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Senjie Lin - One of the best experts on this subject based on the ideXlab platform.
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Spliced leader RNA trans-splicing discovered in Copepods.
Scientific reports, 2015Co-Authors: Feifei Yang, Senjie Lin, Yunyun Zhuang, Yousong Huang, Hongju Chen, David A. Campbell, Nancy R. Sturm, Guangxing LiuAbstract:Copepods are one of the most abundant metazoans in the marine ecosystem, constituting a critical link in aquatic food webs and contributing significantly to the global carbon budget, yet molecular mechanisms of their gene expression are not well understood. Here we report the detection of spliced leader (SL) trans-splicing in calanoid Copepods. We have examined nine species of wild-caught Copepods from Jiaozhou Bay, China that represent the major families of the calanoids. All these species contained a common 46-nt SL (CopepodSL). We further determined the size of CopepodSL precursor RNA (slRNA; 108-158 nt) through genomic analysis and 3′-RACE technique, which was confirmed by RNA blot analysis. Structure modeling showed that the Copepod slRNA folded into typical slRNA secondary structures. Using a CopepodSL-based primer set, we selectively enriched and sequenced Copepod full-length cDNAs, which led to the characterization of Copepod transcripts and the cataloging of the complete set of 79 eukaryotic cytoplasmic ribosomal proteins (cRPs) for a single Copepod species. We uncovered the SL trans-splicing in Copepod natural populations, and demonstrated that CopepodSL was a sensitive and specific tool for Copepod transcriptomic studies at both the individual and population levels and that it would be useful for metatranscriptomic analysis of Copepods.
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Detecting In Situ Copepod Diet Diversity Using Molecular Technique: Development of a Copepod/Symbiotic Ciliate-Excluding Eukaryote-Inclusive PCR Protocol
PloS one, 2014Co-Authors: Zhiling Guo, Edward J. Carpenter, Sheng Liu, Senjie LinAbstract:Knowledge of in situ Copepod diet diversity is crucial for accurately describing pelagic food web structure but is challenging to achieve due to lack of an easily applicable methodology. To enable analysis with whole Copepod-derived DNAs, we developed a Copepod-excluding 18S rDNA-based PCR protocol. Although it is effective in depressing amplification of Copepod 18S rDNA, its applicability to detect diverse eukaryotes in both mono- and mixed-species has not been demonstrated. Besides, the protocol suffers from the problem that sequences from symbiotic ciliates are overrepresented in the retrieved 18S rDNA libraries. In this study, we designed a blocking primer to make a combined primer set (Copepod/symbiotic ciliate-excluding eukaryote-common: CEEC) to depress PCR amplification of symbiotic ciliate sequences while maximizing the range of eukaryotes amplified. We firstly examined the specificity and efficacy of CEEC by PCR-amplifying DNAs from 16 Copepod species, 37 representative organisms that are potential prey of Copepods and a natural microplankton sample, and then evaluated the efficiency in reconstructing diet composition by detecting the food of both lab-reared and field-collected Copepods. Our results showed that the CEEC primer set can successfully amplify 18S rDNA from a wide range of isolated species and mixed-species samples while depressing amplification of that from Copepod and targeted symbiotic ciliate, indicating the universality of CEEC in specifically detecting prey of Copepods. All the predetermined food offered to Copepods in the laboratory were successfully retrieved, suggesting that the CEEC-based protocol can accurately reconstruct the diets of Copepods without interference of Copepods and their associated ciliates present in the DNA samples. Our initial application to analyzing the food composition of field-collected Copepods uncovered diverse prey species, including those currently known, and those that are unsuspected, as Copepod prey. While testing is required, this protocol provides a useful strategy for depicting in situ dietary composition of Copepods.
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detecting in situ Copepod diet diversity using molecular technique development of a Copepod symbiotic ciliate excluding eukaryote inclusive pcr protocol
PLOS ONE, 2014Co-Authors: Zhiling Guo, Edward J. Carpenter, Sheng Liu, Senjie LinAbstract:Knowledge of in situ Copepod diet diversity is crucial for accurately describing pelagic food web structure but is challenging to achieve due to lack of an easily applicable methodology. To enable analysis with whole Copepod-derived DNAs, we developed a Copepod-excluding 18S rDNA-based PCR protocol. Although it is effective in depressing amplification of Copepod 18S rDNA, its applicability to detect diverse eukaryotes in both mono- and mixed-species has not been demonstrated. Besides, the protocol suffers from the problem that sequences from symbiotic ciliates are overrepresented in the retrieved 18S rDNA libraries. In this study, we designed a blocking primer to make a combined primer set (Copepod/symbiotic ciliate-excluding eukaryote-common: CEEC) to depress PCR amplification of symbiotic ciliate sequences while maximizing the range of eukaryotes amplified. We firstly examined the specificity and efficacy of CEEC by PCR-amplifying DNAs from 16 Copepod species, 37 representative organisms that are potential prey of Copepods and a natural microplankton sample, and then evaluated the efficiency in reconstructing diet composition by detecting the food of both lab-reared and field-collected Copepods. Our results showed that the CEEC primer set can successfully amplify 18S rDNA from a wide range of isolated species and mixed-species samples while depressing amplification of that from Copepod and targeted symbiotic ciliate, indicating the universality of CEEC in specifically detecting prey of Copepods. All the predetermined food offered to Copepods in the laboratory were successfully retrieved, suggesting that the CEEC-based protocol can accurately reconstruct the diets of Copepods without interference of Copepods and their associated ciliates present in the DNA samples. Our initial application to analyzing the food composition of field-collected Copepods uncovered diverse prey species, including those currently known, and those that are unsuspected, as Copepod prey. While testing is required, this protocol provides a useful strategy for depicting in situ dietary composition of Copepods.
Zhiling Guo - One of the best experts on this subject based on the ideXlab platform.
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Detecting In Situ Copepod Diet Diversity Using Molecular Technique: Development of a Copepod/Symbiotic Ciliate-Excluding Eukaryote-Inclusive PCR Protocol
PloS one, 2014Co-Authors: Zhiling Guo, Edward J. Carpenter, Sheng Liu, Senjie LinAbstract:Knowledge of in situ Copepod diet diversity is crucial for accurately describing pelagic food web structure but is challenging to achieve due to lack of an easily applicable methodology. To enable analysis with whole Copepod-derived DNAs, we developed a Copepod-excluding 18S rDNA-based PCR protocol. Although it is effective in depressing amplification of Copepod 18S rDNA, its applicability to detect diverse eukaryotes in both mono- and mixed-species has not been demonstrated. Besides, the protocol suffers from the problem that sequences from symbiotic ciliates are overrepresented in the retrieved 18S rDNA libraries. In this study, we designed a blocking primer to make a combined primer set (Copepod/symbiotic ciliate-excluding eukaryote-common: CEEC) to depress PCR amplification of symbiotic ciliate sequences while maximizing the range of eukaryotes amplified. We firstly examined the specificity and efficacy of CEEC by PCR-amplifying DNAs from 16 Copepod species, 37 representative organisms that are potential prey of Copepods and a natural microplankton sample, and then evaluated the efficiency in reconstructing diet composition by detecting the food of both lab-reared and field-collected Copepods. Our results showed that the CEEC primer set can successfully amplify 18S rDNA from a wide range of isolated species and mixed-species samples while depressing amplification of that from Copepod and targeted symbiotic ciliate, indicating the universality of CEEC in specifically detecting prey of Copepods. All the predetermined food offered to Copepods in the laboratory were successfully retrieved, suggesting that the CEEC-based protocol can accurately reconstruct the diets of Copepods without interference of Copepods and their associated ciliates present in the DNA samples. Our initial application to analyzing the food composition of field-collected Copepods uncovered diverse prey species, including those currently known, and those that are unsuspected, as Copepod prey. While testing is required, this protocol provides a useful strategy for depicting in situ dietary composition of Copepods.
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detecting in situ Copepod diet diversity using molecular technique development of a Copepod symbiotic ciliate excluding eukaryote inclusive pcr protocol
PLOS ONE, 2014Co-Authors: Zhiling Guo, Edward J. Carpenter, Sheng Liu, Senjie LinAbstract:Knowledge of in situ Copepod diet diversity is crucial for accurately describing pelagic food web structure but is challenging to achieve due to lack of an easily applicable methodology. To enable analysis with whole Copepod-derived DNAs, we developed a Copepod-excluding 18S rDNA-based PCR protocol. Although it is effective in depressing amplification of Copepod 18S rDNA, its applicability to detect diverse eukaryotes in both mono- and mixed-species has not been demonstrated. Besides, the protocol suffers from the problem that sequences from symbiotic ciliates are overrepresented in the retrieved 18S rDNA libraries. In this study, we designed a blocking primer to make a combined primer set (Copepod/symbiotic ciliate-excluding eukaryote-common: CEEC) to depress PCR amplification of symbiotic ciliate sequences while maximizing the range of eukaryotes amplified. We firstly examined the specificity and efficacy of CEEC by PCR-amplifying DNAs from 16 Copepod species, 37 representative organisms that are potential prey of Copepods and a natural microplankton sample, and then evaluated the efficiency in reconstructing diet composition by detecting the food of both lab-reared and field-collected Copepods. Our results showed that the CEEC primer set can successfully amplify 18S rDNA from a wide range of isolated species and mixed-species samples while depressing amplification of that from Copepod and targeted symbiotic ciliate, indicating the universality of CEEC in specifically detecting prey of Copepods. All the predetermined food offered to Copepods in the laboratory were successfully retrieved, suggesting that the CEEC-based protocol can accurately reconstruct the diets of Copepods without interference of Copepods and their associated ciliates present in the DNA samples. Our initial application to analyzing the food composition of field-collected Copepods uncovered diverse prey species, including those currently known, and those that are unsuspected, as Copepod prey. While testing is required, this protocol provides a useful strategy for depicting in situ dietary composition of Copepods.
Edward J. Carpenter - One of the best experts on this subject based on the ideXlab platform.
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Detecting In Situ Copepod Diet Diversity Using Molecular Technique: Development of a Copepod/Symbiotic Ciliate-Excluding Eukaryote-Inclusive PCR Protocol
PloS one, 2014Co-Authors: Zhiling Guo, Edward J. Carpenter, Sheng Liu, Senjie LinAbstract:Knowledge of in situ Copepod diet diversity is crucial for accurately describing pelagic food web structure but is challenging to achieve due to lack of an easily applicable methodology. To enable analysis with whole Copepod-derived DNAs, we developed a Copepod-excluding 18S rDNA-based PCR protocol. Although it is effective in depressing amplification of Copepod 18S rDNA, its applicability to detect diverse eukaryotes in both mono- and mixed-species has not been demonstrated. Besides, the protocol suffers from the problem that sequences from symbiotic ciliates are overrepresented in the retrieved 18S rDNA libraries. In this study, we designed a blocking primer to make a combined primer set (Copepod/symbiotic ciliate-excluding eukaryote-common: CEEC) to depress PCR amplification of symbiotic ciliate sequences while maximizing the range of eukaryotes amplified. We firstly examined the specificity and efficacy of CEEC by PCR-amplifying DNAs from 16 Copepod species, 37 representative organisms that are potential prey of Copepods and a natural microplankton sample, and then evaluated the efficiency in reconstructing diet composition by detecting the food of both lab-reared and field-collected Copepods. Our results showed that the CEEC primer set can successfully amplify 18S rDNA from a wide range of isolated species and mixed-species samples while depressing amplification of that from Copepod and targeted symbiotic ciliate, indicating the universality of CEEC in specifically detecting prey of Copepods. All the predetermined food offered to Copepods in the laboratory were successfully retrieved, suggesting that the CEEC-based protocol can accurately reconstruct the diets of Copepods without interference of Copepods and their associated ciliates present in the DNA samples. Our initial application to analyzing the food composition of field-collected Copepods uncovered diverse prey species, including those currently known, and those that are unsuspected, as Copepod prey. While testing is required, this protocol provides a useful strategy for depicting in situ dietary composition of Copepods.
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detecting in situ Copepod diet diversity using molecular technique development of a Copepod symbiotic ciliate excluding eukaryote inclusive pcr protocol
PLOS ONE, 2014Co-Authors: Zhiling Guo, Edward J. Carpenter, Sheng Liu, Senjie LinAbstract:Knowledge of in situ Copepod diet diversity is crucial for accurately describing pelagic food web structure but is challenging to achieve due to lack of an easily applicable methodology. To enable analysis with whole Copepod-derived DNAs, we developed a Copepod-excluding 18S rDNA-based PCR protocol. Although it is effective in depressing amplification of Copepod 18S rDNA, its applicability to detect diverse eukaryotes in both mono- and mixed-species has not been demonstrated. Besides, the protocol suffers from the problem that sequences from symbiotic ciliates are overrepresented in the retrieved 18S rDNA libraries. In this study, we designed a blocking primer to make a combined primer set (Copepod/symbiotic ciliate-excluding eukaryote-common: CEEC) to depress PCR amplification of symbiotic ciliate sequences while maximizing the range of eukaryotes amplified. We firstly examined the specificity and efficacy of CEEC by PCR-amplifying DNAs from 16 Copepod species, 37 representative organisms that are potential prey of Copepods and a natural microplankton sample, and then evaluated the efficiency in reconstructing diet composition by detecting the food of both lab-reared and field-collected Copepods. Our results showed that the CEEC primer set can successfully amplify 18S rDNA from a wide range of isolated species and mixed-species samples while depressing amplification of that from Copepod and targeted symbiotic ciliate, indicating the universality of CEEC in specifically detecting prey of Copepods. All the predetermined food offered to Copepods in the laboratory were successfully retrieved, suggesting that the CEEC-based protocol can accurately reconstruct the diets of Copepods without interference of Copepods and their associated ciliates present in the DNA samples. Our initial application to analyzing the food composition of field-collected Copepods uncovered diverse prey species, including those currently known, and those that are unsuspected, as Copepod prey. While testing is required, this protocol provides a useful strategy for depicting in situ dietary composition of Copepods.
Sheng Liu - One of the best experts on this subject based on the ideXlab platform.
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Detecting In Situ Copepod Diet Diversity Using Molecular Technique: Development of a Copepod/Symbiotic Ciliate-Excluding Eukaryote-Inclusive PCR Protocol
PloS one, 2014Co-Authors: Zhiling Guo, Edward J. Carpenter, Sheng Liu, Senjie LinAbstract:Knowledge of in situ Copepod diet diversity is crucial for accurately describing pelagic food web structure but is challenging to achieve due to lack of an easily applicable methodology. To enable analysis with whole Copepod-derived DNAs, we developed a Copepod-excluding 18S rDNA-based PCR protocol. Although it is effective in depressing amplification of Copepod 18S rDNA, its applicability to detect diverse eukaryotes in both mono- and mixed-species has not been demonstrated. Besides, the protocol suffers from the problem that sequences from symbiotic ciliates are overrepresented in the retrieved 18S rDNA libraries. In this study, we designed a blocking primer to make a combined primer set (Copepod/symbiotic ciliate-excluding eukaryote-common: CEEC) to depress PCR amplification of symbiotic ciliate sequences while maximizing the range of eukaryotes amplified. We firstly examined the specificity and efficacy of CEEC by PCR-amplifying DNAs from 16 Copepod species, 37 representative organisms that are potential prey of Copepods and a natural microplankton sample, and then evaluated the efficiency in reconstructing diet composition by detecting the food of both lab-reared and field-collected Copepods. Our results showed that the CEEC primer set can successfully amplify 18S rDNA from a wide range of isolated species and mixed-species samples while depressing amplification of that from Copepod and targeted symbiotic ciliate, indicating the universality of CEEC in specifically detecting prey of Copepods. All the predetermined food offered to Copepods in the laboratory were successfully retrieved, suggesting that the CEEC-based protocol can accurately reconstruct the diets of Copepods without interference of Copepods and their associated ciliates present in the DNA samples. Our initial application to analyzing the food composition of field-collected Copepods uncovered diverse prey species, including those currently known, and those that are unsuspected, as Copepod prey. While testing is required, this protocol provides a useful strategy for depicting in situ dietary composition of Copepods.
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detecting in situ Copepod diet diversity using molecular technique development of a Copepod symbiotic ciliate excluding eukaryote inclusive pcr protocol
PLOS ONE, 2014Co-Authors: Zhiling Guo, Edward J. Carpenter, Sheng Liu, Senjie LinAbstract:Knowledge of in situ Copepod diet diversity is crucial for accurately describing pelagic food web structure but is challenging to achieve due to lack of an easily applicable methodology. To enable analysis with whole Copepod-derived DNAs, we developed a Copepod-excluding 18S rDNA-based PCR protocol. Although it is effective in depressing amplification of Copepod 18S rDNA, its applicability to detect diverse eukaryotes in both mono- and mixed-species has not been demonstrated. Besides, the protocol suffers from the problem that sequences from symbiotic ciliates are overrepresented in the retrieved 18S rDNA libraries. In this study, we designed a blocking primer to make a combined primer set (Copepod/symbiotic ciliate-excluding eukaryote-common: CEEC) to depress PCR amplification of symbiotic ciliate sequences while maximizing the range of eukaryotes amplified. We firstly examined the specificity and efficacy of CEEC by PCR-amplifying DNAs from 16 Copepod species, 37 representative organisms that are potential prey of Copepods and a natural microplankton sample, and then evaluated the efficiency in reconstructing diet composition by detecting the food of both lab-reared and field-collected Copepods. Our results showed that the CEEC primer set can successfully amplify 18S rDNA from a wide range of isolated species and mixed-species samples while depressing amplification of that from Copepod and targeted symbiotic ciliate, indicating the universality of CEEC in specifically detecting prey of Copepods. All the predetermined food offered to Copepods in the laboratory were successfully retrieved, suggesting that the CEEC-based protocol can accurately reconstruct the diets of Copepods without interference of Copepods and their associated ciliates present in the DNA samples. Our initial application to analyzing the food composition of field-collected Copepods uncovered diverse prey species, including those currently known, and those that are unsuspected, as Copepod prey. While testing is required, this protocol provides a useful strategy for depicting in situ dietary composition of Copepods.
Youichi Tsukamoto - One of the best experts on this subject based on the ideXlab platform.
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Simulation of Copepod biomass by a prey–predator model in Hiuchi-nada, central part of the Seto Inland Sea: does Copepod biomass affect the recruitment to the shirasu (Japanese larval anchovy Engraulis japonicus) fishery?
Fisheries Science, 2011Co-Authors: Hiromu Zenitani, Naoaki Kono, Youichi TsukamotoAbstract:We have modeled the prey–predator dynamics between nutrients, phytoplankton, and Copepods in Hiuchi-nada, central part of the Seto Inland Sea. The model parameters were estimated by stepwise regression using data sampled from 2001 to 2005. We re-created the fluctuations in Copepod biomass in the spring–summer of 2001–2004 by model simulation and investigated the relationship between the re-created Copepod biomass and anchovy Engraulis japonicus reproductive success rate in Hiuchi-nada. The anchovy reproductive success rate was proportional to the Copepod biomass during the last 10 days of May, a period that immediately preceded anchovy recruitment. This relationship indicates that a possible key factor in the regulation of anchovy population levels is the fluctuation in abundance of the Copepod assemblage and that the crucial period for anchovy recruitment in Hiuchi-nada would be the period just before anchovy recruitment to the shirasu (body length: approx. 20–35 mm) fishery. These results provide a potential framework for forecasting the anchovy recruitment level that is based on both larval abundance and survival rate as estimated from the biomass of Copepods in the pre-recruitment period of anchovy.
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simulation of Copepod biomass by a prey predator model in hiuchi nada central part of the seto inland sea does Copepod biomass affect the recruitment to the shirasu japanese larval anchovy engraulis japonicus fishery
Fisheries Science, 2011Co-Authors: Hiromu Zenitani, Naoaki Kono, Youichi TsukamotoAbstract:We have modeled the prey–predator dynamics between nutrients, phytoplankton, and Copepods in Hiuchi-nada, central part of the Seto Inland Sea. The model parameters were estimated by stepwise regression using data sampled from 2001 to 2005. We re-created the fluctuations in Copepod biomass in the spring–summer of 2001–2004 by model simulation and investigated the relationship between the re-created Copepod biomass and anchovy Engraulis japonicus reproductive success rate in Hiuchi-nada. The anchovy reproductive success rate was proportional to the Copepod biomass during the last 10 days of May, a period that immediately preceded anchovy recruitment. This relationship indicates that a possible key factor in the regulation of anchovy population levels is the fluctuation in abundance of the Copepod assemblage and that the crucial period for anchovy recruitment in Hiuchi-nada would be the period just before anchovy recruitment to the shirasu (body length: approx. 20–35 mm) fishery. These results provide a potential framework for forecasting the anchovy recruitment level that is based on both larval abundance and survival rate as estimated from the biomass of Copepods in the pre-recruitment period of anchovy.
