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2,168 results for “deletion”
Dataset: Uncovering missing pieces. Duplication and deletion history of arrestins in deuterostomes.
<p>This is the dataset accompanying the following publication: Uncovering missing pieces: Duplication and deletion history of arrestins in deuterostomes. See abstract below. </p> <p>Background<br> The cytosolic arrestin proteins mediate desensitization of activated G protein-coupled receptors (GPCRs) via competition with G proteins for the active phosphorylated receptors. Arrestins in active, including receptor-bound, conformation are also transducers of signaling. Therefore, this protein family is an attractive therapeutic target. The signaling outcome is believed to be a result of structural and sequence-dependent interactions of arrestins with GPCRs and other protein partners. Here we elucidated the detailed evolution of arrestins in deuterostomes.</p> <p>Results<br> Identity and number of arrestin paralogs were determined searching deuterostome genomes and gene expression data. In contrast to standard gene prediction methods, our strategy first detects exons situated on different scaffolds and then solves the problem of assigning them to the correct gene. This increases both the completeness and the accuracy of the annotation in comparison to conventional database search strategies applied by the community. The employed strategy enabled us to map in detail the duplication- and deletion history of arrestin paralogs including tandem duplications, pseudogenizations and the formation of retrogenes. The two rounds of whole genome duplications in the vertebrate stem lineage gave rise to four arrestin paralogs. Surprisingly, visual arrestin ARR3 was lost in the mammalian clades Afrotheria and Xenarthra. Duplications in specific clades, on the other hand, must have given rise to new paralogs that show signatures of diversification in functional elements important for receptor binding and phosphate sensing.</p> <p>Conclusion<br> The current study traces the functional evolution of deuterostome arrestins in unprecedented detail. Based on a precise re-annotation of the exon-intron structure at nucleotide resolution, we infer the gain and loss of paralogs and patterns of conservation, co-variation and selection.</p>
Data from: Major group-B enterovirus populations deleted in the noncoding 5' region of genomic RNA modulate activation of the type I interferon pathway in cardiomyocytes and induce myocarditis
<p>Major 5'-terminally deleted (5'TD) RNA forms of group-B coxsackievirus (CVB-5'TD) has been associated with myocarditis in both mice and humans. Although it is known that interferon-β (IFN-β) signaling is critical for an efficient innate immune response against CVB-induced myocarditis, the link between CVB-5'TD RNA forms and type I IFN signaling in cardiomyocytes remains to be explored. In a mouse model of CVB3/28-induced myocarditis, major early-emerging forms of CVB-5'TD RNA have been characterized as replicative viral populations that impair IFN-β production in the heart. Synthetic CVB3/28 RNA forms mimicking each of these major 5'TD virus populations were transfected in mice and have been shown to modulate innate immune responses in the heart and to induce myocarditis in mice. Remarkably, transfection of synthetic viral RNA with deletions in the secondary structures of the 5'-terminal CVB3 RNA domain I, modifying stem-loops "b", "c" or "d", were found to impair IFN-β production in human cardiomyocytes. In addition, the activation of innate immune response by Poly(I:C), was found to restore IFN-β production and to reduce the burden of CVB-5'TD RNA-forms in cardiac tissues, thereby reducing the mortality rate of infected mice. Overall, our results indicate that major early-emerging CVB3 populations deleted in the domain I of genomic RNA, in the 5' noncoding region, modulate the activation of the type I IFN pathway in cardiomyocytes and induce myocarditis in mice. These findings shed new light on the role of replicative CVB-5'TD RNA forms as key pathophysiological factors in CVB-induced human myocarditis.</p>
DNA large fragment deleting by compact, sequence-motif-free and specific TaqTth-hpRNA assisted with the microhomology-mediated end joining pathway
<p><span>A DNA editing tool TaqTth-hpRNA was developed in this study, composed of a compact recombinant TaqTth nuclease (832 aa) and a simple hairpin-RNA guiding probe (hpRNA). <em>In vitro</em> biochemical studies showed the TaqTth-hpRNA efficiently cleaves artificially synthesized ssDNA without stringent sequence motif like PAM. It can also cleave the genomic DNA of <em>E. coli</em> with ~80% efficiency. The TaqTth-hpRNA cleavage of genomic DNA in mammalian cells generated products with large fragment deletions mediated by the microhomology-mediated end joining (MMEJ) pathway. In addition, the cleavage was sensitive to mismatches in targeted regions, which was applied to specific damage of the <em>APP<sup>lon</sup></em> mutation in Alzheimer’s disease without disrupting the <em>APP<sup>wt</sup></em> locus. It is worth mentioning that the <em>APP<sup>lon</sup></em> sequence has only one base difference from that of <em>APP<sup>wt</sup></em>. The characteristics of small size, no PAM requirement, high specificity, and large deletion products make the TaqTth-hpRNA a potential therapeutic strategy for treating autosomal dominant disorders in the future.</span></p>
A point mutation and large deletion at the candidate avirulence locus AvrMlp7 in the poplar rust fungus correlate with poplar RMlp7 resistance breakdown
<p>Several studies reported the rapid evolution of avirulence (<i>Avr</i>) genes to escape <i>R</i>-mediated plant immunity and identified a variety of mechanisms leading to virulence. The poplar rust fungus <i>Melampsora larici-populina</i> is the most damaging pathogen of poplars. A major adaptive event occurred in 1994 with the breakdown of <i>RMlp7</i> resistance gene in poplar. Population genomics studies identified a locus in the genome of <i>M. larici-populina</i>, which likely corresponds to the <i>AvrMlp7</i> candidate avirulence gene. We used a population genetics approach combined with dedicated qPCR assays on a comprehensive set of 281 isolates, covering 27 years (encompassing the resistance breakdown event), to validate the candidate locus and to assess its polymorphism. We found two mechanisms, a point mutation and a deletion, that allowed the pathogen to escape <i>RMlp7</i>-mediated resistance. Six diploid genotypes were thus characterized at the candidate locus (three avirulent and three virulent). In addition, a temporal analysis revealed that the two virulence alleles pre-existed (harboured as avirulent heterozygous genotypes) since the early samplings and were found in association (as virulent genotypes) at the time of the resistance breakdown.These molecular analyses were complemented by a population genetic analysis of those temporal samples, using 22 microsatellite markers.</p>
Computational models from: Allele-specific activation, enzyme kinetics, and inhibitor sensitivities of EGFR exon 19 deletion mutations in lung cancer
<p>Computational models, compressed molecular dynamics (MD) simulation trajectories, and sample input files for "Allele-specific activation, enzyme kinetics, and inhibitor sensitivities of EGFR exon 19 deletion mutations in lung cancer". An early version of this manuscript is available as a preprint here: https://www.biorxiv.org/content/10.1101/2022.03.16.484661v1</p>
ARPIP: Ancestral sequence Reconstruction with insertions and deletions under the Poisson Indel Process
<p>Modern phylogenetic methods allow inference of ancestral molecular sequences given an alignment and phylogeny relating present day sequences. This provides insight into the evolutionary history of molecules, helping to understand gene function and to study biological processes such as adaptation and convergent evolution across a variety of applications. Here we propose a dynamic programming algorithm for fast joint likelihood-based reconstruction of ancestral sequences under the Poisson Indel Process (PIP). Unlike previous approaches, our method, named ARPIP, enables the reconstruction with insertions and deletions based on an explicit indel model. Consequently, inferred indel events have an explicit biological interpretation. Likelihood computation is achieved in linear time with respect to the number of sequences. Our method consists of two steps, namely finding the most probable indel points and reconstructing ancestral sequences. First, we find the most likely indel points and prune the phylogeny to reflect the insertion and deletion events per site. Second, we infer the ancestral states on the pruned subtree in a manner similar to FastML. We applied ARPIP on simulated datasets and on real data from the Betacoronavirus genus. ARPIP reconstructs both the indel events and substitutions with a high degree of accuracy. Our method fares well when compared to established state-of-the-art methods such as FastML and PAML. Moreover, the method can be extended to explore both optimal and suboptimal reconstructions, include rate heterogeneity through time and more. We believe it will expand the range of novel applications of ancestral sequence reconstruction.</p>
Factor XII deletion mitigates cerebral microbleed load but not hemodynamic dysfunction in the arcAβ mice
<p>Cerebrovascular dysfunction and a prothrombotic state have been found in patients with Alzheimer’s disease (AD). The factor XII (FXII)-driven activated contact system has been implicated in the vascular pathology and inflammation in AD patients and AD mouse models. Here we investigated the effect of genetic deletion of <em>FXII</em> on AD-related vascular dysfunction using magnetic resonance imaging (MRI). AD mouse line ArcAβ, arcAβ/<em>FXII-/-</em>, <em>FXII-/-</em> and non-transgenic littermates of 17 months of age (n = 40) were assessed for 1) cerebral microbleeds (CMB) load using susceptibility weighted imaging (SWI) MRI, 2) cerebral blood flow (CBF) using arterial spin labeling, and 3) vascular reactivity by estimating changes in cerebral blood volume (∆CBV) during hypercapnic stimulus using acetazolamide.</p>
DELETE ME PLEASE
<p>This is the replication package for paper "On the evolution of technical lag in the npm package dependency network" accepted for publication in ICSME 2018.</p>
TAD-fusion score: discovery and ranking the contribution of deletions to genome structure
<p>Datasets and code of the manuscript:</p> <p>Huynh L. & Hormozdiari F., TAD-fusion score: discovery and ranking the contribution of deletions to genome structure.</p> <p> </p>
QC and WGS around the breakpoints of deletions in the compound heterozygous PRKN-deficient PD iPSC line FINi006-A (FI.CS.PRKNDex2/Dex5-7.@40)
<p>BAM files from WGS on the regions of deletions in both <em>PRKN</em> gene alleles of the iPSC line (clone 18) derived using Sendai virus from PRKN 09/090 patient's fibroblasts </p>
Cas9-induced large deletions and small indels are controlled in a convergent fashion
<p>Demultiplexed reads assembled from 150PE Illumina using Pear with following settings: pear-0.9.10-bin-64 -f read1.fq -r read2.fq -n 20 -p 0.01. Unassembled PE reads (estimated at 0.1% of all reads) and reads that failed demux not included. 960 files total, corresponding to 96 wells of the library (95 control or knock-out mES clones and one well intentionally left empty) times two biological replicates times five test gRNAs (non-targetting control g33, chromosome X targetting g15, g48 and gU48 and autosome targetting g148). mES cells are derived from CAST x BL6 cross. Non-targeting control g33 fastq files are not locus-demultiplexed ie would map to g15, g48 and g148 loci. </p>
Data from: HIF prolyl hydroxylase 2/3 deletion disrupts astrocytic integrity and exacerbates neuroinflammation
<p><span>Astrocytes constitute the parenchymal border of the blood-brain barrier (BBB), modulate the exchange of soluble and cellular elements, and are essential for neuronal metabolic support. Thus, astrocytes critically influence neuronal network integrity. In hypoxia, astrocytes upregulate a transcriptional program that has been shown to boost neuroprotection in several models of neurological diseases. We investigated transgenic mice with astrocyte-specific activation of the hypoxia-response program by deleting the oxygen sensors, HIF prolyl-hydroxylase domains 2 and 3 (Phd2/3). We induced Phd2/3 deletion in experimental autoimmune encephalomyelitis (EAE) in a therapeutic approach that led to an exacerbation of the disease mediated by massive immune cell infiltration. We found that Phd2/3-ko astrocytes, though expressing a neuroprotective signature, exhibited a gradual loss of gap-junctional Connexin-43 (Cx43), which was induced by vascular endothelial growth factor-alpha (Vegf-a) expression. These results provide mechanistic insights into astrocyte biology, their critical role in hypoxic states, and in chronic inflammatory CNS diseases.</span></p>
Open-Label Study of ZYN002 Administered as a Transdermal Gel to Children and Adolescents With 22q11.2 Deletion Syndrome
ClinicalTrials.gov study NCT05149898. IPD Sharing: NO. Countries: 2. Publications: 0.
A Study in Previously Untreated Chronic Lymphocytic Leukemia (CLL) Subjects, Excluding Those With the 17p Deletion, to Evaluate Debulking Regimens Prior to Initiating Venetoclax Combination Therapy
ClinicalTrials.gov study NCT03406156. IPD Sharing: YES. Countries: 1. Publications: 0.
Lenalidomide Versus Placebo in Myelodysplastic Syndromes With a Deletion 5q[31] Abnormality
ClinicalTrials.gov study NCT00179621. IPD Sharing: Not stated. Countries: 9. Publications: 4.
A Multicenter Phase 2 Study of Ibrutinib in Patients With Relapsed or Refractory Chronic Lymphocytic Leukemia (CLL) or Small Lymphocytic Lymphoma (SLL) With 17p Deletion
ClinicalTrials.gov study NCT01744691. IPD Sharing: NO. Countries: 9. Publications: 1.
Acalabrutinib in Patients With Relapsed/Refractory and Treatment naïve Deletion 17p CLL/SLL
ClinicalTrials.gov study NCT02337829. IPD Sharing: YES. Countries: 1. Publications: 4.
A Study of the Efficacy of ABT-199 in Subjects With Relapsed/Refractory or Previously Untreated Chronic Lymphocytic Leukemia With the 17p Deletion
ClinicalTrials.gov study NCT01889186. IPD Sharing: YES. Countries: 7. Publications: 4.
Clinical Trial in 22q13 Deletion Syndrome(Phelan-McDermid Syndrome)
ClinicalTrials.gov study NCT01525901. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Lenalidomide Safety/Efficacy in Myelodysplastic Syndromes (MDS) Associated With a Deletion (Del)(5q) Cytogenetic Abnormality
ClinicalTrials.gov study NCT00065156. IPD Sharing: Not stated. Countries: 2. Publications: 4.
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.