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opencc-by-4.0May 2020View details →

Large Scale Computational Analysis of Coding and Non-coding Element Expression in Mycobacterium tuberculosis Unannotated CDS

Large Scale Computational Analysis of Coding and Non-coding Element Expression in Mycobacterium tuberculosis Unannotated CDS data for the Applied Medical Science MSci Research Project.

opencc-zeroJul 2020View details →

Data from: Comparative analysis of DNA repeats and identification of novel Fesreba centromeric element in fescues and ryagrasses

Background Cultivated grasses are an important source of food for domestic animals worldwide. Better knowledge of their genomes can speed up the development of new cultivars with better quality and resistance to biotic and abiotic stresses. The most widely grown grasses are tetraploid ryegrass species ( Lolium spp.) and diploid and hexaploid fescue species (Festuca spp.). In this work, we characterized repetitive DNA sequences and their contribution to genome size in five fescue and two ryegrass species, as well as one fescue and two ryegrass cultivars. Results Partial genome sequences produced by Illumina technology were used for genome-wide comparative analyses using RepeatExplorer pipeline. Retrotransposons were found to be the most abundant repeat types in all seven grass species. Athila element of Ty3/gypsy family showed the most striking differences in copy number between fescues and ryegrasses. The sequence data enabled the assembly of an LTR element Fesreba, which is highly enriched in centromeric and (peri)centromeric regions in all species. A combination of FISH with a probe specific to Fesreba element and immunostaining with CENH3 antibody showed their colocalization and indicated a possible role of Fesreba in centromere function. Conclusions Comparative repeatome analysis in a set of fescues and ryegrasses provided new insights into their genome organization and divergence, including the assembly of LTR element Fesreba. A new LTR element Fesreba was identified and found abundant in centromeric regions of the fescues and ryegrasses. It may have a role in the function of their centromeres.

opencc-by-4.0Jan 2021View details →

Femtosecond-LA-ICP-MS analysis recording variation in trace elements in Amphistegina lessonii from Akajima, Okinawa Prefecture, Japan

The data set comprises of sea surface temperatures, salinity which were recorded from Akajima Island, Okinawa Prefecture, Japan during the year 2003 and 2004. The tidal heights data was generated using the software Tide Predictor for the Akajima Island. The  Element/Ca analysis of larger benthic foraminifera Amphistegina lessonii was carried out by using Femto-second Laser Ablation Inductively Coupled Plasma-Mass Spectrometer (fs-LA-ICP-MS) technique at the Department of Climate Geochemistry, Max Planck Institute for Chemistry. The co-variation and correlation plots of Element/Ca with tidal heights, sea surface temperature and sea surface salinity are also provided.

opencc-zeroJan 2021View details →

Phylogenomic analysis of ultraconserved elements resolves the evolutionary and biogeographic history of Segmented Trapdoor Spiders

The segmented trapdoor spiders (Liphistiidae) are the sole surviving family of the suborder Mesothelae, which forms the sister lineage to all other living spiders. Liphistiids have retained a number of plesiomorphic traits and their present-day distribution is limited to East and Southeast Asia. Studying this group has the potential to shed light on the deep evolutionary history of spiders, but the phylogeny and divergence times of the family have not been resolved with confidence. We performed phylogenomic and molecular dating analyses of 2,765 ultraconserved element loci from 185 liphistiid taxa. Our analyses show that the crown group of Liphistiidae appeared in the mid-Cretaceous at 102 Ma (95% credibility interval 92–113 Ma), but it was not until the Neogene that much of the diversification within the family occurred in mainland Southeast and East Asia. This diversification was coincident with tectonic events such as the extension of the East Asian continental margin, as well as geological upheavals in Indochina induced by the collision between India and Asia. Our study highlights the important role of major tectonic events in shaping the evolutionary history, present-day diversity, and geographical distribution of mesothele and liphistiid spiders.

opencc-zeroDec 2016View details →

Data from: Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements

Phylogenetics is undergoing a revolution as large-scale molecular datasets reveal unexpected but repeatable rearrangements of clades that were previously thought to be disparate lineages. One of the most unusual clades of fishes that has been found using large-scale molecular datasets is an expanded Syngnathiformes including traditional long-snouted syngnathiform lineages (Aulostomidae, Centriscidae, Fistulariidae, Solenostomidae, Syngnathidae), as well as a diverse set of largely benthic-associated fishes (Callionymoidei, Dactylopteridae, Mullidae, Pegasidae) that were previously dispersed across three orders. The monophyly of this surprising clade of fishes has been upheld by recent studies utilizing both nuclear and mitogenomic data, but the relationships among major lineages within Syngnathiformes remain ambiguous; previous analyses have inconsistent topologies and are plagued by low support at deep divergences between the major lineages. In this study, we use a dataset of ultraconserved elements (UCEs) to conduct the first phylogenomic study of Syngnathiformes. UCEs have been effective markers for resolving deep phylogenetic relationships in fishes and, combined with increased taxon sampling, we expected UCEs to resolve problematic syngnathiform relationships. Overall, UCEs were effective at resolving relationships within Syngnathiformes at a range of evolutionary timescales. We find consistent support for the monophyly of traditional long-snouted syngnathiform lineages (Aulostomidae, Centriscidae, Fistulariidae, Solenostomidae, Syngnathidae), which better agrees with morphological hypotheses than previously published topologies from molecular data. This result was supported by all Bayesian and maximum likelihood analyses, was robust to differences in matrix completeness and potential sources of bias, and was highly supported in coalescent-based analyses in ASTRAL when matrices were filtered to contain the most phylogenetically informative loci. While Bayesian and maximum likelihood analyses found support for a benthic-associated clade (Callionymidae, Dactylopteridae, Mullidae, and Pegasidae) as sister to the long-snouted clade, this result was not replicated in the ASTRAL analyses. The base of our phylogeny is characterized by short internodes separating major syngnathiform lineages and is consistent with the hypothesis of an ancient rapid radiation at the base of Syngnathiformes. Syngnathiformes therefore present an exciting opportunity to study patterns of morphological variation and functional innovation arising from rapid but ancient radiation.

opencc-zeroDec 2013View details →

Data from: Analysis of transposable elements in the genome of Asparagus officinalis from high coverage sequence data

Asparagus officinalis is an economically and nutritionally important vegetable crop that is widely cultivated and is used as a model dioecious species to study plant sex determination and sex chromosome evolution. To improve our understanding of its genome composition, especially with respect to transposable elements (TEs), which make up the majority of the genome, we performed Illumina HiSeq2000 sequencing of both male and female asparagus genomes followed by bioinformatics analysis. We generated 17 Gb of sequence (12×coverage) and assembled them into 163,406 scaffolds with a total cumulated length of 400 Mbp, which represent about 30% of asparagus genome. Overall, TEs masked about 53% of the A. officinalis assembly. Majority of the identified TEs belonged to LTR retrotransposons, which constitute about 28% of genomic DNA, with Ty1/copia elements being more diverse and accumulated to higher copy numbers than Ty3/gypsy. Compared with LTR retrotransposons, non-LTR retrotransposons and DNA transposons were relatively rare. In addition, comparison of the abundance of the TE groups between male and female genomes showed that the overall TE composition was highly similar, with only slight differences in the abundance of several TE groups, which is consistent with the relatively recent origin of asparagus sex chromosomes. This study greatly improves our knowledge of the repetitive sequence construction of asparagus, which facilitates the identification of TEs responsible for the early evolution of plant sex chromosomes and is helpful for further studies on this dioecious plant.

opencc-by-4.0Oct 2023View details →

Supplementary tables for the article "LIBS and XRF for the elemental analysis of aquatic organisms"

Supplementary tables with full analytical results (Russian and English versions)

opencc-by-4.0Oct 2023View details →

IODP Expedition 391 ICP-AES elemental analysis (interstitial water)

Elemental concentration in interstitial water samples was measured by inductively coupled plasma - atomic emission spectroscopy (ICP-AES). Data are presented by element-wavelength pair (e.g., more than one calcium line may be reported). Elemental lines for which data do not exist for a particular expedition will not appear.

opencc-zeroMar 2024View details →

Exploring the preservation of a parasitic trace in decapod crustaceans using finite elements analysis

The fossil record of parasitism is poorly understood, due largely to the scarcity of strong fossil evidence of parasites. Understanding the dynamics of preservation for fossil parasitic evidence is critical to contextualizing the fossil record of parasitism. Here, we present the first use of X-ray computed tomography (CT) scanning and finite elements analysis (FEA) to analyze the impact of a parasite-induced fossil trace on host preservation. Seven fossil and modern decapod crustacean specimens with branchial swellings attributed to an epicaridean isopod parasite were CT scanned and examined with FEA to assess differences in the magnitude and distribution of stress between normal and swollen branchial chambers. The results of the FEA show highly localized stress peaks in reaction to point forces, with higher peak stress on the swollen branchial chamber for all specimens, suggesting a possible shape-related decrease in the preservation potential of these parasitic swellings. Broader application of these methods as well as advances in the application of 3D data analysis in paleontology are critical to understanding the fossil record of parasitism and other poorly represented fossil groups.

Fig. 6 in Unraveling the Myotis morass: ultraconserved-element analysis reveals introgression, cryptic diversity, and taxonomic trouble

Fig. 6. Proposed Introgression Pathways identified using quartet asymmetry tests. Sixty-three quartets indicated significant deviation from expectations under incomplete lineage sorting. Pathways are identified by letters with number of supporting quartets in parentheses. Branch lengths are time-calibrated as in Fig. 1.

Fig. 5 in Unraveling the Myotis morass: ultraconserved-element analysis reveals introgression, cryptic diversity, and taxonomic trouble

Fig. 5. Measures of population structure and diversity of the Nearctic Myotis species. (A) ASTRAL_I tree constructed from 2,615 UCE gene trees—dots indicate posterior probability (red> 0.9, blue = 1). (B) Principal component analysis of SNP loci from the UCE sequences—inset in B illustrates the amount of variance explained by PCs 1 to 11. (C) Map of sample collection locations. (D) Neighbor-joining tree constructed from SNPS. Colors in B–D are the same for each individual and are based on the first 3 components of the principal component analysis. Samples marked by * in A and D are individuals with discordant positions on the trees and are discussed further in the text.

Fig. 4 in Unraveling the Myotis morass: ultraconserved-element analysis reveals introgression, cryptic diversity, and taxonomic trouble

Fig. 4. Measures of population structure and diversity of the Neotropical "ruber group." (A) ASTRAL_I tree constructed from 2,615 UCE gene trees—dots indicate posterior probability (red> 0.9, blue = 1). (B) Principal component analysis of SNP loci from the UCE sequences—inset in B illustrates the amount of variance explained by PCs 1 to 11. (C) Map of sample collection locations. (D) Neighbor-joining tree constructed from SNPs. Colors in B–D are the same for each individual and are based on the first 3 components of the principal component analysis.

Fig. 3 in Unraveling the Myotis morass: ultraconserved-element analysis reveals introgression, cryptic diversity, and taxonomic trouble

Fig. 3. Measures of population structure and diversity of Neotropical "albescens group." (A) ASTRAL_I tree constructed from 2,615 UCE gene trees—dots indicate posterior probability (red> 0.9, blue = 1). (B) Principal component analysis of SNP loci from the UCE sequences—inset in B illustrates the amount of variance explained by PCs 1 to 11. (C) Map of sample collection locations. (D) Neighbor-joining tree constructed from SNPs. Colors in B–D are the same for each individual and are based on the first 3 components of the principal component analysis. Individuals indicated with colored symbols in A and D are individuals with discordant positions on the trees and are discussed further in the text.

Fig. 1 in Unraveling the Myotis morass: ultraconserved-element analysis reveals introgression, cryptic diversity, and taxonomic trouble

Fig. 1. (A) Myotis ASTRAL_S species tree inferred from 2,615 UCE gene trees. Pie charts show the percentage of trees supporting each of 3 possible quartet topologies. All branches received posterior probabilities> 0.90. All others indicated with dots. Colored bars on the right of the tree show

Fig. 2 in Unraveling the Myotis morass: ultraconserved-element analysis reveals introgression, cryptic diversity, and taxonomic trouble

Fig. 2. Comparison of tree conflict by marker for 3 broad phylogeographic Myotis groups: (A) Nearctic group; (B) Neotropical "albescens group"; (C) Neotropical "ruber group." This is a subset of individuals shown in Fig. 1A. For each group, the left tree displays the ASTRAL_I UCE phylogeny while the right displays the maximum likelihood Cyt b phylogeny. The same individuals are shown in each tree pair. Lines between trees denote notable topological differences between markers. Colors for highlighting by species are an approximated average color for that species as determined by the first 3 components of the PCAs shown in Figs. 3–5.

opencc-by-4.0Jun 2024View details →

Metadata description regarding a study "Competitiveness and value creation: Longitudinal analysis of sawmills and wood construction element producers in Finland"

This dataset is supplied by a commercial information service and is subject to usage restrictions. As such, the dataset itself cannot be publicly shared. This metadata description offers detailed information about the dataset's content and structure.

opencc-by-4.0May 2018View details →

Geographic Information System of structural elements in the Niobe-Aphrodite Map Area of Venus: a tool for structural and geologic analysis.

The Niobe Aphrodite Map Area covers over 25% of the surface of Venus and extends from 57N to 57S and 60E to 180E. The structural-element map presented here is derived from the1:10 M-scale geologic maps of Niobe Planitia, U.S. Geological Survey I-2467 and Aphrodite Terra, U.S. Geological Survey I-2476. Both maps are in various stages of review and revision overseen by the U.S. Geological Survey on behalf of NASA. Here we present a Geographic Information System (GIS) that contain the different structural elements of the area (deformation structures and lithodemic units), that can be used to analyze relationships between and among suites of structural elements across this large portion of Venus’ surface. Base images and data on which determination of the structural element determination is based can be accessed and downloaded directly in GIS-ready formats through the USGS Map a Planet website (https://astrogeology.usgs.gov/tools/map-a-planet-2).

opennotspecifiedMay 2019View details →

lil, left ilium;; lti, left tibia; pd, pedal digits; and ub, unidentified bony element. The white box indicates the position from which the sample was taken for histological analysis. Scale bars, 10 mm (a, c, d), 20 mm (b). in A new Jurassic scansoriopterygid and the loss of membranous wings in theropod dinosaurs

lil, left ilium;; lti, left tibia; pd, pedal digits; and ub, unidentified bony element. The white box indicates the position from which the sample was taken for histological analysis. Scale bars, 10 mm (a, c, d), 20 mm (b).

opencc-by-4.0Dec 2018View details →

Description of the monitoring analysis and evaluation of the new façade elements for building envelopes in both new construction and renovation.

Deliverable with descritpion of Eco-Binder demo buildings