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67 results for “interspecies”
Dataset associated with article "Robots mediating interactions between animals for interspecies collective behaviors"
<p>This dataset contains results and analysis described in the study "Robots mediating interactions between animals for interspecies collective behaviors", Bonnet, F., Mills, R., Szopek, M., Schönwetter-Fuchs, S., Halloy, J., Bogdan, S., Correia, L., Mondada, F. and Schmickl, T. (2019), <em>Science Robotics</em>, <em>4</em>(28), doi: 10.1126/scirobotics.aau7897</p> <p>Contents: </p> <ul> <li>experimental data (logs from robotic systems, example videos)</li> <li>animal tracking analysis output</li> </ul> <p>See the readme and summary files contained within the archives for further details.</p>
EFSA Project on the use of NAMs to explore interspecies metabolic differences on essential oils as feed additives (Annexes A, B, C, D)
<p>Raw data of phase I and II experiments and PBK model input data and simulation of the EFSA Project on the use of NAMs to explore interspecies metabolic differences on essential oils as feed additives (OC/EFSA/SCER/2021/14).</p>
ATACSeq fastq files associated with the manuscript entitled 'Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion'
<p>This next-generation sequencing dataset is associated with the research manuscript entitled ‘<em>Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion</em>’ (https://www.biorxiv.org/content/10.1101/754002v2).</p> <p>The zipped folder ‘<strong>Zenodo_Saxena_etal_2021_ATACSeq_FastqFiles</strong>’ contains raw/unprocessed ATACSeq Fatsq read files for postnatal day 5 (P5) mouse (Mus) and jerboa (Jac) cartilage samples (Metatarsal = MT; Radius/Ulna = RU).</p> <p>> The <strong>Jac_P5</strong> subfolder contains paired-end reads (R1 and R2) for three jerboa metatarsals (MT1-3) and radius/ulna (RU1-3) biological replicates.</p> <p>> The <strong>Mus_P5</strong> subfolder contains paired-end reads (R1 and R2) for two mouse metatarsals (MT1-2) and radius/ulna (RU1-2) biological replicates.</p>
Figurations of Interspecies Harmony in Literature, Film, and Other Cultural Texts of the English-Speaking World
<p>Dataset 1 version 1.0 and Dataset 2 version 1.0 for the research project:</p> <p>FIGURATIONS OF INTERSPECIES HARMONY IN LITERATURE, FILM, AND OTHER CULTURAL TEXTS OF THE ENGLISH-SPEAKING SPHERE, from the mid-19 to the 21st centuries, funded by the National Science Centre, Poland (grant no. UMO-2020/38/E/HS2/00130). </p> <p> </p> <p>These datasets were used as data in the writing of the article "Non Human Kids of Kiddie Lit: Marjorie Kinnan Rawlings's The Yearling and the Cultural Construction of Animal Narratives as Children's Literature" by Justyna Włodarczyk & Julia Wilde, published open access (CC-BY) in Children's Literature in Education, Sept. 2022</p> <p>DOI: https://doi.org/10.1007/s10583-022-09508-6 </p> <p> </p> <p>The purpose of the two datasets is to provide historical background data for the development of the "boy and dog" literary convention (Dataset 1) and for establishing the frequency of film adaptations of animal fiction (dataset 2). </p> <p> </p>
Interspecies chimerism with human embryonic stem cells generates functional human dopamine neurons at low efficiency
<p>Interspecies chimeras offer great potential for regenerative medicine and creation of human disease models. Whether human pluripotent stem cell (hPSC) derived neurons in an interspecies chimera can differentiate into functional neurons and integrate into host neural circuity is not known. Here we show, using Engrailed 1 (En1) as a development niche that human naïve-like ES cells can incorporate into embryonic and adult mouse brains. Human-derived neurons including tyrosine hydroxylase (TH) positive neurons integrate into the mouse brain at low efficiency. These TH-positive neurons have electrophysiologic properties consistent with their human origin. Additionally, these human-derived neurons in the mouse brain accumulate pathologic phosphorylated α-synuclein in response to α-synuclein preformed fibrils. Optimization of human/mouse chimeras could be utilized to study human neuronal differentiation and human brain disorders.</p>
Site impacts nutrient translocation efficiency in intra- and interspecies miscanthus hybrids on marginal lands
<p class="MsoNormal"><span>Miscanthus</span><span>, a C<sub>4</sub> perennial rhizomatous grass, is capable of growing in varied climates and soil types in Europe, including on marginal lands. It can produce high yields with low nutrient inputs when harvested after complete senescence. Senescence induction and rate depend on complex genetic, environmental, and management interactions. To explore these interactions, we analysed four miscanthus hybrids </span><span>(two novel seed-based hybrids, GRC 3<em> (M. sinensis × sinensis</em>) and GRC 14 (<em>M. sacchariflorus × sinensis)</em>; GRC 15, a<em> </em>novel <em>M. sacchariflorus × sinensis </em>clone; and GRC 9, a standard <em>M.</em></span><em><span> </span></em><em><span>× giganteus</span></em><span> clone</span><span>)</span><span> in Italy, Croatia, Germany and the UK.</span></p> <p class="MsoNormal"><span>Over all trial locations and hybrids, the average aboveground biomass of the three-year-old stands in August 2020 was 15 t DM ha<sup>-1</sup> with nutrient contents of 7.6 mg N g<sup>-1</sup> and 14.6 mg K g<sup>-1</sup>. As expected, delaying the harvest until spring reduced overall yield and nutrient contents (12 t DM ha<sup>-1</sup>,<sup> </sup>3.3 mg N g<sup>-1</sup> and 5.5 mg K g<sup>-1</sup>). At lower latitudes, the late-ripening <em>M.</em> </span><em><span>sacchariflorus × sinensis</span> </em><span>GRC 14 and GRC 15 combined high yields with low nutrient contents. At the most elevated latitude location (UK), the early-ripening </span><em><span>M. sinensis × sinensis</span> </em><span>combined high biomass yields with low nutrient offtakes. The clonal <em>M. × giganteus</em> with intermediate flowering and senescence attained similar low nutrient contents by spring harvest at all four locations.</span></p> <p><span>Seasonal changes in yield and</span><span> nutrie</span><span>nt </span><span>levels analysed in this study provide: 1) a first step towards recommending hybrids for specific locations and end uses in Europe; 2) crucial data for determination of harvest time and practical steps in the valorisation of biomass; and 3) key sustainability data for life cycle assessments. Identification of trade-offs resulting from genetic × environment × management interactions are critical for increasing sustainable biomass supply from miscanthus grown on marginal lands.</span></p>
Assemblies and annotations from the paper "Interspecies hybridization as a route of accessory chromosome origin in fungal species infecting wild grasses"
<div> <p>This repository contains the whole genome assemblies, gene and TE annotations generated and analyzed in the manuscript entitled "Interspecies hybridization as a route of accessory chromosome origin in fungal species infecting wild grasses". </p> <p>Preprint available on BioRxiv:</p> <p>https://www.biorxiv.org/content/10.1101/2024.10.03.616481v1</p> <p> </p> </div>
RNASeq fastq files associated with the manuscript entitled 'Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion'
<p>This next-generation sequencing dataset is associated with the research manuscript entitled ‘<em>Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion</em>’ (https://www.biorxiv.org/content/10.1101/754002v2).</p> <p>The folder ‘<strong>Zenodo_Saxena_etal_2021_RNASeq_FastqFiles</strong>’ contains raw/unprocessed RNASeq Fatsq read files for postnatal day 5 (P5) mouse (Mus) and jerboa (Jac) cartilage samples (Metatarsal = MT; Radius/Ulna = RU).</p> <p>> The <strong>Jac_P5</strong> subfolder contains single-end reads (R1) for five jerboa metatarsals (MT1-5) and radius/ulna (RU1-5) biological replicates. Jac_MT1-3 and Jac_RU1-3 were used in the primary differential expression analysis (n=3). Jac_MT4-5 and Jac_RU4-5 were used for independent validation (n=2) of the the primary analysis. </p> <p>> The <strong>Mus_P5</strong> subfolder contains single-end reads (R1) for five mouse metatarsals (MT1-5) and radius/ulna (RU1-5) biological replicates. Mus_MT1-3 and Mus_RU1,3 & 4 were used in the primary differential expression analysis (n=3). Mus_MT4-5 and Mus_RU4 & 5 were used for independent validation (n=2) of the the primary analysis. </p>
Introgressive hybridization in the west Pacific pen shells (genus Atrina): Restricted interspecies gene flow within the genome
<p>Abstract</p> <p>A compelling interest in marine biology is to elucidate how species boundaries between sympatric free‐spawning marine invertebrates such as bivalve molluscs are maintained in the face of potential hybridization. Hybrid zones provide the natural resources for us to study the underlying genetic mechanisms of reproductive isolation between hybridizing species. Against this backdrop, we examined the occurrence of introgressive hybridization (introgression) between two bivalves distributed in the western Pacific margin, Atrina japonica and Atrina lischkeana, based on single‐nucleotide polymorphisms (SNPs) derived from restriction site‐associated DNA sequencing. Using 1066 ancestry‐informative SNP sites, we also investigated the extent of introgression within the genome to search for SNP sites with reduced interspecies gene flow. A series of our individual‐level clustering analyses including the principal component analysis, Bayesian model‐based clustering, and triangle plotting based on ancestry–heterozygosity relationships for an admixed population sample from the Seto Inland Sea (Japan) consistently suggested the presence of specimens with varying degrees of genomic admixture, thereby implying that the two species are not completely isolated. The Bayesian genomic cline analysis identified 10 SNP sites with reduced introgression, each of which was located within a genic region or an intergenic region physically close to a functional gene. No, or very few, heterozygotes were observed at these sites in the hybrid zone, suggesting that selection acts against heterozygotes. Accordingly, we raised the possibility that the SNP sites are within genomic regions that are incompatible between the two species. Our finding of restricted interspecies gene flow at certain genomic regions gives new insight into the maintenance of species boundaries in hybridizing broadcast‐spawning molluscs.</p>
Interspecies chimerism with human embryonic stem cells generates functional human dopamine neurons at low efficiency
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Introgressive hybridization in the west Pacific pen shells (genus Atrina): Restricted interspecies gene flow within the genome
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Site impacts nutrient translocation efficiency in intra- and interspecies miscanthus hybrids on marginal lands
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Data from: Interspecies interference and monitoring duration affect detection rates in chew cards
Pest monitoring methods should provide unbiased accurate estimates of pest densities and locations, while also minimizing time-in-field and costs. Recent pest mammal monitoring studies have found that chew cards are more effective than conventional mammal monitoring methods, but little experimental work has been done to determine optimal experimental duration or quantify the risks of saturation by one species biasing detections of other species. Here, we used chew cards in three sites within Awarua wetland (Southland, New Zealand) to investigate the optimal amount of time required to detect targeted pest species (rats, possums and mice), and to examine the potential of rats and possums to bias detection rates of other species. We found depressed detections of possums and rats where a contraspecific had been detected on a card, which is consistent with previous studies of a similar duration on interspecies interference. This experiment is the first to analyse the rates at which species detections accrue over the course of a survey, and we found rat detections lagged behind possums for the first four nights. We modelled the effect of survey duration and relative rat abundance on the likelihood of further possum detections. Duration and rat abundance interacted, meaning there are trade-offs to be considered with regard to duration: shorter durations may avoid the risk of saturation in areas of high pest density, but risk not sampling sparse or neophobic populations. Our data suggest that chew cards remain one of the most sensitive pest monitoring tools for rats and possums, compared to conventional methods such as tracking tunnels and wax tags. In areas of moderate pest densities, we suggest that a duration of five nights is optimal for detecting pests. However, in areas of high pest density the sensitivity of chew cards may render them unsuitable because of saturation and interspecies interference effects.
OTU data and analysis files for interspecies comparison of Philippine terrestrial small mammal diets
<p>Island radiations represent unique evolutionary histories in unique ecological contexts. These radiations provide opportunities to investigate ecological diversification in groups that typically exhibit niche partitioning among their constituents, including partitioning of food resources. DNA metabarcoding produces finer levels of diet identification than traditional methods, allowing us to examine dietary niche partitioning in communities or clades in which species share superficially similar diets. Here we use DNA metabarcoding to investigate dietary niche partitioning in an endemic radiation of mammals in the Philippines. Our data reveal niche partitioning as well as phylogenetically-uncorrelated adaptive evolution in this small mammal community. Because 70% of the focal species belong to the tribe Chrotomyini, an endemic Philippine radiation of murid rodents that feed extensively on earthworms, this study sheds light on dietary adaptation and its role in the co-occurrence of closely related species. Our results reveal fine-scale resource partitioning within this community; our data provide compelling evidence for niche partitioning of diet that was masked by previous diet categories and will help in further dissecting the model adaptive radiation of endemic small mammals on Luzon. This study reinforces the notion that DNA metabarcoding can be a valuable tool for investigating both ecological relationships and evolutionary ecology at the community and phylogenetic level, respectively.</p>
Supplementary figure collections 1–3 of 'Interspecies co‐expression analysis of lateral root development using inducible systems in rice, Medicago, and Arabidopsis'
<p>Supplementary figure collections 1–3 of 'Interspecies co‐expression analysis of lateral root development using inducible systems in rice, Medicago, and Arabidopsis' (10.1111/tpj.16481)</p>
Data from: Interspecies interference and monitoring duration affect detection rates in chew cards
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OTU data and analysis files for interspecies comparison of Philippine terrestrial small mammal diets
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Association of poultry vaccination with interspecies transmission and molecular evolution of H5 subtype avian influenza virus
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Analysis code and additional data associated with the manuscript entitled 'Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion'
<p>This dataset is associated with the research manuscript entitled ‘<em>Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion</em>’ (https://www.biorxiv.org/content/10.1101/754002v2).</p> <p>The folder ‘<strong>Zenodo_Saxena_etal_2021_AdditionalData_AnalysisCode</strong>’ contains:</p> <p>> Analysis code used for jerboas-mouse differential RNASeq analysis (<strong>saxena_Interspecies_DESEQ2_analysis.R</strong>).</p> <p>> A folder <strong>Mus_Jac_gtfDir</strong> with two gtf annotation files for 1:1 orthologs in Mouse (musAnno4_1To1Orthologs) and Jerboa (jerboaAnno4_1To1Orthologs) genomes generated with CESAR. This folder also contains two files with mouse or jerboa gene lengths in non-overlapping exons of each gene in the 1:1 orthologous GTF annotations (suffixed "*_exon_lengths_per_gene.txt"). A supporting R library required to run the analysis is provided in this folder (saxena_shared_library_v2.R).</p> <p>>A <strong>STAR_countsDir</strong> folder with STAR generated GeneCounts for mouse and jerboa samples (suffixed "*_SR50"). Subfolders contain metatarsal (MT) and Radius/ulna (RU) STAR Genecounts used in the primary (“*_n=3") and independent validation ("*_n=2") analyses.</p> <p>> A pdf file with <strong>Additional Figures 1 and 2</strong>. Fig 1 shows RNAScope <em>in situs </em>for <em>Galnt17</em> in jerboa and mouse postnatal day 5 cartilages. Fig 2 shows DESeq2 generated MA-plot for jerboa-mouse metatarsal comparisons (n=3).</p> <p>> <strong>Additional Data Tables_1to3</strong> with DESeq2 differential expression results for all of the 17,464 mouse and jerboa orthologs in the primary (n=3, Table1) and independent validation (n=2, Table2) analyses. r-log transformed gene counts for 17,464 mouse and jerboa 1:1 orthologs in metatarsal samples (n=3, Table3).</p>
Dataset for Interspecies interactions determine growth dynamics of biopolymer degrading populations in microbial communities.
<p>This is the dataset (containing raw and annotated image sets, scripts, and growth dynamics) </p>
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International Brain Laboratory public data
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OpenNeuro
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