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At least 145 records · Page 8Linked to original sources
PubMed2001

Relationships of scincid lizards (Mabuya spp; Reptilia: Scincidae) from the Cape Verde islands based on mitochondrial and nuclear DNA sequences.

Partial DNA sequences from two mitochondrial (mt) and one nuclear gene (cytochrome b, 12S rRNA, and C-mos) were used to estimate the phylogenetic relationships among the six extant species of skinks endemic to the Cape Verde Archipelago. The species form a monophyletic unit, indicating a single colonization of the islands, probably from West Africa. Mabuya vaillanti and M. delalandii are sister taxa, as indicated by morphological characters. Mabuya fogoensis and M. stangeri are closely related, but the former is probably paraphyletic. Mabuya spinalis and M. salensis are also probably paraphyletic. Within species, samples from separate islands always form monophyletic groups. Some colonization events can be hypothesized, which are in line with the age of the islands. C-mos variation is concordant with the topology derived from mtDNA.

Animals↗
PubMed1981

The DNA sequences of cloned complex satellite DNAs from Hawaiian Drosophila and their bearing on satellite DNA sequence conservation.

A class of restriction endonuclease fragments near 185 bp in length and comprising approximately 20% of the genomes of 3 species of Hawaiian Drosophila has been cloned using bacteriophage M13. The nucleotide sequences of 14 clones have been determined and the variation between clones has been found to be due to deletions and base changes. Analyses of uncloned material show that the cloning system itself does not introduce the variation. The variation of the basic repeat within and between species is high; 15% due to deletions and 10% due to base changes. The Drosophila data are similar in many respects to both the 23 bp calf satellite results (Pech et al., 1979 b) and those from sequence analyses of the 170 bp primate restriction fragments (Rubin et al., 1979; Donehower et al., 1980, Wu and Manuelidis, 1980). The intraspecies level of base changes and deletions in the calf satellite approaches 25% as does that in the human/African green monkey/baboon comparisons. The between species variation in the primate group is near 35%. Direct sequencing methods thus reveal a widespread sequence heterogeneity in both invertebrate and mammalian satellite systems of long or short repeat length. This heterogeneity does not support the strict sequence conservation implied by the "library" hypothesis, which claims a functional role in speciation for the rigid conservation of satellite DNA sequences (Fry and Salser, 1977). Furthermore the Drosophila and primate data reveal that satellite DNAs can change rapidly, though nonrandomly, at the nucleotide sequence level in a relatively closely knit group such as the Hawaiian species, as well as in more distantly related species from amongst the primates. We draw two major conclusions. There is no universal attribute of satellite DNA sequence per se, the only biological variable to date being the amount of satellite DNA and its effect in the germ line. Many aspects of satellite DNA evolution conform to Kimura's (1979) concepts of neutrality.

Animals↗
PubMed1997

Taxonomic status and phylogenetic relationships of some species of the genus Gammarus (Crustacea, Amphipoda) deduced from mitochondrial DNA sequences.

Mitochondrial DNA nucleotide sequence analysis was used to determine the extent of genetic differentiation among six species of the genus Gammarus (Crustacea, Amphipoda) common in France (G. fossarum, G. pulex, G. lacustris, G. wautieri, G. roeseli, G. marinus). From 23 different populations, 104 specimens were compared to examine their taxonomic status and their phylogenetic relationships. Nucleotide sequences for a 376-base segment of the cytochrome c oxidase subunit I (COI) gene were obtained through direct sequencing of amplified DNA. The strong sequence variability found at the interspecific level, generally masked by morphological or ecological similarities, is consistent with that observed for other crustaceans and supports existing species classifications. A high level of genetic variation was observed at the intraspecific level, suggesting that the COI gene will be a powerful marker for amphipod population biology. Based on the mitochondrial population biology. Based on the mitochondrial DNA results, we propose a phylogenetic hypothesis of the relationships among the six studied species, which is discussed in biogeographic and evolutionary terms.

Animals↗
PubMed1982

Nopaline synthase: transcript mapping and DNA sequence.

The DNA sequence of the nopaline synthase gene (nos) from Agrobacterium tumefaciens Ti plasmid pTiT37 and adjacent regions up to the right border of the T-DNA was determined. The 5' and 3' termini of the polyadenylated nos mRNA, isolated from a T37 tobacco teratoma tumor line, were localized by S1 mapping. The final mRNA is unspliced, encoded by a region of about 1450 bp, and specifies an open reading frame of 413 amino acids. Potential transcriptional signals in the 5' flanking DNA, such as CATAAA ("TATA box") and GGTCACTAT ("CAT box"), bear close resemblance to other eukaryotic promoters. Two putative polyadenylation signals, AATAAA and AATAAT, are found about 135 and 50 bp from the 3' end, respectively. This study may provide information for the development of expression vectors for genes in plant cells; moreover, the structural gene can be used as an easy screenable marker.

Amino Acid Oxidoreductases↗
PubMed1999

Hepatitis C virus-specific DNA sequences in human DNA: differentiation by means of restriction enzyme analysis at the DNA level in healthy, anti-HCV-negative individuals.

This study aimed to look for further HCV-specific sequences at the DNA level of healthy, HCV-negative individuals. Here, the sequence section from nt 57 to nt 328 within the 5'-NCR was assayed. Different combinations of primers were used in the nested PCR without a preceding reverse transcriptase step, resulting in fragments of the expected molecular weight size and also shorter and longer ones. It shows that the major part of the 5'-non-coding region (5'-NCR) of the hepatitis C virus genome is present in the DNA fraction from peripheral blood mononuclear cells (PBMCs) of healthy, anti-HCV-negative individuals tested. Furthermore we designed experiments to prove the specificity of these findings, by using restriction enzymes for digest assays of the target DNA before PCR (pre-PCR digest) and of the products after PCR (post-PCR digest). In conclusion, our study indicates that the main part of the internal ribosome entry site (IRES) structure of HCV at least is contained in the DNA of the individuals tested.

Base Sequence↗
PubMed1994

Atypical regions in large genomic DNA sequences.

Large genomic DNA sequences contain regions with distinctive patterns of sequence organization. We describe a method using logarithms of probabilities based on seventh-order Markov chains to rapidly identify genomic sequences that do not resemble models of genome organization built from compilations of octanucleotide usage. Data bases have been constructed from Escherichia coli and Saccharomyces cerevisiae DNA sequences of > 1000 nt and human sequences of > 10,000 nt. Atypical genes and clusters of genes have been located in bacteriophage, yeast, and primate DNA sequences. We consider criteria for statistical significance of the results, offer possible explanations for the observed variation in genome organization, and give additional applications of these methods in DNA sequence analysis.

Bacteriophage lambda↗
PubMed1988

DNA sequence of the Acinetobacter calcoaceticus catechol 1,2-dioxygenase I structural gene catA: evidence for evolutionary divergence of intradiol dioxygenases by acquisition of DNA sequence repetitions.

The DNA sequence of a 1.6-kilobase-pair SalI-KpnI Acinetobacter calcoaceticus restriction fragment carrying catA, the structural gene for catechol 1,2-dioxygenase I, was determined. The 933-nucleotide gene encodes a protein product with a deduced molecular weight of 34,351. The similarly sized Pseudomonas clcA gene encodes catechol 1,2-dioxygenase II, an enzyme with relatively broad substrate specificity and relatively low catalytic efficiency. Comparison of the catA and clcA sequences demonstrated their common ancestry and suggested that acquisitions of direct and inverted sequence repetitions of 6 to 10 base pairs were frequent events in their evolutionary divergence. The catechol 1,2-dioxygenases proved to be evolutionarily homologous with the alpha and beta subunits of Pseudomonas protocatechuate 3,4-dioxygenase, and analysis of conserved residues in the intradiol dioxygenases revealed conserved histidyl and tyrosyl residues that are probably involved in the ligation of ferric ion in their active sites.

Acinetobacter↗
PubMedDate not supplied

New invariant of DNA sequences.

For a DNA sequence with n bases, one can always associate it with an n x n nonnegative real symmetric matrix whose diagonal entries are zero. Once the matrix is given, its leading eigenvalue is usually calculated and used as an invariant to characterize the DNA sequence. Let M be such a matrix, and lambda1 its leading eigenvalue. Then (1/n)//M//m1 and sqrt [(n-1)/n]//M//F are the lower and upper bounds of lambda1, respectively. Since their arithmetic average is an approximate value of lambda1 and simpler for calculation, we can use it as an alternative invariant to characterize the DNA sequence. The utility of the new parameter is illustrated on the DNA sequences of five species: human, chimpanzee, mouse, rat, and gallus.

Animals↗
PubMedDate not supplied

[Sequence complexity of transcribed unique DNA sequences in genome of mouse P815 mastocytoma cells (author's transl)].

The sequence complexity of nuclear RNA from mouse liver, mouse spleen and highly malignant P815 mastocytoma was measured by nRNA driven hybridization to unique DNA sequences of P815 cells. The unique DNA sequences represent 63% of the total nuclear DNA of P815 cells and their availibility in hybridization experiments was found to be 76%. Of these sequences 7.8% formed hybrids with nuclear RNA of this cell, about 11.5% with mouse spleen and about 14.5% with mouse liver nuclear RNA. Assuming an asymmetrical transcription, the complexities of these transcripts are 2.8 X 10(8) nucleotides for mouse P815 mastocytomas, 4.3 X 10(8) for mouse spleen and about 5.3 X 10(8) nucleotides for mouse liver. Cellular specifity of the transcribed information was analyzed in additivity experiments, in which unique DNA sequences, not complementary to the nuclear RNA of one cell were annealed to the nuclear RNAs of the two other tissues/cells. In these experiments most of the nuclear RNA sequences of P815 cells were found to be also present in the nucleus of mouse liver and spleen. Only a small portion of the unique DNA sequences of P815 mastocytoma (about 1.2% corresponding to 4.4 X 10(7) nucleotides) was found to be complementary only to P815 mastocytoma nuclear RNA.

Animals↗
PubMed1975

Size and distribution of SV 40 DNA Sequences covalently linked with the DNA of permissive mammalian cells.

CV-1 cells productively infected with SV 40 contain viral DNA which is covalently linked with the host cell DNA. These linear duplex viral-host DNA molecules are replicated during the infectious cycle. They can be selectively isolated and purified by two successive cycles of DNA-DNA hybridization and elution steps using first CV-1 cell and then SV 40-DNA immobilized on filters. In an attempt to clarify the nature of the host DNA sequences neighbouring the viral DNA it was found that reiterated host DNA must be within the range of 800 bases from the viral sequences. Reassociation kinetics and treatment of the reassociated viral-host DNA sequences with single strand-specific S1 nuclease have shown that unique host DNA sequences are always present in close neighbourhood of the viral DNA. Most of the SV 40 DNA sequences are probably intergrated as fragments of subgenomic length.

Animals↗
PubMed1994

Identification and elimination of DNA sequences in Taq DNA polymerase.

This study confirms that different preparations of Taq DNA polymerase are contaminated with eubacterial DNA. The contaminants appeared to represent more than one strain or species but were not identified as Thermus aquaticus or Escherichia coli. Differences in microcentrifuge tube composition appeared to affect elimination of the contaminants.

Base Sequence↗
PubMed1980

Presence of Herpesvirus ovis DNA sequences in cellular DNA from sheep lungs affected with jaagsiekte (pulmonary adenomatosis).

To investigate further the possible involvement of Herpesvirus ovis in the aetiology of jaagsiekte, the kinetics of reassociation of viral DNA and DNA isolated from tumour tissue as well as from cell cultures derived from it were studied. Although DNA-DNA hybridization could be demonstrated in 2 cases of jaagsiekte, no correlation was found between the presence of Herpesvirus ovis genome sequences and the occurrence of the disease.

Animals↗
PubMed1999

Gene stability in transgenic aspen (Populus). I. Flanking DNA sequences and T-DNA structure.

The stability of transgenes in the genome of transformed plants depends strongly on their correct physical integration into the host genome as well as on flanking target DNA sequences. For long-lived species like trees, however, no information is available so far concerning inactivation or loss of transgenes due to gene silencing or somatic genome rearrangement events. In this study, four independently transformed 35S-rolC transgenic hybrid aspen plants (Populus tremula L. x tremuloides Michx.), each harbouring one copy of the transgene, were investigated during continuous growth in the greenhouse. In one of these transgenic lines (Esch5:35S-rolC-#1) individuals frequently show phenotypic reversions, while in the remaining three lines (Esch5:35S-rolC-#3, -#5, -#16) the gene was essentially stable. Molecular analysis including PCR, Southern and Northern assays clearly showed that the transgene had been lost in the revertant tissue of the unstable line. Sequencing of T-DNA right and left borders, and flanking DNA regions, in all four transgenic aspen lines revealed no differences either in the type of flanking DNA (G-C to A-T ratio) or with respect to the presence of enhancers or MAR (matrix associated repeats)-like structures. Primers located within the left and right flanking regions in the three stable lines could be used to recover the target sites from the untransformed plants. This was not possible, however, with the unstable line, indicating that at least one flanking sequence does not derive from the plant target DNA but is of unknown origin. PCR using other primer pairs, and inverse PCR analysis, revealed an additional truncated T-DNA copy of 1050 nucleotides adjacent to the left border of the complete copy in this line. Sequencing of this truncated T-DNA revealed that it represented an inverted copy of part of the right half of the original construct. This special feature would allow the inverted repeat to pair with right border sequences of the complete copy. This would explain the frequently observed reversion resulting in transgene loss as due to intrachromosomal base-pairing leading to double-stranded loops of single-stranded DNA during mitotic cell divisions.

Bacterial Proteins↗
PubMed1992

A single-fluor approach to DNA sequence determination using high performance capillary electrophoresis.

The Tabor and Richardson strategy for enzymatic chain termination sequencing of DNA using relative peak intensity has been adapted to high performance capillary gel electrophoresis with laser induced fluorescence detection. This approach to DNA sequencing involves the use of only a single fluor and results in significant reduction in the time required to determine a DNA sequence without the use of highly complicated and expensive instrumentation. We present a modification of the Tabor and Richardson approach employing two reactions, each containing complementary mixtures of only three ddNTP's in the concentration ratio 4:2:1. The DNA sequence is determined by relative peak height and by assigning the missing ddNTP to "gaps" between the peaks. The use of only three terminators/reaction simplifies the software task of differentiating between the termination types and makes more efficient use of the available dynamic range. Both complementary mixes generate complete sequence information and the two data files are combined in order to make a more confident sequence call. This process helps to eliminate errors caused by occasional non-uniform incorporation of ddNTP's or false terminations and also alleviates some of the difficulty associated with reading through compressed regions of the electropherogram.

Base Sequence↗
PubMed1994

Molecular evidence on primate phylogeny from DNA sequences.

Evidence from DNA sequences on the phylogenetic systematics of primates is congruent with the evidence from morphology in grouping Cercopithecoidea (Old World monkeys) and Hominoidea (apes and humans) into Catarrhini, Catarrhini and Platyrrhini (ceboids or New World monkeys) into Anthropoidea, Lemuriformes and Lorisiformes into Strepsirhini, and Anthropoidea, Tarsioidea, and Strepsirhini into Primates. With regard to the problematic relationships of Tarsioidea, DNA sequences group it with Anthropoidea into Haplorhini. In addition, the DNA evidence favors retaining Cheirogaleidae within Lemuriformes in contrast to some morphological studies that favor placing Cheirogaleids in Lorisiformes. While parsimony analysis of the present DNA sequence data provides only modest support for Haplorhini as a monophyletic taxon, it provides very strong support for Hominoidea, Catarrhini, Anthropoidea, and Strepsirhini as monophyletic taxa. The parsimony DNA evidence also rejects the hypothesis that megabats are the sister group of either Primates or Dermoptera (flying lemur) or a Primate-Dermoptera clade and instead strongly supports the monophyly of Chiroptera, with megabats grouping with microbats at considerable distance from Primates. In contrast to the confused morphological picture of sister group relationships within Hominoidea, orthologous noncoding DNA sequences (spanning alignments involving as many as 20,000 base positions) now provide by the parsimony criterion highly significant evidence for the sister group relationships defined by a cladistic classification that groups the lineages to all extant hominoids into family Hominidae, divides this ape family into subfamilies Hylobatinae (gibbons) and Homininae, divides Homininae into tribes Pongini (orangutans) and Hominini, and divides Hominini into subtribes Gorillina (gorillas) and Hominina (humans and chimpanzees). A likelihood analysis of the largest body of these noncoding orthologues and counts of putative synapomorphies using the full range of sequence data from mitochondrial and nuclear genomes also find that humans and chimpanzees share the longest common ancestry.

Animals↗
PubMed2006

Comparative study on DNA sequences of ribosomal DNA and cytochrome c oxidase subunit 1 of mitochondrial DNA among five species of gnathostomes.

The nucleotide sequences of partial 18S, complete internal transcribed spacer region 1 (ITS1), complete 5.8S, complete ITS2 and partial 28S of ribosomal DNA (rDNA) and cytochrome c oxidase subunit 1 of mitochondrial DNA (MCOI) from five species of gnathostomes (G. spinigerum, G. doloresi, G. nipponicum, G. hispidum and G. binucleatum with the former four species being distributed in Japan and Asia) that cause human gnathostomiasis were compared by direct polymerase chain reaction cycle-sequencing. The nucleotide sequences of each region of the18S (613 bp), 5.8S (158 bp) and 28S (598 bp) rDNA from the five species were almost identical. The ITS1 region was different in length for the five species. The nucleotide sequences of each region of ITS2 and partial MCO1 regions were different among the five species. Therefore, these two regions can be used as genetic markers for identification of worms.

Animals↗