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Ronald S Burton - One of the best experts on this subject based on the ideXlab platform.
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efficacy of metabarcoding for identification of Fish Eggs evaluated with mock communities
Ecology and Evolution, 2020Co-Authors: Elena Maria Duke, Ronald S BurtonAbstract:There is urgent need for effective and efficient monitoring of marine Fish populations. Monitoring Eggs and larval Fish may be more informative than that traditional Fish surveys since ichthyoplankton surveys reveal the reproductive activities of Fish populations, which directly impact their population trajectories. Ichthyoplankton surveys have turned to molecular methods (DNA barcoding & metabarcoding) for identification of Eggs and larval Fish due to challenges of morphological identification. In this study, we examine the effectiveness of using metabarcoding methods on mock communities of known Fish egg DNA. We constructed six mock communities with known ratios of species. In addition, we analyzed two samples from a large field collection of Fish Eggs and compared metabarcoding results with traditional DNA barcoding results. We examine the ability of our metabarcoding methods to detect species and relative proportion of species identified in each mock community. We found that our metabarcoding methods were able to detect species at very low input proportions; however, levels of successful detection depended on the markers used in amplification, suggesting that the use of multiple markers is desirable. Variability in our quantitative results may result from amplification bias as well as interspecific variation in mitochondrial DNA copy number. Our results demonstrate that there remain significant challenges to using metabarcoding for estimating proportional species composition; however, the results provide important insights into understanding how to interpret metabarcoding data. This study will aid in the continuing development of efficient molecular methods of biological monitoring for Fisheries management.
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Large interannual variation in spawning in San Diego marine protected areas captured by molecular identification of Fish Eggs
Marine Ecology Progress Series, 2018Co-Authors: Elena Maria Duke, Alice E. Harada, Ronald S BurtonAbstract:Author(s): Duke, Elena | Advisor(s): Burton, Ron S | Abstract: Marine protected areas have become an important management tool that can provide data regarding human impacts on the ocean while protecting exploited species, enhancing biodiversity and protecting ecosystems. Long-term monitoring of reserves is critical to assess how global processes such as natural environmental variation and climate change affect marine populations. We conducted Fish egg surveys in both soft bottom habitat and kelp forest and identify Fish Eggs using DNA barcoding. We compared these data to baseline spawning data established by Harada et al 2015. We documented large inter-annual variability in Fish egg abundance associated with climatic fluctuations, including an El Nino event captured during our sampling years. Interestingly, we observed a phenological shift of peak spawning activity during 2017. We found inter-annual Fish egg abundance may be linked with upwelling regimes and winter temperatures. We found no distinct differences in community composition between habitats we sampled. Through long-term monitoring of Fish spawning we can understand how natural environmental variation such as El Nino events affect Fish populations which will help us predict how temperature increases associated with climate change will affect marine Fish populations. Furthermore, long-term monitoring can help track trends in marine resource availability and evaluate marine reserve efficacy.
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monitoring spawning activity in a southern california marine protected area using molecular identification of Fish Eggs
PLOS ONE, 2015Co-Authors: Alice E. Harada, Elise A Lindgren, Maiko C Hermsmeier, Peter Rogowski, Eric Terrill, Ronald S BurtonAbstract:In order to protect the diverse ecosystems of coastal California, a series of marine protected areas (MPAs) have been established. The ability of these MPAs to preserve and potentially enhance marine resources can only be assessed if these habitats are monitored through time. This study establishes a baseline for monitoring the spawning activity of Fish in the MPAs adjacent to Scripps Institution of Oceanography (La Jolla, CA, USA) by sampling Fish Eggs from the plankton. Using vertical plankton net tows, 266 collections were made from the Scripps Pier between 23 August 2012 and 28 August 2014; a total of 21,269 Eggs were obtained. Eggs were identified using DNA barcoding: the COI or 16S rRNA gene was amplified from individual Eggs and sequenced. All Eggs that were successfully sequenced could be identified from a database of molecular barcodes of California Fish species, resulting in species-level identification of 13,249 Eggs. Additionally, a surface transport model of coastal circulation driven by current maps from high frequency radar was used to construct probability maps that estimate spawning locations that gave rise to the collected Eggs. These maps indicated that currents usually come from the north but water parcels tend to be retained within the MPA; Eggs sampled at the Scripps Pier have a high probability of having been spawned within the MPA. The surface transport model also suggests that although larvae have a high probability of being retained within the MPA, there is also significant spillover into nearby areas outside the MPA. This study provides an important baseline for addressing the extent to which spawning patterns of coastal California species may be affected by future changes in the ocean environment.
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high throughput molecular identification of Fish Eggs using multiplex suspension bead arrays
Molecular Ecology Resources, 2012Co-Authors: Lani U Gleason, Ronald S BurtonAbstract:The location and abundance of Fish Eggs provide information concerning the timing and location of spawning activities and can provide Fishery-independent estimates of spawning biomass. However, the full value of egg and larval surveys is severely restricted because many species’ Eggs and larvae are morphologically similar, making species-level identification difficult. Recent efforts have shown that nearly all species of Fish may be identified by mitochondrial DNA (mtDNA) sequences (e.g. via ‘DNA barcoding’). By taking advantage of a DNA barcode database, we have developed oligonucleotide probes for 23 marine Fish species that produce pelagic Eggs commonly found in California waters. Probes were coupled to fluorescent microspheres to create a suspension bead array. Biotin-labelled primers were used to amplify the mitochondrial cytochrome oxidase subunit I (COI) and 16S ribosomal rRNA genes from individual Fish Eggs. The amplicons were then hybridized to the bead array, and after the addition of a reporter fluorophore, samples were analysed by flow cytometry with Luminex 100 instrumentation. Probes specifically targeted Eggs that are abundant and ⁄or from morphologically indistinguishable species pairs. Results showed that the 33 different probes designed for this study accurately identified all samples when PCR was successful. Suspension bead arrays have a number of benefits over other methods of molecular identification; these arrays permit high multiplexing, simple addition of new probes, high throughput and lower cost than DNA sequencing. The increasing availability of DNA barcode data for numerous Fish faunas worldwide suggests that bead arrays could be developed and widely used for Fish egg, larval and tissue identifications.
Robert J Letcher - One of the best experts on this subject based on the ideXlab platform.
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Determination of carotenoids and all-trans-retinol in Fish Eggs by liquid chromatography-electrospray ionization-tandem mass spectrometry.
Journal of chromatography. B Analytical technologies in the biomedical and life sciences, 2005Co-Authors: Hongxia Li, Sélène T Tyndale, Daniel D Heath, Robert J LetcherAbstract:A novel method was developed for the combined determination of carotenoids and retinoids in Fish Eggs, which incorporates prior analyte isolation using liquid-liquid partitioning to minimize analyte degradation, and fraction analysis using high-performance liquid chromatography-electrospray (positive)-quadrupole mass spectrometry (LC-ESI(+)-MS; SIM or MRM modes). Eggs from Chinook salmon (Oncorhynchus tshawytscha) were used as the model Fish egg matrix. The methodology was assessed and validated for beta-carotene, lutein, zeaxanthin, and beta-cryptoxanthin (molecular ion radicals [M](+)), canthaxanthin and astaxanthin ([M+Na](+) adducts) and all-trans-retinol ([(M+H)-H(2)O](+)). Using replicate egg samples (n=5) spiked with beta-cryptoxanthin and beta-carotene before and after extraction, matrix-sourced ESI(+) enhancement was observed as evidenced by comparable %matrix effect and %process efficiency values for beta-cryptoxanthin and beta-carotene of 114-119%. In aquaculture-raised Eggs from adult Chinook salmon astaxanthin, all-trans-retinol, lutein and canthaxanthin were identified and determined at concentrations of 4.12, 1.06, 0.12 and 0.45 microg/g (egg wet weight), respectively. To our knowledge, this is the first report on a method for LC-MS determination of carotenoids and retinoids in a Fish egg matrix, and the first carotenoid-specific determination in any Fish egg sample.
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Determination of carotenoids and all-trans-retinol in Fish Eggs by liquid chromatography-electrospray ionization-tandem mass spectrometry.
Journal of Chromatography B, 2005Co-Authors: Hongxia Li, Sélène T Tyndale, Daniel D Heath, Robert J LetcherAbstract:Abstract A novel method was developed for the combined determination of carotenoids and retinoids in Fish Eggs, which incorporates prior analyte isolation using liquid-liquid partitioning to minimize analyte degradation, and fraction analysis using high-performance liquid chromatography–electrospray (positive)–quadrupole mass spectrometry (LC–ESI(+)–MS; SIM or MRM modes). Eggs from Chinook salmon (Oncorhynchus tshawytscha) were used as the model Fish egg matrix. The methodology was assessed and validated for β-carotene, lutein, zeaxanthin, and β-cryptoxanthin (molecular ion radicals [M] +), canthaxanthin and astaxanthin ([M + Na]+ adducts) and all-trans-retinol ([(M + H)–H2O]+). Using replicate egg samples (n = 5) spiked with β-cryptoxanthin and β-carotene before and after extraction, matrix-sourced ESI(+) enhancement was observed as evidenced by comparable %matrix effect and %process efficiency values for β-cryptoxanthin and β-carotene of 114–119%. In aquaculture-raised Eggs from adult Chinook salmon astaxanthin, all-trans-retinol, lutein and canthaxanthin were identified and determined at concentrations of 4.12, 1.06, 0.12 and 0.45 μg/g (egg wet weight), respectively. To our knowledge, this is the first report on a method for LC–MS determination of carotenoids and retinoids in a Fish egg matrix, and the first carotenoid-specific determination in any Fish egg sample.
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Determination of carotenoids and all-trans-retinol in Fish Eggs by liquid chromatography-electrospray ionization-tandem mass spectrometry.
Journal of chromatography. B Analytical technologies in the biomedical and life sciences, 2005Co-Authors: Sélène T Tyndale, Daniel D Heath, Robert J LetcherAbstract:A novel method was developed for the combined determination of carotenoids and retinoids in Fish Eggs, which incorporates prior analyte isolation using liquid-liquid partitioning to minimize analyte degradation, and fraction analysis using high-performance liquid chromatography-electrospray (positive)-quadrupole mass spectrometry (LC-ESI(+)-MS; SIM or MRM modes). Eggs from Chinook salmon (Oncorhynchus tshawytscha) were used as the model Fish egg matrix. The methodology was assessed and validated for beta-carotene, lutein, zeaxanthin, and beta-cryptoxanthin (molecular ion radicals [M](+)), canthaxanthin and astaxanthin ([M+Na](+) adducts) and all-trans-retinol ([(M+H)-H(2)O](+)). Using replicate egg samples (n=5) spiked with beta-cryptoxanthin and beta-carotene before and after extraction, matrix-sourced ESI(+) enhancement was observed as evidenced by comparable %matrix effect and %process efficiency values for beta-cryptoxanthin and beta-carotene of 114-119%. In aquaculture-raised Eggs from adult Chinook salmon astaxanthin, all-trans-retinol, lutein and canthaxanthin were identified and determined at concentrations of 4.12, 1.06, 0.12 and 0.45 microg/g (egg wet weight), respectively. To our knowledge, this is the first report on a method for LC-MS determination of carotenoids and retinoids in a Fish egg matrix, and the first carotenoid-specific determination in any Fish egg sample.
Xinbin Duan - One of the best experts on this subject based on the ideXlab platform.
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Species diversity of drifting Fish Eggs in the Yangtze River using molecular identification.
PeerJ, 2018Co-Authors: Liu Mingdian, Dengqiang Wang, Gao Lei, Tian Huiwu, Shaoping Liu, Daqing Chen, Xinbin DuanAbstract:The dam constructions greatly changed the hydrologic conditions in the Yangtze River, and then significantly affected the spawning activities of indigenous river Fish. Monitoring the species composition of drifting Eggs during spawning season is important for protection issues. In this study, we have sampled drifting Fish Eggs in nine locations from 2014 to 2016. Eggs were identified using the mitochondrial cyt b gene sequence. A total of 7,933 Fish Eggs were sequenced successfully and blasted into the NCBI database. Thirty-nine Fish species were identified, and were assigned to four families and two orders. Approximately 64% of the species identified, and 67% of the Eggs, were classified in the Family Cyprinidae. Abundance and Shannon-Wiener diversity index of species were higher in the main river than in tributaries of the river. However, tributaries may be important spawning grounds for some Fish species. The Jaccard's similarity index and river-way distances among sampled stations were negatively correlated suggesting the environment shapes species composition in the sampled spawning grounds. These results showed that mitochondrial DNA sequence is a powerful and effective tool for Fish egg identification in Yangtze River and these data are useful for conservation efforts.
Sélène T Tyndale - One of the best experts on this subject based on the ideXlab platform.
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Determination of carotenoids and all-trans-retinol in Fish Eggs by liquid chromatography-electrospray ionization-tandem mass spectrometry.
Journal of chromatography. B Analytical technologies in the biomedical and life sciences, 2005Co-Authors: Hongxia Li, Sélène T Tyndale, Daniel D Heath, Robert J LetcherAbstract:A novel method was developed for the combined determination of carotenoids and retinoids in Fish Eggs, which incorporates prior analyte isolation using liquid-liquid partitioning to minimize analyte degradation, and fraction analysis using high-performance liquid chromatography-electrospray (positive)-quadrupole mass spectrometry (LC-ESI(+)-MS; SIM or MRM modes). Eggs from Chinook salmon (Oncorhynchus tshawytscha) were used as the model Fish egg matrix. The methodology was assessed and validated for beta-carotene, lutein, zeaxanthin, and beta-cryptoxanthin (molecular ion radicals [M](+)), canthaxanthin and astaxanthin ([M+Na](+) adducts) and all-trans-retinol ([(M+H)-H(2)O](+)). Using replicate egg samples (n=5) spiked with beta-cryptoxanthin and beta-carotene before and after extraction, matrix-sourced ESI(+) enhancement was observed as evidenced by comparable %matrix effect and %process efficiency values for beta-cryptoxanthin and beta-carotene of 114-119%. In aquaculture-raised Eggs from adult Chinook salmon astaxanthin, all-trans-retinol, lutein and canthaxanthin were identified and determined at concentrations of 4.12, 1.06, 0.12 and 0.45 microg/g (egg wet weight), respectively. To our knowledge, this is the first report on a method for LC-MS determination of carotenoids and retinoids in a Fish egg matrix, and the first carotenoid-specific determination in any Fish egg sample.
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Determination of carotenoids and all-trans-retinol in Fish Eggs by liquid chromatography-electrospray ionization-tandem mass spectrometry.
Journal of Chromatography B, 2005Co-Authors: Hongxia Li, Sélène T Tyndale, Daniel D Heath, Robert J LetcherAbstract:Abstract A novel method was developed for the combined determination of carotenoids and retinoids in Fish Eggs, which incorporates prior analyte isolation using liquid-liquid partitioning to minimize analyte degradation, and fraction analysis using high-performance liquid chromatography–electrospray (positive)–quadrupole mass spectrometry (LC–ESI(+)–MS; SIM or MRM modes). Eggs from Chinook salmon (Oncorhynchus tshawytscha) were used as the model Fish egg matrix. The methodology was assessed and validated for β-carotene, lutein, zeaxanthin, and β-cryptoxanthin (molecular ion radicals [M] +), canthaxanthin and astaxanthin ([M + Na]+ adducts) and all-trans-retinol ([(M + H)–H2O]+). Using replicate egg samples (n = 5) spiked with β-cryptoxanthin and β-carotene before and after extraction, matrix-sourced ESI(+) enhancement was observed as evidenced by comparable %matrix effect and %process efficiency values for β-cryptoxanthin and β-carotene of 114–119%. In aquaculture-raised Eggs from adult Chinook salmon astaxanthin, all-trans-retinol, lutein and canthaxanthin were identified and determined at concentrations of 4.12, 1.06, 0.12 and 0.45 μg/g (egg wet weight), respectively. To our knowledge, this is the first report on a method for LC–MS determination of carotenoids and retinoids in a Fish egg matrix, and the first carotenoid-specific determination in any Fish egg sample.
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Determination of carotenoids and all-trans-retinol in Fish Eggs by liquid chromatography-electrospray ionization-tandem mass spectrometry.
Journal of chromatography. B Analytical technologies in the biomedical and life sciences, 2005Co-Authors: Sélène T Tyndale, Daniel D Heath, Robert J LetcherAbstract:A novel method was developed for the combined determination of carotenoids and retinoids in Fish Eggs, which incorporates prior analyte isolation using liquid-liquid partitioning to minimize analyte degradation, and fraction analysis using high-performance liquid chromatography-electrospray (positive)-quadrupole mass spectrometry (LC-ESI(+)-MS; SIM or MRM modes). Eggs from Chinook salmon (Oncorhynchus tshawytscha) were used as the model Fish egg matrix. The methodology was assessed and validated for beta-carotene, lutein, zeaxanthin, and beta-cryptoxanthin (molecular ion radicals [M](+)), canthaxanthin and astaxanthin ([M+Na](+) adducts) and all-trans-retinol ([(M+H)-H(2)O](+)). Using replicate egg samples (n=5) spiked with beta-cryptoxanthin and beta-carotene before and after extraction, matrix-sourced ESI(+) enhancement was observed as evidenced by comparable %matrix effect and %process efficiency values for beta-cryptoxanthin and beta-carotene of 114-119%. In aquaculture-raised Eggs from adult Chinook salmon astaxanthin, all-trans-retinol, lutein and canthaxanthin were identified and determined at concentrations of 4.12, 1.06, 0.12 and 0.45 microg/g (egg wet weight), respectively. To our knowledge, this is the first report on a method for LC-MS determination of carotenoids and retinoids in a Fish egg matrix, and the first carotenoid-specific determination in any Fish egg sample.
Liu Mingdian - One of the best experts on this subject based on the ideXlab platform.
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Species diversity of drifting Fish Eggs in the Yangtze River using molecular identification.
PeerJ, 2018Co-Authors: Liu Mingdian, Dengqiang Wang, Gao Lei, Tian Huiwu, Shaoping Liu, Daqing Chen, Xinbin DuanAbstract:The dam constructions greatly changed the hydrologic conditions in the Yangtze River, and then significantly affected the spawning activities of indigenous river Fish. Monitoring the species composition of drifting Eggs during spawning season is important for protection issues. In this study, we have sampled drifting Fish Eggs in nine locations from 2014 to 2016. Eggs were identified using the mitochondrial cyt b gene sequence. A total of 7,933 Fish Eggs were sequenced successfully and blasted into the NCBI database. Thirty-nine Fish species were identified, and were assigned to four families and two orders. Approximately 64% of the species identified, and 67% of the Eggs, were classified in the Family Cyprinidae. Abundance and Shannon-Wiener diversity index of species were higher in the main river than in tributaries of the river. However, tributaries may be important spawning grounds for some Fish species. The Jaccard's similarity index and river-way distances among sampled stations were negatively correlated suggesting the environment shapes species composition in the sampled spawning grounds. These results showed that mitochondrial DNA sequence is a powerful and effective tool for Fish egg identification in Yangtze River and these data are useful for conservation efforts.