Application of HiCEP to Screening of Radiation Stress-Responsive Genes in the Soil Microarthropod Folsomia candida (Collembola)
The field of ecotoxicogenomics has received increasing attention for its potential to provide insight into pressing ecological issues. However, its applications are limited due to a lack of genetic sequence information for organisms used in ecotoxicological studies. We used high-coverage expression...
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| Veröffentlicht in: | Environmental science & technology 2008-09, Vol.42 (18), p.6997-7002 |
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| creator | Nakamori, Taizo Fujimori, Akira Kinoshita, Keiji Ban-nai, Tadaaki Kubota, Yoshihisa Yoshida, Satoshi |
| description | The field of ecotoxicogenomics has received increasing attention for its potential to provide insight into pressing ecological issues. However, its applications are limited due to a lack of genetic sequence information for organisms used in ecotoxicological studies. We used high-coverage expression profiling (HiCEP), a method that requires no prior sequence knowledge, to examine stress-responsive genes and their dose dependence in the springtail Folsomia candida using γ radiation as the stressor. Radiation-responsive genes and their dose dependency were detected at effective doses for reproduction, and 16 up-regulated transcript-derived fragments (TDFs) were sequenced. Quantitative PCR analysis also found that most of the TDFs were up-regulated. The sequences of the TDFs showed resemblance to known genes, such as glutathione S-transferase and poly(ADP-ribose) polymerase, but most showed no similarity to any genes in the gene databases. These results suggest that HiCEP is effective for discovering differently expressed genes and their dose dependence, even in organisms for which few sequence data are available. The limited length of the TDFs, however, may impede functional annotation of the genes. In conclusion, HiCEP is useful for ecotoxicogenomic studies in which various organisms with few available genomic resources are involved. |
| doi_str_mv | 10.1021/es801128q |
| format | Article |
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However, its applications are limited due to a lack of genetic sequence information for organisms used in ecotoxicological studies. We used high-coverage expression profiling (HiCEP), a method that requires no prior sequence knowledge, to examine stress-responsive genes and their dose dependence in the springtail Folsomia candida using γ radiation as the stressor. Radiation-responsive genes and their dose dependency were detected at effective doses for reproduction, and 16 up-regulated transcript-derived fragments (TDFs) were sequenced. Quantitative PCR analysis also found that most of the TDFs were up-regulated. The sequences of the TDFs showed resemblance to known genes, such as glutathione S-transferase and poly(ADP-ribose) polymerase, but most showed no similarity to any genes in the gene databases. These results suggest that HiCEP is effective for discovering differently expressed genes and their dose dependence, even in organisms for which few sequence data are available. The limited length of the TDFs, however, may impede functional annotation of the genes. In conclusion, HiCEP is useful for ecotoxicogenomic studies in which various organisms with few available genomic resources are involved.</description><identifier>ISSN: 0013-936X</identifier><identifier>EISSN: 1520-5851</identifier><identifier>DOI: 10.1021/es801128q</identifier><identifier>PMID: 18853822</identifier><identifier>CODEN: ESTHAG</identifier><language>eng</language><publisher>Washington, DC: American Chemical Society</publisher><subject>Animals ; Applied sciences ; Arthropods ; Arthropods - genetics ; Arthropods - radiation effects ; Collembola ; Dose-Response Relationship, Radiation ; Ecotoxicology and Human Environmental Health ; Exact sciences and technology ; Folsomia candida ; Gamma Rays ; Gene Expression Profiling ; Genes ; Genes, Insect ; Genetics ; Pollution ; Polymerase Chain Reaction ; Radiation ; RNA, Messenger - genetics ; RNA, Messenger - metabolism ; Sequence Analysis, RNA ; Soil ; Soil microorganisms ; Soil sciences ; Soils ; Stress, Physiological - genetics ; Stress, Physiological - radiation effects ; Up-Regulation - radiation effects</subject><ispartof>Environmental science & technology, 2008-09, Vol.42 (18), p.6997-7002</ispartof><rights>Copyright © 2008 American Chemical Society</rights><rights>2008 INIST-CNRS</rights><rights>Copyright American Chemical Society Sep 15, 2008</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-a550t-b38d3372e30d6d7773279687b341639bf9ac5a5e272ac093c8f449887a86724f3</citedby><cites>FETCH-LOGICAL-a550t-b38d3372e30d6d7773279687b341639bf9ac5a5e272ac093c8f449887a86724f3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://pubs.acs.org/doi/pdf/10.1021/es801128q$$EPDF$$P50$$Gacs$$H</linktopdf><linktohtml>$$Uhttps://pubs.acs.org/doi/10.1021/es801128q$$EHTML$$P50$$Gacs$$H</linktohtml><link.rule.ids>315,781,785,2766,27081,27929,27930,56743,56793</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=20660627$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/18853822$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Nakamori, Taizo</creatorcontrib><creatorcontrib>Fujimori, Akira</creatorcontrib><creatorcontrib>Kinoshita, Keiji</creatorcontrib><creatorcontrib>Ban-nai, Tadaaki</creatorcontrib><creatorcontrib>Kubota, Yoshihisa</creatorcontrib><creatorcontrib>Yoshida, Satoshi</creatorcontrib><title>Application of HiCEP to Screening of Radiation Stress-Responsive Genes in the Soil Microarthropod Folsomia candida (Collembola)</title><title>Environmental science & technology</title><addtitle>Environ. Sci. Technol</addtitle><description>The field of ecotoxicogenomics has received increasing attention for its potential to provide insight into pressing ecological issues. However, its applications are limited due to a lack of genetic sequence information for organisms used in ecotoxicological studies. We used high-coverage expression profiling (HiCEP), a method that requires no prior sequence knowledge, to examine stress-responsive genes and their dose dependence in the springtail Folsomia candida using γ radiation as the stressor. Radiation-responsive genes and their dose dependency were detected at effective doses for reproduction, and 16 up-regulated transcript-derived fragments (TDFs) were sequenced. Quantitative PCR analysis also found that most of the TDFs were up-regulated. The sequences of the TDFs showed resemblance to known genes, such as glutathione S-transferase and poly(ADP-ribose) polymerase, but most showed no similarity to any genes in the gene databases. These results suggest that HiCEP is effective for discovering differently expressed genes and their dose dependence, even in organisms for which few sequence data are available. The limited length of the TDFs, however, may impede functional annotation of the genes. In conclusion, HiCEP is useful for ecotoxicogenomic studies in which various organisms with few available genomic resources are involved.</description><subject>Animals</subject><subject>Applied sciences</subject><subject>Arthropods</subject><subject>Arthropods - genetics</subject><subject>Arthropods - radiation effects</subject><subject>Collembola</subject><subject>Dose-Response Relationship, Radiation</subject><subject>Ecotoxicology and Human Environmental Health</subject><subject>Exact sciences and technology</subject><subject>Folsomia candida</subject><subject>Gamma Rays</subject><subject>Gene Expression Profiling</subject><subject>Genes</subject><subject>Genes, Insect</subject><subject>Genetics</subject><subject>Pollution</subject><subject>Polymerase Chain Reaction</subject><subject>Radiation</subject><subject>RNA, Messenger - genetics</subject><subject>RNA, Messenger - metabolism</subject><subject>Sequence Analysis, RNA</subject><subject>Soil</subject><subject>Soil microorganisms</subject><subject>Soil sciences</subject><subject>Soils</subject><subject>Stress, Physiological - genetics</subject><subject>Stress, Physiological - radiation effects</subject><subject>Up-Regulation - radiation effects</subject><issn>0013-936X</issn><issn>1520-5851</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2008</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpl0V1rFDEUBuBBFLtWL_wDEgTRXozmY_Ixl3XbbYWK624F78KZTMamZpJpMlv0yr_ulF12Qa8CycPLOXmL4iXB7wmm5IPNChNC1d2jYkY4xSVXnDwuZhgTVtZMfD8qnuV8izGmDKunxRFRijNF6az4czoM3hkYXQwodujSzc-XaIxobZK1wYUfD7craN2WrMdkcy5XNg8xZHdv0YUNNiMX0Hhj0To6jz47kyKk8SbFIbZoEX2OvQNkILSuBfRuHr23fRM9nDwvnnTgs32xO4-Lb4vz6_llefXl4tP89KoEzvFYNky1jElqGW5FK6VkVNZCyYZVRLC66WowHLilkoLBNTOqq6paKQlKSFp17Lh4u80dUrzb2Dzq3mVjvYdg4yZrySslBZN4kq__kbdxk8I0nJ5-j1SCMTqhky2aNs052U4PyfWQfmuC9UMnet_JZF_tAjdNb9uD3JUwgTc7ANmA7xIE4_LeUSwEFlROrtw6l0f7a_8O6acWkkmur5dr_VF8Xa7OFkKvDrlg8mGJ_wf8C5_rrbo</recordid><startdate>20080915</startdate><enddate>20080915</enddate><creator>Nakamori, Taizo</creator><creator>Fujimori, Akira</creator><creator>Kinoshita, Keiji</creator><creator>Ban-nai, Tadaaki</creator><creator>Kubota, Yoshihisa</creator><creator>Yoshida, Satoshi</creator><general>American Chemical Society</general><scope>BSCLL</scope><scope>IQODW</scope><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>7QO</scope><scope>7ST</scope><scope>7T7</scope><scope>7U7</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>P64</scope><scope>SOI</scope><scope>7SS</scope><scope>F1W</scope><scope>H95</scope><scope>L.G</scope><scope>M7N</scope></search><sort><creationdate>20080915</creationdate><title>Application of HiCEP to Screening of Radiation Stress-Responsive Genes in the Soil Microarthropod Folsomia candida (Collembola)</title><author>Nakamori, Taizo ; Fujimori, Akira ; Kinoshita, Keiji ; Ban-nai, Tadaaki ; Kubota, Yoshihisa ; Yoshida, Satoshi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a550t-b38d3372e30d6d7773279687b341639bf9ac5a5e272ac093c8f449887a86724f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2008</creationdate><topic>Animals</topic><topic>Applied sciences</topic><topic>Arthropods</topic><topic>Arthropods - genetics</topic><topic>Arthropods - radiation effects</topic><topic>Collembola</topic><topic>Dose-Response Relationship, Radiation</topic><topic>Ecotoxicology and Human Environmental Health</topic><topic>Exact sciences and technology</topic><topic>Folsomia candida</topic><topic>Gamma Rays</topic><topic>Gene Expression Profiling</topic><topic>Genes</topic><topic>Genes, Insect</topic><topic>Genetics</topic><topic>Pollution</topic><topic>Polymerase Chain Reaction</topic><topic>Radiation</topic><topic>RNA, Messenger - genetics</topic><topic>RNA, Messenger - metabolism</topic><topic>Sequence Analysis, RNA</topic><topic>Soil</topic><topic>Soil microorganisms</topic><topic>Soil sciences</topic><topic>Soils</topic><topic>Stress, Physiological - genetics</topic><topic>Stress, Physiological - radiation effects</topic><topic>Up-Regulation - radiation effects</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Nakamori, Taizo</creatorcontrib><creatorcontrib>Fujimori, Akira</creatorcontrib><creatorcontrib>Kinoshita, Keiji</creatorcontrib><creatorcontrib>Ban-nai, Tadaaki</creatorcontrib><creatorcontrib>Kubota, Yoshihisa</creatorcontrib><creatorcontrib>Yoshida, Satoshi</creatorcontrib><collection>Istex</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Environment Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Toxicology Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environment Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>ASFA: Aquatic Sciences and Fisheries Abstracts</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 1: Biological Sciences & Living Resources</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) Professional</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><jtitle>Environmental science & technology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Nakamori, Taizo</au><au>Fujimori, Akira</au><au>Kinoshita, Keiji</au><au>Ban-nai, Tadaaki</au><au>Kubota, Yoshihisa</au><au>Yoshida, Satoshi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Application of HiCEP to Screening of Radiation Stress-Responsive Genes in the Soil Microarthropod Folsomia candida (Collembola)</atitle><jtitle>Environmental science & technology</jtitle><addtitle>Environ. Sci. Technol</addtitle><date>2008-09-15</date><risdate>2008</risdate><volume>42</volume><issue>18</issue><spage>6997</spage><epage>7002</epage><pages>6997-7002</pages><issn>0013-936X</issn><eissn>1520-5851</eissn><coden>ESTHAG</coden><abstract>The field of ecotoxicogenomics has received increasing attention for its potential to provide insight into pressing ecological issues. However, its applications are limited due to a lack of genetic sequence information for organisms used in ecotoxicological studies. We used high-coverage expression profiling (HiCEP), a method that requires no prior sequence knowledge, to examine stress-responsive genes and their dose dependence in the springtail Folsomia candida using γ radiation as the stressor. Radiation-responsive genes and their dose dependency were detected at effective doses for reproduction, and 16 up-regulated transcript-derived fragments (TDFs) were sequenced. Quantitative PCR analysis also found that most of the TDFs were up-regulated. The sequences of the TDFs showed resemblance to known genes, such as glutathione S-transferase and poly(ADP-ribose) polymerase, but most showed no similarity to any genes in the gene databases. These results suggest that HiCEP is effective for discovering differently expressed genes and their dose dependence, even in organisms for which few sequence data are available. The limited length of the TDFs, however, may impede functional annotation of the genes. In conclusion, HiCEP is useful for ecotoxicogenomic studies in which various organisms with few available genomic resources are involved.</abstract><cop>Washington, DC</cop><pub>American Chemical Society</pub><pmid>18853822</pmid><doi>10.1021/es801128q</doi><tpages>6</tpages></addata></record> |
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| subjects | Animals Applied sciences Arthropods Arthropods - genetics Arthropods - radiation effects Collembola Dose-Response Relationship, Radiation Ecotoxicology and Human Environmental Health Exact sciences and technology Folsomia candida Gamma Rays Gene Expression Profiling Genes Genes, Insect Genetics Pollution Polymerase Chain Reaction Radiation RNA, Messenger - genetics RNA, Messenger - metabolism Sequence Analysis, RNA Soil Soil microorganisms Soil sciences Soils Stress, Physiological - genetics Stress, Physiological - radiation effects Up-Regulation - radiation effects |
| title | Application of HiCEP to Screening of Radiation Stress-Responsive Genes in the Soil Microarthropod Folsomia candida (Collembola) |
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