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123 results for “454”
Data from: Exploring Symbiodinium diversity and host specificity in Acropora corals from geographical extremes of Western Australia with 454 amplicon pyrosequencing
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Data from: Allele discovery of ten candidate drought-response genes in Austrian oak using a systematically informatics approach based on 454 amplicon sequencing
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Data from: A 454 survey reveals the community composition and core microbiome of the common bed bug (Cimex lectularius) across an urban landscape
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Data from: Comparison of 454 pyrosequencing methods for characterizing the major histocompatibility complex of nonmodel species and the advantages of ultra deep coverage
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Data from: Microsatellite markers from the Ion Torrent: a multi-species contrast to 454 shotgun sequencing
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Data from: Evaluation of two approaches to genotyping MHC class I in a passerine – CE-SSCP and 454 pyrosequencing
Genes of the highly dynamic major histocompatibility complex (MHC) are directly linked to individual fitness and are of high interest in evolutionary ecology and conservation genetics. Gene duplication and positive selection usually lead to high levels of polymorphism in the MHC region, making genotyping of MHC a challenging task. Here, we compare the performance of two methods for MHC class I genotyping in a passerine with highly duplicated MHC class I genes: capillary electrophoresis single strand conformation polymorphism (CE-SSCP) analysis and 454 GS FLX Titanium pyrosequencing. According to our findings, the number of MHC variants (called alleles for simplicity) detected by CE-SSCP is significantly lower than detected by 454. To resolve discrepancies between the two methods we cloned and Sanger sequenced a MHC class I amplicon for an individual with high number of alleles. We found a perfect congruence between cloning/Sanger sequencing results and 454. Thus, in case of multi-locus amplification, CE-SSCP considerably underestimates individual MHC diversity. However, numbers of alleles detected by both methods are significantly correlated, although the correlation is weak (r = 0.32). Thus, in systems with highly duplicated MHC, 454 provides more reliable information on individual diversity than CE-SSCP.
Data from: Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species
Microsatellites are ubiquitous in Eukaryotic genomes. A more complete understanding of their origin and spread can be gained from a comparison of their distribution within a phylogenetic context. Although information for model species is accumulating rapidly, it is insufficient due to a lack of species depth, thus intragroup variation is necessarily ignored. As such, apparent differences between groups may be overinflated and generalizations cannot be inferred until an analysis of the variation that exists within groups has been conducted. In this study, we examined microsatellite coverage and motif patterns from 454 shotgun sequences of 154 Eukaryote species from eight distantly related phyla (Cnidaria, Arthropoda, Onychophora, Bryozoa, Mollusca, Echinodermata, Chordata and Streptophyta) to test if a consistent phylogenetic pattern emerges from the microsatellite composition of these species. It is clear from our results that data from model species provide incomplete information regarding the existing microsatellite variability within the Eukaryotes. A very strong heterogeneity of microsatellite composition was found within most phyla, classes and even orders. Autocorrelation analyses indicated that while microsatellite contents of species within clades more recent than 200 Mya tend to be similar, the autocorrelation breaks down and becomes negative or non-significant with increasing divergence time. Therefore, the age of the taxon seems to be a primary factor in degrading the phylogenetic pattern present among related groups. The most recent classes or orders of Chordates still retain the pattern of their common ancestor. However, within older groups, such as classes of Arthropods, the phylogenetic pattern has been scrambled by the long independent evolution of the lineages.
FIGURE 8. Bellottia apoda. IIPB 454 in Atlantic occurrence of the genus Bellottia (Teleostei, Bythitidae) with two new species from the Western North Atlantic
FIGURE 8. Bellottia apoda. IIPB 454/1982. SL 52.
Raw sequencing data of Anaplamsa phagocytophilum loci (ankA, msp4, groEL) obtained from 454 and parameter files to clean these data using MOTHUR
<p>A compressed archive including: i) raw sequences in ssf file; ii) Mothur oligo files to sort out sequences among loci and individual samples.</p>
Figures 453- 454 from: van Achterberg C, Shaw MR, Quicke DLJ (2020) Revision of the western Palaearctic species of Aleiodes Wesmael (Hymenoptera, Braconidae, Rogadinae). Part 2: Revision of the A. apicalis group. ZooKeys 919: 1-259. https://doi.org/10.3897/zookeys.919.39642
Figures 453- 454 Aleiodes krulikowskii (Kokujev), ♀, lectotype 453 habitus lateral 454 ovipositor sheath lateral.
Figure 3 from: Gradinarov D (2014) The mermithid species Isomermis lairdi (Nematoda, Mermithidae), previously only known in Africa, found in Europe. ZooKeys 454: 1-11. https://doi.org/10.3897/zookeys.454.7577
Figure 3 - Tail region of male Isomermis lairdi from Jeleznitsa with spicules and genital papillae, lateral view. Scale bar: 100 µm.
Figure 2 from: Gradinarov D (2014) The mermithid species Isomermis lairdi (Nematoda, Mermithidae), previously only known in Africa, found in Europe. ZooKeys 454: 1-11. https://doi.org/10.3897/zookeys.454.7577
Figure 2 - Main morphological characters of Isomermis lairdi from Jeleznitsa (A–H). A, B Mature male, anterior region with terminal mouth opening (A) and amphid (B), lateral view. C Female postparasitic juvenile, posterior end with tail appendage D Mature female, posterior end E Female, vulvar region with vagina F Male, spicules G Male postparasitic juvenile, tail region with tail appendage H Mature male, tail region. Scale bars: A, B: 50 µm; C–F: 70 µm; G, H: 100 µm.
FIGURE 454 in A revision of the genera and species of the Neotropical family Mesembrinellidae (Diptera: Oestroidea)
FIGURE 454. Female sternites of Souzalopesiella facialis (Aldrich).
FIGURE 454 in A revision of the genera and species of the Neotropical family Mesembrinellidae (Diptera: Oestroidea)
FIGURE 454. Female sternites of Souzalopesiella facialis (Aldrich).
FIGURES 451–454 in New species (130) of the hyperdiverse aquatic beetle genus Hydraena Kugelann from Papua New Guinea, and a preliminary analysis of areas of endemism (Coleoptera: Hydraenidae) 2944
FIGURES 451–454. Geographical distributions of Hydraena species.
Figure 4 from: Román-Valencia C, Ruiz-C. R, Taphorn D, García-Alzate C (2014) A new species of Hemibrycon (Characiformes, Characidae) from the upper San Juan River drainage, Pacific versant, Colombia. ZooKeys 454: 109-125. https://doi.org/10.3897/zookeys.454.6954
Figure 4 - Upper and lower jaws of Hemibrycon sanjuanensis sp. n. IUQ 3695, 55.5 mm SL, A Premaxilla B Maxilla C Lower jaw. Scale bar = 1 mm.
Figure 3 from: Román-Valencia C, Ruiz-C. R, Taphorn D, García-Alzate C (2014) A new species of Hemibrycon (Characiformes, Characidae) from the upper San Juan River drainage, Pacific versant, Colombia. ZooKeys 454: 109-125. https://doi.org/10.3897/zookeys.454.6954
Figure 3 - Representation of the Canonical Variables (CV canonical variable 1 is the X axis and canonical variable 2 is the Y axis) for Hemibrycon sanjuanensis sp. n., Hemibrycon cairoense and Hemibrycon dariensis.
Figure 2 from: Román-Valencia C, Ruiz-C. R, Taphorn D, García-Alzate C (2014) A new species of Hemibrycon (Characiformes, Characidae) from the upper San Juan River drainage, Pacific versant, Colombia. ZooKeys 454: 109-125. https://doi.org/10.3897/zookeys.454.6954
Figure 2 - Distribution and location of Hemibrycon sanjuanensis sp. n. in the Alto San Juan River, Risaralda state, Colombia.
Figure 1 from: Román-Valencia C, Ruiz-C. R, Taphorn D, García-Alzate C (2014) A new species of Hemibrycon (Characiformes, Characidae) from the upper San Juan River drainage, Pacific versant, Colombia. ZooKeys 454: 109-125. https://doi.org/10.3897/zookeys.454.6954
Figure 1 - Hemibrycon sanjuanensis sp. n., holotype IUQ 3693. 53.5 mm SL, Colombia, Risaralda State, Pueblo Rico Municipality, El Recreo, upper San Juan River Basin, Aguas Claras River, tributary of the Tatamá River. Scale 1 cm.
Figures 33-38 from: Tian M, Yin H, Huang S (2014) Du'an Karst of Guangxi: a kingdom of the cavernicolous genus Dongodytes Deuve (Coleoptera, Carabidae, Trechinae). ZooKeys 454: 69-107. https://doi.org/10.3897/zookeys.454.7269
Figures 33-38 - Male genitalia of Dongodytes (s. str.) species (median lobe and parameres in lateral view, apical part of median lobe in dorsal view). 33–34 Dongodytes (s. str.) elongatus sp. n. 35–36 Dongodytes (s. str.) lani sp. n. 37–38 Dongodytes (s. str.) troglodytes sp. n.
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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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.