Single nucleotide polymorphisms identification in expressed genes of Schistosoma mansoni
Single nucleotide polymorphism (SNP) markers have been shown to be useful in genetic investigations of medically important parasites and their hosts. In this paper, we describe the prediction and validation of SNPs in ESTs of Schistosoma mansoni. We used 107,417 public sequences of S. mansoni and id...
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Veröffentlicht in: | Molecular and biochemical parasitology 2007-08, Vol.154 (2), p.134-140 |
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container_title | Molecular and biochemical parasitology |
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creator | Simões, Mariana Bahia, Diana Zerlotini, Adhemar Torres, Kleider Artiguenave, François Neshich, Goran Kuser, Paula Oliveira, Guilherme |
description | Single nucleotide polymorphism (SNP) markers have been shown to be useful in genetic investigations of medically important parasites and their hosts. In this paper, we describe the prediction and validation of SNPs in ESTs of
Schistosoma mansoni. We used 107,417 public sequences of
S. mansoni and identified 15,614 high-quality candidate SNPs in 12,184 contigs. The presence of predicted SNPs was observed in well characterized antigens and vaccine candidates such as those coding for myosin; Sm14 and Sm23; cathepsin B and triosephosphate isomerase (TPI). Additionally, SNPs were experimentally validated for the cathepsin B. A comparative model of the
S. mansoni cathepsin B was built for predicting the possible consequences of amino acid substitutions on the protein structure. An analysis of the substitutions indicated that the amino acids were mostly located on the surface of the molecule, and we found no evidence for a significant conformational change of the enzyme. However, at least one of the substitutions could result in a structural modification of an epitope. |
doi_str_mv | 10.1016/j.molbiopara.2007.04.003 |
format | Article |
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Schistosoma mansoni. We used 107,417 public sequences of
S. mansoni and identified 15,614 high-quality candidate SNPs in 12,184 contigs. The presence of predicted SNPs was observed in well characterized antigens and vaccine candidates such as those coding for myosin; Sm14 and Sm23; cathepsin B and triosephosphate isomerase (TPI). Additionally, SNPs were experimentally validated for the cathepsin B. A comparative model of the
S. mansoni cathepsin B was built for predicting the possible consequences of amino acid substitutions on the protein structure. An analysis of the substitutions indicated that the amino acids were mostly located on the surface of the molecule, and we found no evidence for a significant conformational change of the enzyme. However, at least one of the substitutions could result in a structural modification of an epitope.</description><identifier>ISSN: 0166-6851</identifier><identifier>EISSN: 1872-9428</identifier><identifier>DOI: 10.1016/j.molbiopara.2007.04.003</identifier><identifier>PMID: 17568698</identifier><language>eng</language><publisher>Netherlands: Elsevier B.V</publisher><subject>Animals ; Antigens, Helminth - genetics ; Cathepsin B ; Cathepsin B - chemistry ; Cathepsin B - genetics ; Comparative modeling ; Computational biology ; Fatty Acid Transport Proteins - genetics ; Genes, Helminth - genetics ; Helminth Proteins - genetics ; Models, Molecular ; Myosins - genetics ; Polymorphism, Single Nucleotide ; Schistosoma mansoni ; Schistosoma mansoni - genetics ; Single nucleotide polymorphism ; Triose-Phosphate Isomerase - genetics</subject><ispartof>Molecular and biochemical parasitology, 2007-08, Vol.154 (2), p.134-140</ispartof><rights>2007 Elsevier B.V.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c508t-459a61f7009cb83a57697113ea7196533a127553dcda165dbd339877bc0bbef23</citedby><cites>FETCH-LOGICAL-c508t-459a61f7009cb83a57697113ea7196533a127553dcda165dbd339877bc0bbef23</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.molbiopara.2007.04.003$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>230,314,780,784,885,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/17568698$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Simões, Mariana</creatorcontrib><creatorcontrib>Bahia, Diana</creatorcontrib><creatorcontrib>Zerlotini, Adhemar</creatorcontrib><creatorcontrib>Torres, Kleider</creatorcontrib><creatorcontrib>Artiguenave, François</creatorcontrib><creatorcontrib>Neshich, Goran</creatorcontrib><creatorcontrib>Kuser, Paula</creatorcontrib><creatorcontrib>Oliveira, Guilherme</creatorcontrib><title>Single nucleotide polymorphisms identification in expressed genes of Schistosoma mansoni</title><title>Molecular and biochemical parasitology</title><addtitle>Mol Biochem Parasitol</addtitle><description>Single nucleotide polymorphism (SNP) markers have been shown to be useful in genetic investigations of medically important parasites and their hosts. In this paper, we describe the prediction and validation of SNPs in ESTs of
Schistosoma mansoni. We used 107,417 public sequences of
S. mansoni and identified 15,614 high-quality candidate SNPs in 12,184 contigs. The presence of predicted SNPs was observed in well characterized antigens and vaccine candidates such as those coding for myosin; Sm14 and Sm23; cathepsin B and triosephosphate isomerase (TPI). Additionally, SNPs were experimentally validated for the cathepsin B. A comparative model of the
S. mansoni cathepsin B was built for predicting the possible consequences of amino acid substitutions on the protein structure. An analysis of the substitutions indicated that the amino acids were mostly located on the surface of the molecule, and we found no evidence for a significant conformational change of the enzyme. However, at least one of the substitutions could result in a structural modification of an epitope.</description><subject>Animals</subject><subject>Antigens, Helminth - genetics</subject><subject>Cathepsin B</subject><subject>Cathepsin B - chemistry</subject><subject>Cathepsin B - genetics</subject><subject>Comparative modeling</subject><subject>Computational biology</subject><subject>Fatty Acid Transport Proteins - genetics</subject><subject>Genes, Helminth - genetics</subject><subject>Helminth Proteins - genetics</subject><subject>Models, Molecular</subject><subject>Myosins - genetics</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Schistosoma mansoni</subject><subject>Schistosoma mansoni - genetics</subject><subject>Single nucleotide polymorphism</subject><subject>Triose-Phosphate Isomerase - genetics</subject><issn>0166-6851</issn><issn>1872-9428</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2007</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkU9vFCEYh4nR2G31KxhO3mYKw_DvYqKNVZMmHmqT3ggD72zZzMAIs4399qXZjdVTTyTwvD9-8CCEKWkpoeJ8185pGkJabLZtR4hsSd8Swl6hDVWya3TfqddoU1HRCMXpCTotZUcI4VKIt-iESi6U0GqDbq9D3E6A495NkNbgAS9pephTXu5CmQuuO3ENY3B2DSniEDH8WTKUAh5vIULBacTXrsJrKmm2eLaxpBjeoTejnQq8P65n6Oby66-L783Vz28_Lj5fNY4TtTY911bQURKi3aCYrQW1pJSBlVQLzpilneSceectFdwPnjGtpBwcGQYYO3aGPh1yl_0wg3e1bbaTWXKYbX4wyQbz_0kMd2ab7g3VSsie1oCPx4Ccfu-hrGYOxcE02QhpX4wksuuUehmkWuq-72UF1QF0OZWSYfzbhhLz5M_szLM_8-TPkN5Uf3X0w7-veR48CqvAlwMA9U_vA2RTXIDowIcMbjU-hZdveQSd3rRS</recordid><startdate>20070801</startdate><enddate>20070801</enddate><creator>Simões, Mariana</creator><creator>Bahia, Diana</creator><creator>Zerlotini, Adhemar</creator><creator>Torres, Kleider</creator><creator>Artiguenave, François</creator><creator>Neshich, Goran</creator><creator>Kuser, Paula</creator><creator>Oliveira, Guilherme</creator><general>Elsevier B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20070801</creationdate><title>Single nucleotide polymorphisms identification in expressed genes of Schistosoma mansoni</title><author>Simões, Mariana ; Bahia, Diana ; Zerlotini, Adhemar ; Torres, Kleider ; Artiguenave, François ; Neshich, Goran ; Kuser, Paula ; Oliveira, Guilherme</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c508t-459a61f7009cb83a57697113ea7196533a127553dcda165dbd339877bc0bbef23</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2007</creationdate><topic>Animals</topic><topic>Antigens, Helminth - genetics</topic><topic>Cathepsin B</topic><topic>Cathepsin B - chemistry</topic><topic>Cathepsin B - genetics</topic><topic>Comparative modeling</topic><topic>Computational biology</topic><topic>Fatty Acid Transport Proteins - genetics</topic><topic>Genes, Helminth - genetics</topic><topic>Helminth Proteins - genetics</topic><topic>Models, Molecular</topic><topic>Myosins - genetics</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Schistosoma mansoni</topic><topic>Schistosoma mansoni - genetics</topic><topic>Single nucleotide polymorphism</topic><topic>Triose-Phosphate Isomerase - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Simões, Mariana</creatorcontrib><creatorcontrib>Bahia, Diana</creatorcontrib><creatorcontrib>Zerlotini, Adhemar</creatorcontrib><creatorcontrib>Torres, Kleider</creatorcontrib><creatorcontrib>Artiguenave, François</creatorcontrib><creatorcontrib>Neshich, Goran</creatorcontrib><creatorcontrib>Kuser, Paula</creatorcontrib><creatorcontrib>Oliveira, Guilherme</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Molecular and biochemical parasitology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Simões, Mariana</au><au>Bahia, Diana</au><au>Zerlotini, Adhemar</au><au>Torres, Kleider</au><au>Artiguenave, François</au><au>Neshich, Goran</au><au>Kuser, Paula</au><au>Oliveira, Guilherme</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Single nucleotide polymorphisms identification in expressed genes of Schistosoma mansoni</atitle><jtitle>Molecular and biochemical parasitology</jtitle><addtitle>Mol Biochem Parasitol</addtitle><date>2007-08-01</date><risdate>2007</risdate><volume>154</volume><issue>2</issue><spage>134</spage><epage>140</epage><pages>134-140</pages><issn>0166-6851</issn><eissn>1872-9428</eissn><abstract>Single nucleotide polymorphism (SNP) markers have been shown to be useful in genetic investigations of medically important parasites and their hosts. In this paper, we describe the prediction and validation of SNPs in ESTs of
Schistosoma mansoni. We used 107,417 public sequences of
S. mansoni and identified 15,614 high-quality candidate SNPs in 12,184 contigs. The presence of predicted SNPs was observed in well characterized antigens and vaccine candidates such as those coding for myosin; Sm14 and Sm23; cathepsin B and triosephosphate isomerase (TPI). Additionally, SNPs were experimentally validated for the cathepsin B. A comparative model of the
S. mansoni cathepsin B was built for predicting the possible consequences of amino acid substitutions on the protein structure. An analysis of the substitutions indicated that the amino acids were mostly located on the surface of the molecule, and we found no evidence for a significant conformational change of the enzyme. However, at least one of the substitutions could result in a structural modification of an epitope.</abstract><cop>Netherlands</cop><pub>Elsevier B.V</pub><pmid>17568698</pmid><doi>10.1016/j.molbiopara.2007.04.003</doi><tpages>7</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Animals Antigens, Helminth - genetics Cathepsin B Cathepsin B - chemistry Cathepsin B - genetics Comparative modeling Computational biology Fatty Acid Transport Proteins - genetics Genes, Helminth - genetics Helminth Proteins - genetics Models, Molecular Myosins - genetics Polymorphism, Single Nucleotide Schistosoma mansoni Schistosoma mansoni - genetics Single nucleotide polymorphism Triose-Phosphate Isomerase - genetics |
title | Single nucleotide polymorphisms identification in expressed genes of Schistosoma mansoni |
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