Search results for "Base Sequence"

Why Nuclear Ribosomal DNA Spacers (ITS) Tell Different Stories in Quercus

2001

The molecular systematics of Quercus (Fagaceae) was recently assessed by two teams using independently generated ITS sequences. Although the results disagreed in several remarkable features, the phylogenetic trees for either hypothesis were highly supported by bootstrap resampling. We have reanalyzed the ITS sequences used by both teams (eight taxa) to reveal the underlying patterns of this divergence. Within species, conspicuous length and G + C% divergence were evident in most sequence comparisons. In addition, a high rate of substitutions and deletions involving highly conserved motifs in both ITS spacers were present in a set of sequences. This was coupled with a less thermodynamic stab…

Interplay between RNA structure and protein evolution in HIV-1.

2010

The genomes of many RNA viruses contain abundant secondary structures that have been shown to be important for understanding the evolution of noncoding regions and synonymous sites. However, the consequences for protein evolution are less well understood. Recently, the secondary structure of the HIV-1 RNA genome has been experimentally determined. Using this information, here we show that RNA structure and proteins do not evolve independently. A negative correlation exists between the extent of base pairing in the genomic RNA and amino acid variability. Relaxed RNA structures may favor the accumulation of genetic variation in proteins and, conversely, sequence changes driven by positive sel…

Long-range translational coupling in single-stranded RNA bacteriophages: an evolutionary analysis

1998

In coliphage MS2 RNA a long-distance interaction (LDI) between an internal segment of the upstream coat gene and the start region of the replicase gene prevents initiation of replicase synthesis in the absence of coat gene translation. Elongating ribosomes break up the repressor LDI and thus activate the hidden initiation site. Expression studies on partial MS2 cDNA clones identified base pairing between 1427-1433 and 1738-1744, the so-called Min Jou (MJ) interaction, as the molecular basis for the long-range coupling mechanism. Here, we examine the biological significance of this interaction for the control of replicase gene translation. The LDI was disrupted by mutations in the 3'-side an…

The cis-regulatory sequences required for expression of the Drosophila melanogaster adult cuticle gene ACP65A.

2009

Post-embryonic development in insects requires successive molts. Molts are triggered by ecdysteroids, and the nature of the molt (larval, pupal or adult) is determined by juvenile hormones. The genes encoding cuticle proteins are targets of both classes of hormones, and therefore are interesting models to study hormone action at the molecular level. The Drosophila ACP65A cuticle gene is expressed exclusively during the synthesis of the adult exoskeleton, in epidermal domains synthesising flexible cuticle. We have examined the cis -regulatory sequences of ACP65A using phylogenetic comparisons and functional analysis, and find that only about 180 bp are essential, including an 81 bp intron. T…

Screening for multiple hereditary hypercoagulability factors using the amplification refractory mutation system

2003

Many hereditary factors have been implicated in the development of arterial and/or venous thromboembolic diseases. A number of these risk factors can be identified by the amplification refractory mutation system (ARMS). However, the underlying technical conditions for performing ARMS are highly variable, and depend on which risk factors are being analyzed. We have now developed a novel ARMS-based system to simultaneously screen for multiple hypercoagulability factors under identical PCR conditions. This can greatly simplify the process of screening for hereditary hypercoagulability.

Nucleotide sequence of the 18S rDNA from the microalgaNanochlorum eucaryotum

1988

The human complement component C8B gene: structure and phylogenetic relationship

1993

The eighth component of human complement (C8) is a serum protein that consists of three chains (alpha, beta and gamma), encoded by three separate genes, viz., C8A, C8B, and C8G. In serum, the beta-subunit is non-covalently bound to the disulfide-linked alpha-gamma subunit. Using a full-length C8 beta cDNA probe, we isolated several clones from human genomic lambda DNA libraries. Four lambda clones covering the complete cDNA sequence were characterized by TaqI restriction mapping and were "shotgun" subcloned into M13. C8 beta-cDNA-positive clones were partially sequenced to characterize the 12 exons of the gene with sizes from 69 to 347 bp. All intron-exon junctions followed the GT-AG rule. …

Two distinct amplification events of the c-myc locus in a colorectal tumour.

2008

Southern hybridisation of genomic DNA extracted from a human primary colorectal carcinoma revealed amplification of a fragment containing the wild-type c-myc locus. Two additional rearranged DNA fragments, lying upstream of c-myc, fused to distant non-contiguous sequences from the same chromosome, with an opposite configuration (head to head vs. head to tail), were also found to be amplified. Sequences analysis suggested that these rearrangements resulted from illegitimate recombination at two distinct points within the DNA sequence just upstream of the c-myc ORF and further that these events triggered two different amplification mechanisms, only one of which, involving a strand invasion ev…

Molecular Structure of a Gypsy Element of Drosophila Subobscura (Gypsyds) Constituting a Degenerate Form of Insect Retroviruses

1996

We have determined the nucleotide sequence of a 7.5 kb full-size gypsy element from Drosophila subobscura strain H-271. Comparative analyses were carried out on the sequence and molecular structure of gypsy elements of D.subobscura (gypsyDs), D.melanogaster (gypsyDm) and D.virilis (gypsyDv). The three elements show a structure that maintains a common mechanism of expression. ORF1 and ORF2 show typical motifs of gag and pol genes respectively in the three gypsy elements and could encode functional proteins necessary for intracellular expansion. In the three ORF1 proteins an arginine-rich region was found which could constitute a RNA binding motif. The main differences among the gypsy element…

Accelerated Evolution of Fetuin-A (FETUA, also AHSG) is Driven by Positive Darwinian Selection, not GC-Biased Gene Conversion

2009

article i nfo Human Fetuin-A (FETUA, also termed AHSG) is a serum protein composed of two cystatin-like domains D1 and D2 of together 235 amino acids (aa) and an unrelated domain D3 of 114 aa. Though the protein plays a role in diverse physiological and pathological processes, comparably little is known about sequence evolution of FETUA. We therefore analyzed its molecular evolution on the basis of coding sequences of 16 primate species. Ratios of non-synonymous to synonymous substitution rates (dn/ds= ω) suggest that a previously reported acceleration of sequence evolution of exon 7, which encodes domain D3, is driven by positive selection instead of neutral evolution. Irrespective of the …