea…
Peripheral T-cell lymphoma classification: the matter of cellular derivation.
2011
Peripheral T-cell lymphomas (PTCLs) represent approximately 12% of all non-Hodgkin's lymphomas in Western countries. They are quite heterogeneous as far as morphology and phenotype are concerned. Furthermore, until now, PTCLs could not be referred to specific normal counterparts, in contrast to B-cell-derived non-Hodgkin's lymphomas. In particular, in the last edition of the WHO classification of Tumors of the Hematopoietic and Lymphoid Tissues, for the majority of nodal PTCLs (including the not otherwise specified type and anaplastic large-cell lymphoma), the postulated cell of origin remained undefined. However, in the last few years, high-throughput genomic techniques, especially gene-ex…
Liver-primed memory T cells generated under noninflammatory conditions provide anti-infectious immunity.
2013
SummaryDevelopment of CD8+ T cell (CTL) immunity or tolerance is linked to the conditions during T cell priming. Dendritic cells (DCs) matured during inflammation generate effector/memory T cells, whereas immature DCs cause T cell deletion/anergy. We identify a third outcome of T cell priming in absence of inflammation enabled by cross-presenting liver sinusoidal endothelial cells. Such priming generated memory T cells that were spared from deletion by immature DCs. Similar to central memory T cells, liver-primed T cells differentiated into effector CTLs upon antigen re-encounter on matured DCs even after prolonged absence of antigen. Their reactivation required combinatorial signaling thro…
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 …