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List of validated primers of gilthead sea bream (Sparus aurata) and European seabass (DIcentrarchus labrax) developed in PerformFISH project (D2.3)
<p>The document contains all the primers identified for the screening of genes tested for their potential as biomarkers to predict quality performance in gilthead sea bream and European sea bass larvae and juveniles in the context of PERFORMFISH (WP2). The spreadsheet has the following information: Pathway, phisiologic process in which the gene is involved; name of protein that gene produces; gene code; acession nº, code given in the consulted databases and the sequence extracted for primer design; FW and RV primer, forward and reverse primer sequence specific for target gene; melt temperature, optimized temperature that primers work at ; amplicon size, size in base pairs of the product produced with the primers; eff%, efficency of primers; r2; source, the origin of the primers, "in house" or "literature" (including available DOI. Each pair of primers are classified using a "traffic light" system indicating their validation status.</p>
Codebook - Knowledge-Action Platforms (Data & Policy article) Bream McIntosh et al.,
<p>Codebook used for Round 2 coding against key criteria of a 'Platform' definition that responds to matrix coding of Sustainability Knowledge Action Platforms. To accompany the article in Data & Policy 'The role of sustainability knowledge-action platforms in advancing multi-stakeholder engagement on sustainability'.</p>
FIGURE 5 in Differential expression of HPG-axis genes in autotetraploids derived from red crucian carp Carassius auratus red var., × blunt snout bream Megalobrama amblycephala,
FIGURE 5 Mean (+SD) relative expression of gnrh2, fshb, lhb, fshr and lhr messenger (m)RNA in (a) the breeding season () 2n, and () 4n and (b) the non-breeding season in Carassius auratus red var. () 2n, and () 4n. (RCC,) and autotetraploid C. auratus red var. ♀ × Megalobrama amblycephala ♂ (4nRR,). T, gene detected in the testis; O, gene detected in the ovary. *, significant difference between RCC and 4nRR (P <0.05)
FIGURE 4 Deduced amino-acid sequences for the Gnrh2 in Differential expression of HPG-axis genes in autotetraploids derived from red crucian carp Carassius auratus red var., × blunt snout bream Megalobrama amblycephala,
FIGURE 4 Deduced amino-acid sequences for the Gnrh2 () and Lhr () genes in Carassius auratus red var. (RCC) and autotetraploid C. auratus red var. ♀ × Megalobrama amblycephala ♂ (4nRR)
FIGURE 2 in Differential expression of HPG-axis genes in autotetraploids derived from red crucian carp Carassius auratus red var., × blunt snout bream Megalobrama amblycephala,
FIGURE 2 (a) The mature eggs (scale bar = 100 μm) and (b) mature sperm (scale bar = 10 μm) of autotetraploid Carrasius auratus red var. ♀ x Megalobrama amblycephala ♂ (4nRR)
FIGURE 3 in Differential expression of HPG-axis genes in autotetraploids derived from red crucian carp Carassius auratus red var., × blunt snout bream Megalobrama amblycephala,
FIGURE 3 Reverse-transcription (RT)-PCR analysis of the expression of (a) gnrh2, (b) fshb, (c) lhb, (d) fshr and (e) lhr messenger (m)RNA in various tissues of autotetraploid Carrasius auratus red var. ♀ x Megalobrama amblycephala ♂ (4nRR). The upper strip of each panel (a)–(e) shows the positive control of actin gene while the lower strip of each panel shows the RT-PCR amplification of the target gene
FIGURE 1 in Differential expression of HPG-axis genes in autotetraploids derived from red crucian carp Carassius auratus red var., × blunt snout bream Megalobrama amblycephala,
FIGURE 1 The gonadal structure of Carassius auratus red var. [RCC; (a)–(c)] and autotetraploids C. auratus red var. ♀ × Megalobrama amblycephala ♂ [4nRR; (d)–(f)]: (a) ovary of 7 month-old RCC containing many phase II and a few phase III oocytes; (b) ovary of 12 month-old RCC showing many mature phase IV ova; (c) testis of 12 month-old RCC with numerous mature sperms () and a small amount of spermatocytes () in the lobules of testes; (d) ovary of 7 month-old 4nRR containing phase II and a few phase III oocytes; (e) ovary of 12 month-old 4nRR with numerous mature phase IV ova; (f) testis of 12 month-old 4nRR with numerous mature sperms () and a small amount of spermatocytes () in the lobules of testes, the scale bars: (a), (b), (d), and (e) = 100 μm; (c) and (f) = 10 μm
Fig. 2 in Two new Myxobolus spp. (Myxozoa: Myxobolidae) from white bream, Blicca bjoerkna (Linnaeus, 1758) developing in basifilamental location of gills
Fig. 2. Schematic illustration of Myxobolus spp. myxospores. a – M. bjoerknae sp. n. in frontal view, b – in sutural view; c – M. lamellobasis sp. n. in frontal view, d – in sutural view. Scale bar: 10 µm.
Fig. 3 in Two new Myxobolus spp. (Myxozoa: Myxobolidae) from white bream, Blicca bjoerkna (Linnaeus, 1758) developing in basifilamental location of gills
Fig. 3. Histological section of the cartilaginous gill arch of white bream. p – plasmodium of Myxobolus bjoerknae sp. n., c – cartilaginous base of the filaments, f – gill filament, ct – connective tissue; arrows indicate gill lamellae. Haematoxylin and eosin staining (H & E). Scale bar: 100 µm.
Fig. 1. a in Two new Myxobolus spp. (Myxozoa: Myxobolidae) from white bream, Blicca bjoerkna (Linnaeus, 1758) developing in basifilamental location of gills
Fig. 1. a – spores of Myxobolus bjoerknae sp. n. infecting the cartilaginous gill arch in frontal view; inset: spores in sutural view; b – spores of M. lamellobasis sp. n. from the base of the gill filaments in frontal view; inset: spores in sutural view. Scale bars: 10 µm.
Fig. 5 in Two new Myxobolus spp. (Myxozoa: Myxobolidae) from white bream, Blicca bjoerkna (Linnaeus, 1758) developing in basifilamental location of gills
Fig. 5. Phylogenetic tree generated by Bayesian inference (GTR + I + Γ model) based on a 1613 bp-long alignment of 18S rDNA sequences of 43 myxosporean taxa. New Myxobolus spp. sequences are in bold. Ceratomyxa shasta was chosen as outgroup. Posterior probabilities are shown at nodes. NCBI accession numbers are in brackets.
Data from: Balanced replacement of fish meal with Hermetia illucens meal allows efficient hepatic nutrient metabolism and increased fillet lipid quality in gilthead sea bream (Sparus aurata) juveniles
<p>In the present study, gilthead sea bream (<em>Sparus aurata</em>) juveniles were reared using sustainable feeds containing insect meal from <em>Hermetia illucens</em> larvae and poultry by-products meal. Proteomics and Proton Nuclear Magnetic Resonance-based metabolomics analysis were used to assess the metabolic impact of tested dietary formulations in sea bream liver, whereas the composition of muscle fillet was characterized by means of metabolomics and gas chromatography of fatty acids methyl esters. Replacing fish meal with insect meal in a 5% fish meal diet did not substantially alter metabolism of dietary nutrients, leading to small but statistically detectable effects solely on lauric acid content of sea bream fillet, and few alterations in some markers of immune response, such as leukocyte elastase inhibitor-like, granzyme B (G,H)-like, and two associated ortholog groups namely serpin B, and chymase). Liver morphology confirmed the absence of structural damage or inflammation in the insect meal-fed group, which showed a lower amount of hepatic lipid deposition and accumulation, too.</p>
Dataset for image analysis of LCDV susceptibility in sea bream
<p>This dataset comprises the photographs used to carry out the genetic estimates of LCDV susceptibility in sea bream. The numbers 1-499 correspond to batch1 and 500-100 to batch2</p>
FIGURE 6 in Parascolopsis akatamae, a new species of dwarf monocle bream (Perciformes Nemipteridae) from the Indo-West Pacific, with redescription of closely related species P. eriomma
FIGURE 6. Maximum likelihood phylogeny derived from partial sequences of the mitochondrial cytochrome oxidase subunit I for the genus Parascolopsis and closely related species. Numbers at branches indicate bootstrap probabilities based on 1,000 replications. DDBJ/EMBL/GenBank accession numbers are shown in parentheses.
FIGURE 4 in Parascolopsis akatamae, a new species of dwarf monocle bream (Perciformes Nemipteridae) from the Indo-West Pacific, with redescription of closely related species P. eriomma
FIGURE 4. Biofluorescence emission patterns of Parascolopsis akatamae n. sp. (A–C, OCF-P4098, holotype, 160.5 mm SL) and P. eriomma (D–F, OCF-P4097, 154.4 mm SL). A) lateral view, under white light; B) lateral view, under blue light; C) ventral view, under blue light; D) lateral view, under white light; E) lateral view, under blue light; F) ventral view, under blue light.
FIGURE 5 in Parascolopsis akatamae, a new species of dwarf monocle bream (Perciformes Nemipteridae) from the Indo-West Pacific, with redescription of closely related species P. eriomma
FIGURE 5. Distribution of Parascolopsis akatamae n. sp. and P. eriomma. Closed markers are based on specimens examined during this study; open markers are based on literature records (identified from color photographs).
FIGURE 2 in Parascolopsis akatamae, a new species of dwarf monocle bream (Perciformes Nemipteridae) from the Indo-West Pacific, with redescription of closely related species P. eriomma
FIGURE 2. Fresh specimens of Parascolopsis akatamae n. sp. (A–D) and P. eriomma (E–F) at different growth stages. A) OCF-P4119, 98.3 mm SL, Okinawa-jima Island, Japan; B) OCF-P4071, 140.1 mm SL, Okinawa-jima Island, Japan; C) OCF- P4123, 179.7 mm SL, Okinawa-jima Island, Japan; D) OCF-P4089, 252.7 mm SL, Ishigaki-jima Island, Japan; E) OCF-P4212, 139.6 mm SL, Okinawa-jima Island, Japan; F) OCF-P3889, 172.8 mm SL, Okinawa-jima Island, Japan.
FIGURE 3 in Parascolopsis akatamae, a new species of dwarf monocle bream (Perciformes Nemipteridae) from the Indo-West Pacific, with redescription of closely related species P. eriomma
FIGURE 3. Relationships of length of forked part of caudal fin to standard length (A) and length of longest dorsal-fin spine to eye diameter (B) in Parascolopsis akatamae n. sp. (blue markers) and P. eriomma (red markers). Large squares indicates data from holotypes. Regression equations for (A) P. akatamae: y = 0.1473x + 2.4922, R2 = 0.9729; P. eriomma: y = 0.104x + 5.7483, R2 = 0.9234, and (B), P. akatamae: y = 1.7484x - 4.865, R2 = 0.8817; P. eriomma: y = 1.5366x + 5.3993, R2 = 0.8184.
FIGURE 1. Parascolopsis akatamae n in Parascolopsis akatamae, a new species of dwarf monocle bream (Perciformes Nemipteridae) from the Indo-West Pacific, with redescription of closely related species P. eriomma
FIGURE 1. Parascolopsis akatamae n. sp. (A) and P. eriomma (B–C). A) fresh specimen, OCF-P4098, holotype, 160.5 mm SL, Okinawa-jima Island, Japan; B) fresh specimen, OCF-P4097, 154.4 mm SL, Okinawa-jima Island, Japan; C) preserved specimen, FMNH 52247, holotype, 190.9 mm SL, Kaohsiung, Taiwan.
Data from: Exploring neutral and adaptive processes in expanding populations of gilthead sea bream, Sparus aurata L., in the North-East Atlantic
Recent studies in empirical population genetics have highlighted the importance of taking into account both neutral and adaptive genetic variation in characterizing microevolutionary dynamics. Here we explore the genetic population structure and the footprints of selection in four populations of the warm-temperate coastal fish, the gilthead sea bream (Sparus aurata), whose recent northward expansion has been linked to climate change. Samples were collected at four Atlantic locations, including Spain, Portugal, France and the South of Ireland, and genetically assayed using a suite of species-specific markers, including 15 putatively neutral microsatellites and 23 Expressed Sequence Tag-linked (ESTs) markers, as well as a portion of the mitochondrial DNA (mtDNA) Control Region. Two of the putatively neutral markers, Bld-10 and Ad-10, bore signatures of strong directional selection, particularly in the newly established Irish population, though the potential 'surfing effect' of rare alleles at the edge of the expansion front was also considered. Analyses after the removal of these loci suggest low but significant population structure likely affected by some degree of gene flow counteracting random genetic drift. No signal of historic divergence was detected at mtDNA. BLAST searches conducted with all 38 markers used failed to identify specific genomic regions associated to adaptive functions. However, the availability of genomic resources for this commercially valuable species is rapidly increasing, bringing us closer to the understanding of the interplay between selective and neutral evolutionary forces, shaping population divergence of an expanding species in a heterogeneous milieu.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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OpenNeuro
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