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1,283 results for “Copying”
IO Islamic 1665. Ta'rîkh-i-'âlamârâi-'abbâsî, A Complete Copy of Iskandar Munshî's History of Shâh 'Abbâs the Great
<p>IO Islamic 1665. Ta’rîkh-i-‘âlamârâi-‘abbâsî, A Complete Copy of Iskandar Munshî’s History of Shâh ‘Abbâs the Great</p>
IO Islamic 1441. Ta'rîkh-i-'âlamârâi-'abbâsî, A Complete Copy of Iskandar Munshî's History of Shâh 'Abbâs the Great
<p>IO Islamic 1441. Ta’rîkh-i-‘âlamârâi-‘abbâsî, A Complete Copy of Iskandar Munshî’s History of Shâh ‘Abbâs the Great</p>
IO Islamic 298. Ta'rîkh-i-'âlamârâi-'abbâsî, A Complete Copy of Iskandar Munshî's History of Shâh 'Abbâs the Great
<p>IO Islamic 298. Ta’rîkh-i-‘âlamârâi-‘abbâsî, A Complete Copy of Iskandar Munshî’s History of Shâh ‘Abbâs the Great</p>
IO Islamic 003. Abdallâhnama, A Copy of the Extremely Rare History of the Shaibânî Khâns of Transoxania
<p>IO Islamic 003. Abdallâhnama, A Copy of the Extremely Rare History of the Shaibânî Khâns of Transoxania</p>
Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers
<p>Introduction: Antimicrobial resistant (AMR) genes in bacteria are often carried on plasmids. Since these plasmids can spread the AMR genes between bacteria, it is important to know if the genes are located on highly transferable plasmids or in the more stable chromosomes. Whole genome sequence (WGS) analysis makes it easy to determine if a strain contains a resistance gene, however, it is not easy to determine if the gene is located on the chromosome or on a plasmid as genome sequence assembly generally results in 50-300 DNA fragments (contigs). With our newly developed prediction tool, we analyze the composition of these contigs to predict their likely source, plasmid or chromosomal. This information can be used to determine if a resistant gene is chromosomally located or on a plasmid. The tool is optimized for 19 different bacterial species, including Campylobacter, E. coli, and Salmonella, and can also be used for metagenomic assemblies.</p> <p>Methods: The tool identifies the number of chromosomal marker genes, plasmid replication genes and plasmid typing genes using CheckM and DIAMOND Blast, and determines pentamer frequencies and contig sizes per contig. A prediction model was trained using Random Forest on an extensive set of plasmids and chromosomes from 19 different bacterial species and validated on separate test sets of known chromosomal and plasmid contigs of the different bacteria. Results: Prediction of plasmid contigs was nearly perfect when calculated based on number of correctly predicted bases, with up to 99% specificity and 99% sensitivity. Prediction of small contigs remains difficult, since these contigs consists primarily of repeated sequences present in both plasmid and chromosome, e.g. transposases.</p> <p>Conclusion: The newly developed tool is able to determine if contigs are chromosomal or plasmid with a very high specificity and sensitivity (up to 99%) and can be very useful to analyze WGS data of bacterial genomes and their antimicrobial resistance genes.</p> <p>Plasmid databases can be downloaded from: http://klif.uu.nl/download/plasmid_db/</p> <p>Data used for training can be downloaded here: http://klif.uu.nl/download/plasmid_db/trainingsets2/</p>
Avian MHC copy number variation is associated with helminth richness
<p>Genes of the Major Histocompatibility Complex (MHC) play a key role in the adaptive immunity of vertebrates, as they encode receptors responsible for recognition of antigens. Evolutionary history of the MHC proceeded through numerous gene duplications, which increases the spectrum of pathogens recognized by individuals. Although pathogen-mediated selection is believed to be a primary driver of MHC expansion over evolutionary times, empirical evidence for this association is virtually lacking. Here, we used an extensive dataset on MHC class II copy number variation in non-passerine birds to test for an evolutionary correlation with helminth parasite richness. As expected, our phylogenetically-informed modelling revealed a positive association between MHC copy number and total helminth richness, even after controlling for a broad spectrum of ecological and life-history traits. Thus, total helminth richness appears to be the most important correlate of MHC copy number, supporting a leading role of pathogen-mediated selection in the evolution of MHC in birds. Our results provide some of the first, although correlative, evidence linking parasitism to inter-specific variation in MHC copy number among birds.</p>
Phylogeny and biogeography of Fagus (Fagaceae) based on 28 nuclear single/low‐copy loci
<p><i>Fagus</i> L. is a key component in temperate deciduous broadleaf forests of the Northern Hemisphere. However, its biogeographic history has not been examined under the framework of a fully resolved and reasonably time-calibrated phylogeny. In this study, we sequenced 28 nuclear single/low-copy loci (18,555 bp in total) of 11 <i>Fagus</i> species/segregates and seven outgroups. Phylogenetic trees were reconstructed using both concatenation-based (ML, MP, BI) and coalescent-based methods (StarBEAST2, ASTRAL). The monophyly of two subgenera (<i>Fagus</i> and <i>Engleriana</i>) and most sections was well supported, except for sect. <i>Lucida</i>, which was paraphyletic with respect to sect. <i>Longipetiolata</i>. We also found a major phylogenetic conflict among North American, East Asian and West Eurasian lineages of subgen. <i>Fagus</i>. Three segregates that have isolated distribution (<i>F. </i><i>mexicana</i>,<i> F. multinervis</i>, and <i>F. orientalis</i>) were independent evolutionary units. Biogeographic analysis with fossils suggested that <i>Fagus</i> could have originated in North Pacific region in late Early Eocene. Major diversifications coincided with a climate aberration at the Eocene/Oligocene boundary and the global cooling since Mid-Miocene. The Late Miocene accelerated global cooling and the Pleistocene glaciations would have driven beeches into East Asia, North America and West Eurasia. Meanwhile, range reduction and extinction in high latitudes, in central Asia and in western North America converged to form beech modern distribution pattern. This study provides a first attempt to disentangle the biogeographic history of beeches in the context of a nearly resolved and time-calibrated phylogeny, which may shed new insights into the formation of the temperate biome in the Northern Hemisphere.</p>
NanoString nCounter copy number variation assay
<p>The sex chromosomes often follow unusual evolutionary trajectories. In particular, the sex-limited Y and W chromosomes frequently exhibit a small but unusual gene content in numerous species, where many genes have undergone massive gene amplification. The reasons for this remain elusive with a number of recent studies implicating meiotic drive, sperm competition, genetic drift and gene conversion in the expansion of gene families. However, our understanding is primarily based on Y chromosome studies, and the W chromosome has been largely overlooked. Here, we conduct a comprehensive investigation into the abundance, variability, and evolution of ampliconic genes on the W both across and within avian species. We find a striking deficit of gene families on the duck W chromosome, as well as conservation in W-linked gene copy number across duck breeds, indicating that gene amplification may not be such a general feature of sex chromosome evolution as Y studies would initially suggest. Furthermore, we show that gene families have expanded independently in the duck and chicken. In particular, using contrasts between modern chicken and duck breeds selected for different female-specific selection regimes and their wild ancestors, we investigate the factors driving the expansion of HINTW, a prominent ampliconic gene family hypothesized to play a role in female reproduction and oogenesis. While we find that HINTW is ampliconic in both species, our results support a role of female-specific selection in driving gene amplification in the chicken but not the duck, challenging the assumption that HINTW is key for female fecundity across the avian phylogeny.</p>
Koranic Science, a Copy of Kashshâf [IO Islamic 563]
<ul> <li>al-Qurʼān القرآن الكريم</li> <li><strong>This manuscript is now IO Islamic 563 in the India Office collections.</strong></li> <li><strong>[metadata:</strong><a href="https://de.wikipedia.org/wiki/Otto_Loth"> <strong>Otto Loth, </strong></a><strong><em><a href="http://doi.org/10.5281/zenodo.3923636">A Catalogue of the Arabic Manuscripts in the Library of the India Office</a></em>, (volume 1), no. 53 here with further notations and hyperlinks]</strong>.</li> </ul> <p>53.</p> <p>563. Size 14 in. by 7<sup>1/2</sup> in.; foll. 796. Twenty-nine lines in a page.</p> <p>Another copy of the <em>Kashshâf</em>. Well written, by Burhân b. Ḥâmid. Ornamented and gilt. Some glosses.</p>
Koranic Science, a Copy of Kashshâf [58]
<ul> <li>al-Qurʼān القرآن الكريم</li> <li><strong>This manuscript is now IO Islamic 23 in the India Office collections.</strong></li> <li><strong>[metadata:</strong><a href="https://de.wikipedia.org/wiki/Otto_Loth"> <strong>Otto Loth, </strong></a><strong><em><a href="http://doi.org/10.5281/zenodo.3923636">A Catalogue of the Arabic Manuscripts in the Library of the India Office</a></em>, (volume 1), no. 58 here with further notations and hyperlinks]</strong>.</li> </ul> <p>58.</p> <p>23. Size 12<sup>1/4</sup> in. by 7<sup>3/4</sup> in.; foll. 454. Twenty-five lines in a page.</p> <p>An edition of the <em>Kashshâf </em>“mixed” with the text of the Koran, entitled کاشف الکشّاف. The Editor, who calls himself DARWÎSH, says in his short Preface:</p> <p>نحمده علی ما شرح صدور اولو(sic) البصائر بکشف قوامض الحکم... اما بعد فیقول العبد المغمور بکثرةً التشویش، العبد الاقل درویش، ان العلامة الزمخشری قد ابدع فی تفسیره للکشاف، (الکr.) و بذل جهده و اناف، کما قیل * ان التفاسیر فی الدنیا بلا عدد* و ان من بینها الکشاف کالشافی* لکنه لزخارة فضله و وفور علمه اقتصر فی اکثر المواضع علی بیان اللفظ بالتفسیر، فکان ادراکه علی الطلاب عسیر، (sic) فخطر ببال هذا العبد الضعیف المعترف بقلة البضاعة، و لسوالف ایامه بالاضاعة، ان یثبت قبل التفسیر بالآیات، و ان یکون للآیة کلها او بعضها بات، (sic)</p> <p>This is the First Part, concluding with Sû. 16.</p> <p>Well written. Foll. 256 and 263 should be transposed.</p> <p>[Hastings.]</p> <p> </p>
Data from: Mining from transcriptomes: 315 single-copy orthologous genes concatenated for the phylogenetic analyses of Orchidaceae
Phylogenetic relationships are hotspots for orchid studies with controversial standpoints. Traditionally, the phylogenies of orchids are based on morphology and subjective factors. Although more reliable than classic phylogenic analyses, the current methods are based on a few gene markers and PCR amplification, which are labor intensive and cannot identify the placement of some species with degenerated plastid genomes. Therefore, a more efficient, labor-saving and reliable method is needed for phylogenic analysis. Here, we present a method of orchid phylogeny construction using transcriptomes. Ten representative species covering five subfamilies of Orchidaceae were selected, and 315 single-copy orthologous genes extracted from the transcriptomes of these organisms were applied to reconstruct a more robust phylogeny of orchids. This approach provided a rapid and reliable method of phylogeny construction for Orchidaceae, one of the most diversified family of angiosperms. We also showed the rigorous systematic position of holomycotrophic species, which has previously been difficult to determine because of the degenerated plastid genome. We concluded that the method presented in this study is more efficient and reliable than methods based on a few gene markers for phylogenic analyses, especially for the holomycotrophic species or those whose DNA sequences have been difficult to amplify. Meanwhile, a total of 315 single-copy orthologous genes of orchids are offered and more informative loci could be used in the future orchid phylogenetic studies.
Data from: A phylogeny of the genus Amaranthus (Amaranthaceae), based on several low-copy nuclear loci and chloroplast regions
The genus Amaranthus (pigweeds) is a group of ∼74 monoecious or dioecious annual species native to every continent but Antarctica, frequently associated with natural and human disturbance, with several economically important domesticated and weedy species. We set out to reconstruct the phylogeny of Amaranthus, with broad geographic sampling, in order to answer questions about biogeographic relationships in the genus and the monophyly of the subgenera. Fifty-eight species were included inmaximum parsimony and Bayesian phylogenetic analyses based on ITS and three low-copy nuclear genes (A36, G3PDH, and Waxy), as well as two chloroplast regions (trnL5′-trnL3′ and matK/trnK). Topology tests were also employed to test taxonomic hypotheses about incongruence between trees and the monophyly of clades containing Galápagos species. Our analyses support the origin of the genus in the Americas, with a single long-distance dispersal event to the Old World, and both nuclear and chloroplast trees recover three to fourmajor clades, roughly corresponding to three subgenera recognized based on morphology. However, there are species in all of these clades that were not predicted based on morphology, and we discover previously unsuspected relationships between Galápagos species and species from the North American Southwest, which comprise small monophyletic groups outside of the three recognized subgenera. Additionally, an important herbicide resistant weed species (A. palmeri) and its sister species are placed into different large clades based on nuclear or chloroplast data, suggesting a chloroplast capture event. These results will provide a basis for further exploration of the evolution of weedy ecological strategies in the group.
Data from: Conserved genetic regions across angiosperms as tools to develop single copy nuclear markers in gymnosperms: an example using cycads
Several individuals of the Caribbean Zamia clade and other cycad genera were used to identify single copy nuclear genes for phylogeographic and phylogenetic studies in Cycadales. Two strategies were employed to select target loci: 1) a tblastX search of Arabidopsis conserved ortholog sequence (COS) set and, 2) a tblastX search of Arabidopsis-Populus-Vitis-Oryza Shared Single Copy genes (APVO SSC) against the EST Zamia databases in Genbank. From the first strategy, 30 loci were selected, and from the second, 16 loci. In both cases the matching Genbank accessions of Zamia were used as a query for retrieving highly similar sequences from Cycas, Picea, Pinus species or Ginko biloba. After retrieving and aligning all the sequences in each locus, intron predictions were completed to assist in primer design. PCR was carried out in three rounds to detect paralogous loci. A total of 29 loci were successfully amplified as a single band of which 20 were likely single copy loci. These loci showed different diversity and divergence levels. A preliminary screening allowed us to select 8 promising loci (40S, ATG2, BG, GroES, GTP, LiSH, PEX4 and TR) for the Z. pumila complex and 4 loci (COS26, GroES, GTP and HTS) for all other cycad genera.
Data from: Primers for Castilleja and their utility across Orobanchaceae: II. Single-copy nuclear loci
Premise of the study: We developed primers targeting nuclear loci in Castilleja with the goal of reconstructing the evolutionary history of this challenging clade. These primers were tested across other major clades in Orobanchaceae to assess their broader utility. Methods and Results: We assembled low-coverage genomes for three taxa in Castilleja and developed primer combinations for the single-copy conserved ortholog set (COSII) and the pentatricopeptide repeat (PPR) gene family. These primer combinations were designed to take advantage of the Fluidigm microfluidic PCR platform and are well suited for high-throughput sequencing applications. Eighty-seven primers were designed for Castilleja, and 27 were found to have broader utility in Orobanchaceae. Conclusions: These results demonstrate the utility of these primers, not only across Castilleja, but for other lineages within Orobanchaceae as well. This expanded molecular toolkit will be an asset to future phylogenetic studies in Castilleja and throughout Orobanchaceae.
Paternally inherited P-element copy number affects the magnitude of hybrid dysgenesis in Drosophila simulans and D. melanogaster
<p class="CxSpFirst">Transposable elements (TEs) are repetitive regions of DNA that are able to self-replicate and reinsert themselves throughout host genomes. Since the discovery of TEs, a prevalent question has been whether increasing TE copy number has an effect on the fitness of their hosts. <i>P</i>-elements (PEs) in <i>Drosophila</i> are a well-studied TE that has strong phenotypic effects. When a female without PEs (M) is crossed to a male with them (P), the resulting females are often sterile, a phenomenon called hybrid dysgenesis (HD). Here, we used short and long-read sequenced to infer the number of PEs in the genomes of dozens of isofemale lines from two <i>Drosophila</i> species and measured whether the magnitude of HD was correlated with the number of PEs in the paternal genome. Consistent with previous reports, we find evidence for a positive correlation between the paternal PE copy number and the magnitude of HD in progeny from ♀M ´ ♂ P crosses for both species. Other crosses are not affected by the number of PE copies. We also find that the correlation between the strength of HD and PE copy number differs between species which suggest there are genetic differences that might make some genomes more resilient to the potentially deleterious effects of TEs. Our results suggest that PE copy number interacts with other factors in the genome and the environment to cause HD and that the importance of these interactions is species-specific.</p>
Data from: Distribution and functionality of copy number variation across European cattle populations
Copy number variation (CNV), which is characterized by large-scale losses or gains of DNA fragments, contributes significantly to genetic and phenotypic variation. Assessing CNV across different European cattle populations might reveal genetic changes responsible for phenotypic differences, which have accumulated throughout the domestication history of cattle as consequences of evolutionary forces that act upon them. To explore pattern of CNVs across European cattle, we genotyped 149 individuals, that represent different European regions, using the Illumina Bovine HD Genotyping array. A total of 9,944 autosomal CNVs were identified in 149 samples using a Hidden Markov Model (HMM) as employed in PennCNV. Animals originating from several breeds of British Isles, and Balkan and Italian regions, on average, displayed higher abundance of CNV counts than Dutch or Alpine animals. A total of 923 CNV regions (CNVRs) were identified by aggregating CNVs overlapping in at least two animals. The hierarchical clustering of CNVRs indicated low differentiation and sharing of high-frequency CNVRs between European cattle populations. Various CNVRs identified in the present study overlapped with olfactory receptor genes and genes related to immune system. In addition, we also detected a CNV overlapping the Kit gene in English longhorn cattle which has previously been associated with color-sidedness. To conclude, we provide a comprehensive overview of CNV distribution in genome of European cattle. Our results indicate an important role of purifying selection and genomic drift in shaping CNV diversity that exists between different European cattle populations.
Data from: Dynamics of copy number variation in host races of the pea aphid
Copy number variation (CNV) makes a major contribution to overall genetic variation and is suspected to play an important role in adaptation. However, aside from a few model species, the extent of CNV in natural populations has seldom been investigated. Here, we report on CNV in the pea aphid Acyrthosiphon pisum, a powerful system for studying the genetic architecture of host plant adaptation and speciation thanks to multiple host races forming a continuum of genetic divergence. Recent studies have highlighted the potential importance of chemosensory genes, including the gustatory and olfactory receptor gene families (Grs and Ors, respectively), in the process of host race formation. We used targeted re-sequencing to achieve a very high depth of coverage, and thereby revealed the extent of CNV of 434 genes, including 150 chemosensory genes, in 104 individuals distributed across eight host races of the pea aphid. We found that CNV was widespread in our global sample, with a significantly higher occurrence in multigene families, especially in Ors, and a decrease in the probability of complete gene duplication or deletion (CDD) with increase in coding sequence length. Genes with CDD variants were usually more polymorphic for copy number, especially in the P450 gene family where toxin resistance may be related to gene dosage. We found that Grs were over-represented among genes discriminating host races, as were CDD genes and pseudogenes. Our observations shed new light on CNV dynamics and are consistent with CNV playing a role in both local adaptation and speciation.
Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics (output data)
<p>This contains the output results of CalicoST (inferred CNAs and cancer clones), results of comparison methods, and CNAs inferred from WES data of 13 samples across four cancer types.</p> <p>In this updated version, we also included the simulated data and the results from CalicoST and other methods in CalicoST_simulation_deposit.zip. README contains the details of deposited files.</p>
FIGURE. Neotype of Euphorbia leandriana Boiteau, Boiteau s.n. (P, specimen formerly in spiritu), designated in the present paper. A, B. details of the specimen; C. specimen with copy of the original spirit label (lost), likely by J. Bosser. Credits: Muséum national d'histoire naturelle, Paris (A–C). in Novelties in Malagasy Euphorbia (Euphorbiaceae)
FIGURE. Neotype of Euphorbia leandriana Boiteau, Boiteau s.n. (P, specimen formerly in spiritu), designated in the present paper. A, B. details of the specimen; C. specimen with copy of the original spirit label (lost), likely by J. Bosser. Credits: Muséum national d'histoire naturelle, Paris (A–C).
Rational Design and Construction of Multi-Copy Biomanufacturing Islands in Mammalian Cells
<p>Data underlying the figures in the publication “Rational design and construction of multi-copy biomanufacturing islands in mammalian cells”, published in <em>Nucleic Acids Res.</em>, <strong>2022</strong>, 50(1), 561-578.</p> <p>DOI:10.1093/nar/gkab1214</p> <p> </p> <p>Table of contents:</p> <p><strong>1. tableSx.zip: </strong>8 .zip archives containing the raw data for the Tables S1-S8.</p> <p><strong>2. bioIslands_Supp_Figs_Info_Tables.pdf</strong></p> <p> </p> <p>Data Availability Statement</p> <p> DNA sequences specifying all coding and regulatory elements used to assemble our multiple gene constructs are provided in the Supplementary Data. Novel sequences have been deposited in the NCBI database. Accession numbers are provided in Supplementary Tables S2-S7.</p> <p> The gene diversifier and optimizer software is freely available for download at https://github.com/altamurr/Gene-Diversifier.</p> <p> Flow cytometry data has been deposited in FlowRepository. Links to FlowRepository are available in the section “Flow Cytometry Data” in the Supplementary Data.</p> <p> Microbial and mammalian strains as well as plasmid constructs used to complete this study are available under a Material Transfer Agreement.</p> <p> </p>
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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.