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At least 631 records · Page 35Linked to original sources
PubMed1997

Differentiation of Coxiella burnetii by sequence analysis of the gene (com1) encoding a 27-kDa outer membrane protein.

The gene (com1) encoding a 27-kDa outer membrane protein in 21 strains of Coxiella burnetii from a variety of clinical and geographical sources was sequenced for strain differentiation. The com1 gene was highly conserved among all the strains tested but there were several differences in nucleotide and deduced amino acid sequences. Based on the com1 gene-specific nucleotides and deduced amino acids, the 21 strains were divided into four groups. Group 1 contained 14 strains originating from ticks, cattle and human cases of acute Q fever. Groups 2 and 3 included 2 and 3 strains, respectively, originating from human cases of chronic Q fever. Group 4 contained 2 strains originating from a human case of acute Q fever and a goat with abortion. The results indicated that the strains originating from ticks, cattle and human cases of acute Q fever differed at the molecular level from those of human chronic Q fever. This study suggests that a sequence analysis of the com1 gene can be used for strain differentiation of C. burnetii.

Amino Acid Sequence↗
PubMed2005

[Cloning and sequence analysis of ITS gene of Leishmania donovani isolates from different epidemic foci in China].

This study was directed to determine the nucleotide sequence of the ITS (internal transcribed spacer) gene of Leishmania donovani isolates from desert foci (L. d XJ771), hill foci (L. d SC10) and plain foci (L. d SD2), and to find out the differences of the sequences of ITS gene among these three isolates. The specific ITS fragments from nuclear DNA of three Leishmania isolates were amplified by PCR, cloned into PMD18-T vector, and then sequenced by the dideoxy chain termination method. Sequence analysis showed that the amplified DNA fragments of the three isolates were 1 086 bp (L. d XJ771), 1 027 bp (L. d SC10) and 1 028 bp (L. d SD2). There were obvious sequence differences among L. d XJ771, L. d SC10 and L. d SD2. The differences between L. d XJ771 (desert foci isolate) and L. d SC10 (hill foci isolate) were less than the differences between L. d XJ771 (desert foci isolate ) and L. d SD2. (plain foci isolate).

China↗
PubMed2004

Cloning and sequencing analysis of the repressor gene of temperate mycobacteriophage L1.

The wild-type and temperature-sensitive (ts) repressor genes were cloned from the temperate mycobacteriophage L1 and its mutant L1cIts391, respectively. A sequencing analysis revealed that the 131st proline residue of the wild-type repressor was changed to leucine in the ts mutant repressor. The 100% identity that was discovered between the two DNA regions of phages L1 and L5, carrying the same sets of genes including their repressor genes, strengthened the speculation that L1 is a minor variant of phage L5 or vice versa. A comparative analysis of the repressor proteins of different mycobacteriophages suggests that the mycobacteriophage-specific repressor proteins constitute a new family of repressors, which were possibly evolved from a common ancestor. Alignment of the mycobacteriophage-specific repressor proteins showed at least 7 blocks (designated I-VII) that carried 3-8 identical amino acid residues. The amino acid residues of blocks V, VI, and some residues downstream to block VI are crucial for the function of the L1 (or L5) repressor. Blocks I and II possibly form the turn and helix 2 regions of the HTH motif of the repressor. Block IV in the L1 repressor is part of the most charged region encompassing amino acid residues 72-92, which flanks the putative N-terminal basic (residues 1-71) and C-terminal acidic (residues 93-183) domains of L1 repressor.

Amino Acid Sequence↗
PubMed2004

Comparative sequence analysis of imprinted genes between human and mouse to reveal imprinting signatures.

We performed a comparative genomic sequence analysis between human and mouse for 24 imprinted genes on human chromosomes 1, 6, 7, 11, 13, 14, 15, 18, 19, and 20. The MEME program was used to search for motifs within conserved sequences among the imprinted genes and we then used the MAST program to analyze for the presence or absence of motifs in the imprinted genes and 128 nonimprinted genes. Our analysis identified 15 motifs that were significantly enriched in the imprinted genes. We generated a logistic regression model by combining multiple motifs as input variables and the 24 imprinted genes and the 128 nonimprinted genes as a training set. The accuracy, sensitivity, and specificity of our model were 98, 92, and 99%, respectively. The model was further validated by an open test on 12 additional imprinted genes. The motifs identified in this study are novel imprinting signatures, which should improve our understanding of genomic imprinting and the role of genomic imprinting in human diseases.

Amino Acid Motifs↗
PubMed1995

Sequence analysis of leukotoxin secretion determinants from a Pasteurella haemolytica-like organism.

The pHLBD genes encoding the secretion functions for the 105 kDa RTX leukotoxin of Pasteurella haemolytica-like (PHL) organism has been cloned and sequenced. Like analogous genes from other RTX determinants, the pHLBD genes lie immediately downstream from the leukotoxin structural gene, pHLA. Although isolated from a diverse group of gram-negative organisms, the pHLBD genes and the characterized RTX BD genes from other organisms exhibit a high degree of homology at both the DNA and predicted amino acid sequence levels. We have previously reported the cloning of the leukotoxin gene (pHLCA) (Chang et al., Infect. Immun. 61:2089-2095), which encodes a 105-kda polypeptide with cytotoxic activity. DNA sequence analysis of the pHLBD genes shows 83.93% and 86.05% homologous to that of P. haemolytica IktBD genes, respectively.

ATP-Binding Cassette Transporters↗
PubMed1990

Cloning and sequence analysis of the cDNA for arachidonate 12-lipoxygenase of porcine leukocytes.

The complete amino acid sequence of arachidonate 12-lipoxygenase (EC 1.13.11.31) of porcine leukocytes was deduced by cloning and sequence analysis of DNA complementary to its mRNA. The sequence was confirmed by automated Edman degradation of the N-terminal regions of the native enzyme and its proteolytic fragments. The cDNA had an open reading frame encoding 662 amino acid residues with a calculated molecular weight of 74,911. Amino acid residues 533-545, Cys-(Xaa)3-Cys-(Xaa)3-His-(Xaa)3-His, showed significant homology to the short cysteine- or histidine-containing sequences proposed as the metal-binding domains of transcription factors and various metal-containing proteins [Berg, J. M. (1986) Science 232, 485-487]. The amino acid sequence of 12-lipoxygenase exhibited 86% identity with human reticulocyte 15-lipoxygenase and showed 41% identity with human leukocyte 5-lipoxygenase. The 12-lipoxygenase cDNA recognized a 3.4-kilobase mRNA species in various porcine cell types, with the largest amount in leukocytes, followed by pituitary, lung, jejunum, and spleen.

Amino Acid Sequence↗
PubMed1989

Identification by sequence analysis of chemotactic factors for monocytes produced by normal and transformed cells stimulated with virus, double-stranded RNA or cytokine.

A monocyte chemotactic activity was found to be released by various types of cultured human cells after appropriate stimulation: normal diploid fibroblasts, peripheral blood mononuclear cells or monocytes isolated therefrom, and a number of tumor cell lines, including osteosarcoma (MG-63) and hepatoma (Malavu) but not melanoma (Bowes) cells. Cultures of diploid human fibroblasts and these tumor cells stimulated with interleukin (IL) 1 or double-stranded RNA [poly(rI).poly(rC)], or infected with viruses (measles or rubella viruses) were found to produce chemotactic activity for both monocytes and granulocytes. Media collected from fibroblasts treated with E. coli or IL 6 did not contain such activity. Granulocyte and monocyte chemotactic activities were serologically distinct, and could be separated by successive chromatographical procedures. While the granulocyte chemotactic activity of both fibroblasts and MG-63 cells had previously been identified as granulocyte chemotactic protein/IL 8, the monocyte chemotactic activity from MG-63 cells was identified by amino acid sequence analysis as a different protein recently described to be released by human glioma and myelomonocytic cell lines. In view of the similarity in their chromatographical behavior, monocyte chemotactic activities from fibroblasts, MG-63 cells and fresh monocytes can probably be assigned to identical molecules. Cultures of unfractionated peripheral blood cells, however, were found to release an additional monocyte chemotactic protein, identifiable by amino acid sequence analysis as platelet factor 4.

Amino Acid Sequence↗
PubMed1994

Systematic use of automated fluorescence-based sequence analysis of amplified genomic DNA for rapid detection of point mutations.

Several approaches are now available for screening populations for known mutations in a given gene. However, for detection of multiple mutations in a population that has not been characterized or for detection of new mutations, the value and efficiency of these screening procedures decreases. Although more than 100 different beta-thalassemia mutations have so far been described, the spectrum of mutations in the Eastern Mediterranean and Israel has not been defined in detail. We have used automated fluorescence-based DNA sequence analysis of PCR-amplified genomic DNA employing a cycle-sequencing strategy coupled with advanced analysis software to rapidly detect beta-thalassemia mutations in Israeli patients. This method enabled rapid identification of eight different mutations in 10 patients, including two rare mutations, one of which has never been described in this geographic region. Our results show that automated fluorescence-based DNA sequence analysis of amplified genomic DNA is a rapid and reliable method for detection of point mutations and small deletions or insertions in both heterozygous and homozygous states. This approach is particularly effective for a relatively small gene such as beta-globin, but it can also be used for rapid detection of mutations in large genes by first sequencing clusters of exons and intron/exon borders.

Automation↗
PubMed2000

New approaches for innovations in sensitive Edman sequence analysis by design of a wafer-based chip sequencer.

In the last few years the development of new mass spectrometric techniques enabled fast and sensitive protein analysis by the introduction of mass spectrometry (MS) fingerprinting and MS/MS sequencing. For these methods mixtures of peptide fragments of the proteins can be employed, whereas the Edman degradation method requests purified peptides. On the other hand, Edman sequencing has the advantages that interpretation of the data is more simple, extended sequences can be derived, and reliable sequence information on unknown proteins is possible. Hence, Edman chemistry as an alternative technique to MS is still valuable. But higher sensitivity of the sequencers is needed in order to meet modern demands, e.g. in proteomics research. We designed a wafer-based chip sequencer for protein and peptide sequencing in the femto- to attomole range. The main advantage of our new design is the complete integration of dead volume free valves together with reactor and converter and volume-measuring loops within one wafer-based system. In this system aggressive chemicals and solvents for the Edman degradation can be delivered in sub-microliter amounts, which allows a considerable shortening of the degradation cycles. Further, we developed sensitive maintenance and tightness tests to prove a precise and reproducible delivery of the chemicals and the reduction of drying times as compared with conventional sequencers. Real parallel processing of several samples can easily be implemented. The system is designed to serve future needs in protein research.

Indicators and Reagents↗
PubMed1997

Cloning and nucleotide sequence analysis of a Brucella abortus gene encoding an 18 kDa immunoreactive protein.

A DNA fragment encoding an approximately 18 kDa protein from Brucella abortus strain 2308 was cloned and expressed in Escherichia coli. This recombinant protein, designated BA18K, reacted in Western blot analysis with sera obtained from experimentally and naturally infected animals including mice, goats, dogs and humans. Restriction enzyme analysis of the plasmid (pBA28) encoding BA18K revealed the presence of an approximately 8.7 kbp Sau3A genomic DNA fragment within the vector and subsequent subcloning and Western blot analysis limited the region encoding BA18K to an approximately 3.0 kbp Pst 1 DNA fragment. DNA sequence analysis of this region identified an open reading frame capable of encoding a protein of 177 amino acids with a predicted relative molecular mass of 17529. Comparison of the deduced amino acid sequence of BA18K with those in the protein sequence databases yielded no homology with previously described proteins from other bacterial genera. These searches did, however, indicate that BA18K is identical to the previously described outer membrane protein (OMP) from B. abortus strain 544 designated Omp 19.

Amino Acid Sequence↗
PubMed2001

Charge-state-dependent sequence analysis of protonated ubiquitin ions via ion trap tandem mass spectrometry.

One of the major factors governing the "top-down" sequence analysis of intact multiply protonated proteins by tandem mass spectrometry is the effect of the precursor ion charge state on the formation of product ions. To more fully understand this effect, electrospray ionization coupled to a quadrupole ion trap mass spectrometer, collision-induced dissociation, and gas-phase ion/ion reactions have been employed to examine the fragmentation of the [M + 12H]12+ to [M + H]+ ions of bovine ubiquitin. At low charge states (+1 to +6), loss of NH3 or H2O from the protonated precursor and directed cleavage at aspartic acid residues was observed. At intermediate charge states, (+7, +8, and +9), extensive nonspecific fragmentation of the protein backbone was observed, with 50% sequence coverage obtained from the [M + 8H]8+ ion alone. At high charge states, (+10, +11, +12), the single dominant channel that was observed was the preferential fragmentation of a single proline residue. These data can be readily explained in terms of the current model for intramolecular proton mobilization, that is, the "mobile proton model", the mechanisms for amide bond dissociation developed for protonated peptides, as well as the structures of the multiply charged ions of ubiquitin in the gas phase, examined by ion mobility and hydrogen/deuterium exchange measurements.

Amino Acid Sequence↗
PubMed1998

Comparative sequence analysis of a gene-rich cluster at human chromosome 12p13 and its syntenic region in mouse chromosome 6.

The Human Genome Project has created a formidable challenge: the extraction of biological information from extensive amounts of raw sequence. With the increasing availability of genomic sequence from other species, one approach to extracting coding and regulatory element information is through cross-species sequence comparison. To assess the strengths and weaknesses of this methodology for large-scale sequence analysis, 227 kb of mouse sequence syntenic to a gene-rich cluster on human chromosome 12p13 was obtained. Primarily through percent identity plots (PIPs) of SIM comparative sequence alignments, the sequence of coding regions, putative alternative exons, conserved noncoding regions, and correlation in repetitive element insertions were easily determined. The analysis demonstrated that the number, order, and orientation of all 17 genes are conserved between the two species, whereas two human pseudogenes are absent in mouse. In addition, apart from MIRs, no direct correlation of distribution or position of the majority of repetitive elements between the two species is seen. Finally, in examining the synonymous and nonsynonymous substitution rates in the conserved genes, a large variation in nonsynonymous rates is observed indicating that the genes in this region are diverging at different rates. This study indicates the utility and strength of large-scale cross-species sequence comparisons in the extraction of biological information from raw sequence, especially when combined with other computational tools such as GRAIL and BLAST.

Amino Acid Sequence↗
PubMed2000

Genomic sequence analysis of Fugu rubripes CFTR and flanking genes in a 60 kb region conserving synteny with 800 kb of human chromosome 7.

To define control elements that regulate tissue-specific expression of the cystic fibrosis transmembrane regulator (CFTR), we have sequenced 60 kb of genomic DNA from the puffer fish Fugu rubripes (Fugu) that includes the CFTR gene. This region of the Fugu genome shows conservation of synteny with 800-kb sequence of the human genome encompassing the WNT2, CFTR, Z43555, and CBP90 genes. Additionally, the genomic structure of each gene is conserved. In a multiple sequence alignment of human, mouse, and Fugu, the putative WNT2 promoter sequence is shown to contain highly conserved elements that may be transcription factor or other regulatory binding sites. We have found two putative ankyrin repeat-containing genes that flank the CFTR gene. Overall sequence analysis suggests conservation of intron/exon boundaries between Fugu and human CFTR and revealed extensive homology between functional protein domains. However, the immediate 5' regions of human and Fugu CFTR are highly divergent with few conserved sequences apart from those resembling diminished cAMP response elements (CRE) and CAAT box elements. Interestingly, the polymorphic polyT tract located upstream of exon 9 is present in human and Fugu but absent in mouse. Similarly, an intron 1 and intron 9 element common to human and Fugu is absent in mouse. The euryhaline killifish CFTR coding sequence is highly homologous to the Fugu sequence, suggesting that upregulation of CFTR in that species in response to salinity may be regulated transcriptionally.

Amino Acid Sequence↗
PubMed1998

Saguenay Lac Saint Jean cytochrome oxidase deficiency: sequence analysis of nuclear encoded COX subunits, chromosomal localization and a sequence anomaly in subunit VIc.

A biochemically distinct form of cytochrome oxidase (COX) deficiency found in the Saguenay region of Quebec is an autosomal recessive trait. The cDNA sequences of all 10 nuclear-encoded subunits from a patient's fibroblasts showed normal coding sequence. Sequences for subunit VIc in two atypical patients showed a heterozygous base substitution. Subunit VIc was localized to chromosome 18.

Animals↗
PubMed1999

Sequence analysis of 16S rRNA genes amplified from two ribosomal RNA gene clusters of Bifidobacterium bifidum.

Two rRNA gene clusters were detected in the genome of Bifidobacterium bifidum KCTC 3202T using Southern blot analysis. To analyse the sequences of the 16S rRNA genes from rrnA and rrnB, 16S rDNAs were amplified by PCR using DNA fragments purified from gel slices containing each of the rRNA gene clusters. The amplified 16S rDNAs from rrnA and rrnB were cloned into vectors and three clones of each gene sequenced. The resultant sequences were confirmed by direct sequencing of the 16S rDNAs from rrnA and rrnB. Sequence differences were not found between rrnA and rrnB in 1488 bp of the 16S rRNA genes.

Bifidobacterium↗
PubMed2001

Cloning and sequence analysis of cnaA gene encoding the catalytic subunit of calcineurin from Aspergillus oryzae.

Calcineurin has been implicated in ion-homeostasis, stress adaptation in yeast and for hyphal growth in filamentous fungi. Genomic DNA and cDNA encoding the catalytic subunit of calcineurin (cnaA) were isolated from Aspergillus oryzae. The cnaA open reading frame extended to 1727 bp and encoded a putative protein of 514 amino acids. Comparative analysis of the nucleotide sequence of cnaA genomic DNA and cDNA confirmed the presence of three introns and a highly conserved calmodulin binding domain. The deduced amino acid sequence was homologous to calcineurin A from Aspergillus nidulans (92%), Neurospora crassa (84%), human (67%), Saccharomyces cerevisiae (58%) and Schizosaccharomyces pombe (54%). Further, A. oryzae cnaA cDNA complemented S. cerevisiae calcineurin disruptant strain (Deltacmp1 Deltacmp2), which was not viable in the presence of high concentrations of NaCl (1.2 M) and at alkaline pH 8.5.

Amino Acid Sequence↗
PubMed2002

Sequence analysis of 5'-flanking region of human pax-5 gene exon 1B.

Pax-5 gene is important transcription factor in B-lymphopoiesis and B-cell development. To understand the regulatory mechanism of pax-5 expression, the immediate 5'-flanking region (6 671 bp) of human pax-gene exon 1B was isolated and characterized. Analysis of the total sequence showed that the proximal promoter includes 3 CAT boxes, 1 SP1 and 1 E box. However, there was no consensus sequence for a TATA box in the 5'-flanking region. Putative regulatory sites of further upstream in the sequence revealed 6 LMO(2)COM, 5 NFAT, 2 LPOLYA-B, 3 GATA1, 2 AP4, 10 MZF1, 1 ETS1-B, 1 GATA3, 1 NKX25, 2 RORA1, 1 LYF1, 2 Ikaros2, 2 TCF11, 1 GATA-C and 1 FREAC7. Therefore, the 5'-flanking region of human pax-5 exon 1B could be involved in regulating the expression of human pax-5 and B-cell differentiation and development.

5' Flanking Region↗