Search results for "alignment"
showing 7 items of 627 documents
Crystallization and preliminary crystallographic study of a pheromone-binding protein from the cockroachLeucophaea maderae
2002
Pheromone-binding proteins (PBPs) are small helical proteins (13-18 kDa) present in various sensory organs of moths and other insect species. An antennal protein from the cockroach Leucophaea maderae (LmaPBP) has been found to share all the hallmarks of the PBP family and is expressed specifically in the female adult antennae, the gender that perceives the sex pheromone. Here, the crystallization of LmaPBP expressed as a recombinant protein in Escherichia coli periplasm is reported. Crystals of LmaPBP were obtained by the sitting-drop vapour-diffusion method using a nanodrop-dispensing robot. The protein crystallizes in two different crystal forms. Form 1 belongs to space group P1, with uni…
Genomic structure and promoter analysis of pathogen-inducedrepatgenes fromSpodoptera exigua
2009
The repat gene family encodes midgut proteins overexpressed in response to pathogen infection in the lepidopteran Spodoptera exigua. Up-regulation of repat genes has been observed after challenging the larvae with both Bacillus thuringiensis toxins and after infection with the baculovirus Autographa californica multiple nucleopolyhedrovirus. In our study, PCR amplification of the genomic region and genome walking were used to obtain the genomic structure and the sequence of the 5'-upstream region of repat1 and repat2, two of the most phylogenetically distant members of the repat family. A similar gene structure between repat1 and repat2 has been found, with conserved exon-intron positions a…
Isolation of Mhc class I cDNAs from the axolotl Ambystoma mexicanum.
1997
Class I major histocompatibility complex (Mhc) cDNA clones were isolated from axolotl mRNA by polymerase chain reaction (PCR) and by screening a cDNA phage library. The nucleotide and predicted amino acid sequences show definite similarities to the Mhc class Ialpha molecules of higher vertebrates. Most of the amino acids in the peptide binding region that dock peptides at their N and C termini in mammals are conserved. Several amino acids considered to be important for the interaction of beta2-microglobulin with the Mhc alpha chain are also conserved in the axolotl sequence. The fact that axolotl class I A cDNAs are ubiquitously expressed and highly polymorphic in the alpha1 and alpha2 doma…
Ordering and dewetting in spin-coated films of a liquid crystalline main chain polymer
2006
Abstract The ordering of spin-coated films of a main-chain smectic liquid crystalline polymer with an azobenzene group connected by flexible spacers to a phenyl malonate unit has been studied as a function of film thickness using scanning force microscopy and UV/Vis spectroscopy. Already the as-prepared films are characterized by a significant out-of-plane orientation of the azobenzene groups. Annealing of films thicker than 7 nm results in aggregation and homeotropical alignment of azobenzene groups forming smectic layers parallel to the substrate. An optically isotropic mesophase was found upon annealing in the temperature range of smectic mesophase. Films thinner than the bilayer thickne…
CARE: context-aware sequencing read error correction.
2020
Abstract Motivation Error correction is a fundamental pre-processing step in many Next-Generation Sequencing (NGS) pipelines, in particular for de novo genome assembly. However, existing error correction methods either suffer from high false-positive rates since they break reads into independent k-mers or do not scale efficiently to large amounts of sequencing reads and complex genomes. Results We present CARE—an alignment-based scalable error correction algorithm for Illumina data using the concept of minhashing. Minhashing allows for efficient similarity search within large sequencing read collections which enables fast computation of high-quality multiple alignments. Sequencing errors ar…
On temporal deixis and cognitive models in early Indo-European
2013
Crosslinguistic evidence suggest that there are two different (often coexistent) basic cognitive models for time, on the basis of which the world’s languages express time in terms of conceptual metaphor from the source spatial domain to the target temporal domain: i) the Time-based (Time-Reference-Point) model, in which time is conceptualized in terms of sequentially arrayed objects moving in space, so that a temporal event is relative to another earlier or later temporal event; ii) the Ego-based (Ego-Reference-Point) model, which is considered to have a more complex structure in which times are conceptualized as objects relative to a canonical deictic observer (Ego) located at the hic et n…
A Framework to Support Business-IT Alignment in Enterprise Architecture Decision Making
2008
First published in the proceedings of the EBRF 2007 conference ”Research Forum to Understand Business in Knowledge Society”, September 25-27, Jyväskylä, Finland Business-IT alignment is one of the key concerns of general management and chief information officers. It is commonly recognized as an important instrument for realizing organizational effectiveness. Achieving business-IT alignment requires often change in the way managers regard IT and it demands co-operation between general and IT management. The challenge of aligning business- and IT-related concerns and requirements in architecture decision making situations is the focus of this study. As one possible solution, we present a fram…