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2,960 results for “elements”
A bacterial toxin-antitoxin system as a native defence element against RNA phages
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DNA gains and losses in gigantic genomes do not track differences in transposable element-host silencing interactions
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Transposable element accumulation drives size differences among polymorphic Y chromosomes in Drosophila
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Stream Elemental Cycling (LTER Synthesis Working Group)
A global compilation of stream chemistry data was synthesized to evaluate spatial and temporal trends in solutes with a particular focus on dissolved organic matter and nitrogen (inorganic and organic forms). Data span a global array of streams and rivers ranging from the tropics to the arctic. Data include concentrations of dissolved organic nitrogen, nitrate, ammonium, total dissolved nitrogen, and dissolved organic carbon. Data set also includes other measures of physical-chemical properties where available. Data from different sites span various amounts of time and some sites include intensive sampling while other data represent extensive sampling protocols. Two data sets are provided: 1) the synthesize data product (“All Sites Combined) and 2) “Data All Median” which provides median values for each site.
Elevation, mesh elements, and strickler roughness coefficient for the Virginia Coastal Reserve
 This dataset contains a mesh and associated elements for the southern Delmarva Peninsula
Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements
<p><em>Austropuccinia psidii</em>, originating in South America, is a globally invasive fungal plant pathogen that causes rust disease on Myrtaceae. Several biotypes are recognized, with the most widely distributed pandemic biotype spreading throughout the Asia-Pacific and Oceania regions over the last decade. <em>Austropuccinia</em><em> psidii</em> has a broad host range with more than 480 myrtaceous species. Since first detected in Australia in 2010, the pathogen has caused the near extinction of at least three species and negatively affected commercial production of several Myrtaceae. To enable molecular and evolutionary studies into <em>A. psidii</em> pathogenicity, we assembled a highly contiguous genome for the pandemic biotype. With an estimated haploid genome size of just over 1 Gb (gigabases), it is the largest assembled fungal genome to date. The genome has undergone massive expansion via distinct transposable element (TE) bursts. Over 90% of the genome is covered by TEs predominantly belonging to the Gypsy superfamily. These TE bursts have likely been followed by deamination events of methylated cytosines to silence the repetitive elements. This in turn led to the depletion of CpG sites in transposable elements and a very low overall GC content of 33.8%. The overall gene content is highly conserved, when compared to other closely related Pucciniales, yet the intergenic distances are increased by an order of magnitude indicating a general insertion of TEs between genes. Overall, we show how transposable elements shaped the genome evolution of <em>A. psidii</em> and provide a greatly needed resource for strategic approaches to combat disease spread. Please cite the authors if using this data: https://academic.oup.com/g3journal/article/11/3/jkaa015/6007476</p>
Additional data for the publication "Rare Earth Elements in oyster shells: provenance discrimination and potential vital effects"
<p>Rare Earth Elements (REE) and yttrium measurements from modern (Marennes-Oléron, France) oyster shells collected by LA-ICP-MS. This dataset is used in the publication 'Rare Earth Elements in oyster shells: provenance discrimination and potential vital effects'.</p>
Suspended photonic crystal membranes in AlGaAs heterostructures for integrated multi-element optomechanics
<p>The figures in [Sushanth Kini Manjeshwar et.al (arXiv:2004.12454)] were produced with the data stored here. The data were produced by the provided scripts. Please read the Readme.txt for the overview of the structure of the data and how to use the scripts to re-generate the data or use it to produce new data.</p>
Large Scale Computational Analysis of Coding and Non-coding Element Expression in Mycobacterium tuberculosis Unannotated CDS
<p>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. </p>
Three needle Sorter 1 element, effect of the lateral needles on the probe
<p>In this Dataset it is possible to observe the effect of the lateral needles, or stigmators, of the Sorter1 on a slightly out of focus probe.</p> <p>The theory behind this device can be found at <strong><a href="https://doi.org/10.1016/j.ultramic.2019.112861">10.1016/j.ultramic.2019.112861</a></strong></p>
Off-Axis electron holography data for phase reconstruction of the Sorter 1 element with applied potential
<p>Here reported the dataset used for the reconstraction of the phase of the electron wave functions after interaction with the Sorter 1 Element.</p>
In-focus and Out of focus images of the 11-needles Sorter 2 element
<p>In this dataset it is possible to observe a series of out of focus images of the Sorter 2 element, where the potentials were varied:</p> <p>-V1 is the electrostatic potential on the external needles;</p> <p>-V2 on the even needles;</p> <p>-V3 on the remaining off needles</p> <p>We are able to control the applied electrostatic potential individually on each odd needle, while the even ones are all connected and at the same potential, thanks to a custom made aperture holder by Thermofisher.</p>
Data from: Comparative analysis of DNA repeats and identification of novel Fesreba centromeric element in fescues and ryagrasses
<p>Background<br> 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.</p> <p>Results<br> 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.</p> <p>Conclusions<br> 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.</p>
The impact of local population genetic background on the spread of the selfish element Medea-1 in red flour beetles
<p>Selfish genetic elements have been found in the genomes of many species, yet our understanding of their evolutionary dynamics is only partially understood. A number of distinct selfish <i>Medea</i> elements are naturally present in many populations of the red flour beetle (<i>Tribolium castaneum</i>). Although these <i>Medea</i> elements are predicted by models to increase in frequency within populations because any offspring of a <i>Medea</i>-bearing mother that do not inherit at least one <i>Medea</i> allele will die, experiments demonstrating an increase in a naturally occuring <i>Medea</i> element are lacking. Our survey of the specific <i>Medea </i>element<i>, </i>M<sup>1</sup>, in the United States showed that it had a patchy geographic distribution. From the survey it could not be determined if this distribution was caused by a slow process of M<sup>1</sup> colonization of discrete populations or if some populations lacked M<sup>1</sup> because they had genetic factors conferring resistance to the <i>Medea </i>mechanism. We show that populations with naturally low to intermediate M<sup>1</sup> frequencies likely represent transient states during the process of <i>Medea</i> spread. Furthermore, we find no evidence that genetic factors are excluding M<sup>1</sup> from US populations where the element is not presently found. We also show how a known suppressor of <i>Medea</i> can impair the increase of M<sup>1</sup> in populations and discuss the implications of our findings for pest-management applications of <i>Medea</i> elements.</p>
Combined-evidence analyses of ultraconserved elements and morphological data: an empirical example in iguanian lizards
<p>Genomic datasets generated by next-generation sequencing are increasingly prevalent in phylogenetics, but morphological data are required to phylogenetically place fossils, corroborate molecular hypotheses, and date phylogenies. Combined-evidence analyses provide an integrative assessment of tree topology. However, no attempt has been made to simultaneously analyze next-generation genomic datasets and morphological data, and the future of morphology in the context of genomic data is uncertain. I conducted combined-evidence analyses that include genomic and morphological datasets, specifically, with ultraconserved elements and two morphological matrices. In unweighted maximum likelihood and Bayesian combined-evidence analyses, morphological signal was dwarfed by the ultraconserved elements, and some node support values were reduced relative to ultraconserved element-only analyses. Increasing the weight of morphological characters allowed those data to influence the tree, but weighting subjectivity should be considered in future analyses. More attempts should be made to simultaneously analyze genomic and morphological datasets.</p>
Data from: Biological stoichiometry of oleaginous microalgal lipid synthesis: The role of N:P supply ratios and growth rate on microalgal elemental and biochemical composition
<p>Biological Stoichiometry is an ecological framework connecting the balance of elements to the functioning of organisms. Here, we applied this framework to study the relationships between carbon:nitrogen:phosphorus (C:N:P) ratios and synthesis of industrial high value biochemicals in the highly oleaginous alga <em>Tetradesmus bernardii.</em> We expected an increase in protein content with increasing cellular N content and decreasing C:N stoichiometry, and an increase in lipid content with increasing C:N and C:P stoichiometry. We tested these hypotheses by exposing <em>T. bernardii</em> to N and P limitation at a range of N:P supply ratios in chemostats set at low and high dilution rates. Following expectations, the cellular protein content increased with the N content, and decreased with cellular C:N ratios across all treatments. Carbohydrates and lipids largely followed the relative availability of C and increased under both N and P limitation, with higher C:N and C:P ratios. Specifically, lipid content increased by 100–125% upon N and P limitation, with a shift towards more neutral lipids at the cost of glycolipids and phospholipids. Generally, we observed a re-allocation of cellular C from protein to carbohydrates upon modest N limitation, and towards lipids under P and severe N limitation. Our results demonstrate stoichiometrically predictable patterns of industrially valuable compounds in an oleaginous microalga.</p>
The insertion of a mitochondrial selfish element into the nuclear genome and its consequences: supporting data sets and scripts
<p>Supplementary data sets and script for the article "The insertion of a mitochondrial selfish element into the nuclear genome and its consequences".</p> <p>The original source code with versioning is available at https://gitlab.gwdg.de/molsysevol/umag_11064 .</p>
The sunflower (Helianthus annuusL.) genome reflects a recent history of biased accumulation of transposable elements
<p>Aside from polyploidy, transposable elements are the major drivers of genome size increases in plants. Thus, understanding the diversity and evolutionary dynamics of transposable elements in sunflower (<i>Helianthus annuus</i> L.), especially given its large genome size (∼3.5 Gb) and the well‐documented cases of amplification of certain transposons within the genus, is of considerable importance for understanding the evolutionary history of this emerging model species. By analyzing approximately 25% of the sunflower genome from random sequence reads and assembled bacterial artificial chromosome (BAC) clones, we show that it is composed of over 81% transposable elements, 77% of which are long terminal repeat (LTR) retrotransposons. Moreover, the LTR retrotransposon fraction in BAC clones harboring genes is disproportionately composed of chromodomain‐containing <i>Gypsy</i> LTR retrotransposons ('chromoviruses'), and the majority of the intact chromoviruses contain tandem chromodomain duplications. We show that there is a bias in the efficacy of homologous recombination in removing LTR retrotransposon DNA, thereby providing insight into the mechanisms associated with transposable element (TE) composition in the sunflower genome. We also show that the vast majority of observed LTR retrotransposon insertions have likely occurred since the origin of this species, providing further evidence that biased LTR retrotransposon activity has played a major role in shaping the chromatin and DNA landscape of the sunflower genome. Although our findings on LTR retrotransposon age and structure could be influenced by the selection of the BAC clones analyzed, a global analysis of random sequence reads indicates that the evolutionary patterns described herein apply to the sunflower genome as a whole.</p>
Data from: Protein-encoding ultraconserved elements provide a new phylogenomic perspective of Oestroidea flies (Diptera, Calyptratae)
<p>The diverse superfamily Oestroidea with more than 15,000 known species includes among others, blow flies, flesh flies, bot flies, and the diverse tachinid flies. Oestroidea exhibit strikingly divergent morphological and ecological traits, but even with a variety of data sources and inferences there is no consensus on the relationships among major Oestroidea lineages. Phylogenomic inferences derived from targeted enrichment of ultraconserved elements or UCEs have emerged as a promising method for resolving difficult phylogenetic problems at varying timescales. To reconstruct phylogenetic relationships among families of Oestroidea, we obtained UCE loci exclusively derived from the transcribed portion of the genome making them suitable for larger and more integrative phylogenomic studies using other genomic and transcriptomic resources. We analysed datasets containing 37–2,077 UCE loci from 98 representatives of all oestroid families (except Ulurumyiidae and Mystacinobiidae) and seven calyptrate outgroups, with a total concatenated aligned length between 10–550 Mb. About 35% of the sampled taxa consisted of museum specimens (2–92 years old), of which 85% resulted in successful UCE enrichment. Our maximum likelihood and coalescent-based analyses produced well-resolved and highly supported topologies. With the exception of Calliphoridae and Oestridae, all included families were recovered as monophyletic with the following conclusions: Oestroidea is monophyletic with Mesembrinellidae as sister to the remaining oestroid families; Oestridae is paraphyletic with respect to Sarcophagidae; Polleniidae is sister to Tachinidae; Rhinophoridae sister to (Luciliinae (Toxotarsinae (Melanomyinae + Calliphorinae))); Phumosiinae is sister to Chrysomyinae and Bengaliinae is sister to Rhiniidae. These results support the ranking of most calliphorid subfamilies as separate families.</p>
Evaluating Elements of Web-based Data Enrichment for Pseudo-Relevance Feedback Retrieval
<p>This data archive accompanies our work, in which we analyze a pseudo-relevance retrieval method that is based on the results of web search engines. By enriching topics with text data from web search engine result pages and linked contents, we train topic-specific and cost-efficient classifiers that can be used to search test collections for relevant documents. Building up on attempts that were initially made at TREC Common Core 2018 by Grossman and Cormack, we address the questions of system performance over time considering different search engines, queries and test collections. Our experimental results show how and to which extent the considered components affect the retrieval performance. Overall, the analyzed method is robust in terms of average retrieval performance and a promising way to use web content for the data enrichment of relevance feedback methods.</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
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.