Search results for "homology"

orthoFind Facilitates the Discovery of Homologous and Orthologous Proteins

2015

Finding homologous and orthologous protein sequences is often the first step in evolutionary studies, annotation projects, and experiments of functional complementation. Despite all currently available computational tools, there is a requirement for easy-to-use tools that provide functional information. Here, a new web application called orthoFind is presented, which allows a quick search for homologous and orthologous proteins given one or more query sequences, allowing a recurrent and exhaustive search against reference proteomes, and being able to include user databases. It addresses the protein multidomain problem, searching for homologs with the same domain architecture, and gives a si…

Relative Rigid Cohomology and Deformation of Hypersurfaces

2010

Phylogenetic analysis of Lymnaeid snails based on 18S rDNA sequences.

1997

The 18S rDNA sequences of the six most common European Lymnaeidae species (Mollusca:Gastropoda:Basommatophora) have been obtained by direct PCR cycle sequencing and silver staining methods. The sequence alignment and secondary structures of the 18S rRNA gene of Lymnaea stagnalis, L. auricularia, L. peregra, L. palustris, L. glabra, and L. truncatula are analyzed. This gene proves to be a good marker for both specific determination and supraspecific lymnaeid phylogeny. The malacological importance is evident, considering the specific determination problems of individual snails and the present systematic chaos in Lymnaeidae due to their pronounced morphoanatomic uniformity, which makes a clas…

Quotients of the Dwork Pencil

2012

In this paper we investigate the geometry of the Dwork pencil in any dimension. More specifically, we study the automorphism group G of the generic fiber of the pencil over the complex projective line, and the quotients of it by various subgroups of G. In particular, we compute the Hodge numbers of these quotients via orbifold cohomology.

Evidence for a modular structure of the homologous repetitive C-terminal carbohydrate-binding sites of Clostridium difficile toxins and Streptococcus…

1992

The homologous C-terminal repeats of Clostridium difficile toxins (ToxA and ToxB) and streptococcal glucosyltransferases appear to mediate protein-carbohydrate interactions at cellular binding sites with sugar moieties as substrates. A consensus sequence of 134 repeating units from gram-positive bacteria indicates that these repeats have a modular design with (i) a stretch of aromatic amino acids proposed to be involved in the primary carbohydrate-protein interaction, (ii) an amplification of this interaction by repetition of the respective sequences, and (iii) a second domain, not characterized, that is responsible for carbohydrate specificity.

Downregulation of a Chitin Deacetylase-Like Protein in Response to Baculovirus Infection and Its Application for Improving Baculovirus Infectivity

2009

ABSTRACT Several expressed sequence tags (ESTs) with homology to chitin deacetylase-like protein (CDA) were selected from a group of Helicoverpa armigera genes whose expression changed after infection with H. armigera single nucleopolyhedrovirus (HearNPV). Some of these ESTs coded for a midgut protein containing a chitin deacetylase domain (CDAD). The expressed protein, HaCDA5a, did not show chitin deacetylase activity, but it showed a strong affinity for binding to chitin. Sequence analysis showed the lack of any chitin binding domain, described for all currently known peritrophic membrane (PM) proteins. HaCDA5a has previously been detected in the H. armigera PM. Such localization, togethe…

Functional characterization of ORCTL2--an organic cation transporter expressed in the renal proximal tubules.

1998

AbstractChromosome 11p15.5 harbors a gene or genes involved in Beckwith-Wiedemann syndrome that confer(s) susceptibility to Wilms' tumor, rhabdomyosarcoma, and hepatoblastoma. We have previously identified a transcript at 11p15.5 which encodes a putative membrane transport protein, designated organic cation transporter-like 2 (ORCTL2), that shares homology with tetracycline resistance proteins and bacterial multidrug resistance proteins. In this report, we have investigated the transport properties of ORCTL2 and show that this protein can confer resistance to chloroquine and quinidine when overexpressed in bacteria. Immunohistochemistry analyses performed with anti-ORCTL2 polyc.onal antibod…

Evo-devo mechanisms underlying the continuum between homology and homoplasy

2015

The different manifestations of equivalence and similarity in structure throughout evolution suggest a continuous and hierarchical process that starts out with the origin of a morphological novelty, unit, or homologue. Once a morphological unit has originated, its properties change subsequently into variants that differ, in magnitude, from the original properties found in the common ancestor. We will look into the nature of morphological units and their degrees of modification, which will provide the starting point for restructuring the concept of “homology,” keeping the use of homology as the identity of an anatomical part, and homogeny, as the specific variation of that anatomical part du…

Production and characterisation of recombinant forms of human pulmonary surfactant protein C (SP-C):Structure and surface activity

2006

  Udgivelsesdato: 2006-Apr Surfactant protein C (SP-C) is an essential component for the surface tension-lowering activity of the pulmonary surfactant system. It contains a valine-rich alpha helix that spans the lipid bilayer, and is one of the most hydrophobic proteins known so far. SP-C is also an essential component of various surfactant preparations of animal origin currently used to treat neonatal respiratory distress syndrome (NRDS) in preterm infants. The limited supply of this material and the risk of transmission of infectious agents and immunological reactions have prompted the development of synthetic SP-C-derived peptides or recombinant humanized SP-C for inclusion in new prepar…

Specific expression of a TRIM-containing factor in ectoderm cells affects the skeletal morphogenetic program of the sea urchin embryo

2011

In the indirect developing sea urchin embryo, the primary mesenchyme cells (PMCs) acquire most of the positional and temporal information from the overlying ectoderm for skeletal initiation and growth. In this study, we characterize the function of the novel gene strim1, which encodes a tripartite motif-containing (TRIM) protein, that adds to the list of genes constituting the epithelial-mesenchymal signaling network. We report that strim1 is expressed in ectoderm regions adjacent to the bilateral clusters of PMCs and that its misexpression leads to severe skeletal abnormalities. Reciprocally, knock down of strim1 function abrogates PMC positioning and blocks skeletogenesis. Blastomere tran…