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3,109 results for “sequence analysis”
FIG. 4 in Foraminiferal biostratigraphy, facies and sequence stratigraphy analysis across the K-Pg Boundary in Hazara, Lesser Himalayas (Dhudial Section)
FIG. 4. — Field photograph of the studied Dhudial Section: A, stratigraphic contacts of different ages; B, authigenic quartz near the boundary; C, Outcrop view of probable OAE3.
Oxylobus (Asteraceae) analysis DNA sequence data
<p>A molecular phylogenetic investigation was carried out to clarify aspects of the systematics of <i>Oxylobus</i>, a primarily Mexican alpine genus of Eupatorieae. Analysis of sequence data from two nuclear (nrDNA ITS, ETS) and three plastid markers (<i>rbcL</i>, <i>ndhF</i>, <i>matK</i>) confirmed the monophyly of <i>Oxylobus</i> and placed species of <i>Ageratina</i> as its sister group. A survey of 56 samples of <i>Oxylobus</i> using nrDNA ITS and ETS provided support for the currently accepted species, and showed the recently described <i>O. coyulensis</i> to be distinct and the sister group to the rest of the genus. The results also confirmed the placement of <i>O. juarezensis</i> in synonymy with <i>O. subglabrus</i>. The results of a broad survey of <i>Ageratina</i> for ITS data showed that it is likely not monophyletic as currently circumscribed. The phylogenetic results also highlighted the distinctiveness of <i>Piqueria</i> and <i>Piqueriopsis</i> as a distinct clade at the base of Eupatorieae.</p>
Alignments of Sequence Data for Phylogenetic Analysis of Damsel
<p>Initially described in 1882, <i>Chromis enchrysurus</i>, the Yellowtail Reeffish, was redescribed in 1982 to account for an observed color morph that possesses a white tail instead of a yellow one, but morphological and geographic boundaries between the two color morphs were not well understood. Taking advantage of newly collected material from submersible studies of deep reefs and photographs from rebreather dives, we sought to determine whether the white-tailed <i>Chromis</i> is actually a color morph of <i>Chromis enchrysurus</i> or a distinct species. These alignments for mitochondrial genes cytochrome b and cytochrome c oxidase subunit I were used to generate phylogenetic trees that separated <i>Chromis enchrysurus</i> and the white-tailed <i>Chromis</i> into two reciprocally monophyletic clades. Genetic, morphological, and biogeographic data all indicate that the white-tailed <i>Chromis</i> is a distinct species, herein described as <i>Chromis vanbebberae </i>sp. nov. The discovery of a new species within a conspicuous group such as damselfishes in a well-studied region of the world highlights the importance of deep-reef exploration in documenting undiscovered biodiversity.</p>
Data from: Diagnostic yield in epileptic encephalopathies is improved by genome sequencing and re-analysis
<p><b>Objective:</b> To assess the benefits and limitations of whole genome sequencing (WGS) compared to exome sequencing (ES) or multigene panel (MGP) in the molecular diagnosis of developmental and epileptic encephalopathies (DEE).</p> <p><b>Methods: </b>We performed WGS of 30 comprehensively phenotyped DEE patient trios that were undiagnosed after first-tier testing, including chromosomal microarray (CMA), and either research ES (n=15) or diagnostic MGP (n=15).</p> <p><b>Results</b>: 8 diagnoses were made in the 15 individuals who received prior ES (53%): 3 individuals had complex structural variants; 5 had ES-detectable variants which now had additional evidence for pathogenicity. 11 diagnoses were made in the 15 MGP-negative individuals (68%); the majority (n=10) involved genes not included in the panel, particularly in individuals with post-neonatal onset of seizures and those with more complex presentations including movement disorders, dysmorphic features and/or multi-organ involvement. 42% of diagnoses were autosomal recessive or X-chromosome linked.</p> <p><span><span><b>Conclusion:</b> WGS was able to improve diagnostic yield over ES primarily through the detection of complex structural variants (n=3). The higher diagnostic yield was otherwise better attributed to the power of re-analysis rather than inherent advantages of the WGS platform. Additional research is required to assist in the assessment of pathogenicity of novel non-coding and complex structural variants and further improve diagnostic yield for patients with DEE and other neurogenetic disorders.</span></span></p>
DNA sequence data use in phylogenetic analysis of eastern North American stitchworts
<p>Generic delimitation in Caryophyllaceae has been a challenge, and has been informed most recently by use of molecular phylogenetic data. In this study, analysis of 29 samples from the small segregate <em>Mononeuria</em> using nuclear ITS and plastid <em>rps16</em> data revealed it to be polyphyletic. The type species <em>Mononeuria patula</em> as well as two others (<em>M. muscorum</em> and <em>M. paludicola</em>) were shown to belong to the <em>Sabulina</em> clade. The remaining species formed a clade that also included the previously monotypic <em>Geocarpon</em> and was sister to a heterogeneous group that included the Hawaiian <em>Schiedea</em> and three other monotypic genera, <em>Honckenya</em>, <em>Wilhelmsia</em>, and <em>Triplateia</em>. Although several nomenclatural options are available, we propose to place the species from this clade into a single genus, <em>Geocarpon</em>, which basically follows the most recent treatment after exclusion of <em>Sabulina</em> species, but with the necessary new genus placements. New combinations are proposed: <em>Sabulina muscorum</em>, <em>Sabulina paludicola</em>, <em>Geocarpon carolinianum, Geocarpon cumberlandensis</em>, <em>Geocarpon glabrum</em>, <em>Geocarpon groendlandicum</em>, <em>Geocarpon nuttallii</em>, and <em>Geocarpon uniflorum.</em> Analysis of the sequence data revealed remarkable variability among populations of <em>Sabulina</em> (formerly <em>Mononeuria</em>) <em>patula</em>, <em>Sabulina</em> (formerly <em>Mononeuria) paludicola</em>, and <em>Geocarpon </em>(formerly <em>Mononeuria</em>) <em>groenlandicum</em>, suggesting that cryptic species may be present. The data also suggested that broader sampling of <em>Sabulina</em> and <em>Geocarpon</em> could lead to increased understanding of the timing and origins of occupation of calcareous glades and rock outcrop habitats in eastern North America.</p>
research data supporting "Revealing the organization of catalytic sequence-defined oligomers via combined molecular dynamics simulations and network analysis"
<p>This repository contains all the data generated and analyzed including the starting structures, the input files, the trajectory files, the output data from cpptraj and network analyses, and in-house scripts used to prepare the network and module files shown in the paper <strong>"Revealing the organization of catalytic sequence-defined oligomers via combined molecular dynamics simulations and network analysis"</strong> published in <strong>Journal of Chemical Information and Modeling</strong> (DOI: 10.1021/acs.jcim.2c00101). </p>
Data from: Sequence-based association analysis reveals an MGST1 eQTL with pleiotropic effects on bovine milk composition
[No abstract entered]
Single nucleus sequencing analysis of rat hippocampus reveals the landscape of latent phase temporal lobe epilepsy
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Atomistic Predictions and Network-Based Allosteric Analysis of Conformational Ensembles for the State-Switching ABL Kinase Mutants Using Combination of Alanine Sequence Scanning and Shallow Subsampling in AlphaFold2
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Fig. 1 in MITOCHONDRIAL 16S AND 12S rRNA SEQUENCE ANALYSIS IN FOUR SALMONID SPECIES FROM ROMANIA
Fig. 1. Variable sites in 16S rRNA (1) and 12S rRNA (2). The numbers represent the position occupied in the 16S rRNA, and 12S rRNA respectively. Identical sites are indicated by the symbol "·" and
supplemental files for Assembly and analysis of sequence from a spring and winter type Camelina sativa by whole genome PacBio HiFi technologies
<p><span>Supplemental files for Assembly and analysis of sequence from a spring and winter type <em>Camelina sativa</em> by whole genome PacBio HiFi technologies</span></p>
Figure 3 from: Anslan S, Nilsson RH, Wurzbacher C, Baldrian P, Tedersoo L, Bahram M (2018) Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding. MycoKeys 39: 29-40. https://doi.org/10.3897/mycokeys.39.28109
Figure 3 - Number of OTUs per sample for Illumina data recorded from a) pipeline-generated OTU tables (median differences = 38 OTUs) and from b) filtered OTU tables (median differences = 12 OTUs). The Galaxy workflow was excluded here.
Figure 2 from: Anslan S, Nilsson RH, Wurzbacher C, Baldrian P, Tedersoo L, Bahram M (2018) Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding. MycoKeys 39: 29-40. https://doi.org/10.3897/mycokeys.39.28109
Figure 2 - OTU accumulation curves of the evaluated pipelines for a) PacBio and b) Illumina datasets.
Fig. 3 in Phylogenetic analysis of the genus Argia Rambur, 1842 (Odonata: Coenagrionidae), based on morphological characters of larvae and mitochondrial DNA sequences
Fig. 3 Phylogenetic hypothesis recovered by Bayesian inference from the total evidence data set
Analysis of Public Short-Read RNA-Sequencing Data: PRJNA543316
<p><strong><span>PRJNA543316</span></strong></p> <p><span>Metformin is a front-line drug in the treatment of type-2 diabetes mellitus (T2DM). In addition to its antigluconeogenic and insulin-sensitizing properties, it has emerged as a potent inhibitor of the inflammatory response of macrophages. Specifically, metformin has been shown to reduce transcript levels of Il1b, the gene encoding the pro-inflammatory cytokine interleukin (IL)-1b, during long-term exposure of macrophages to the bacterial cell-wall component lipopolysaccharide (LPS). However, the extent to which metformin affects the early transcriptional response to LPS has never been investigated. Here, we show that metformin affects transcript levels of a large yet selective subset of LPS-responsive genes after only two hours of LPS exposure, mostly counteracting the effect of LPS rather than enhancing it. The affected genes are implicated in a variety of biological functions, in particular cellular movement and trafficking. Intriguingly, metformin affects transcript levels of Il1b at this early time point as well, but through a molecular mechanism fundamentally different from the regulation observed after longer exposure. While down-regulation of Il1b by metformin during the late stages of the LPS response has been shown to rely on stabilization of hypoxia-inducible factor (HIF)-1α and production of IL-10, Il1b inhibition at the early stage requires AMP-activated protein kinase (AMPK) activation but is independent of HIF-1α and IL-10. These results reveal an unexpected complexity in the anti-inflammatory properties of metformin and demonstrate that Il1b is down-regulated by distinct mechanisms in the early and late stages of the LPS response. Overall design: Bone-marrow-derived macrophages from WT C57Bl/6 mice were either left untreated, stimulated with 100 ng/ml LPS for 2 h or pretreated with 5 mM metformin for 6 h and then stimulated with 100 ng/ml LPS for 2 h.</span></p> <p><span>Pipeline: FastQ -> FastQC -> fastp -> STAR -> samtools -> multiQC</span></p>
Seq2scFv: a toolkit for the comprehensive analysis of display libraries from long-read sequencing platforms
<p>Annotation of full-length scFvs sequenced with PacBio using Seq2scFv (https://github.com/ngs-ai-org/seq2scfv). </p> <p>Raw files were obtained from publicly available dataset generated by Nannini and colleagues in "Combining phage display with SMRTbell next-generation sequencing for the rapid discovery of functional scFv fragments." <em>MAbs</em>. Vol. 13. No. 1. Taylor & Francis, 2021.</p> <p>The results of the annotation are organized in directories. These correspond to the different steps of the tutorial presented in the Seq2scFv repository. </p> <p>├── 1.Preprocessed<br>├── 2.Catalogued<br>├── 3.vscan<br>├── 4.scFv_split<br>├── 5.Linkers<br>├── 6.Flags<br>├── 7.Counts<br>└── focus_libs.txt</p> <p>This entry also contains the code provided in the GitHub repository.</p>
Sequence data and structural data utilized in the study and analysis of grain protein function prediction.
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Data from: PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data
The pairwise sequentially Markovian coalescent (PSMC) method uses the genome sequence of a single individual to estimate demographic history covering a time span of thousands of generations. Although originally designed for whole-genome data, we here use simulations to investigate its applicability to reference genome-aligned restriction site associated DNA (RAD) data. We find that RAD data can potentially be used for PSMC analysis, but at present with limitations. The key factor is the proportion (p) of the genome that the RAD data covers. In our simulations, a proportion of 10% can still retain a substantial amount of coalescent information, whereas for 1% estimation becomes unreliable. The performance depends strongly on mutation rate (μ) and recombination rate (r) and is proportional to μ*p/r. When the value of this term is low, increasing the amount of data and number of iterations helps restoring the power of the estimation. We subsequently analyse one whole-genome-sequenced and 17 RAD-sequenced three-spined sticklebacks (Gasterosteus aculeatus) from a lake in Greenland. The whole-genome sequence suggests a relatively recent expansion and decline within ca. 4000–40 000 generations ago, possibly reflecting postglacial expansion and founding of the lake population. RAD data, where chromosomes from 10 individuals are combined, identify a similar pattern. Our study provides guidance about the use of PSMC analysis and suggests measures that can improve its utility for RAD data. Finally, the study shows that RAD loci in general contain coalescent information that can be used for developing more targeted methods.
FIGURE 2 in Mitochondrial DNA sequence analysis of the spectacled salamander, Salamandrina terdigitata (Urodela: Salamandridae), supports the existence of two distinct species
FIGURE 2. Map of Italy showing the sampling sites of Salamandrina terdigitata.
TNT file for phylogenetic analysis of the moss class Polytrichopsida composed of morphological and sequence level characters
<p>PREMISE OF THE STUDY: When fossils are sparse in morphologically divergent lineages, phylogenetic analyses based on morphology may support hypotheses of relationships incongruent with those supported by gene sequence data. Integration of morphological and sequence data from conservative gene regions may reconcile such situations by circumscribing the search space of combined analyses.</p> <p>METHODS: We revisited the phylogeny of Polytrichopsida, a highly divergent group of mosses, in parsimony analyses. We supplemented the existing morphological matrix with sequence data of four genes (nt 18S, cp rbcL & rps4, mt nad5) commonly used in mosses; we included both fossils and extant terminals that lack sequence data.</p> <p>KEY RESULTS: We recovered patterns of relationships largely congruent with those supported by analyses of sequence data from a higher number of terminals. Analyses including all terminals recovered one optimal tree with Alophosia and the fossil Meantoinea forming a clade sister to the rest of the ingroup. Outgroup sampling experiments produced congruent topologies for most ingroup relationships.</p> <p>CONCLUSIONS: The potential of total-evidence analyses sampling conservative genes to alleviate conflict with morphology-based hypotheses should be tested in groups with denser fossil record. Although bryophyte fossils have been deemed fragmentary, it was recently shown that integrating fossils in total-evidence analyses may not reduce phylogenetic resolution. Therefore, total-evidence analyses incorporating fossils bear promise for clarifying bryophyte phylogenetic relationships. In Polytrichopsida, a group with a long evolutionary history, we cannot assume, a priori, that currently known fossils, which date back to only c. 140 Ma ago, represent the oldest lineages.</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.