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At least 253 records · Page 14Linked to original sources
PubMed2002

Phylogenetics of Miscanthus, Saccharum and related genera (Saccharinae, Andropogoneae, Poaceae) based on DNA sequences from ITS nuclear ribosomal DNA and plastid trnLintron and trnL-F intergenic spacers.

DNA sequences were used to assess the monophyly and inter-relationships of Miscanthus, Saccharumand related genera in the Saccharum complex. Three DNA regions were sequenced, including the trnLintron and the trnL-F intergenic spacer of the plastid genome and the ITS region of nuclear ribosomal DNA (nrDNA). Because it was more variable, the ITS region proved most suitable for phylogenetic reconstruction at this level, and the results indicate that Miscanthus s.l. and Saccharum s.l. are polyphyletic. A set of species from Saccharum section Ripidium(clade a) do not group closely with any members of Saccharum s.l. A number of Miscanthus species from eastern or south-eastern Asia represent a monophyletic group with a basic chromosome number of 19 (clade b), but the other species from Africa and the Himalayas are clearly excluded. There is support for a monophyletic Saccharum s.s. clade including S. officinarumand S. spontaneum that is sister to Miscanthus s.s(clade c). There is no evidence to support the division of some Saccharum s.l. into the genera currently known as Erianthus and Narenga. Saccharum contortum( =Erianthus contortus), S. narenga (= Narenga porphyrocoma) and Erianthus rockii, group more closely with Miscanthus fuscus, a species from the Himalayas and also with the African Miscanthus s.l. species (= Miscanthidium, clade d).

Journal Article↗
PubMed2002

Mycobacterium avium subsp. paratuberculosis strains from cattle and sheep can be distinguished by a PCR test based on a novel DNA sequence difference.

A DNA sequence differing between sheep and cattle types of Mycobacterium avium subsp. paratuberculosis was identified and used to develop a PCR test. The test unequivocally distinguished all sheep types from cattle types and was negative for a wide range of other strains from the Mycobacterium avium-Mycobacterium intracellulare complex. The test will be useful for epidemiological purposes, particularly in hosts such as deer that can be easily infected with either type.

Animals↗
PubMed1997

DNA sequence of Bacillus subtilis (natto) NR-1 gamma-glutamyltranspeptidase gene, ggt.

The ggt encoding gamma-glutamyltranspeptidase (GGT) from Bacillus subtilis (natto) was cloned and sequenced. The DNA sequence contains a single open reading frame of 1761 bp that might be translated to a protein of 587 amino acid residues, and indicates that B. subtilis (natto) GGT is synthesized as prepro-GGT and processed later into large and small subunits. The putative catabolite responsive element (CRE) was located upstream of the ggt coding region.

Amino Acid Sequence↗
PubMed2001

Differences in DNA-sequence recognition between the DNA-binding domain fragment and the full-length molecule of the heat-shock transcription factor of schistosome.

Binding and inhibition studies reveal that the DNA-binding domain (DBD) fragment and the full-length molecule of the heat-shock transcription factor of schistosome (SmHSF) differ in DNA sequence recognition. SmHSF does not recognize the ideal HSE consensus sequence (nGAAnnTTCnnGAAn) but recognizes a variant HSE that contains nGTAn instead of nGAAn in the third pentamer. The DBD reacts efficiently with the ideal HSE sequence and with lower affinity with the variant HSE sequence. These findings suggest that elements inside and outside the DBD contribute to the DNA-binding specificity of HSF.

Animals↗
PubMed1999

Side-entry excitation and detection of square capillary array electrophoresis for DNA sequencing.

In high throughput DNA sequencing based on capillary electrophoresis, efficient coupling of the laser to each capillary is a challenge. Our group previously reported two multiple point irradiation schemes. The present work describes a more efficient excitation and detection method in which the laser light propagates through the capillary array without undergoing a serious reduction in power. An array of square capillaries (340 microns O.D. x 75 microns I.D.) was sandwiched between two fused-silica plates with an index-matching solution in between. The light was directed into the channel across the capillary array from the side. DNA sequences of PGEM/U from 24 capillaries were obtained even with a relatively low-power laser. The excitation scheme can be scaled up to hundreds of capillaries to achieve high-speed, high-throughput DNA sequencing, genetic typing and drug screening.

Electrophoresis, Capillary↗
PubMed1984

DNA sequence analysis of crown gall tumor T-DNA encoding the 0.7 kb transcript.

Crown gall tumor formation involves integration into the plant genome of DNA sequences (the T-region) of tumor-inducing (Ti) plasmids present in Agrobacterium tumefaciens. The T-DNA of the tumor expresses several gene products. Little is known about the function or regulation of expression of the 0.7kb transcript, which represents a relatively abundant T-DNA transcript in octopine-type tumors. In this report, a detailed structural analysis of the gene encoding the 0.7 kb transcript has been obtained by DNA sequence analysis of T-DNA isolated from A6S/2 tumor line. An indication of the structural characteristics of the protein product is obtained from the predicted amino acid sequence. The sequences flanking the open reading frame show characteristics with other eucaryotic genes. The corresponding DNA sequence of the inducing Ti plasmid (pTiA6) is identical with that of the DNA sequence from the tumor. Comparison of this gene sequence with the corresponding region of another Ti plasmid (pTiAch5) shows several differences in the 5' flanking sequence, but the nucleotide sequence of the coding region and 3' flanking region are identical.

Amino Acid Sequence↗
PubMed2004

Rényi continuous entropy of DNA sequences.

Entropy measures of DNA sequences estimate their randomness or, inversely, their repeatability. L-block Shannon discrete entropy accounts for the empirical distribution of all length-L words and has convergence problems for finite sequences. A new entropy measure that extends Shannon's formalism is proposed. Renyi's quadratic entropy calculated with Parzen window density estimation method applied to CGR/USM continuous maps of DNA sequences constitute a novel technique to evaluate sequence global randomness without some of the former method drawbacks. The asymptotic behaviour of this new measure was analytically deduced and the calculation of entropies for several synthetic and experimental biological sequences was performed. The results obtained were compared with the distributions of the null model of randomness obtained by simulation. The biological sequences have shown a different p-value according to the kernel resolution of Parzen's method, which might indicate an unknown level of organization of their patterns. This new technique can be very useful in the study of DNA sequence complexity and provide additional tools for DNA entropy estimation. The main MATLAB applications developed and additional material are available at the webpage . Specialized functions can be obtained from the authors.

Animals↗
PubMed1995

A new algorithm for DNA sequence assembly.

Since the advent of rapid DNA sequencing methods in 1976, scientists have had the problem of inferring DNA sequences from sequenced fragments. Shotgun sequencing is a well-established biological and computational method used in practice. Many conventional algorithms for shotgun sequencing are based on the notion of pairwise fragment overlap. While shotgun sequencing infers a DNA sequence given the sequences of overlapping fragments, a recent and complementary method, called sequencing by hybridization (SBH), infers a DNA sequence given the set of oligomers that represents all subwords of some fixed length, k. In this paper, we propose a new computer algorithm for DNA sequence assembly that combines in a novel way the techniques of both shotgun and SBH methods. Based on our preliminary investigations, the algorithm promises to be very fast and practical for DNA sequence assembly.

Algorithms↗
PubMed2001

On-line nanoliter cycle sequencing reaction with capillary zone electrophoresis purification for DNA sequencing.

An integrated system for DNA sequencing based on a nanoreactor for cycle-sequencing reaction coupled with on-line capillary zone electrophoresis (CZE) for purification and capillary gel electrophoresis (CGE) for separation is presented. Less than 100 nl of premixed reagent solution, which includes dye-labeled terminator pre-mix, bovine serum albumin and template, was hydrodynamically injected into a fused-silica capillary (75 microm I.D.) inside a laboratory-made microthermocycler for cycle sequencing reaction. In the same capillary, the reaction products were purified by CZE followed by on-line injection of the DNA fragments into another capillary for CGE. Over 540 base pairs (bp) of DNA can be separated and the bases called for single-standed DNA with 0.9% error rate. The total time was about 3.5 h, or a cycle time of 2 h with staggered operation. For double-stranded DNA, a longer reaction time was required and base calling up to 490 bp with 1.2% error rate was achieved. The whole system is readily adaptable to automated multiplex operation for DNA sequencing or polymerase chain reaction analysis.

Base Sequence↗
PubMed2002

Biosensors for DNA sequence detection.

DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

Biosensing Techniques↗
PubMed1997

Similarities inferred from the studies of long range correlations among mitochondrial DNA sequences.

Existence of long range correlations within the DNA sequences of living organism has immense importance in understanding the language of DNA sequences. Recently it has been reported that long range correlations occur in DNA sequences. Some investigators claimed that these type of correlations occur only on intron containing DNA sequences. Some observers, however, have the opinion that long range correlations do not distinguish between the intron containing DNA sequences and intronless DNA sequences. The biological origin of long range correlations in the DNA sequences is not clearly known. In this paper we have demonstrated that long range correlations also occur on intronless mitochondrial DNA sequences, indicating that these special type of correlations are not the unique features for intron containing DNA sequences. We have also demonstrated that long range correlations simply originate in the region around which there is a large variation of pyrimidine and purine ratios. The similarities among the mitochondrial DNA sequences can be inferred by computing the fractal exponents in the region where there is a large variation of pyrimidine and purine ratio, as well as in the region where the ratio of pyrimidine and purine fluctuates in a nearly constant manner. In other words the similarities among the mitochondrial DNA sequences cannot be inferred by calculating the fractral exponents for the whole sequence.

Animals↗
PubMed1995

Isolation and characterization of a Pseudomonas aeruginosa genomic DNA sequence, encoding a putative DNA helicase belonging to superfamily I.

The isolation and characterization of a 2,122 bp DNA fragment from a Pseudomonas aeruginosa genomic library containing a 1,495 bp open reading frame (ORF) encoding a putative DNA helicase is described. The deduced amino acid (498 residues) sequence derived from this ORF, exhibited a high degree of homology to the rep and uvrD helicases of Escherichia coli (55 and 38% identities, respectively), and to those of Staphylococcus aureus and Haemophilus influenzae (43 and 39% identities, respectively), all of them belonging to superfamily I.

Amino Acid Sequence↗
PubMed1994

Sequence analysis of 16S rRNA from mycoplasmas by direct solid-phase DNA sequencing.

Automated solid-phase DNA sequencing was used for determination of partial 16S ribosomal DNA sequences of mycoplasmas. The sequence information was used to establish phylogenetic relationships of 11 different mycoplasmas whose 16S rRNA sequences had not been determined earlier. A biotinylated fragment corresponding to positions 344 to 939 in the Escherichia coli sequence was generated by PCR. The PCR product was immobilized onto streptavidin-coated paramagnetic beads, and direct sequencing was performed in both directions. One previously unclassified avian mycoplasma was found to belong to the Mycoplasma lipophilum cluster of the hominis group. Microheterogeneities were discovered in the rRNA operons of Mycoplasma mycoides subsp. mycoides (SC type), confirming the existence of two different rRNA operons. The 16S rRNA sequence of M. mycoides subsp. capri was identical to that of M. mycoides subsp. mycoides (type SC), except that no microheterogeneities were revealed. Furthermore, automated solid-phase DNA sequencing was used to identify a mycoplasmal contamination of a cell culture as Mycoplasma hyorhinis, which proved to be very difficult by conventional methods. The results suggest that the direct solid-phase DNA sequencing procedure is a powerful tool for identification of mycoplasmas and is also useful in taxonomic studies.

Base Sequence↗
PubMed1992

Direct sequencing of baculovirus genomic DNA: sequence determination of the engineered respiratory syncytial virus chimeric FG gene.

Primer-directed enzymatic sequencing has proven to be an efficient and effective method for sequencing various size double-stranded DNA templates. We previously developed a primer-directed sequencing procedure for using double-stranded cosmid (50 kb) DNAs as template. We are interested in using this method to directly sequence larger DNA templates. Towards this goal we applied this method to directly sequence an engineered gene that had been transferred and integrated into the 130-kb baculovirus genome. Both crudely prepared and CsCl gradient-banded baculovirus DNAs were tested and reasonable sequencing ladders were obtained for both types of DNA templates. As little as 3 micrograms of gradient-banded baculovirus DNA were found to be sufficient to obtain film exposure times similar to those observed for cosmid size templates, 24 to 48 h. Effectiveness of the described method was demonstrated by obtaining the complete sequence of the engineered respiratory syncytial virus chimeric FG gene (2.5 kb in length) directly from the recombinant baculovirus "Baculo-FG" genome. Thus, our results demonstrate first, that double-stranded DNA templates as large as 130 kb can be sequenced directly and second, that the nucleotide sequence of engineered genes integrated within the baculovirus genome can be determined without the use of any intermediate steps of procedures.

Amino Acid Sequence↗
PubMed1992

Structural heterogeneity in the R173 family of rye-specific repetitive DNA sequences.

The rye-specific R173 family of repeated DNA sequences consists of ca. 15,000 individual copies per diploid rye (Secale cereale) genome and is distributed over all 7 rye chromosomes in a dispersed manner. Individual R173 elements vary in size between 3 and 6 kb, are generally not arranged as tandem repeats and are flanked by both multi-copy and single-copy sequences. DNA sequence analysis of three R173 elements (R173-1, R173-2 and R173-3) demonstrated a high degree of homology in conserved domains. The structure of R173-1 was quite different from the other two elements: long direct repeats, which represent a rye-specific repetitive sequence, were found at the ends and a 600 bp long domain was replaced by an unrelated sequence of approximately equal size. R173-2 and R173-3 were extremely similar to each other with the exception of a terminal truncation of R173-2. No open reading frames for proteins greater than 20 kDa were present and a database search failed to detect significant homologies to published protein sequences. Despite the transposon like genomic organisation of the R173 family, individual elements lacked sequence features frequently associated with transposons and retrotransposons. In contrast, two of the regions flanking R173 elements showed strong DNA homologies to a 850 bp long region of a proposed wheat retrotransposon and to a 300 bp long region downstream of the wheat Glu-D1 gene.

Base Sequence↗
PubMed1983

Kilo-sequencing: an ordered strategy for rapid DNA sequence data acquisition.

A strategy for rapid DNA sequence acquisition in an ordered, nonrandom manner, while retaining all of the conveniences of the dideoxy method with M13 transducing phage DNA template, is described. Target DNA 3 to 14 kb in size can be stably carried by our M13 vectors. Suitable targets are stretches of DNA which lack an enzyme recognition site which is unique on our cloning vectors and adjacent to the sequencing primer; current sites that are so useful when lacking are Pst, Xba, HindIII, BglII, EcoRI. By an in vitro procedure, we cut RF DNA once randomly and once specifically, to create thousands of deletions which start at the unique restriction site adjacent to the dideoxy sequencing primer and extend various distances across the target DNA. Phage carrying a desired size of deletions, whose DNA as template will give rise to DNA sequence data in a desired location along the target DNA, may be purified by electrophoresis alive on agarose gels. Phage running in the same location on the agarose gel thus conveniently give rise to nucleotide sequence data from the same kilobase of target DNA.

Base Sequence↗