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Homology Search (homology + search)
Selected AbstractsVascular smooth muscle cell growth-promoting factor/F-spondin inhibits angiogenesis via the blockade of integrin ,v,3 on vascular endothelial cellsJOURNAL OF CELLULAR PHYSIOLOGY, Issue 3 2001Yoshito Terai Vascular smooth muscle cell growth-promoting factor (VSGP) was originally isolated from bovine ovarian follicular fluid as a stimulator of vascular smooth muscle cell proliferation. Homology searches indicate that bovine and human VSGPs are orthologs of rat F-spondin. Here, we examined whether recombinant human VSGP/F-spondin affected the biological activities of endothelial cells. VSGP/F-spondin did not affect the proliferation of human umbilical vein endothelial cells (HUVECs); however, it did inhibit VEGF- or bFGF-stimulated HUVEC migration. To clarify the mechanism of this inhibitory effect, we examined the adhesion of HUVECs to extracellular matrix proteins. VSGP/F-spondin specifically inhibited the spreading of HUVECs on vitronectin via the functional blockade of integrin ,v,3. As a result, VSGP/F-spondin inhibited the tyrosine phosphorylation of focal adhesion kinase (FAK) when HUVECs were plated on vitronectin. Moreover, VSGP/F-spondin inhibited the activation of Akt when HUVECs on vitronectin were stimulated with VEGF. VSGP/F-spondin inhibited tube formation by HUVECs in vitro and neovascularization in the rat cornea in vivo. These results indicate that VSGP/F-spondin inhibits angiogenesis at least in part by the blockade of endothelial integrin ,v,3. © 2001 Wiley-Liss, Inc. [source] SLIC-1/sorting nexin,20: A novel sorting nexin that directs subcellular distribution of PSGL-1EUROPEAN JOURNAL OF IMMUNOLOGY, Issue 2 2008Ulrich Abstract P-Selectin glycoprotein ligand-1 (PSGL-1) is a mucin-like glycoprotein expressed on the surface of leukocytes that serves as the major ligand for the selectin family of adhesion molecules and functions in leukocyte tethering and rolling on activated endothelium and platelets. Previous studies have implicated the highly conserved cytoplasmic domain of PSGL-1 in regulating outside-in signaling of integrin activation. However, molecules that physically and functionally interact with this domain are not completely defined. Using a yeast two-hybrid screen with the cytoplasmic domain of PSGL-1 as bait, a novel protein designated selectin ligand interactor cytoplasmic-1 (SLIC-1) was isolated. Computer-based homology search revealed that SLIC-1 was the human orthologue for the previously identified mouse sorting nexin,20. Direct interaction between SLIC-1 and PSGL-1 was specific as indicated by co-immunoprecipitation and motif mapping. Colocalization experiments demonstrated that SLIC-1 contains a Phox homology domain that binds phosphoinositides and targets the PSGL-1/SLIC-1 complex to endosomes. Deficiency in the murine homologue of SLIC-1 did not modulate PSGL-1-dependent signaling nor alter neutrophil adhesion through PSGL-1. We conclude that SLIC-1 serves as a sorting molecule that cycles PSGL-1 into endosomes with no impact on leukocyte recruitment. [source] Partial genomic organization of ribosomal protein S7 gene from malaria vector Anopheles stephensiINSECT SCIENCE, Issue 2 2007RAJNIKANT DIXIT Abstract In this study, we describe the partial genomic organization of ribosomal protein S7 gene isolated from the mosquito Anopheles stephensi. Initially a 558 bp partial cDNA sequence was amplified as precursor mRNA sequence containing 223 bp long intron. 5, and 3, end sequences were recovered using end specific rapid amplification of cDNA ends (RACE) polymerase chain reaction. The full-length cDNA sequence was 914 nucleotide long with an open reading frame capable of encoding 192 amino acid long protein with calculated molecular mass of 22 174 Da and a pI point of 9.94. Protein homology search revealed > 75% identity to other insect's S7 ribosomal proteins. Analysis of sequence alignment revealed several highly conserved domains, one of which is related to nuclear localization signal (NLS) region of human rpS7. Interestingly, intron nucleotide sequence comparison with A. gambiae showed a lesser degree of conservation as compared to coding and untranslated regions. Like this, early studies on the genomic organization and cDNA/ Expressed sequence tag analysis (EST) could help in genome annotation of A. stephensi, and would be likely to be sequenced in the future. [source] Rapid and accurate identification of microorganisms contaminating cosmetic products based on DNA sequence homologyINTERNATIONAL JOURNAL OF COSMETIC SCIENCE, Issue 6 2005Y. Fujita Synopsis The aim of this study was to develop rapid and accurate procedures to identify microorganisms contaminating cosmetic products, based on the identity of the nucleotide sequences of the internal transcribed spacer (ITS) region of the ribosomal RNA coding DNA (rDNA). Five types of microorganisms were isolated from the inner portion of lotion bottle caps, skin care lotions, and cleansing gels. The rDNA ITS region of microorganisms was amplified through the use of colony-direct PCR or ordinal PCR using DNA extracts as templates. The nucleotide sequences of the amplified DNA were determined and subjected to homology search of a publicly available DNA database. Thereby, we obtained DNA sequences possessing high similarity with the query sequences from the databases of all the five organisms analyzed. The traditional identification procedure requires expert skills, and a time period of approximately 1 month to identify the microorganisms. On the contrary, 3,7 days were sufficient to complete all the procedures employed in the current method, including isolation and cultivation of organisms, DNA sequencing, and the database homology search. Moreover, it was possible to develop the skills necessary to perform the molecular techniques required for the identification procedures within 1 week. Consequently, the current method is useful for rapid and accurate identification of microorganisms, contaminating cosmetics. Résumé Le but de cette étude est de développer une procédure rapide et fiable pour identifier les micro-organismes contaminant les produits cosmétiques. Cette procédure repose sur l'identification des séquences des nucléotides des espaceurs transcrits internes (Internal Transcribed Spacer ou région ITS), de l'ADN codant pour l'ARN ribosomique (rADN). Cinq types de micro-organismes sont isolés sur la partie intérieure des bouchons des flacons de lotions pour le soin de la peau et de gels lavants. Les régions ITS rADN des micro-organismes sont amplifiées grâce à l'utilisation de la méthode ,colony-direct PCR, ou ,ordinal PCR, en utilisant les extraits d'ADN comme matrices. Les séquences de nucléotides de l'ADN amplifiées sont évaluées et soumises à une recherche homologique dans une librairie d'ADN disponible au public. Ainsi, grâce aux bases de données, nous obtenons des séquences d'ADN qui possèdent une similaritéélevée avec les séquences recherchées des cinq organismes analysés. La procédure d'identification classique exige des compétences d'experts et une période d'environ un mois pour identifier les micro-organismes. D'autre part, il faut 3 à 7 jours pour terminer toutes les procédures utilisées dans la méthode ici décrite, y compris l'isolation et la culture des organismes, le séquençage de l'ADN et la recherche dermatologique dans les bases de données. De plus, il est possible en 1 semaine de développer les compétences nécessaires pour mettre en ,uvre les techniques moléculaires requises pour les procédures d'identification. Cette méthode est donc utile pour une identification rapide et fiable des micro-organismes qui contaminent les cosmétiques. [source] Penicillium chrysogenum glucose oxidase , a study on its antifungal effectsJOURNAL OF APPLIED MICROBIOLOGY, Issue 6 2004É. Leiter Abstract Aims:, Purification and characterization of the high molecular mass Candida albicans -killing protein secreted by Penicillium chrysogenum. Methods and Results:, The protein was purified by a combination of ultrafiltration, chromatofocusing and gel filtration. Enzymological characteristics [relative molecular mass (Mr) = 155 000, subunit structure ,2 with Mr,, = 76 000, isoelectric point (pI) = 5·4] were determined using SDS-PAGE and 2D-electrophoresis. N-terminal amino acid sequencing and homology search demonstrated that the antifungal protein was the glucose oxidase (GOX) of the fungus. The enzyme was cytotoxic for a series of bacteria, yeasts and filamentous fungi. Vitamin C (1·0 mg ml,1) prevented oxidative cell injuries triggered by 0·004 U GOX in Emericella nidulans cultures but bovine liver catalase was ineffective even at a GOX : catalase activity ratio of 0·004 : 200 U. A secondary inhibition of growth in E. nidulans cultures by the oxygen-depleting GOX,catalase system was likely to replace the primary inhibition exerted by H2O2. Conclusions:,Penicillium chrysogenum GOX possesses similar enzymological features to those described earlier for other Penicillium GOXs. Its cytotoxicity was dependent on the inherent antioxidant potential of the test micro-organisms. Significance and Impact of the Study:,Penicillium chrysogenum GOX may find future applications in glucose biosensor production, the disinfection of medical implants or in the food industry as an antimicrobial and/or preservative agent. [source] Identification of Escherichia coli O172 O-antigen gene cluster and development of a serogroup-specific PCR assayJOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2004H. Guo Abstract Aim:, To characterize the locus for O-antigen biosynthesis from Escherichia coli O172 type strain and to develop a rapid, specific and sensitive PCR-based method for identification and detection of E. coli O172. Methods and Results:, DNA of O-antigen gene cluster of E. coli O172 was amplified by long-range PCR method using primers based on housekeeping genes galF and gnd Shot gun bank was constructed and high quality sequencing was performed. The putative genes for synthesis of UDP-FucNAc, O-unit flippase, O-antigen polymerase and glycosyltransferases were assigned by the homology search. The evolutionary relationship between O-antigen gene clusters of E. coli O172 and E. coli O26 is shown by sequence comparison. Genes specific to E. coli O172 strains were identified by PCR assays using primers based on genes for O-unit flippase, O-antigen polymerase and glycosyltransferases. The specificity of PCR assays was tested using all E. coli and Shigella O-antigen type strains, as well as 24 clinical E. coli isolates. The sensitivity of PCR assays was determined, and the detection limits were 1 pg ,l,1 chromosomal DNA, 0·2 CFU g,1 pork and 0·2 CFU ml,1 water. The total time required from beginning to end of the procedure was within 16 h. Conclusion:, The O-antigen gene cluster of E. coli O172 was identified and PCR assays based on O-antigen specific genes showed high specificity and sensitivity. Significance and Impact of the Study:, An O-antigen gene cluster was identified by sequencing. The specific genes were determined for E. coli O172. The sensitivity of O-antigen specific PCR assay was tested. Although Shiga toxin-producing O172 strains were not yet isolated from clinical specimens, they may emerge as pathogens. [source] Identification of the genes associated with a virulent strain of Porphyromonas gingivalis using the subtractive hybridization techniqueMOLECULAR ORAL MICROBIOLOGY, Issue 1 2008M. Tachibana-Ono Background/aims:,Porphyromonas gingivalis, a major etiological organism implicated in periodontal disease, can be classified into virulent and avirulent strains. Our aim was to identify a gene for the virulence of P. gingivalis. Methods:, The subtractive hybridization technique was employed to identify the genes specific to P. gingivalis W83, a virulent strain. In this study, P. gingivalis W83 was used as the tester strain, and P. gingivalis ATCC 33277 was the driver strain. The prevalence of W83-specific genes was determined by Southern blot analysis of several P. gingivalis strains. Results:, We obtained 575 colonies using the subtractive hybridization technique. From among these, 26 DNA fragments were subjected to a homology search using the BLAST program. Compared with strain ATCC 33277, strain W83 contained 12 unique clones. The specificities of the isolated DNA fragments were analyzed among four P. gingivalis strains by Southern blot analysis. Five genes showed specificity for strain W83 compared with strain ATCC 33277. All five genes were also identified in strain W50. Conclusions:, The subtractive hybridization technique was effective in screening the two strains for specific DNA sequences, some of which might be responsible for determining virulence. The results suggested that several genes specific to strain W83 were associated with its virulence. Further analysis of these DNA fragments will provide important information on the pathogenesis of virulent P. gingivalis strains. [source] A shared promoter region suggests a common ancestor for the human VCX/Y, SPANX, and CSAG gene families and the murine CYPT familyMOLECULAR REPRODUCTION & DEVELOPMENT, Issue 2 2008Martin A. Hansen Abstract Many testis-specific genes from the sex chromosomes are subject to rapid evolution, which can make it difficult to identify murine genes in the human genome. The murine CYPT gene family includes 15 members, but orthologs were undetectable in the human genome. However, using refined homology search, sequences corresponding to the shared promoter region of the CYPT family were identified at 39 loci. Most loci were located immediately upstream of genes belonging to the VCX/Y, SPANX, or CSAG gene families. Sequence comparison of the loci revealed a conserved CYPT promoter-like (CPL) element featuring TATA and CCAAT boxes. The expression of members of the three families harboring the CPL resembled the murine expression of the CYPT family, with weak expression in late pachytene spermatocytes and predominant expression in spermatids, but some genes were also weakly expressed in somatic cells and in other germ cell types. The genomic regions harboring the gene families were rich in direct and inverted segmental duplications (SD), which may facilitate gene conversion and rapid evolution. The conserved CPL and the common expression profiles suggest that the human VCX/Y, SPANX, and CSAG2 gene families together with the murine SPANX gene and the CYPT family may share a common ancestor. Finally, we present evidence that VCX/Y and SPANX may be paralogs with a similar protein structure consisting of C terminal acidic repeats of variable lengths. Mol. Reprod. Dev. 75: 219,229, 2008. © 2007 Wiley-Liss, Inc. [source] Structure of the minimized ,/,-hydrolase fold protein from Thermus thermophilus HB8ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 12 2007Yong Xie The gene encoding TTHA1544 is a singleton found in the Thermus thermophilus HB8 genome and encodes a 131-amino-acid protein. The crystal structure of TTHA1544 has been determined at 2.0,Å resolution by the single-wavelength anomalous dispersion method in order to elucidate its function. There are two molecules in the asymmetric unit. Each molecule consists of four ,-helices and six ,-strands, with the ,-strands composing a central ,-sheet. A structural homology search revealed that the overall structure of TTHA1544 resembles the ,/,-hydrolase fold, although TTHA1544 lacks the catalytic residues of a hydrolase. These results suggest that TTHA1544 represents the minimized ,/,-hydrolase fold and that an additional component would be required for its activity. [source] Solution structure of Arabidopsis thaliana protein At5g39720.1, a member of the AIG2-like protein familyACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 6 2006Betsy L. Lytle The three-dimensional structure of Arabidopsis thaliana protein At5g39720.1 was determined by NMR spectroscopy. It is the first representative structure of Pfam family PF06094, which contains protein sequences similar to that of AIG2, an A. thaliana protein of unknown function induced upon infection by the bacterial pathogen Pseudomonas syringae. The At5g39720.1 structure consists of a five-stranded ,-barrel surrounded by two ,-helices and a small ,-sheet. A long flexible ,-helix protrudes from the structure at the C-terminal end. A structural homology search revealed similarity to three members of Pfam family UPF0131. Conservation of residues in a hydrophilic cavity able to bind small ligands in UPF0131 proteins suggests that this may also serve as an active site in AIG2-like proteins. [source] Purification and characterization of 66-kDa glycoprotein from human breast carcinomaCANCER SCIENCE, Issue 9 2007Renqing Feng We extracted a 66-kDa glycoprotein (GP-1D8) from breast invasive ductal carcinoma tissues. The monoclonal antibody (mAb) against GP-1D8 was prepared in our laboratory. Western blotting with the purified protein using the mAb demonstrated a single band of 66 kDa. Immunocytochemical and immunohistochemical analysis revealed strong expression of GP-1D8 protein in the cytoplasm of MCF-7 cells and different types of breast carcinoma tissues, but GP-1D8 is absent in normal breast and benign breast tumor tissues. Glycosylation analysis showed GP-1D8 contained methylated salic acid. GP-1D8 was identified using mass-spectrometric techniques and N -terminal sequencing. These data were used to identify the protein through the SWISSPROT protein sequence database and BLAST homology search. These results showed GP-1D8 had some similarity to human albumin precursor. Co-immunoprecipitation assays of lysate from MCF-7 cells and mass spectrometric analysis revealed the interaction of GP-1D8 with ,-tubulin. This is the first time human breast carcinoma tissues and MCF-7 cells have been shown to express a 66-kDa glycoprotein similar to human albumin precursor. These results might be important in the detection of novel potential biomarkers and may provide insight into the molecular mechanisms of tumorigenesis. (Cancer Sci 2007; 98: 1344,1349) [source] Hemagglutinating activity and corresponding putative sequence identity from Curcuma aromatica rhizomeJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 6 2008Ponpimol Tiptara Abstract BACKGROUND:Curcuma aromatica is a medicinal plant belonging to the Zingiberaceae family with an incomplete genome sequence. It has been reported that extract from the rhizome of this plant contains haemagglutinating activity. In this study the profile of fractions containing hemagglutinating activity is described. RESULTS: Following extraction with saline buffer, the protein solution was fractionated by ammonium sulfate precipitation. Ion-exchange chromatography was completed on fast-flow SP-Sepharose, as well as gel filtration chromatography on Superdex 75. The active fractions were then separated by one-dimensional sodium dodecyl sulfate,polyacrylamide gel electrophoresis and labeled proteins were digested with trypsin. The digest bands were analyzed by reversed-phase liquid chromatography,tandem mass spectrometry. Inferred peptide sequences were used in Mascot searching and mass spectrometry-driven BLAST (MS-BLAST) homology searches allowed the recognition of related proteins in other species of Viridiplantae. Six putative proteins from nine bands showed similarity with lectin sequences. CONCLUSION: This study reports the identification of six lectins from the Curcuma aromatica rhizome achieved by mass spectrometry using MS-BLAST algorithms to search for homology between de novo determined peptide sequences and protein sequences available in sequence databases. Copyright © 2008 Society of Chemical Industry [source] The secretome of Pleurotus sapidusPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 18 2005Holger Zorn Dr. Abstract Due to their unique capability to attack lignified biopolymers, extracellular enzymes of white-rot fungi enjoy an increasing interest in various fields of white biotechnology. The edible fungus Pleurotus sapidus was selected as a model organism for the analysis of the secretome by means of 2-DE. For enzyme production, the fungus was grown in submerged cultures either on peanut shells or on glass wool as a carrier material. Identification of the secreted enzymes was performed by tryptic digestion, ESI-MS/MS ab initio sequencing, and homology searches against public databases. The spectrum of secreted enzymes comprised various types of hydrolases and lignolytic enzymes of the manganese peroxidase/versatile peroxidase family. While peptidases were secreted mainly by the cultures grown on peanut shells, versatile peroxidase type enzymes dominated in the cultures grown on glass wool. [source] The complete mitochondrial genome of the domestic red deer (Cervus elaphus) of New Zealand and its phylogenic position within the family CervidaeANIMAL SCIENCE JOURNAL, Issue 5 2010Kenta WADA ABSTRACT We determined the complete nucleotide sequence of the mitochondrial genome of the semidomestic red deer (Cervus elaphus) of New Zealand. The genome was 16 357 bp long and contained 13 protein-coding genes, 12SrRNA, 16SrRNA, 22 tRNAs and a D-loop as found in other mammals. Database homology searches showed that the mitochondrial DNA (mtDNA) sequence from the New Zealand semidomestic deer was similar to partial mtDNA sequences from the European, Norwegian (C. e. atlanticus) and Spanish red deer (C. e. hispanicus). Phylogenetic analysis of the mitochondrial protein-coding regions revealed two well-defined monophyletic clades in subfamilies Cervinae and Muntiacinae. However, red deer and Sika deer were not found to be close relatives. The analysis did identify the red deer as a sister taxon of a Samber/Sika deer clade, although it was more closely related to the Samber than the Sika group. [source] Characterization of the major allergens of Pachycondyla chinensis in ant sting anaphylaxis patientsCLINICAL & EXPERIMENTAL ALLERGY, Issue 4 2009E. K. Lee Summary Background The ant species Pachycondyla chinensis, which has spread from Far Eastern Asia to New Zealand and North America, induces anaphylactic reactions in human with its sting. However, the major allergens of P. chinensis have not yet been characterized. Methods We selected seven patients with histories of anaphylaxis induced by P. chinensis. Two-dimensional electrophoresis (2-DE) was used to identify the major allergens. We subsequently performed Western blots for P. chinensis -specific IgEs, N-terminal amino acid sequencing, ESI-MS/MS, and RT-PCR using primers based on the N-terminal sequence. Results Six of the anaphylactic subjects had an IgE specific to a 23 kDa allergen of P. chinensis. Two candidates for major allergens, 23 kDa (pI 8.7) and 25 kDa (pI 6.2), were revealed by 2-DE using P. chinensis -specific IgE immunoblotting. In N-terminal sequencing and ESI-MS/MS analysis, 23 kDa (pI 8.7) and 25 kDa (pI 6.2) allergens, belonging to the protein families of antigen 5, were identified and share marked amino acid sequence similarity. The 23 kDa allergen is 206 amino acids in length and homology searches showed 54.0% and 50.0% homology with Sol i 3 and Ves v 5, respectively. Conclusion The major allergens of P. chinensis are 23 kDa (pI 8.7) and 25 kDa (pI 6.2) proteins that belong to the antigen 5 family of proteins. [source] | ||||||||||||||||