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At least 1,279 records · Page 71Linked to original sources
PubMed2000

Sequence, structural, and evolutionary analysis of prokaryotic ribosomal protein L11 methyltransferases.

The Escherichia coli PrmA enzyme catalyzes methylation of the large ribosomal subunit protein L11. Database homology searches, multiple sequence alignment, and structure prediction allowed to dissect the primary structure of PrmA into two domains and assign putative functional or structural roles to invariant or highly conserved residues. Evolutionary relationships within the PrmA family were also analyzed. The topology of the branching order agrees to a large extent with the consensus phylogeny of Eubacteria, with the exception of beta and epsilon subdivisions of Proteobacteria, which most probably had their original prmA genes replaced by copies acquired via the lateral gene transfer from gamma-Proteobacteria and some close relative of the ancestor of gramnegative bacteria, respectively.

Amino Acid Sequence↗
PubMed1998

Parallel Protein Information Analysis (PAPIA) System Running on a 64-Node PC Cluster.

Protein information analysis is widely regarded as a key technology in drug design, macromolecular engineering, and understanding genome sequences. Because vast amount of calculations are required, further speed-up for protein information analysis is very much in demand. We have implemented the PAPIA (PArallel Protein Information Analysis) system on the RWC PC cluster IIa (PAPIA cluster) which consists of 64 Pentium Pro 200MHz microprocessors. The PAPIA system performs fast parallel processing for typical calculations in protein analysis, such as structure similarity search, sequence homology search and multiple sequence alignment, nearly 60 times faster than a single processor. We have started a WWW service (http://www.rwcp.or.jp/papia/), allowing any biologist to easily submit jobs to the PAPIA system through a WWW browser. The user can experience the power of current parallel processing technology.

Journal Article↗
PubMed2001

[Identification of notoginseng(Panax notoginseng) and its adulterants using DNA sequencing].

OBJECTIVE: To analyze the nuclear ribosomal RNA small subunit (18S rRNA) and chloroplast matK gene sequence of notoginseng (Panax notoginseng) in order to provide molecular evidence for its genuine origin identification. METHODS: To sequence 18S rRNA and matK genes of Panax notoginseng and its four adulterants such as P. japonicus, Curcuma phaeocaulis, C. wenyujin, C. kwangsiensis using PCR direct sequencing and to detect their variation of sequences. RESULTS: The sequence length of notoginseng and its adulterants is 1809-1811 bp for 18S rRNA gene and 1259-1548 bp for matK gene, respectively. Multiple sequence alignment shows that there are much sequence variation between notoginseng and its adulterants. CONCLUSION: DNA sequencing is an accurate and reliable method in origin identification of the genuine notoginseng.

Amino Acid Sequence↗
PubMed2001

Molecular cloning and characterization of Mycobacterium bovis BCG pcp gene encoding pyrrolidone carboxyl peptidase.

The Mycobacterium bovis bacilli Calmette-Guerin (BCG) pcp gene that encodes the pyrrolidone carboxyl peptidase (Pcp) was cloned from a lambdagtll genomic library and sequenced. The nucleotide sequence contains a 669 bp open reading frame coding for a protein of 222 amino acid residues with a calculated molecular mass of 23,209 Da. The deduced amino acid sequence is highly homologous to the Pcps from Bacillus amyloliquefaciens, Pseudomonas fluorescens, Bacillus subtilis, Streptococcus pyogenes, and Staphylococcus aureus. A multiple sequence alignment revealed highly conserved domains. The BCG pcp gene was overexpressed in Escherichia coli. The Pcp was purified to homogeneity. The recombinant protein was further confirmed by an enzymatic assay.

Amino Acid Sequence↗
PubMed2001

MHC class II proteins contain a potential binding site for the verotoxin receptor glycolipid CD77.

Globotriaosyl ceramide or CD77 functions as a cell surface receptor for toxins of the Shiga toxin/verotoxin family and as a marker for germinal center stage B-cells. The B-cell protein CD19 and the interferon-alpha receptor possess verotoxin-like amino acid sequences in their extracellular domains, and CD77 has been shown to function in CD19-mediated adhesion and interferon-induced growth inhibition. The Burkitt's lymphoma cell line, Daudi, is similar to germinal center B-cells in their expression of CD77, CD19 and MHC class II molecules. Using the multiple sequence alignment program, ClustalW, we have identified a verotoxin-like amino acid sequence on the beta-chain of human and murine MHC class II molecules. Binding of CD77 at this site could modulate the peptide-binding properties of these MHC class II molecules. Using Western blot analysis of whole cell extracts, we found that CD77-positive Daudi cells have higher levels of HLA-D proteins than VT500 cells, a Daudi-derived CD77-deficient mutant cell line. In contrast, MHC class II-mediated adhesion and surface expression are similar in the two cell lines. Therefore, CD77 could play a functional or regulatory role in MHC class II-mediated functions specifically relating to antigen presentation by B-cells to T helper cells.

Amino Acid Sequence↗
PubMed2002

Refining structural and functional predictions for secretasome components by comparative sequence analysis.

Comparative sequence analysis of presenilins reveals the conserved transmembrane domain shared with leukocyte antigen CD47, possibly involved in signal transduction. Sensitive techniques of multiple sequence alignment extend the earlier observation of the aminopeptidase homology domain in nicastrin to suggest that this protein may be a catalytically active component of secretasome involved in proteolysis or co-proteolysis of presenilin or beta-amyloid.

Amino Acid Sequence↗
PubMed2000

Motifs of the caldesmon family.

Seven highly conserved regions were found in caldesmon molecules from various sources using the multiple sequence alignment method. Their localization coincides with regions where the binding sites to other proteins were postulated. Less conserved and highly divergent regions of the sequences are described as well. These results could refine the planning of caldesmon gene manipulations and accelerate the precise localization of binding sites in the caldesmon molecule and, as a consequence, this could help to elucidate its function in smooth muscle contraction.

Actins↗
PubMed2002

First molecular characterization of an unequal homologous alu-mediated recombination event responsible for hemophilia.

The large number of Alu repeats in the human genome provides abundant opportunities for unequal homologous recombination events that are responsible of several human diseases. We here describe a novel large FVIII gene deletion from a severe hemophilia A patient in which Alu-repetitive elements are directly involved in the origin of the mutation. Using a long-fragment PCR method, a approximately 23 kb deletion was delimited between introns 24 and 25. The resulting FVIII gene had a hybrid 2317-bp intron and lacked exon 25. Absence of exon 25 was confirmed at the RNA level. Multiple sequence alignment of this hybrid intron and normal introns 24 and 25 provided evidence of an homologous recombination event between two Alu repeats and the exact breakpoints were delimited to a 16 bp region. To our knowledge, this is the first report of hemophilia caused by unequal homologous Alu/Alu recombination. This mechanism, commonly related to genetic human disorders, may be involved in a significant number of hemophilia cases considering that FVIII is coded by an Alu-rich gene.

Alu Elements↗
PubMed2002

[DNA sequencing and molecular identification of Patchouli and its substitute wrinkled gianthyssop].

AIM: To analyze sequences of the nuclear ribosomal RNA small subunit (18S rRNA) gene and the chloroplast matK gene of crude drug Patchouli (Pogostemon cablin) in order to provide molecular evidence for identification of Patchouli drug. METHODS: To sequence the entire 18S rRNA gene and partial matK gene of Patchouli from Guangzhou and its substitute Wrinkled Gianthyssop (Agastache rugosa) from Sichuan using PCR direct sequencing and to detect the homology of two gene sequences between these two crude drugs. RESULTS: The complete 18S rRNA gene sequence is 1,805 bp in length for Patchouli from Guangzhou whereas 1,794 bp for Wrinkled Gianthyssop from Sichuan. The 3'-end sequence of matK gene is 521 bp (747-1,268 nt from upstream of matK gene) for these two crude drugs. Based on multiple sequence alignment, it is found that there are 18 variable sites and 11 aligned gap sites in 18S rRNA sequence, 49 variable sites in 3'-matK sequence between these two crude drugs. The homology is 98.4% for 18S rRNA and 90.6% for 3'-matK between two crude drugs, respectively. CONCLUSION: DNA sequencing can provide an accurate and reliable tool in the crude drug identification of Patchouli and its substitute Wrinkled Gianthyssop.

Agastache↗
PubMed2002

[DNA profiling of Pogostemon cablin chemotypes differing in essential oil composition].

AIM: To provide molecular evidence for quality evaluation and GAP production of Pogostemon cablin (Blanco) Benth. cultivated in different regions in Guangdong and Hainan provinces, China, by comparing two sequences (1.2 kb of plastid matK gene and 1.8 kb of nuclear 18S rRNA gene) and two chemotypes (Pogostone-type and Patchouliol-type in essential oil composition). METHODS: PCR direct sequencing was applied to detemine the matK and 18S rRNA sequences for six samples of Pogostemon cablin from different localities. RESULTS: The matK sequences of six samples of Pogostemon cablin from different regions of cultivation are 1,245 bp in length, which coding 415 amino acids of protein (maturase), and 18S rRNA sequences are 1,803-1,805 bp in size. Based on multiple sequence alignment, there are 47 variable sites in the matK sequence of these six samples, 17 in the 18S rRNA sequence. The cluster tree reconstructed by UPGMA method shows that the sequence divergence both in matK and 18S rRNA genes among six samples of Pogostemon cablin was well correlative with their regions of cultivation and intraspecific chemotypes of essential oil composition. CONCLUSION: Combining with chemical and biogeographical data, DNA sequencing can become a powerful tool in the key technique-species identification of quality evaluation and GAP production of Pogostemon cablin.

Base Sequence↗
PubMed2002

[matK and its nucleotide sequencing of crude drug chuanxiong and phylogenetic relationship between their species from China and Japan].

AIM: To provide more molecular evidences for species relationship between Chuanxiong (Ligusticum chuanxiong Hort.) from China and Japanese Chuanxiong (Senkyu in Japanese) (Cnidium officinale Makino). METHODS: To sequence such two genes as internal transcribed spacer (ITS) from nuclear rDNA and maturase for lysine (matK) in tRNA(lys) (UUU) intron from chloroplast DNA of both Ligusticum chuanxiong and Cnidium officinale using PCR direct sequencing and to analyze the sequence variation of two genes between these two species. RESULTS: The matK gene sequence of Ligusticum chuanxiong and Cnidium officinale is 1268 bp in length, coding 422 amino acids of maturase protein. ITS gene sequence 699 bp, consisting of 54 bp of 18S rRNA-3', 215 bp of ITS1, 162 bp of 5.8S rRNA, 222 bp of ITS2, 46 bp of 26S rRNA-5'. Multiple sequence alignment shows that the sequence of two genes between dried crude drug and fresh voucher material of Ligusticum chuanxiong and Cnidium officinale, there is 1 variable site (T-->C) in matK (upstream at 595 nt) and ITS (ITS1 at 54 nt) between Ligusticum chuanxiong and Cnidium officinale. CONCLUSION: Based on homology analysis of two genes plastid matK and nuclear ITS, the origin of Chuanxiong from China and Japan ought to be identical, the scientific name Cnidium officinale of Japanese Chuanxiong should be changed to Ligusticum chuanxiong.

Amino Acid Sequence↗
PubMed2003

[Initial analysis of complete genome sequences of SARS coronavirus].

Multiple sequence alignment among 12 complete SARS coronavirus (SARS-CoV) sequences reveals that the major parts of 29708 b of the genomes have 99.82% identical bases. Forty two nucleotide mismatches were found in addition to the five and six gaps in two genomes. Among them, 28 mismatches result in changes of amino acid in the encoded proteins. Analysis of the changes implies possible effect on the Spike and Membrane protein of the virus, while most of the other changes seem not very significant to alter the structure and function of the proteins. These results have been released on the anti-sars web site maintained by the Centre of Bioinformatics, Peking University (antisars.cbi.pku.edu.cn) and may be of help for further experimental study.

Amino Acid Sequence↗
PubMed2003

[Comparison of specific genomic DNA fragment between Microtus fortis calamorum and Microtus fortis fortis].

Microtus fortis(Taxonomy ID: 100897), also named as reed vole, is classified as Microtus, Micotinae, Cricetidae, Rodentia, Mammalia on taxonomy. Microtus fortis mainly distributes in China. Some areas of Russia, North Korea and Mongolia close to Northeast borderland of China also have a small number of Microtus fortis in distribution. Microtus fortis in China has principally 4 subspecies, and most of them live is the drainage area of Yangtse River. Schistosoma japonicum (one of commonly parasites in China) can infect about 40 kinds of mammalian animals, including the human being, but could not infect Microtus foris. It is known as the only animal in Dongting Lake region of China which has the ability of natural resistance to Schistosoma japonicum. The Microtus fortis domesticated in laboratory has the same biological characteristics as the wild one and these characteristics could be inherited to its progeny steadily. We got a specific DNA fragment from genomic library of Microtus fortis. This DNA fragment in genomic DNA of human beings, Kunming mice, Balb/c mice and C57BL/6J mice could not be detected by dot blot hybridization and PCR, apart from genomic DNA of Microtus fortis. In this report, the differences of genomic DNA in 34 Microtus fortis were compared between Microtus fortis calamorum(Dongting Lake region of southern China) and Microtus fortis fortis (Ningxia province of northern China). The residing localion of these two subspecies is far away about 1,200 kilometers from each other. The genomic DNA of Microtus fortis calamorum and Microtus fortis fortis were extracted and amplified by PCR according to the specific genomic DNAs sequence of Microtus fortis reported previously (Accession number in GenBank: AF277394). The amplified DNA fragments were inserted into pGEM-T easy vector and sequenced. The DNA fragment sequencing results from the two subspecies were compared to detect whether there was any difference. 19 alleles were found from Microtus fortis (20 of Microtus fortis calamorum and 14 of Microtus fortis fortis). The results of multiple sequence alignment showed that 25 single nucleotide polymorphism (SNP) sites were existed in the different Microtus fortis individuals, including transition (G-->A,A-->G,T-->C,C-->T), transversion(G-->T,A-->T,T-->A,C-->A), insertion (CA) and deletion (TGTTTT). The difference of genomic DNA from two subspecies were obvious, especially on the sites of 146, 192, 223, 224 and 235. The insertion of CA on the sites of 223 and 224 as well as A-->G transition on the site of 235 was only occurred in Microtus fortis fortis. They are not found in Microtus fortis calamorum so far. They could be divided into two groups according to phylogenetic tree analysis results, one was the genomic DNA of Microtus fortis calamorum and the other one was that of Microtus fortis fortis. However, the homologues reached up to 98% between two subspecies. These results are very important for us to further understand the genetic background, biological characteristics, evolutionary rule and the anti-schistosoma japonicum mechanism of Microtus fortis at the molecular levels. The specific base changes of the DNA fragment between the two subspecies are probably correlative with the animal immigration, survival conditions, and species evolution.

Animals↗
PubMed1992

The VPH1 gene encodes a 95-kDa integral membrane polypeptide required for in vivo assembly and activity of the yeast vacuolar H(+)-ATPase.

Yeast vacuolar acidification-defective (vph) mutants were identified using the pH-sensitive fluorescence of 6-carboxyfluorescein diacetate (Preston, R. A., Murphy, R. F., and Jones, E. W. (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 7027-7031). Vacuoles purified from yeast bearing the vph1-1 mutation had no detectable bafilomycin-sensitive ATPase activity or ATP-dependent proton pumping. The peripherally bound nucleotide-binding subunits of the vacuolar H(+)-ATPase (60 and 69 kDa) were no longer associated with vacuolar membranes yet were present in wild type levels in yeast whole cell extracts. The VPH1 gene was cloned by complementation of the vph1-1 mutation and independently cloned by screening a lambda gt11 expression library with antibodies directed against a 95-kDa vacuolar integral membrane protein. Deletion disruption of the VPH1 gene revealed that the VPH1 gene is not essential for viability but is required for vacuolar H(+)-ATPase assembly and vacuolar acidification. VPH1 encodes a predicted polypeptide of 840 amino acid residues (molecular mass 95.6 kDa) and contains six putative membrane-spanning regions. Cell fractionation and immunodetection demonstrate that Vph1p is a vacuolar integral membrane protein that co-purifies with vacuolar H(+)-ATPase activity. Multiple sequence alignments show extensive homology over the entire lengths of the following four polypeptides: Vph1p, the 116-kDa polypeptide of the rat clathrin-coated vesicles/synaptic vesicle proton pump, the predicted polypeptide encoded by the yeast gene STV1 (Similar To VPH1, identified as an open reading frame next to the BUB2 gene), and the TJ6 mouse immune suppressor factor.

Amino Acid Sequence↗
PubMed1992

Computational sequence analysis revisited: new databases, software tools, and the research opportunities they engender.

The increasing quantity and complexity of sequences and structural data for proteins and nucleic acids create both problems and opportunities for biomedical researchers. Fortunately, a new generation of practical computer tools for data analysis and integrated information retrieval is emerging. Recent developments in fast database searching, multiple sequence alignment, and molecular modeling are discussed and windows-based, mouse-driven software for CD-ROM and network information retrieval are described. Each method is illustrated with a practical example pertinent to lipid research. In particular, the connection among cholesteryl ester transfer protein, bactericidal permeability-increasing protein, and lipopolysaccharide-binding proteins is determined; novel repetitive sequence motifs in mammalian farnesyltransferase subunits and related yeast prenyltransferases are derived; biochemical insights from a three-dimensional model of human apolipoprotein D based on two insect lipocalins are discussed; the relationship between apolipoprotein D and gross cystic disease fluid protein from human breast is reviewed; and prospects for modeling apolipoprotein E-related proteins are described. In addition, information on a number of general and special-purpose sequence, motif, and structural databases is included.

Amino Acid Sequence↗
PubMed2003

Search-based optimization.

The problem of determining the minimum cost hypothetical ancestral sequences for a given cladogram is known to be NP-complete (Wang and Jiang, 1994). Traditionally, point estimations of hypothetical ancestral sequences have been used to gain heuristic, upper bounds on cladogram cost. These include procedures with such diverse approaches as non-additive optimization of multiple sequence alignment, direct optimization (Wheeler, 1996), and fixed-state character optimization (Wheeler, 1999). A method is proposed here which, by extending fixed-state character optimization, replaces the estimation process with a search. This form of optimization examines a diversity of potential state solutions for cost-efficient hypothetical ancestral sequences and can result in greatly more parsimonious cladograms. Additionally, such an approach can be applied to other NP-complete phylogenetic optimization problems such as genomic break-point analysis.

Animals↗
PubMed2003

Analysis of low-density lipoprotein receptor gene mutations in a Chinese patient with clinically homozygous familial hypercholesterolemia.

OBJECTIVE: To screen the point mutation of the low-density lipoprotein receptor (LDL-R) gene in Chinese familial hypercholesterolemia (FH) patients, characterize the relationship between the genotype and the phenotype and discuss the molecular pathological mechanism of FH. METHODS: A patient with clinical phenotype of homozygous FH and her parents were investigated for mutations in the promoter and all eighteen exons of the LDL-R gene. Screening was carried out using Touch-down PCR and direct DNA sequencing; multiple alignment analysis by DNASIS 2.5 was used to find base alteration, and the LDL-R gene mutation database was searched to identify the alteration. In addition, the apolipoprotein B gene (apo B) was screened for known mutations (R3500Q) that cause familial defective apo B100 (FDB) by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). RESULTS: Two new heterozygous mutations in exons 4 and 9 of the LDL-R gene were identified in the proband (C122Y and T383I) as well as her parents. Both of the mutations have not been published in the LDL-R gene mutation database. No mutation of apo B100 (R3500Q) was observed. CONCLUSION: Two new mutations (C112Y and T383I) were found in the LDL-R gene, which may result in FH and may be particularly pathogenetic genotypes in Chinese people.

Adult↗
PubMed2003

[Cloning and expression of tumor necrosis factor (TNFalpha) cDNA from red seabream pagrus major].

A fragment of TNFalpha cDNA sequence from red seabream was cloned by homology cloning approach with two degenerated primers which were designed based on the conserved regions of other animals' TNF sequences. The sequence was elongated by 3' and 5' RACE to get the full length CDS sequence. This sequence contained 1264 nucleotides that included a 5' UTR of 85 bp, a 3' UTR of 514 bp and an open reading frame (ORF) of 666 bp which could encode 222 amino acids propeptide. In 3' UTR, there were several mRNA instability motifs and three endotoxin-responsive sequences, but the sequence lacked the polyadenylation signal. The deduced peptide had a clear transmembrane domain, a TNFalpha family signature and a TNF2 family profile. The cell attachment sequence and the glycosaminoglycan attachment sites were also found in the sequence. The red seabream TNF sequence shared relatively high similarity with both mammalian TNFalpha and TNFbeta by multiple sequence alignments. Phylogenetic analysis showed that the piscine TNFalpha were located independently in a different branch compared with mammalian TNFalpha and TNFbeta. Based on the primary and secondary structure analysis and gene expression study, we could concluded that the red seabream TNF should be a TNFalpha, not TNFbeta. RT-PCR was used to study TNFalpha transcript expression. 24 h after the red seabream was challenged by Vibrio anguillarum, the RS TNFalpha transcript expression were detected in blood, brain, gill, heart, head kidney, kidney, liver, muscle and spleen. Results showed that TNFalpha mRNA was constitutively expressed in parts of the tissues both in stimulated and unstimulated fish and the expression could be enhanced after the pathogen infection.

Amino Acid Sequence↗