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At least 811 records · Page 45Linked to original sources
PubMed1997

Characterization of Borrelia lusitaniae sp. nov. by 16S ribosomal DNA sequence analysis.

We determined the complete sequence of the rrs gene from five strains of genomic species PotiB2. Both distance and parsimony methods were used to infer the evolutionary relationships of the rrs gene sequence of this genomic species in comparison with the rrs gene sequence of Borrelia valaisiana and the rrs gene sequences of Borrelia burgdorferi sensu lato species obtained from sequence databases. The phylogenetic analysis revealed that the genomic species PotiB2 strains clustered in a separate lineage, which was consistent with data from previous DNA-DNA hybridization experiments (D. Postic, M. V. Assous, P. A. D. Grimont, and G. Baranton, Int. J. Syst. Bacteriol. 44:743-752, 1994). A PCR-restriction fragment length polymorphism analysis was used to identify genomic species PotiB2 and to differentiate it from B. burgdorferi sensu lato species. Moreover, signature nucleotide positions were identified for each B. burgdorferi sensu lato species. In accordance with DNA relatedness values, our findings suggest that genomic species PotiB2 can be more clearly defined and identified, and we propose that it should be referred to as a new species, Borrelia lusitaniae. The type strain is PotiB2.

Bacterial Proteins↗
PubMed2000

Autoantibodies in the sera of patients with rheumatic heart disease: characterization of myocardial antigens by two-dimensional immunoblotting and N-terminal sequence analysis.

The concept of antigenic mimicry in autoimmune diseases such as rheumatic fever has been under investigation for decades and the range of cross-reactive tissue antigens for streptococcal-induced antibodies identified in rheumatic heart disease is still expanding. To identify heart tissue-reactive antigens which may be implicated in the secondary immunopathogenesis of rheumatic fever, sera from 56 patients with acute rheumatic heart disease were probed in two-dimensional Western blots for reactivity against heart tissue antigens. After two-dimensional immunoblot analysis, proteins were submitted to N-terminal amino acid sequence analysis. This analysis identified creatine kinase, two mitochondrial proteins and, at a low level, various stress proteins as cross-reactive myocardial antigens. Therefore, in addition to myosin, creatine kinase may represent another major antigen for autoreactive antibodies in rheumatic heart disease. Mitochondrial proteins have been implicated in the pathogenesis of inflammatory heart disease for some years, and in this study we have identified two mitochondrial proteins as relevant antigens in rheumatic heart disease.

Aconitate Hydratase↗
PubMed1998

[Detection of TT virus DNA and sequence analysis of partial gene of TTV in sera from blood donors].

In order to investigate TTV infection in blood donors, 262 sera samples from blood donors were detected by nested--PCR method using primers from ORF1 of TTV genome DNA. The results showed that 18 of 58(31.0%) serum samples from blood donors with elevated transaminase level were positive for TTV DNA. 30 of 204 (14.7%) sera samples from blood donors with normal transaminase levels were positive for TTV DNA. There were significant difference between them (chi 2 = 38.1, P < 0.05). Five products of PCR for TTV DNA were purified and cloned to T Vector. The sequence analysis showed that there were above 97% nucleotide identity among AB008394 (from Japan), TTVCHNI (from China) and our 5 isolates from blood donors. The results suggest that there exists TTV infection among blood donors in China. TTV may be transmitted by blood transfusion. Our isolates, AB008394 and TTVCHN1 share a same genotype.

Base Sequence↗
PubMed2002

Differentiation of medicinal Cordyceps species by rDNA ITS sequence analysis.

Chongcao (the sexual stage of Cordyceps sinensis) is an important traditional Chinese fungal drug commonly used as a tonic and/or drug for hundreds of years. Recently, due to an increased demand for Cordyceps sinensis, the isolation of the fungus from the environment has been insufficient, and so other species of Cordyceps or artificially cultured Cordyceps sinensis mycelium as a conidial form (asexual stage) has been used to substitute for wild Cordyceps sinensis. There are more than ten Cordyceps species, and their related asexual species that also carry the name Chongcao on commercial markets. Since the value of each Chongcao may differ by more than 100-fold, the authentication of Chongcao is essential to secure their efficacy. However, the identification of the origin of a particular species, especially of its bio-products on the market, is difficult. Here, DNA sequence analysis of the rDNA ITS (internal transcribed spacer) was exploited to differentiate the medicinal species Cordyceps sinensis from several related Cordyceps species, such as, e. g., C. militaris, C. gunnii and their asexual stages. The data demonstrate that the rDNA ITS sequences of C. sinensis collected from different geographical regions are almost identical and are significantly different from the substitutes, so that they could be easily distinguished at the DNA level. Furthermore, based on the highly divergent ITS region of rDNA, a pair of species-specific primers were designed and used for the rapid identification of Cordyceps sinensis.

Base Sequence↗
PubMed2001

3'-Terminal sequence analysis of the RNA genome of the Indian isolate of cardamom mosaic virus: a new member of genus Macluravirus of potyviridae.

Cardamom mosaic virus, a possible member of the family Potyviridae has been associated with the mosaic disease (Katte disease) of small cardamom in India. A virus isolated from the symptomatic cardamom leaves was positive in ELISA only with antiserum to the Guatemalan isolate of cardamom mosaic virus and not with a number of other potyviruses. The size of the viral RNA (8.5 kb) and the molecular weight of the coat protein (CP) (38 kDa) were determined. A 1.8-kb product containing the partial nuclear inclusion body (NIb) gene, the entire coat protein gene and the 3' untranslated region (UTR) was amplified by reverse transcription (RT) and polymerase chain reaction (PCR), cloned and sequenced. The viral origin of the clone was confirmed by Northern hybridization with viral RNA. The experimentally determined N-terminal sequence of the CP matched with the deduced amino acid sequence of the CP gene. Sequence analysis of the clone suggests that the cardamom mosaic virus is a member of the Maclurvirus genus of the family Potyviridae.

3' Untranslated Regions↗
PubMed2006

Cloning and sequence analysis of 2 different acetylcholinesterase genes in Rhopalosiphum padi and Sitobion avenae.

Two genes encoding different acetylcholinesterases (AChE) were successfully cloned from 2 species of aphid, Rhopalosiphum padi (L.) and Sitobion avenae (F.). They were named Rp.AChE1 (GenBank accession No. AY707318), Rp.AChE2 (AY667435), Sa.AChE1 (AY707319), and Sa.AChE2 (AY819704), and were 2133, 2363, 2131, and 2362 bp in length and encoded 664, 676, 664, and 676 amino acids, respectively. All of them shared the characteristics of the AChE family: catalytic tiads, 3 intra-chain disulfide bridges, an acyl pocket, and the conservative aromatic residues for the active site of the gorge. Sequence analysis revealed that Rp.AChE1 and Sa.AChE1 showed higher identity to the reported orthologous genes of Drosophila AChE, and Rp.AChE2 and Sa.AChE2 to paralogous genes. However, in each of the aphids, the 2 genes from the same species shared only 29% identity between one another. It was therefore concluded that each of the aphids has 2 different AChE genes, which are either orthologous or paralogous to Drosophila AChE. The high conservation of AChE1 and AChE2 indicated that 2 acetylcholinesterases exist popularly and that both might function in aphids.

Acetylcholinesterase↗
PubMed2004

Identification, molecular cloning, and sequence analysis of a deoxyribose aldolase in Streptococcus mutans GS-5.

Bacterial fitness in the environment, where nutrients are limited and competition is intense, plays a central role in survival and virulence of the organisms. Deoxyribose aldolase, found in several species of bacteria, is known to be involved in the catabolism of deoxynucleosides arising from dead cells, thereby giving a selective advantage to the microorganisms with a capability to consume DNA as an alternative carbon and energy source. A gene encoding a deoxyribose aldolase gene ( deoC) was identified in the cariogenic Streptococcus mutans strain GS-5 by comparative sequence analysis and gene cloning. The gene encodes a protein of 220 amino acids, having a predicted molecular weight of 23.3 kDa with a p I of 5.44. The gene was cloned into the expression vector pFLAG-1, and the biological function of the gene product was analyzed by a complementation assay with a deoC(-) Escherichia coli mutant SPhi063. Transformation of the E. coli SPhi063 with the plasmid construct allowed this organism to grow on glucose minimal medium supplemented with 2 mM deoxyadenosine or deoxythymidine. These results showed activity of deoxyribose aldolase, confirming the identity of the gene. Utilization of exogenous deoxynucleotides as a carbon and energy source may confer a survival and growth advantage to S. mutans over other bacteria in dental plaque, suggesting that deoxyribose aldolase may be a contributing factor to virulence.

Aldehyde-Lyases↗
PubMed1993

Mass spectrometry of proteins and peptides: sensitive and accurate mass measurement and sequence analysis.

The study of proteins and peptides by mass spectrometry has been advanced by the development of matrix-assisted laser desorption/ionization and electrospray ionization. Proteins with masses > 100 kDa may be measured accurately at picomole sensitivities. Sequence analysis of peptides in mixtures at subpicomole quantities is possible by tandem mass spectrometry. Practical applications of the new technology to biological research are illustrated.

Amino Acid Sequence↗
PubMed2005

Prevalence and partial sequence analysis of human T cell lymphotropic virus type I in China.

A total of 145,293 serum samples were collected from volunteer blood donors in 13 provinces of China and tested for anti-HTLV antibody using an ELISA licensed in China. Thirty were positive for anti-HTLV by ELISA and 19 of those 30 samples were confirmed positive using a supplemental immunoblot assay. Anti-HTLV-I was detected only in samples from Fujian province (a Southern province) where the positivity rate was approximately 0.05%. The region encoding gp46 from 5 of the 19 antibody positive samples was amplified and sequenced. Sequence analysis indicated that these isolates belong to HTLV-I genotype A. These data suggest that HTLV-I is not endemic throughout China and the virus may be restricted to a particular region.

Antibodies, Viral↗
PubMed2004

Computational identification and sequence analysis of stop codon readthrough genes in Oryza sativa.

Using an approach based on the Readthrough Candidate Extraction System (RCES), we extracted 111 candidates from 9620 gene sequences of rice. The results of homology search and sequence analysis demonstrated that these candidates included actual readthrough genes that would be important for further investigating the mechanism of translation termination regulated by readthrough event, and could also give some useful clues for functional genome annotation. Between the candidates and non-candidates of gene sequences in rice, there exist significant base biases at the positions surrounding the stop codons. These positions, especially both -1 and +4, are referred to as part of an extended stop signal. In candidates, G at position -1, and G or C at position +4 are much more favored than that in non-candidates. Both stop sequence patterns, GUAGC and GUGAG, might drive high readthrough efficiency in rice. Secondary structure analysis revealed that the -1 and +1 amino acids around the first stop codon of candidates have a strong bias toward arginine, particularly the +1 position (20.7%), which indicated that the amino acids at the readthrough region being frequently located in the hydrophilic region of beta-turn might be a determinant for efficient translation termination or not.

Base Sequence↗
PubMed2000

Sequence analysis of E2 glycoprotein genes of classical swine fever viruses: identification of a novel genogroup in Thailand.

Thirty classical swine fever viruses (CSFV) isolated in Thailand between 1988 and 1996 were characterised by genetic sequence analysis of a part of their E2 coding regions, comparing the new data with that for representative reference viruses from other countries and continents. Thai isolates were divided into three distinct genogroups, indicating multiple origins for the outbreaks. Eighteen isolates from 1988-1995 form a new genogroup not previously described from any other geographical region. Eleven isolates from 1988-1995 are in the same genogroup as old US and European strains represented by reference strains Alfort 187 and Brescia. The viruses of this group seem to have died out in Europe but still persist in Thailand. One recent isolate from 1996 represents another previously described genogroup being closely related to Italian viruses isolated in the same year.

Animals↗
PubMed2006

cDNA cloning, sequence analysis and molecular modeling of a new peptide from the scorpion Buthotus saulcyi venom.

In this study, the cDNA of a new peptide from the venom of the scorpion, Buthotus saulcyi, was cloned and sequenced. It codes for a 64 residues peptide (Bsaul1) which shares high sequence similarity with depressant insect toxins of scorpions. The differences between them mainly appear in the loop1 which connects the beta-strand1 to the alpha-helix and seems to be functionally important in long chain scorpion neurotoxins. This loop is three amino acids longer in Bsaul1 compared to other depressant toxins. A comparative amino acid sequence analysis done on Bsaul1 and some of alpha-, beta-, excitatory and depressant toxins of scorpions showed that Bsaul1 contains all the residues which are highly conserved among long chain scorpion neurotoxins. Structural model of Bsaul1 was generated using Ts1 (a beta-toxin that competes with the depressant insect toxins for binding to Na(+) channels) as template. According to the molecular model of Bsaul1, the folding of the polypeptide chain is being composed of an anti-parallel three-stranded beta-sheet and a stretch of alpha- helix, tightly bound by a set of four disulfide bridges. A striking similarity in the spatial arrangement of some critical residues was shown by superposition of the backbone conformation of Bsaul1 and Ts1.

Amino Acid Motifs↗
PubMed2005

Application of multilocus sequence analysis (MLSA) for rapid identification of Enterococcus species based on rpoA and pheS genes.

The aim of this study was to evaluate the use of RNA polymerase alpha subunit (rpoA) and phenylalanyl-tRNA synthase (pheS) gene sequences as species identification tools for enterococci. Ninety-six representative strains comprising all currently recognized Enterococcus species were examined. rpoA gene sequences generated a robust classification into species groups similar to the one based on 16S rRNA gene sequence analysis. On the other hand, the pheS gene is a fast-evolving clock even better suited for species delineation than the rpoA gene, but not for recognition of species groups within Enterococcus as determined by both rpoA and 16S rRNA genes. All enterococcal species were clearly differentiated on the basis of their rpoA and pheS sequences. Evaluation of intraspecies variation showed that both rpoA and pheS genes have a high degree of homogeneity among strains of the same species. Strains of the same enterococcal species have at least 99% rpoA and 97% pheS gene sequence similarity, whereas, different enterococcal species have at maximum 97% rpoA and 86% pheS gene sequence similarity. It was concluded that both genes can be used as reliable tools for identification of clinical and environmental species of Enterococcus and are efficient screening methods for the detection of novel species. The sequence data obtained in this study were compared to the available atpA and 16S rRNA gene sequences. The MLSA approach to Enterococcus taxonomy provides portable, highly reproducible data with lower costs for rapid identification of all enterococcal species.

Bacterial Typing Techniques↗
PubMed1990

RNA2 of grapevine fanleaf virus: sequence analysis and coat protein cistron location.

The nucleotide sequence of the genomic RNA2 (3774 nucleotides) of grapevine fanleaf virus strain F13 was determined from overlapping cDNA clones and its genetic organization was deduced. Two rapid and efficient methods were used for cDNA cloning of the 5' region of RNA2. The complete sequence contained only one long open reading frame of 3555 nucleotides (1184 codons, 131K product). The analysis of the N-terminal sequence of purified coat protein (CP) and identification of its C-terminal residue have allowed the CP cistron to be precisely positioned within the polyprotein. The CP produced by proteolytic cleavage at the Arg/Gly site between residues 680 and 681 contains 504 amino acids (Mr 56019) and has hydrophobic properties. The Arg/Gly cleavage site deduced by N-terminal amino acid sequence analysis is the first for a nepovirus coat protein and for plant viruses expressing their genomic RNAs by polyprotein synthesis. Comparison of GFLV RNA2 with M RNA of cowpea mosaic comovirus and with RNA2 of two closely related nepoviruses, tomato black ring virus and Hungarian grapevine chrome mosaic virus, showed strong similarities among the 3' non-coding regions but less similarity among the 5' end non-coding sequences than reported among other nepovirus RNAs.

Amino Acid Sequence↗
PubMed1991

Bst DNA polymerase permits rapid sequence analysis from nanogram amounts of template.

A simple, rapid method is presented for the enzymatic sequence analysis of nanogram amounts of single-stranded or double-stranded DNA. This approach employs the thermostable DNA polymerase from Bacillus sterothermophilus and exploits its ability to efficiently extend all of the template-primer complex, even at low substrate concentrations. The procedure requires few pipetting steps, no preannealing step and very short reaction time. This method can significantly reduce the cost associated with DNA polymerase and the amount of template and time required to perform the enzymatic sequencing reactions. As little as a 10-ng aliquot of such sequencing reactions can be analyzed on a fluorescence-based capillary gel electrophoresis instrument recently developed in our laboratory. This highly sensitive detection, in conjunction with the ability to efficiently sequence nanogram amounts of template, strongly suggests the feasibility of direct DNA sequencing of single bacteriophage M13 plaques without prior amplification.

Bacteriophages↗
PubMed2000

Cloning and sequence analysis of the Candida boidinii ADE2 gene.

Candida boidinii ADE2 gene (phosphoribosyl-5-aminoimidazole carboxylase; AIRC, EC 4. 1. 1. 21) has been cloned by homology to the Saccharomyces cerevisiae ADE2 gene. The cloned C. boidinii ADE2 gene complemented the ade2 mutation of S. cerevisiae. Sequence analysis showed a single open reading frame of 1719 nucleotides coding for a polypeptide of 573 residues. Comparison of the deduced amino acid sequence with those of AIRC enzymes from other yeasts showed marked homology among yeast AIRCs.

Amino Acid Sequence↗
PubMed1994

Identification of succinimide sites in proteins by N-terminal sequence analysis after alkaline hydroxylamine cleavage.

Under favorable conditions, Asp or Asn residues can undergo rearrangement to a succinimide (cyclic imide), which may also serve as an intermediate for deamidation and/or isoaspartate formation. Direct identification of such succinimides by peptide mapping is hampered by their lability at neutral and alkaline pH. We determined that incubation in 2 M hydroxylamine, 0.2 M Tris buffer, pH 9, for 2 h at 45 degrees C will specifically cleave on the C-terminal side of succinimides without cleavage at Asn-Gly bonds; yields are typically approximately 50%. N-terminal sequence analysis can then be used to identify an internal sequence generated by cleavage of the succinimide, hence identifying the succinimide site.

Amino Acid Sequence↗