Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
317
datasets available to search
ShareScore release 0.9.0
Dataset results
317 results for “gene structure”
Data from: Limited gene dispersal and spatial genetic structure as stabilizing factors in an ant-plant mutualism
Comparative studies of the population genetics of closely associated species are necessary to properly understand the evolution of these relationships because gene flow between populations affects the partners' evolutionary potential at the local scale. As a consequence (at least for antagonistic interactions), asymmetries in the strength of the genetic structures of the partner populations can result in one partner having a co-evolutionary advantage. Here, we assess the population genetic structure of partners engaged in a species-specific and obligatory mutualism: the Neotropical ant-plant, Hirtella physophora, and its ant associate, Allomerus decemarticulatus. Although the ant cannot complete its life cycle elsewhere than on H. physophora and the plant cannot live for long without the protection provided by A. decemarticulatus, these species also have antagonistic interactions: the ants have been shown to benefit from castrating their host plant and the plant is able to retaliate against too virulent ant colonies. We found similar short dispersal distances for both partners, resulting in the local transmission of the association and, thus, inbred populations in which too virulent castrating ants face the risk of local extinction due to the absence of H. physophora offspring. On the other hand, we show that the plant populations probably experienced greater gene flow than did the ant populations, thus enhancing the evolutionary potential of the plants. We conclude that such levels of spatial structure in the partners' populations can increase the stability of the mutualistic relationship. Indeed, the local transmission of the association enables partial alignments of the partners' interests, and population connectivity allows the plant retaliation mechanisms to be locally adapted to the castration behaviour of their symbionts.
Oxytenanthera abyssinica (A. Rich.) Munro; lowland bamboo (Poaceae, Bambusinea) in Ethiopia: Genetic diversity, population structure and gene flow analysis
<p><span>As one of the most important non-timber forest resources, a potential alternative to wood and wood product and fastest-growing plant in the world (91 cm (35 in) per day), bamboo is a member of the grass family (Poaceae) and constitutes a single subfamily Bambusoideae. 67% of total area of bamboo in Africa and 7% of world total is contributed by Ethiopia giving more than 1.44 million hectares. Silica gel dried young fresh leaves from 130 individuals of O. abyssinica were collected for DNA extraction and PCR amplification. Each of the PCR amplified ISSR fragments using 19 ISSR primers were used to study band pattern and heterozigosity, level of polymorphism, calculating marker efficiency, Nei`s (H) and Shannon (I) genetic diversity, analysis of molecular variance (AMOVA), analysis for cluster, principal coordinates (PCoA) and admixture results. High genetic variation at species level was observed with the percentage of the polymorphic loci (PPL) = 84.48%. The H, I, observed number of alleles (Na) and effective number of alleles (Ne) at species level was 0.2702, 0.4061, 1.8448, and 1.4744, respectively, showing a relatively high level of genetic diversity. However, the genetic differentiation at the population level was relatively low. AMOVA using grouped populations revealed that, most of the diversity was distributed within the populations (61.05%) with F<sub>ST</sub> = 0.38949, F<sub>SC</sub> = 0.10486 and F<sub>CT</sub> = 0.31797. Cluster analysis grouped the populations into sharply distinct clusters, which could be attributed to cross pollination nature of the plant and long lived to the area. STRUCTURE analyses for all population and excluding Gambella population gives different result K = 2 and K = 11. Using these markers, we find strong evidence linking geographic origin of diversity and samples from Gambella Region found different from others and might tell the availability of additional bamboo species in the country.</span></p>
FIGURE 1 in Analysis of primary structure loops from Hairpins 35 and 48 of the Nematoda SSU rRNA gene provides further evidence that the genera Tripylina Brzeski, 1963, Trischistoma Cobb, 1913 and Rhabdolaimus de Man, 1880 are members of Enoplida
FIGURE 1. Localisation of synapomorphic molecular traits in 18S r RNA genes of Enoplida. A. Fragments of alignments of aligned gene sequences corresponding to SSU rRNA regions of hairpins 35 and 48. Presumed synapomorphies of Trichistoma, Tripylina and other Enoplida are marked and given a dark background. B. Secondary structures of Hairpin 35 of Loricera foveata. C. Secondary structures of Hairpin 35 of Trischistoma and Tripylina. Arrowed, 1280 A → G substitution. D. Secondary structures of Hairpin 48 of Loricea foveata. E. Secondary structures of Hairpin 48 of Trischistoma and Tripylina. Arrowed: 1820 G → Y substitution.
Atomic-Resolution Structure of the Protein Encoded by Gene V of fd Bacteriophage in Complex with Viral ssDNA Determined by Magic-Angle Spinning Solid-State NMR
<p>F-specific filamentous phages, elongated particles with circular single-stranded DNA encased in a symmetric protein capsid, undergo an intermediate step, where thousands of homodimers of a non-structural protein, gVp, bind to newly synthesized strands of DNA, preventing further DNA replication and preparing the circular genome in an elongated conformation for assembly of a new virion structure at the membrane. While the structure of the free homodimer is known, the ssDNA-bound conformation has yet to be determined. We report an atomic-resolution structure of the gVp monomer bound to ssDNA of fd phage in the nucleoprotein complex elucidated via Magic-Angle Spinning solid-state NMR. The model presents significant conformational changes with respect to the free form. These modifications facilitate the binding mechanism and possibly promote cooperative binding in the assembly of the gVp-ssDNA complex.</p> <p>The raw NMR data used for structure determination are uploaded as original Bruker directories from topspin version 3.5. Processing details are given in the supporting Information of the manuscript. PDB ID is 8ACZ. BMRB accession number is 51391.</p>
Dataset to article "Distinct traits of structural and regulatory evolutional conser-vation of human genes with specific focus on major cancer mo-lecular pathways"
<p>Abstract: Evolution of protein coding genes has both structural and regulatory components. The first can be assessed by measuring the ratio of non-synonymous to synonymous nucleotide sub-stitutions. The second component can be measured as the normalized proportion of transposable elements that used as the regulatory elements. For the first time, we characterized in parallel the regulatory and structural evolutionary profiles for 10,890 human genes and 2,972 molecular pathways. We observed ~0.1 correlation between the structural and regulatory metrics at the gene level, which appeared much higher (~0.4) at the pathway level. We deposited the data in the publicly available database RetroSpect accessible at https://retrospect.oncobox.com. We also analyzed evolutionary dynamics of six cancer pathways of two major axes: Notch/WNT/Hedgehog and AKT/mTOR/EGFR. The Hedgehog pathway had both components slower, whereas the Akt pathway had clearly accelerated structural evolution. In particular, the major hub nodes Akt and beta-catenin showed both components strongly decreased, whereas two major regulators of Akt TCL1 and CTMP had outstandingly high evolutionary rates. We al-so noticed structural conservation of serine/threonine kinases and the genes related to guanosine metabolism in cancer signaling: GPCRs, G proteins, and small regulatory GTPases (Src, Rac, Ras); however, this was compensated by the accelerated regulatory evolution.</p>
Gene structure prediction results and execution commands and options by GINGER and similar tools
<p>Gene structure prediction results, execution commands, and options by GINGER and similar tools</p> <ul> <li>genome.tar.gz ... genome sequence data used for benchmark test in the paper. </li> <li>input_of_EVM.tar.gz ... input dataset for EVM</li> <li>input_of_GINGER.tar.gz ... input dataset for GINGER</li> <li>input_of_MAKER.tar.gz ... input dataset for MAKER</li> <li>reference_annotation.tar.gz ... gff data used for benchmark test in the paper.</li> <li>result_of_EVM.tar.gz .... results and stats information of EVM (including intermediate result file of <em>C.elegans</em>, <em>D. melanogaster</em>, <em>O. sativa</em>, <em>D. rerio</em>, and <em>H. sapiens</em>)</li> <li>result_of_GINGER.tar.gz .... results and stats information of GINGER (including intermediate result files of <em>C.elegans</em>)</li> <li>result_of_MAKER.tar.gz .... results and stats information of MAKER (including intermediate result files of <em>C.elegans</em>)</li> </ul>
Fig. 7 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice
Fig. 7. Expression profiles analysis of OsFBNs under different temperature stresses. Eleven OsFBN genes in rice were detected for their transcript levels in leave tissues of seedlings at the three-leaf stage with different time intervals after the 35 ̊C (heat stress) and 6 ̊C (cold stress) stresses in the growth chamber, separately. The OsUBQ gene was used as a normalization control; data was measured as the mean values ± SD of three replicates, respectively.
Fig. 4 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice
Fig. 4. Phylogenetic and exon-intron structure analysis of FBN family genes in rice and Arabidopsis. The phylogenetic analysis was performed using the amino acid sequences of 25 FBN family proteins in rice and Arabidopsis (Left). The unrooted phylogenetic tree was generated by the neighbor-joining method and displayed using MEGA7 software. Numbers above or below branches of the evolution tree indicated the bootstrap values; The exon-intron structures of 25 FBN family genes in rice and Arabidopsis were analyzed (Right), the exons were represented by yellow boxes, the UTR by blue, black lines connecting two exons were introns. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 6 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice
Fig. 6. The in vitro lipid binding assays of PAP-domains. A and C, schematic representations of the mutant residues in OsFBN2 and OsFBN4 proteins in the in vitro lipid binding assays. B and D, the in vitro lipid-binding activity assays were performed by a fluorescence lipid probe P-96 (1 mM), fatty acids with C12:0, C14:0, C16:0, C18:0, C20:0, C22:0, with each (0.5 mM) of wild type (Wt) and mutant fusion protein (Mut) of PAP domains in OsFBN2 and OsFBN4 proteins, respectively. Detection experiments were performed with three biological replicates. * and ** symbols indicated the significant difference levels of P <0.05 or P <0.01 between mutant and wild type, respectively.
Fig. 5 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice
Fig. 5. Subcellular localization of CTP domains-fused GFP proteins. These constructs of p35S-FBN1-11-CTP-GFP or p35S-Trxm5-GFP, separately, were transiently expressed in Nicotiana benthamiana mesophyll cells. The co-localizations of fluorescence patterns of CTP domains of ten OsFBN proteins except OsFBN8 fused GFP were observed with the autofluorescence of chlorophyll in chloroplasts in protoplasts. The Trxm5-GFP was used as a chloroplast marker.
Fig. 3 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice
Fig. 3. PKC domain analysis of FBN11 clade in plants. A, Homology analysis of PKC domain sequences in FBN11 clades; B, evolutionary tree analysis of PKC domain in five plant species (Oryza sativa (Os), Selaginella moellendorffii (Smo), Arabidopsis thaliana (At), Glycine max (Gm), and Zea mays (Zm)) and algae (Monoraphidium neglectum (Mon), Chlorella sorokiniana (Chlo), Chlamydomonas sp. UWO 241 (Chla), and Haemato coccus lacustris (Hae); C, the conserved motif analysis of PKC domain in FBN11 protein clades in higher plants.
Fig. 2 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice
Fig. 2. Box-plot graphs and motif analysis of CTP and PAP-domain in plants. The protein sequences of CTP domains and PAP domains were analyzed in six plant species: Selaginella moellendorffii (Smo), Physcomitrella patens (Ppa), Arabidopsis thaliana (At), Glycine max (Gm), Oryza sativa (Os), and Zea mays (Zm), The grand average of hydropathicity (GRAVY) and isoelectric point (pI) of CTP domains of FBN1-11 protein clades were showed in A and B, respectively; The GRAVY and pI of PAP domains in FBN1-11 protein clades were showed in C and D, respectively; The dotted line represented the average values of GRAVY and pI, respectively; The conserved motif sequence of PAP domains in these plants were showed in E.
Fig. 1 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice
Fig. 1. Phylogenetic tree analysis of 121 fibrillin family proteins from 10 representative species. The neighbor-joining tree was constructed using the sequences of 121 fibrillin family proteins in ten representative species: Synechococcus sp. PCC 7002 (Ssp), Erysimum siliculosus (Esi), Emiliania huxleyii (Ehu), Thalassiosira pseudonana (Tps), Chlamydomonas reinhardtii (Cre), Volvox carteri (Vca), Physcomitrella patens (Ppa), Selaginella moellendorffii (Smo), Arabidopsis thaliana (At) and Oryza sativa (Os). Bootstrap values were indicated on the branches. Each fibrillin protein was labeled by its name (Table S3). The green and red color meant the proteins present in algae or terrestrial plant, respectively; the blue color represents the proteins present in both algae and terrestrial plants. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Human Genomic Population Structure and Phenotype-genotype Variation in ADME Genes in Four Populations
ClinicalTrials.gov study NCT02789527. IPD Sharing: UNDECIDED. Countries: 4. Publications: 1.
Data from: Targeted re-sequencing of five Douglas-fir provenances reveals population structure and putative target genes of positive selection
Open the record for dataset details and reuse information.
Data from: Genetic structure and shell shape variation within a rocky shore whelk suggests both diverging and constraining selection with gene flow
Open the record for dataset details and reuse information.
Data from: The 5S rDNA gene family in mollusks: characterization of transcriptional regulatory regions, prediction of secondary structures, and long-term evolution, with special attention to Mytilidae mussels
Open the record for dataset details and reuse information.
Data from: Nearly complete rRNA genes from 371 Animalia: updated structure-based alignment and phylogenetic analysis
Open the record for dataset details and reuse information.
Data from: Geographic population structure of the African malaria vector Anopheles gambiae suggests a role for the forest-savannah biome transition as a barrier to gene flow
Open the record for dataset details and reuse information.
Data from: Limited gene dispersal and spatial genetic structure as stabilizing factors in an ant-plant mutualism
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.