Search results for " sequence"

Computing with Rational Symmetric Functions and Applications to Invariant Theory and PI-algebras

2012

The research of the first named author was partially supported by INdAM. The research of the second, third, and fourth named authors was partially supported by Grant for Bilateral Scientific Cooperation between Bulgaria and Ukraine. The research of the fifth named author was partially supported by NSF Grant DMS-1016086.

Substrate determinants for cleavage in cis and in trans by the hepatitis C virus NS3 proteinase

1995

Processing of the hepatitis C virus polyprotein is accomplished by a series of cotranslational and posttranslational cleavages mediated by host cell signalases and two virally encoded proteinases. Of these the NS3 proteinase is essential for processing at the NS3/4A, NS4A/4B, NS4B/5A, and NS5A/5B junctions. Processing between NS3 and NS4A occurs in cis, implying an intramolecular reaction mechanism, whereas cleavage at the other sites can also be mediated in trans. Sequence analysis of the amino termini of mature cleavage products and comparisons of amino acid residues around the scissile bonds of various hepatitis C virus isolates identified amino acid residues which might contribute to su…

Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix

2015

AbstractBackgroundLife history traits like developmental time, age and size at maturity are directly related to fitness in all organisms and play a major role in adaptive evolution and speciation processes. Comparative genomic or transcriptomic approaches to identify positively selected genes involved in species divergence can help to generate hypotheses on the driving forces behind speciation. Here we use a bottom-up approach to investigate this hypothesis by comparative analysis of orthologous transcripts of four closely related EuropeanRadixspecies.ResultsSnails of the genusRadixoccupy species specific distribution ranges with distinct climatic niches, indicating a potential for natural …

Cloning and sequencing of the chicken egg-white avidin-encoding gene and its relationship with the avidin-related genes Avrl-Avr5

1995

Abstract The gene encoding chicken egg-white avidin (Avd) was amplified from chromosomal DNA, cloned and sequenced. The entire coding region of preavidin (pre-Avd) containing four exons was identified by comparing the Avd gene (1119 bp) with the cDNA. It had a high identity percentage (91–95%) with the previously isolated Avd-related genes 1–5 (Avrl–Avr5) . Interestingly, comparison of Avd with the Avr genes showed that the introns were better conserved (on average 97%) than the exons (90%). The Avd gene, as well as the cDNA, encodes a Gln residue at position 53 of the mature protein, which is in contrast to the previously determined amino-acid sequence.

Evolutionary analysis of G-proteins in early metazoans: Cloning of α- and β-subunits from the sponge Geodia cydonium1The sequences reported here have…

1998

G-protein-coupled (seven-transmembrane segment)-receptors represent a major group of metazoan receptors, involved in transduction of extracellular signals. The G-proteins, which are made up of Galpha/beta/gamma-subunits, link the receptors to the effector system(s). To analyze the phylogenetic relationships among the metazoan alpha-subunits of G-proteins, cDNAs of alpha-subunits were isolated from Geodia cydonium, a marine sponge belonging to the lowest metazoan phylum, Porifera. One encodes a putative isotype of a stimulator of the adenylyl cyclase (Galpha s), another one a putative inhibitor of the adenylyl cyclase (Galpha i/o) and the third one a putative activator of phospholipase C (Ga…

A Novel Chitin-binding Protein from the Vestimentiferan Riftia pachyptila Interacts Specifically with β-Chitin

2001

Abstract A cDNA from Riftia pachyptila was cloned. It encodes a novel 21.3-kDa protein from the worm protective tube, named RCBP (for Riftia chitin-binding protein). On the basis of partial tube-peptide sequences previously obtained, experiments using reverse transcriptase-mediated polymerase chain reaction and rapid amplification of cDNA ends led to the complete cDNA sequence. Analysis of its deduced amino acid sequence shows the presence of two chitin-binding domains. These domains are closely related to type 2 chitin-binding domains that are restricted to the animal kingdom. We showed by affinity assay and immunogold labeling that RCBP is the first protein so far known that binds specifi…

Nucleotide sequence of Clostridium difficile toxin A.

1990

Sequencing and analysis of the gene encoding the α-toxin of Clostridium novyi proves its homology to toxins A and B of Clostridium difficile

1995

A library of total Clostridium novyi DNA was established and screened for the alpha-toxin gene (tcn alpha) by hybridization with oligonucleotides derived from a partial N-terminal sequence and by using specific antisera. Overlapping subgenic tcn alpha fragments were isolated and subsequently the total sequence of tcn alpha was determined. The 6534 nucleotide open reading frame encodes a polypeptide of M(r) 250,166 and pI 5.9. The N-terminal alpha-toxin (Tcn alpha) sequence MLITREQLMKIASIP determined by Edman degradation confirmed the identity of the reading frame and the assignment of the translation start point. The toxin is not modified posttranslationally at its N-terminus nor does it co…

A study on recovering the cloud top-height from infra-red video sequences

2004

In this paper we present some preliminary results on an opticalfow based technique aimed at recovering the cloud-top height from infra-red image sequences. The recovery of the cloud-top height from satellite infra-red images is an important topic in meteorological studies, and is traditionally based on the analysis of the temperature maps. In this work we explore the feasibility for this problem of a technique based on a robust multi-resolution opticalfow algorithm. The robustness is achieved adopting a Least Median of Squares paradigm. The algorithm has been tested on semi-synthetic data (i.e. real data that have been synthetically warped in order to have a reliable ground truth for the mo…

SMART: Unique splitting-while-merging framework for gene clustering

2014

© 2014 Fa et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Successful clustering algorithms are highly dependent on parameter settings. The clustering performance degrades significantly unless parameters are properly set, and yet, it is difficult to set these parameters a priori. To address this issue, in this paper, we propose a unique splitting-while-merging clustering framework, named "splitting merging awareness tactics" (SMART), which does not require any a priori knowledge of either the number …