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244 results for “Model Organisms”
Data from: Sequence Capture using PCR-generated Probes (SCPP): a cost-effective method of targeted high-throughput sequencing for non-model organisms
Recent advances in high-throughput sequencing library preparation and subgenomic enrichment methods have opened new avenues for population genetics and phylogenetics of non-model organisms. To multiplex large numbers of indexed samples while sequencing predominantly orthologous, targeted regions of the genome, we propose modifications to an existing, in-solution capture that utilizes PCR products as target probes to enrich library pools for the genomic subset of interest. The sequence capture using PCR-generated probes (SCPP) protocol requires no specialized equipment, is highly flexible, and significantly reduces experimental costs for projects where a modest scale of genetic data is optimal (25-100 genomic loci). Our alterations enable application of this method across a wider phylogenetic range of taxa and result in higher capture efficiencies and coverage at each locus. Efficient and consistent capture over multiple SCPP experiments and at various phylogenetic distances is demonstrated, extending the utility of this method to both phylogeographic and phylogenomic studies.
Domain organization of lentiviral and betaretroviral surface envelope glycoproteins modeled with AlphaFold
The surface envelope glycoproteins of non-primate lentiviruses and betaretroviruses share sequence similarity with the inner proximal domain b-sandwich of the human immunodeficiency virus type 1 (HIV-1) gp120 glycoprotein that faces the transmembrane glycoprotein as well as patterns of cysteine and glycosylation site distribution that points to a similar two-domain organization in at least some lentiviruses. Here, high reliability models of the surface glycoproteins obtained with the AlphaFold algorithm are presented for the gp135 glycoprotein of the small ruminant caprine arthritis-encephalitis (CAEV) and visna lentiviruses and the betaretroviruses jaagsiekte sheep retrovirus (JSRV), mouse mammary tumor virus (MMTV) and consensus human endogenous retrovirus type K (HERV-K). The models confirm and extend the inner domain structural conservation in these viruses and identify two outer domains with a putative receptor binding site in the CAEV and visna virus gp135. The location of that site is consistent with patterns of sequence conservation and glycosylation site distribution in gp135. In contrast, a single domain is modeled for the JSRV, MMTV and HERV-K betaretrovirus envelope proteins that is highly conserved structurally in the proximal region and structurally diverse in apical regions likely to interact with cell receptors. The models presented here identify sites in small ruminant lentivirus and betaretrovirus envelope glycoproteins likely to be critical for virus entry and virus neutralization by antibodies and will facilitate their functional and structural characterization.
MIMICS-BC_v1.0: Modeling biochar effects on soil organic carbon on croplands in a microbial decomposition model
<p>The code and data of MIMICS-BC_v1.0 related to the manuscript in submission</p>
Supplementary material 4 from: Reip HS, Wesener T (2018) Intraspecific variation and phylogeography of the millipede model organism, the Black Pill Millipede Glomeris marginata (Villers, 1789) (Diplopoda, Glomerida, Glomeridae). In: Stoev P, Edgecombe GD (Eds) Proceedings of the 17th International Congress of Myriapodology, Krabi, Thailand. ZooKeys 741: 93-131. https://doi.org/10.3897/zookeys.741.21917
POPART-data : Explanation note: POPART-data file of haplotypes in format NEXUS.
Supplementary material 5 from: Reip HS, Wesener T (2018) Intraspecific variation and phylogeography of the millipede model organism, the Black Pill Millipede Glomeris marginata (Villers, 1789) (Diplopoda, Glomerida, Glomeridae). In: Stoev P, Edgecombe GD (Eds) Proceedings of the 17th International Congress of Myriapodology, Krabi, Thailand. ZooKeys 741: 93-131. https://doi.org/10.3897/zookeys.741.21917
ESTIMATES-data : Explanation note: ESTIMATES-data file of haplotypes as text file.
Figure 8 from: Reip HS, Wesener T (2018) Intraspecific variation and phylogeography of the millipede model organism, the Black Pill Millipede Glomeris marginata (Villers, 1789) (Diplopoda, Glomerida, Glomeridae). In: Stoev P, Edgecombe GD (Eds) Proceedings of the 17th International Congress of Myriapodology, Krabi, Thailand. ZooKeys 741: 93-131. https://doi.org/10.3897/zookeys.741.21917
Figure 8 Mapped genetic p-distance to geographical distance of all analysed specimen-pairs (4,656) of Glomeris marginata. Solid line: linear trend line with linear function and coefficient of determination R². Circles: see text below and Table 5.
Figure 5 from: Reip HS, Wesener T (2018) Intraspecific variation and phylogeography of the millipede model organism, the Black Pill Millipede Glomeris marginata (Villers, 1789) (Diplopoda, Glomerida, Glomeridae). In: Stoev P, Edgecombe GD (Eds) Proceedings of the 17th International Congress of Myriapodology, Krabi, Thailand. ZooKeys 741: 93-131. https://doi.org/10.3897/zookeys.741.21917
Figure 5 Modified biogeographic regions of France, based on http://inpn.mnhn.fr/programme/rapportage-directives-nature/presentation.
Figure 7 from: Reip HS, Wesener T (2018) Intraspecific variation and phylogeography of the millipede model organism, the Black Pill Millipede Glomeris marginata (Villers, 1789) (Diplopoda, Glomerida, Glomeridae). In: Stoev P, Edgecombe GD (Eds) Proceedings of the 17th International Congress of Myriapodology, Krabi, Thailand. ZooKeys 741: 93-131. https://doi.org/10.3897/zookeys.741.21917
Figure 7 Molecular phylogenetic analysis of Glomeris species by the maximum likelihood method. Midpoint rooted. Bootstrap values in % at nodes. All collapsed nodes have a bootstrap value of 100%. Scale bar: 10 % genetic ML distance.
Figure 3 from: Reip HS, Wesener T (2018) Intraspecific variation and phylogeography of the millipede model organism, the Black Pill Millipede Glomeris marginata (Villers, 1789) (Diplopoda, Glomerida, Glomeridae). In: Stoev P, Edgecombe GD (Eds) Proceedings of the 17th International Congress of Myriapodology, Krabi, Thailand. ZooKeys 741: 93-131. https://doi.org/10.3897/zookeys.741.21917
Figure 3 Distribution map of all successfully sequenced samples of G. marginata (blue dots). Base map: Shuttle Radar Topography Mission elevation data of the Deutsche Zentrum für Luft- und Raumfahrt (SRTM-3), accessed with GLOBALMAPPER v17.
Figure 12 from: Reip HS, Wesener T (2018) Intraspecific variation and phylogeography of the millipede model organism, the Black Pill Millipede Glomeris marginata (Villers, 1789) (Diplopoda, Glomerida, Glomeridae). In: Stoev P, Edgecombe GD (Eds) Proceedings of the 17th International Congress of Myriapodology, Krabi, Thailand. ZooKeys 741: 93-131. https://doi.org/10.3897/zookeys.741.21917
Figure 12 Extrapolation of rarefaction curves with ESTIMATES of the COI sequences of Glomeris marginata. Blue line = estimation with premise of mean number (404 haplotypes); Horizontal yellow line = 95% satisfaction of mean number (384 haplotypes); Green and red line = curve at the 95% upper and lower boundary.
Figure 2 from: Reip HS, Wesener T (2018) Intraspecific variation and phylogeography of the millipede model organism, the Black Pill Millipede Glomeris marginata (Villers, 1789) (Diplopoda, Glomerida, Glomeridae). In: Stoev P, Edgecombe GD (Eds) Proceedings of the 17th International Congress of Myriapodology, Krabi, Thailand. ZooKeys 741: 93-131. https://doi.org/10.3897/zookeys.741.21917
Figure 2 A G. marginata, brown and black form occurring in sympatry, Germany, Rügen, 2016. B–G Similar coloured species of Glomeris analyzed in this study B G. marginata, with a single specimen of G. intermedia in the upper left part, Germany, Landskrone, 2015 C G. intermedia Latzel, 1884, with sympatric G. marginata, Germany, Landskrone, 2015 D G. annulata Brandt, 1833, France, Gard, Courry, 2015 E G. cf. lugubris Attems, 1952, Spain, Cádiz/ Sierra de Grazalema, 2008, preserved specimenF G. cf. maerens Attems, 1927, Spain, Aragón/Teruel, 2010, preserved specimen G G. maerens, Spain, Tarragona/Montsià, 2017; B–D photographed by Jan Philip Oeyen.
Figure 10 from: Reip HS, Wesener T (2018) Intraspecific variation and phylogeography of the millipede model organism, the Black Pill Millipede Glomeris marginata (Villers, 1789) (Diplopoda, Glomerida, Glomeridae). In: Stoev P, Edgecombe GD (Eds) Proceedings of the 17th International Congress of Myriapodology, Krabi, Thailand. ZooKeys 741: 93-131. https://doi.org/10.3897/zookeys.741.21917
Figure 10 TCS-Network of haplotypes of Glomeris marginata with distribution region. Numbers behind region = consecutive haplotype number of DNASP-output. Haplotype accumulations: Red oval = Haplotype lineage I; Yellow oval = Haplotype lineage II; Blue oval = Haplotype lineage III; Green circle = Haplotype lineage IV; Black oval = Haplotype lineage V. Dashes on node connecting lines are representing single nucleotide mutations.
Figure 1 from: Reip HS, Wesener T (2018) Intraspecific variation and phylogeography of the millipede model organism, the Black Pill Millipede Glomeris marginata (Villers, 1789) (Diplopoda, Glomerida, Glomeridae). In: Stoev P, Edgecombe GD (Eds) Proceedings of the 17th International Congress of Myriapodology, Krabi, Thailand. ZooKeys 741: 93-131. https://doi.org/10.3897/zookeys.741.21917
Figure 1 Glomeris marginata (Villers, 1789) colour morphs. A main coloration form, center immature specimens showing the perplexa colour pattern; Germany, Landskrone B strongly lightened adult perplexa pattern, France, Pays de la Loire C red mutant, Germany, Bonn D strongly red-banded form, from France, Montauroux E more weakly red-brown banded from, France, same population as D. A, D, E photographed by Jan Philip Oeyen B by ZFMK C by Dennis Rödder.
Figure 4 from: Reip HS, Wesener T (2018) Intraspecific variation and phylogeography of the millipede model organism, the Black Pill Millipede Glomeris marginata (Villers, 1789) (Diplopoda, Glomerida, Glomeridae). In: Stoev P, Edgecombe GD (Eds) Proceedings of the 17th International Congress of Myriapodology, Krabi, Thailand. ZooKeys 741: 93-131. https://doi.org/10.3897/zookeys.741.21917
Figure 4 Modified biogeographic regions of Germany, based on Naturräumliche Großregionen of Germany, Meynen and Schmithüsen (1953–1962) and http://commons.wikimedia.org/wiki/File:Deutschland_Naturraeumliche_Grossregionen.png
Figure 11 from: Reip HS, Wesener T (2018) Intraspecific variation and phylogeography of the millipede model organism, the Black Pill Millipede Glomeris marginata (Villers, 1789) (Diplopoda, Glomerida, Glomeridae). In: Stoev P, Edgecombe GD (Eds) Proceedings of the 17th International Congress of Myriapodology, Krabi, Thailand. ZooKeys 741: 93-131. https://doi.org/10.3897/zookeys.741.21917
Figure 11 Individual based rarefaction curve calculated with ESTIMATES and with 10,000 replicates (simulated collections) of the COI sequences of Glomeris marginata. Vertical lines indicating 95% lower and upper boundary.
Figure 6 from: Reip HS, Wesener T (2018) Intraspecific variation and phylogeography of the millipede model organism, the Black Pill Millipede Glomeris marginata (Villers, 1789) (Diplopoda, Glomerida, Glomeridae). In: Stoev P, Edgecombe GD (Eds) Proceedings of the 17th International Congress of Myriapodology, Krabi, Thailand. ZooKeys 741: 93-131. https://doi.org/10.3897/zookeys.741.21917
Figure 6 Distribution of nucleotide differences in % between specimen pairs of Glomeris marginata and to outgroup specimens.
Figure 9 from: Reip HS, Wesener T (2018) Intraspecific variation and phylogeography of the millipede model organism, the Black Pill Millipede Glomeris marginata (Villers, 1789) (Diplopoda, Glomerida, Glomeridae). In: Stoev P, Edgecombe GD (Eds) Proceedings of the 17th International Congress of Myriapodology, Krabi, Thailand. ZooKeys 741: 93-131. https://doi.org/10.3897/zookeys.741.21917
Figure 9 Maximum likelihood tree based on the mtDNA COI gene of 97 Glomeris marginata. Midpoint rooted. Roman numerals: Haplotype lineages I–V. Colour morphs of G. marginata: Common black = none; G = grey; R = red border; P = perplexa-markings. Scale bar = 1 % genetic ML distance.
A Bayesian framework for estimating parameters of a generic toxicokinetic model for the bioaccumulation of organic chemicals by benthic invertebrates: proof of concept with PCB153 and two freshwater species.
<p>R Codes and corresponding .csv data files for estimating toxicokinetic model parameters for both chironomids and gammarids exposed to PCB153.</p>
Image-derived models of cell organization changes during differentiation and drug treatments
PC12 cells are a popular model system to study changes driving and accompanying neuronal differentiation. While attention has been paid to changes in transcriptional regulation and protein signaling, much less is known about the changes in organization that accompany PC12 differentiation. Fluorescence microscopy can provide extensive information about these changes, although it is difficult to continuously observe changes over many days of differentiation. We describe a generative model of differentiation-associated changes in cell and nuclear shape and their relationship to mitochondrial distribution constructed from images of different cells at discrete time points. We show that the model accurately represents complex cell and nuclear shapes and learn a regression model that relates cell and nuclear shape to mitochondrial distribution; the predictive accuracy of the model increases during differentiation. Most importantly, we propose a method, based on cell matching and interpolation, to produce realistic simulations of the dynamics of cell differentiation from only static images. We also found that the distribution of cell shapes is hollow: most shapes are very different from the average shape. Finally, we show how the method can be used to model nuclear shape changes of human induced pluripotent stem cells resulting from drug treatments. [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text]
Modeling organic aerosol over Europe in summer conditions with the VBS-GECKO parameterization: sensitivity to secondary organic compound properties and IVOC emissions [Dataset]
<p>This dataset is composed of simulation outputs of the CHIMERE model that were used to evaluate the VBS-GECKO SOA parameterization as described in the study :</p> <p>Lannuque, V., Couvidat, F., Camredon, M., Aumont, B., and Bessagnet, B. : Modelling organic aerosol over Europe in summer conditions with the VBS-GECKO parameterization: sensitivity to secondary organic compound properties and IVOC emissions, Atmos. Chem. Phys., <em>to be submitted soon</em>.<br> <br> <strong>Please cite the original ACP article when using these data in a publication.</strong></p> <p><br> The paper also contains more information about how these data were obtained.</p> <p>The dataset is composed of 34 netcdf files. The 17 "daily" files gather the daily averages and the 17 "profile" files present the average day profiles.</p> <p>Victor Lannuque</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
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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.