Search results for "Sequence Alignment"
showing 10 items of 447 documents
Isolation and characterization of five Fox (Forkhead) genes from the sponge Suberites domuncula.
2003
Fox or Forkhead genes constitute a subgroup of the helix-turn-helix class of transcription factors with a characteristic and highly conserved DNA binding domain. To date, around 100 different Fox genes have been reported ranging from yeast to humans; these have been classified into 18 subclasses (A to P). Fox proteins are responsible for a wide range of functions and key roles in early developmental processes, during organogenesis and also for the function of the major organs and tissues in the adult. Here, we report the isolation and phylogenetic characterization of five members of the Fox family from the sponge Suberites domuncula. Four of them (Sd-FoxL2, Sd-FoxP, Sd-FoxD and Sd-FoxF) fal…
Molecular cloning of rat G-protein-coupled receptor kinase 6 (GRK6) from brain tissue, and its mRNA expression in different brain regions and periphe…
1997
The rat G-protein-coupled receptor kinase 6 (GRK6) cDNA was cloned from rat brain tissue by a combination of reverse-transcription polymerase chain reactions (RT-PCR), based on homology to the cloned human GRK6, and rapid amplification of cDNA ends (RACE-PCR). We obtained a clone of 2817 bp with an open reading frame of 1731 bp encoding for a protein of 576 amino acids that is 96.7% identical and 97.9% similar to its human counterpart. mRNA was detectable in all brain areas examined. In addition, GRK6 was expressed in skeletal muscle, small intestine, aorta, liver, heart, lung, thymus, stomach, uterus and kidney.
A heterochromatic P sequence in the D. subobscura genome.
1994
The study of a heterochromatic P sequence of D. subobscura reveals that it is a degraded element, located at the centromeric region of the A chromosome (X chromosome in this species), and that it is strongly diverged from the euchromatic P sequences previously described in this species. This heterochromatic sequence is composed of some P element fragments embedded in undefined beta-heterochromatic sequences. These mosaic P sequences do not show any transcriptional activity and seem to be ancient parasites of the D. subobscura genome. Phylogenetic analyses indicate that both the euchromatic and heterochromatic P sequences of D. subobscura could come from an ancestral element which was presen…
Characterization and phylogenetic analysis of a cDNA encoding the Fes/FER related, non-receptor protein-tyrosine kinase in the marine sponge Sycon ra…
1998
Abstract In search of ancient versions of phylogenetically conserved genes/proteins, which are typical for multicellular animals, we have decided to analyse marine sponges (Porifera), the most ancient and most primitive metazoan organisms. We report here the complete nucleotide sequence of Sycon raphanus cDNA coding for a 879 aa long protein (100 kDa), which displays high overall similarity in primary structure and organization of domains with non-receptor tyrosine kinases (TKs) from the Fes/FER family. The encoded protein, which we named Fes/FER_SR, has a highly conserved, 260 aa long tyrosine kinase domain at the C-terminus. Amino-terminal to the catalytic domain is an 85 aa long SH2 doma…
Src proteins/src genes: from sponges to mammals
2004
The genome of marine sponge Suberites domuncula, a member of the most ancient and most simple metazoan phylum Porifera, encodes at least five genes for Src-type proteins, more than, i.e., Caenorhabditis elegans or Drosophila melanogaster (two in each). Three proteins, SRC1SD, SRC2SD and SRC3SD, were fully characterized. The overall homology (identity+similarity) among the three S. domuncula Srcs (68-71%) is much lower than the sequence conservation between orthologous Src proteins from freshwater sponges (82-85%). It is therefore very likely that several src genes/proteins were already present in the genome of Urmetazoa, the hypothetical metazoan ancestor. We have identified in the S. domun…
Immunoglobulin-like domain is present in the extracellular part of the receptor tyrosine kinase from the marine sponge Geodia cydonium.
1994
We have isolated and characterized two cDNAs from the marine sponge Geodia cydonium coding for a new member of a receptor tyrosine kinase of class II. The deduced amino acid sequence shows two characteristic domains: (i) the tyrosine kinase domain; and (ii) and immunoglobulin-like domain. The latter part shows high homology to the vertebrate C2 type immunoglobulin domain. This result demonstrates that immunoglobulin domains are not recent achievements of higher animals but exist also in those animals which have diverged from other organisms about 800 million years ago.
Divergent Distribution in Vascular and Avascular Mammalian Retinae Links Neuroglobin to Cellular Respiration
2005
The visual function of the vertebrate retina relies on sufficient supply with oxygen. Neuroglobin is a respiratory protein thought to play an essential role in oxygen homeostasis of neuronal cells. For further understanding of its function, we compared the distribution of neuroglobin and mitochondria in both vascular and avascular mammalian retinae. In the vascular retinae of mouse and rat, oxygen is supplied by the outer choroidal, deep retinal, and inner capillaries. We show that in this type of retina, mitochondria are concentrated in the inner segments of photoreceptor cells, the outer and the inner plexiform layers, and the ganglion cell layer. These are the same regions in which oxyge…
The Implication of Xyloglucan Endotransglucosylase/Hydrolase (XTHs) in Tomato Fruit Infection by Penicillium expansum Link. A
2007
In general, cell wall-degrading enzymes produced by plant pathogenic fungi are considered important pathogenicity factors. In this work, we evaluate the implication of xyloglucan endotransglucosylase/ hydrolase (XTHs), a potential hemicellulosic repairing enzyme, in the infection mechanism process by the fungus. This study investigated the SIXTHS expresion and xyloglucan endotransglucosylase (XET) activity during infection of two tomato fruit cultivars by Penicillium expansum Link. A. In infected fruits, XET specific activity decreased drastically after long infection periods, 24 and 48 h for Canario and Money Maker tomato fruits, respectively. Real Time RT-PCR of eleven SIXTHS also showed …
UVPAR: fast detection of functional shifts in duplicate genes.
2006
Abstract Background The imprint of natural selection on gene sequences is often difficult to detect. A plethora of methods have been devised to detect genetic changes due to selective processes. However, many of those methods depend heavily on underlying assumptions regarding the mode of change of DNA sequences and often require sophisticated mathematical treatments that made them computationally slow. The development of fast and effective methods to detect modifications in the selective constraints of genes is therefore of great interest. Results We describe UVPAR, a program designed to quickly test for changes in the functional constraints of duplicate genes. Starting with alignments of t…
gcType : a high-quality type strain genome database for microbial phylogenetic and functional research
2020
Abstract Taxonomic and functional research of microorganisms has increasingly relied upon genome-based data and methods. As the depository of the Global Catalogue of Microorganisms (GCM) 10K prokaryotic type strain sequencing project, Global Catalogue of Type Strain (gcType) has published 1049 type strain genomes sequenced by the GCM 10K project which are preserved in global culture collections with a valid published status. Additionally, the information provided through gcType includes >12 000 publicly available type strain genome sequences from GenBank incorporated using quality control criteria and standard data annotation pipelines to form a high-quality reference database. This …