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218 results for “Aquaculture”
Fig. 5 in Negative effects of Kudoa islandica n. sp. (Myxosporea: Kudoidae) on aquaculture and wild fisheries in Iceland
Fig. 5. (A) and (B) Muscle section from lumpfish, Cyclopterus lumpus, fixed 24 h post mortem. (A) Ruptured Kudoa plasmodia with subsequent liberation of mature spores causing focal necrosis of the muscle fibre enveloping the plasmodium. (B) Higher magnification showing liberated spores (arrows) and a focal necrosis in the vicinity of the spores (asterisk). (C) Muscle section of an uninfected fish at approx. 48 h p.m. (D) Section of muscle of a heavily infected fish at approximately 48 h p.m. showing extensive myoliquefaction (asterisk). (E) A close up of the affected area showing numerous Kudoa spores (arrowhead) and the associated liquefactive necrosis. Scale bars: (A) = 50 µm, (B) = 10 µm, (C) and (D) = 200 µm, (E) = 10 µm. Abbreviations: MF = Muscle fibres, AC = Adipocytes.
Fig. 2 in Negative effects of Kudoa islandica n. sp. (Myxosporea: Kudoidae) on aquaculture and wild fisheries in Iceland
Fig. 2. (A) Stained histological section of a lumpfish muscle showing a considerable portion of the muscle fibres substituted with Kudoa islandica n. sp. plasmodia. (B) A single infection. (C) A double infection. (D) Multiple infection; numerous plasmodia developing inside a single muscle fibre, separated from each other and the muscle tissue with a thin membrane (arrows). (E) Plasmodial membranes separating two plasmodia (arrows). Inside each plasmodium are numerous mature Kudoa spores. Scale bars: (A) = 300 µm (B) and (C) = 25 µm; (D) = 150 µm; (E) = 5 µm.
The First Highly Contiguous Genome Assembly of Pikeperch (Sander lucioperca), an Emerging Aquaculture Species in Europe
<p><strong>Supporting data for "The First Highly Contiguous Genome Assembly of Pikeperch (<em>Sander lucioperca</em>), an Emerging Aquaculture Species in Europe"</strong></p> <p>===========================================================================================</p> <p><strong>Abstract:</strong></p> <p>--------</p> <p>The pikeperch (<em>Sander lucioperca</em>) is a fresh and brackish water Percid fish natively inhabiting the northern hemisphere. This species is emerging as a promising candidate for intensive aquaculture production in Europe. Specific traits like cannibalism, growth rate and meat quality require genomics based understanding, for an optimal husbandry and domestication process. Still, the aquaculture community is lacking an annotated genome sequence to facilitate genome-wide studies on pikeperch. Here, we report the first highly contiguous draft genome assembly <em>S. lucioperca</em>. In total, 413 and 66 giga base pairs of DNA sequencing raw data were generated with Illumina platform and PacBio Sequel System, respectively. The PacBio data were assembled into a final assembly size of ~900 Mb covering 89% of the 1,014 Mb estimated genome size. The draft genome consisted of 1,966 contigs ordered into 1,313 scaffolds. The contig and scaffold N50 lengths are 3.0 Mb and 4.9 Mb, respectively. The identified repetitive structures accounted for 39% of the genome. We utilized homologies to other ray-finned fishes, and ab initio gene prediction methods to predict 21,249 protein-coding genes in the <em>S. lucioperca </em>genome, of which 88% were functionally annotated by either sequence homology or protein domains and signatures search. The assembled genome spans 97.6% and 96.3% of Vertebrate respectively Actinopterygii single-copy orthologs. The outstanding mapping rate (99.9%) of genomic PE-reads on the assembly suggests an accurate and nearly complete genome reconstruction. This draft genome sequence is the first genomic resource for this promising aquaculture species. It will provide an impetus for genomic-based breeding studies targeting phenotypic and performance traits of captive pikeperch.</p> <p> </p> <p><strong>Files:</strong></p> <p>------</p> <p><a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/sanlu.cds.renamed.fa">sanlu.cds.renamed.fa </a> - Coding sequences of predicted protein-coding genes </p> <p><a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/sanlu.genes.filt.gff3">sanlu.genes.filt.gff3 </a> - gff3 file of predicted protein coding genes</p> <p><a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/sanlu.genes.pep.fa">sanlu.genes.pep.fa </a> - predicted peptide sequences </p> <p><a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/sanlu.genome.ctg.fasta">sanlu.genome.ctg.fasta </a> - <em>Sander lucioperca</em> genome assembly at contig-level</p> <p><a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/sanlu.genome.scf.fa">sanlu.genome.scf.fa </a> - <em>Sander lucioperca</em> genome assembly at scaffold-level</p> <p><a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/Sanlu.genome.masked.fasta">Sanlu.genome.masked.fasta </a>- Repeats-masked <em>Sander lucioperca</em> genome assembly at scaffold-level</p> <p><a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/Sanlu.genome.repeats.gff">Sanlu.genome.repeats.gff </a> - Gff3 file of predicted repeats in <em>Sander lucioperca</em> genome</p> <p><a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/Additional_File_2.xlsx">Additional_File_2.xlsx </a> - Functional annotations of <em>Sander lucioperca </em>genes by SwissProt, NR RefSeq, TrEMBL and InterPro databases</p> <p><a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/sanlu.repeats.lib.fasta">sanlu.repeats.lib.fasta </a> - Predicted repeats library in <em>Sander lucioperca </em>in FASTA format</p> <p><a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/sanlu_miRNA.csv">sanlu_miRNA.csv </a> Predicted micro RNA families in CSV tab file </p> <p><a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/sanlu_miRNA.bed">sanlu_miRNA.bed </a> - Predicted micro RNA families in BED file format</p> <p><a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/sanlu_miRNA.html">sanlu_miRNA.html </a><a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/sanlu_miRNA.bed"> </a> - Predicted micro RNA families in HTML</p> <p><a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/sanlu_rRNA.fasta">sanlu_rRNA.fasta </a> - Predicted ribosomal RNA (rRNA) sequences in FASTA file format</p> <p><a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/sanlu_rRNA.gff">sanlu_rRNA.gff </a> - Predicted ribosomal RNA (rRNA) sequences in GFF file format</p> <p><a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/trna.genes.csv">trna.genes.csv </a> - Predicted transfer RNA (tRNA) genes in CSV tab file</p> <p><a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/SpeciesTree_rooted_node_labels.txt">SpeciesTree_rooted_node_labels.txt </a> - Predicted phylogenetic tree in NEWICK format</p> <p><a href="https://zenodo.org/api/files/808d4d80-6012-4046-bc3c-73b9792b5d8c/SpeciesTreeAlignment.fa">SpeciesTreeAlignment.fa </a> - Species tree alignment in FASTA, based on 1.1 single copy orthologs</p> <p> </p>
Figure 1 in Androgenic hormones in crustacean aquaculture: a review
Figure 1. Male crayfish showing location of male reproductive tract accessible via the base of the fifth walking leg. ag = androgenic gland, g = gonopore, t = testes, and vd = vas deferens (adapted from Mead, 2008).
Fig. 5 in Freshwater parameters in the state of Rio Grande do Sul, southern Brazil, and their influence on fish distribution and aquaculture
Fig. 5. Mean waterborne (A) iron and (B) manganese in various cities of Rio Grande do Sul in the period of 1996 to 2011 (Source CORSAN/RS).
Fig. 3 in Freshwater parameters in the state of Rio Grande do Sul, southern Brazil, and their influence on fish distribution and aquaculture
Fig. 3. Water alkalinity in different cities of Rio Grande do Sul in the period of 1996 to 2011 (A) mean, (B) minimum and (C) maximum values (Source CORSAN/RS).
Fig. 1 in Freshwater parameters in the state of Rio Grande do Sul, southern Brazil, and their influence on fish distribution and aquaculture
Fig. 1. Water pH in different cities of Rio Grande do Sul in the period of 1996 to 2011 (A) mean, (B) minimum and (C) maximum values (Source CORSAN/RS).
Colony forming unit (CFU) data accompanying publication: Bacterial microbiome dynamics in commercial integrated aquaculture systems growing Ulva in abalone effluent water.
<p>Excel sheet with colony forming unit (CFU) data from an abalone farm growing the green seaweed <em>Ulva </em>in abalone effluent water. This dataset characterises the bacterial communities isolated from abalone effluent water entering and leaving the <em>Ulva </em>raceways, as well as from <em>Ulva </em>itself. Dataset is accompanied by two SigmaPlot files showing statistical analyses (statistical outcomes also available in publication).</p>
Consumer Survey Data, Low Trophic Aquaculture
<p>The data is collected based on the designed questionnaire and by a survey company. These consumer preferences in relation to these attributes will be examined through surveys with representative samples from four different countries representing the four zones of the Atlantic Ocean: 1) Brazil, 2) South Africa, 3) Europe (Germany or France), and 4) USA/Canada. The data will be used to analyse consumer awareness and acceptance of low trophic species and sustainable production methods.</p>
Data set to 'Microplastics in aquaculture - potential impacts on inflammatory processes in Nile tilapia'
<p>Raw and analyzed data sets to the publication 'Microplastics in aquaculture - potential impacts on inflammatory processes in Nile tilapia'</p>
Data for: Mediterranean Sea heatwaves jeopardize greater amberjack's (Seriola dumerili) aquaculture productivity through impacts on the fish microbiota.
<p>The data in this repository with the DOI 10.5281/zenodo.8414745 is licensed under a Creative Commons Attribution 4.0 International License.<br> For more information, see https://creativecommons.org/licenses/by/4.0.</p> <p>Physicochemical, microbiome and growth data for:</p> <p>Paper title: Mediterranean Sea heatwaves jeopardize greater amberjack’s (Seriola dumerili) aquaculture productivity through impacts on the fish microbiota<br> Paper DOI: 10.3389/fmars.2023.1168953 </p> <p>Code repository DOI for reproducing the Figures: https://doi.org/10.1038/s43705-023-00243-7</p> <p>Corresponding Author</p> <p>Name: Pablo Sanchez<br> LEITAT Technological Center, 08225, Terrassa, Spain<br> Address: Carrer Innovació, 2, 08225 Terrassa, Barcelona, Spain<br> Email: psanchez@leitat.org<br> </p> <p> </p>
Quantification of the value of selected Nature's Contributions to People provided by Low Trophic Species aquaculture
<p>This dataset was generated by the work on quantification of Nature’s Contributions to People (NCPs) provided by Low Trophic Species (LTS) aquaculture. The quantification and analysis of selected NCPs was performed based on selected indicators using data from the case studies within the AquaVitae project and literature reviews.</p>
Mapping Nature's Contributions to People provided by Low Trophic Species aquaculture and knowledge gaps
<p>This dataset was generated by the work on quantification of Nature’s Contributions to People (NCPs) provided by Low Trophic Species (LTS) aquaculture. As a first step of this work, the identification of the NCPs provided by LTS aquaculture (based on the case studies investigated within AquaVitae) and the identification of current knowledge gaps in terms of qualitative contributions of LTS aquaculture to the NCPs was performed based on expert judgements and literature review.</p> <p>The ecosystem services framework from IPBES – Nature’s Contributions to People was adopted in this work.</p>
Parasites under pressure: salmon lice may adapt to depth-based preventions in aquaculture
<p>Experiment 1. Vertical distribution of copepodids (mixed family groups) in 80 cm columns over time (min) at two pressures.</p> <p>Experiment 2. Vertical distribution of copepodids (individual families) in 80 cm columns at three pressures.</p> <p>Experiment 2 (traits). For each family: body size, egg string length, estimated fecundity and estimated egg size of mother; development times and column distributions (i.e. proportion of copepodids at top of columns) of offspring.</p>
Data from: Emerging risks of non-native species escapes from aquaculture: call for policy improvements in China and other developing countries
<p><span>1. Global aquaculture relies heavily on the farming of non-native aquatic species (hereafter, NAS). NAS escapes from aquaculture facilities can result in serious aquatic bio-invasions, which</span> has been <span>an important issue in the FAO <i>Blue Growth Initiative</i>. A r</span>egulatory quagmire regarding NAS farming and escapes, however, exists in most developing countries.</p> <p><span>2. We discuss aquaculture expansion and NAS escapes, illustrate emerging risks, and propose recommendations for improved aquaculture management</span> across developing countries and particularly for<span> China. </span></p> <p>3. <span>In </span>China<span>,</span> 68 NAS are known to have successfully established feral populations in natural habitats due to recurrent leakages or escapes; among the 68 NAS, 52<span> represent risks to native aquatic ecosystems. In addition to affecting a country's own biodiversity and ecosystem functions, NAS escapees can also threaten the </span>biosecurity<span> of shared waters in neighboring countries.</span></p> <p>4. <i>Policy implications</i>. <span>Non-native aquatic species (NAS) </span>escapes have already had adverse ecological effects in China and other developing countries. The importance of this problem, however, is not adequately recognized by current conservation policies in developing countries. To conserve biodiversity and to support the<span> goal of FAO's</span> sustainable aquaculture, developing countries <span>should now take responsible actions</span> to address NAS escapes <span>through policy and management improvements. Specifically, these</span> countries should pass comprehensive legislation, establish effective agencies and national standards and planning, and enhance integrated research and education to deal with risk assessment, prevention, monitoring, and control of <span>NAS</span> escapes. Given that China is the world's largest aquacultural producer, China can create a model for other developing countries that will increase the biosecurity and sustainability of global aquaculture.</p>
Data from: Oyster aquaculture impacts Zostera marina epibiont community composition in Akkeshi-ko estuary, Japan
Coastal fisheries are in decline worldwide, and aquaculture has become an increasingly popular way to meet seafood demand. While finfish aquaculture can have substantial adverse effects on coastal ecosystems due mostly to necessary feed inputs, bivalves graze on natural phytoplankton and are often considered for their positive ecosystem services. We conducted two independent studies to investigate the effects of long-line Crassostrea gigas oyster aquaculture on Zostera marina seagrass beds and associated epibiont communities in Akkeshi-ko estuary, Japan. Results from both studies yielded no evidence of an effect of oyster aquaculture on the morphology, density, or biomass of Z. marina, but significant differences were apparent in the epibiont community. Reference seagrass beds located away from aquaculture had higher seagrass epiphyte loads and higher abundances of amphipods. Conversely, seagrass beds below aquaculture lines had higher sessile polychaete biomass and higher isopod abundances. Our results suggest that the presence of oyster aquaculture may have indirect effects on seagrass by changing epibiont community composition and relative abundances of species. One proposed mechanism is that cultured oysters feed on epiphytic diatoms and epiphyte propagules before they can settle on the seagrass, which reduces epiphyte loads and influences subsequent faunal settlement. If carefully implemented and monitored, long-line oyster aquaculture may be a sustainable option to consider as bivalve aquaculture expands to meet global seafood demand, but further work is needed to fully assess and generalize the community-level effects on seagrass epibionts.
Data on the occurrence of Anisakids in fishery products from aquaculture in European countries (Jan 2010 – Sept 2023)
<p><span>This file contains data on Anisakids in fishery products from aquaculture in European countries covering studies published between January 2010 and September 2023. </span><span>The systematic review protocol used to identify and extract the information is available<strong> at <a href="../records/10270810">https://zenodo.org/records/10270810</a>.</strong></span></p>
Genetic parentage reconstruction as a practical tool applied to aquaculture and restoration programs for the European flat oyster, Ostrea edulis
<p>Preserving and maximizing genetic diversity in conservation programs, including for restocking, are of high importance. The threatened European flat oyster (<em>Ostrea edulis</em>) is currently the subject of several applied conservation and restocking programs, but concerns have been raised over potential negative side effects of these programs, for example due to our limited knowledge about the genetic effects in natural populations of releasing offspring of hatchery origin. Here, we developed a cost-effective, easily applicable and highly reliable method to assess the genetic diversity and parental contributions in flat oyster hatchery production based on analyses of 17 microsatellite loci. We analyzed broodstock and hatchery-produced spat (total n = 289) and compared diversity to that in wild samples of adults and spat from the broodstock source in the Limfjorden (total n = 190). Based on four hatchery tank experiments, we found that five swarming events (larval releases) were characterized by a single maternal and multiple paternal contributions, and that the number of contributing parents varied greatly both among individual tanks, and between swarming events within tank. On average, the effective number of breeders was only one third of the actual broodstock size. Although the broodstock exhibited high genetic variation, the high reproductive skew resulted in produced seed representing only a relatively small subset of this variation. The work demonstrates potential impact of hatchery reared offspring on decreasing genetic diversity in wild populations, but also that genetic monitoring can be integrated in conservation programs to minimize negative effects on restoration and supplementary restocking programs that utilize hatchery reared spats to support natural populations.</p>
Fig 8 in Capacıty utılızatıon ın aquaculture ın Turkey
Fig 8: Farm capacities according to the regions
Fig 6 in Capacıty utılızatıon ın aquaculture ın Turkey
Fig 6: The number of farms according to the regions
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.