Development of taxonomic rRNA-targeted probes of two harmful algae: Prorocentrum minimum and Kareniamikimotoi by fluorescence in situ hybridization
Harmful algal blooms recently have been under the spotlight throughout the world, because of their negative impact on the marine environment, aquaculture, fisheries as well as public health. The development of methods for rapid and precise identification and quantification of causative species is es...
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description | Harmful algal blooms recently have been under the spotlight throughout the world, because of their negative impact on the marine environment, aquaculture, fisheries as well as public health. The development of methods for rapid and precise identification and quantification of causative species is essential for the warning andmonitoring of blooms, among which the techniques based on taxonomic probes are themost favored. In this study, two harmful algae, i.e.,
Prorocentrum minimum
and
Karenia mikimotoi
were taken into consideration. The partial large subunit rDNA (D1-D2) of both species were firstly PCR-amplified, cloned and sequenced. The obtained sequences were then introduced to carry out alignment analysis for gene specific regions. Three respective candidate probes for each species were designed and used to screen the optimal probe by performing fluorescence in situ hybridization (FISH) tests. The results showed that the probes Pmin0443 and Kmik0602 displayed the best hybridization for
P. minimum
and
K. mikimotoi
, respectively. Both the specific (taxonomic) (Pmin0443 and Kmik0602) and the control probes (UniC0512 and UniR0499) were used for cross-reactivity tests with other microalgae in our laboratory. The probes Pmin0443 and Kmik0602 are specific and could be served as taxonomic probes introduced into the techniques targeting rRNA, such as FISH, sandwich hybridization, and DNA-microarray assay of
P. minimum
and
K. mikimotoi
in the future. Finally, FISH analyses with both probes were performed on the simulated field samples. The probes could hybridize exclusively with the target cells well, and no significant difference (
p
>0.05) was observed in the cell densities of the samples determined by FISH and light microscopy (LM). All suggest that the probes are specific and could be introduced into FISH for the monitoring of both harmful algae. |
doi_str_mv | 10.1007/s13131-013-0278-4 |
format | Article |
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Prorocentrum minimum
and
Karenia mikimotoi
were taken into consideration. The partial large subunit rDNA (D1-D2) of both species were firstly PCR-amplified, cloned and sequenced. The obtained sequences were then introduced to carry out alignment analysis for gene specific regions. Three respective candidate probes for each species were designed and used to screen the optimal probe by performing fluorescence in situ hybridization (FISH) tests. The results showed that the probes Pmin0443 and Kmik0602 displayed the best hybridization for
P. minimum
and
K. mikimotoi
, respectively. Both the specific (taxonomic) (Pmin0443 and Kmik0602) and the control probes (UniC0512 and UniR0499) were used for cross-reactivity tests with other microalgae in our laboratory. The probes Pmin0443 and Kmik0602 are specific and could be served as taxonomic probes introduced into the techniques targeting rRNA, such as FISH, sandwich hybridization, and DNA-microarray assay of
P. minimum
and
K. mikimotoi
in the future. Finally, FISH analyses with both probes were performed on the simulated field samples. The probes could hybridize exclusively with the target cells well, and no significant difference (
p
>0.05) was observed in the cell densities of the samples determined by FISH and light microscopy (LM). All suggest that the probes are specific and could be introduced into FISH for the monitoring of both harmful algae.</description><identifier>ISSN: 0253-505X</identifier><identifier>EISSN: 1869-1099</identifier><identifier>DOI: 10.1007/s13131-013-0278-4</identifier><language>eng</language><publisher>Heidelberg: The Chinese Society of Oceanography</publisher><subject>Algae ; Algal blooms ; Aquaculture ; Climatology ; Cross-reactivity ; DNA ; DNA microarrays ; DNA probes ; Earth and Environmental Science ; Earth Sciences ; Ecology ; Engineering Fluid Dynamics ; Environmental Chemistry ; Eutrophication ; Fish ; Fisheries ; Fluorescence ; Fluorescence in situ hybridization ; Hybridization ; Karenia mikimotoi ; Light microscopy ; Marine ; Marine & Freshwater Sciences ; Marine environment ; Marine fish ; Microscopy ; Morphology ; Nucleotide sequence ; Oceanography ; Optical microscopy ; Phytoplankton ; Plankton ; Polyculture (aquaculture) ; Probes ; Prorocentrum minimum ; Public health ; rRNA ; Sensors ; Target cells ; Taxonomy ; Water quality</subject><ispartof>Acta oceanologica Sinica, 2013-02, Vol.32 (2), p.66-75</ispartof><rights>The Chinese Society of Oceanography and Springer-Verlag Berlin Heidelberg 2013</rights><rights>The Chinese Society of Oceanography and Springer-Verlag Berlin Heidelberg 2013.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c329t-4d556f1b370d704993333810aed276440c8696200b4cb63cfbce0050067528c93</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s13131-013-0278-4$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/1284579345?pq-origsite=primo$$EHTML$$P50$$Gproquest$$H</linktohtml><link.rule.ids>314,776,780,21368,27903,27904,33723,33724,41467,42536,43784,51298,64362,64364,64366,72216</link.rule.ids></links><search><creatorcontrib>Chen, Guofu</creatorcontrib><creatorcontrib>Wang, Quanfu</creatorcontrib><creatorcontrib>Zhang, Chunyun</creatorcontrib><creatorcontrib>Zhang, Baoyu</creatorcontrib><creatorcontrib>Wang, Guangce</creatorcontrib><creatorcontrib>Lu, Douding</creatorcontrib><creatorcontrib>Xu, Zhong</creatorcontrib><creatorcontrib>Yan, Peishen</creatorcontrib><title>Development of taxonomic rRNA-targeted probes of two harmful algae: Prorocentrum minimum and Kareniamikimotoi by fluorescence in situ hybridization</title><title>Acta oceanologica Sinica</title><addtitle>Acta Oceanol. Sin</addtitle><description>Harmful algal blooms recently have been under the spotlight throughout the world, because of their negative impact on the marine environment, aquaculture, fisheries as well as public health. The development of methods for rapid and precise identification and quantification of causative species is essential for the warning andmonitoring of blooms, among which the techniques based on taxonomic probes are themost favored. In this study, two harmful algae, i.e.,
Prorocentrum minimum
and
Karenia mikimotoi
were taken into consideration. The partial large subunit rDNA (D1-D2) of both species were firstly PCR-amplified, cloned and sequenced. The obtained sequences were then introduced to carry out alignment analysis for gene specific regions. Three respective candidate probes for each species were designed and used to screen the optimal probe by performing fluorescence in situ hybridization (FISH) tests. The results showed that the probes Pmin0443 and Kmik0602 displayed the best hybridization for
P. minimum
and
K. mikimotoi
, respectively. Both the specific (taxonomic) (Pmin0443 and Kmik0602) and the control probes (UniC0512 and UniR0499) were used for cross-reactivity tests with other microalgae in our laboratory. The probes Pmin0443 and Kmik0602 are specific and could be served as taxonomic probes introduced into the techniques targeting rRNA, such as FISH, sandwich hybridization, and DNA-microarray assay of
P. minimum
and
K. mikimotoi
in the future. Finally, FISH analyses with both probes were performed on the simulated field samples. The probes could hybridize exclusively with the target cells well, and no significant difference (
p
>0.05) was observed in the cell densities of the samples determined by FISH and light microscopy (LM). All suggest that the probes are specific and could be introduced into FISH for the monitoring of both harmful algae.</description><subject>Algae</subject><subject>Algal blooms</subject><subject>Aquaculture</subject><subject>Climatology</subject><subject>Cross-reactivity</subject><subject>DNA</subject><subject>DNA microarrays</subject><subject>DNA probes</subject><subject>Earth and Environmental Science</subject><subject>Earth Sciences</subject><subject>Ecology</subject><subject>Engineering Fluid Dynamics</subject><subject>Environmental Chemistry</subject><subject>Eutrophication</subject><subject>Fish</subject><subject>Fisheries</subject><subject>Fluorescence</subject><subject>Fluorescence in situ hybridization</subject><subject>Hybridization</subject><subject>Karenia mikimotoi</subject><subject>Light microscopy</subject><subject>Marine</subject><subject>Marine & Freshwater Sciences</subject><subject>Marine environment</subject><subject>Marine fish</subject><subject>Microscopy</subject><subject>Morphology</subject><subject>Nucleotide sequence</subject><subject>Oceanography</subject><subject>Optical microscopy</subject><subject>Phytoplankton</subject><subject>Plankton</subject><subject>Polyculture (aquaculture)</subject><subject>Probes</subject><subject>Prorocentrum minimum</subject><subject>Public health</subject><subject>rRNA</subject><subject>Sensors</subject><subject>Target cells</subject><subject>Taxonomy</subject><subject>Water quality</subject><issn>0253-505X</issn><issn>1869-1099</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9kc1uFDEQhEeISCwJD8DNEhcuhvbfeMwtCuFHRAEhkLhZHo9n4zC2F9sDLK_BC-OwOSAk6D705atSl6rrHhJ4QgDk00JYWwyEYaBywPxOtyFDrzABpe52G6CCYQHi073ufinXAIIIJjfdz-fuq1vSLrhYUZpRNd9TTMFblN9fnuJq8tZVN6FdTqMrv4lvCV2ZHOZ1QWbZGvcMvcspJ9sc8hpQ8NGHdk2c0BuTXfQm-M8-pJo8GvdoXtaUXWm4dchHVHxd0dV-zH7yP0z1KZ50R7NZintwe4-7jy_OP5y9whdvX74-O73AllFVMZ-E6GcyMgmTBK4UazMQMG6isuccbMvfU4CR27Fndh6ta7kBeinoYBU77h4ffFu4L6srVQff_loWE11aiyZUkZ5ILvuGPvoLvU5rju073SDVA-Fq-B9F6MCFVIyLRpEDZXMqJbtZ77IPJu81AX1Tpj6UqVuZ-qZMzZuGHjSlsXHr8h_O_xT9AvrdooA</recordid><startdate>20130201</startdate><enddate>20130201</enddate><creator>Chen, Guofu</creator><creator>Wang, Quanfu</creator><creator>Zhang, 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by fluorescence in situ hybridization</title><author>Chen, Guofu ; Wang, Quanfu ; Zhang, Chunyun ; Zhang, Baoyu ; Wang, Guangce ; Lu, Douding ; Xu, Zhong ; Yan, Peishen</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c329t-4d556f1b370d704993333810aed276440c8696200b4cb63cfbce0050067528c93</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Algae</topic><topic>Algal blooms</topic><topic>Aquaculture</topic><topic>Climatology</topic><topic>Cross-reactivity</topic><topic>DNA</topic><topic>DNA microarrays</topic><topic>DNA probes</topic><topic>Earth and Environmental Science</topic><topic>Earth Sciences</topic><topic>Ecology</topic><topic>Engineering Fluid Dynamics</topic><topic>Environmental Chemistry</topic><topic>Eutrophication</topic><topic>Fish</topic><topic>Fisheries</topic><topic>Fluorescence</topic><topic>Fluorescence in situ hybridization</topic><topic>Hybridization</topic><topic>Karenia mikimotoi</topic><topic>Light microscopy</topic><topic>Marine</topic><topic>Marine & Freshwater Sciences</topic><topic>Marine environment</topic><topic>Marine fish</topic><topic>Microscopy</topic><topic>Morphology</topic><topic>Nucleotide sequence</topic><topic>Oceanography</topic><topic>Optical microscopy</topic><topic>Phytoplankton</topic><topic>Plankton</topic><topic>Polyculture (aquaculture)</topic><topic>Probes</topic><topic>Prorocentrum minimum</topic><topic>Public health</topic><topic>rRNA</topic><topic>Sensors</topic><topic>Target cells</topic><topic>Taxonomy</topic><topic>Water quality</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Chen, Guofu</creatorcontrib><creatorcontrib>Wang, Quanfu</creatorcontrib><creatorcontrib>Zhang, Chunyun</creatorcontrib><creatorcontrib>Zhang, Baoyu</creatorcontrib><creatorcontrib>Wang, Guangce</creatorcontrib><creatorcontrib>Lu, Douding</creatorcontrib><creatorcontrib>Xu, Zhong</creatorcontrib><creatorcontrib>Yan, Peishen</creatorcontrib><collection>CrossRef</collection><collection>Environment Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Oceanic Abstracts</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Earth, Atmospheric & Aquatic Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>ASFA: Aquatic Sciences and Fisheries Abstracts</collection><collection>ProQuest Central 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Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Chen, Guofu</au><au>Wang, Quanfu</au><au>Zhang, Chunyun</au><au>Zhang, Baoyu</au><au>Wang, Guangce</au><au>Lu, Douding</au><au>Xu, Zhong</au><au>Yan, Peishen</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Development of taxonomic rRNA-targeted probes of two harmful algae: Prorocentrum minimum and Kareniamikimotoi by fluorescence in situ hybridization</atitle><jtitle>Acta oceanologica Sinica</jtitle><stitle>Acta Oceanol. Sin</stitle><date>2013-02-01</date><risdate>2013</risdate><volume>32</volume><issue>2</issue><spage>66</spage><epage>75</epage><pages>66-75</pages><issn>0253-505X</issn><eissn>1869-1099</eissn><abstract>Harmful algal blooms recently have been under the spotlight throughout the world, because of their negative impact on the marine environment, aquaculture, fisheries as well as public health. The development of methods for rapid and precise identification and quantification of causative species is essential for the warning andmonitoring of blooms, among which the techniques based on taxonomic probes are themost favored. In this study, two harmful algae, i.e.,
Prorocentrum minimum
and
Karenia mikimotoi
were taken into consideration. The partial large subunit rDNA (D1-D2) of both species were firstly PCR-amplified, cloned and sequenced. The obtained sequences were then introduced to carry out alignment analysis for gene specific regions. Three respective candidate probes for each species were designed and used to screen the optimal probe by performing fluorescence in situ hybridization (FISH) tests. The results showed that the probes Pmin0443 and Kmik0602 displayed the best hybridization for
P. minimum
and
K. mikimotoi
, respectively. Both the specific (taxonomic) (Pmin0443 and Kmik0602) and the control probes (UniC0512 and UniR0499) were used for cross-reactivity tests with other microalgae in our laboratory. The probes Pmin0443 and Kmik0602 are specific and could be served as taxonomic probes introduced into the techniques targeting rRNA, such as FISH, sandwich hybridization, and DNA-microarray assay of
P. minimum
and
K. mikimotoi
in the future. Finally, FISH analyses with both probes were performed on the simulated field samples. The probes could hybridize exclusively with the target cells well, and no significant difference (
p
>0.05) was observed in the cell densities of the samples determined by FISH and light microscopy (LM). All suggest that the probes are specific and could be introduced into FISH for the monitoring of both harmful algae.</abstract><cop>Heidelberg</cop><pub>The Chinese Society of Oceanography</pub><doi>10.1007/s13131-013-0278-4</doi><tpages>10</tpages></addata></record> |
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source | Springer Nature - Complete Springer Journals; ProQuest Central UK/Ireland; Alma/SFX Local Collection; ProQuest Central |
subjects | Algae Algal blooms Aquaculture Climatology Cross-reactivity DNA DNA microarrays DNA probes Earth and Environmental Science Earth Sciences Ecology Engineering Fluid Dynamics Environmental Chemistry Eutrophication Fish Fisheries Fluorescence Fluorescence in situ hybridization Hybridization Karenia mikimotoi Light microscopy Marine Marine & Freshwater Sciences Marine environment Marine fish Microscopy Morphology Nucleotide sequence Oceanography Optical microscopy Phytoplankton Plankton Polyculture (aquaculture) Probes Prorocentrum minimum Public health rRNA Sensors Target cells Taxonomy Water quality |
title | Development of taxonomic rRNA-targeted probes of two harmful algae: Prorocentrum minimum and Kareniamikimotoi by fluorescence in situ hybridization |
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