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115 results for “data deletion”
Data for: Dysregulation of mTOR signaling mediates common neurite and migration defects in both idiopathic and 16p11.2 deletion autism neural precursor cells
<p>Autism spectrum disorder (ASD) is defined by common behavioral characteristics, raising the possibility of shared pathogenic mechanisms. Yet, vast clinical and etiological heterogeneity suggests personalized phenotypes. Surprisingly, our iPSC studies find that six individuals from two distinct ASD subtypes, idiopathic and 16p11.2 deletion, have common reductions in neural precursor cell (NPC) neurite outgrowth and migration even though whole genome sequencing demonstrates no genetic overlap between the datasets. To identify signaling differences that may contribute to these developmental defects, an unbiased phospho-(p)-proteome screen was performed. Surprisingly, despite the genetic heterogeneity, hundreds of shared p-peptides were identified between autism subtypes including the mTOR pathway. mTOR signaling alterations were confirmed in all NPCs across both ASD subtypes and mTOR modulation rescued ASD phenotypes and reproduced autism NPC-associated phenotypes in control NPCs. Thus, our studies demonstrate that genetically distinct ASD subtypes have common defects in neurite outgrowth and migration which are driven by the shared pathogenic mechanism of mTOR signaling dysregulation.</p>
Data from: Deletion of an sRNA primes development in a multicellular bacterium
<p>Small non-coding RNAs (sRNAs) are essential in regulating gene expression during many biological processes. The myxobacteria gene <em>pxr</em> encodes an sRNA known to block fruiting-body development, an aggregative multicellular process triggered by starvation. Deletion of <em>pxr</em> allows <em>Myxococcus xanthus </em>cells<em> </em>to develop in the presence of nutrients. However, potential Pxr binding targets and most genes regulated by Pxr remain unknown. Here, we found that the absence of <em>pxr </em>expression dramatically alters the temporal dynamics of development, thus suggesting an important new role of this sRNA in myxobacterial ecology. We transcriptionally profiled vegetative cells of <em>M. xanthus </em>strains<em> </em>possessing vs lacking <em>pxr</em> and found that over half of the genes impacted by <em>pxr </em>deletion during growth are linked to development, including known and potentially novel critical regulators. Many other genes are associated with general metabolic processes, which Pxr regulates positively. Our study discovers new phenotypic effects of Pxr regulation of likely ecological importance, identifies the suite of genes this sRNA controls during vegetative growth, reveals a previously unknown developmental regulator and provides new insights into the early molecular regulation of myxobacterial development.</p>
BRAIN Journal-High Performance Data mining by Genetic Neural Network-Figure 5. Insertion and Deletion Hidden Layer in NN
<p>Change in NN structure is other method that we used to optimization of solution[18].<br> Insertion a hidden layer caused to mutation operator is much natural. As connection with father and<br> mother nodes is easily[20],[21]. Weights of node and errors automatically calculated.<br> For each stage of the implementation of the mutation operator in genetic algorithms, neural<br> networks, only one of the nodes in the hidden layer is selected and inserted. These layers are<br> inserted on condition that the definition does not harm the network structure and the action is<br> meaningful. As an added layer can adjust the weights and the connection to the parent node of a network<br> layer to be removed.</p>
Data for: Dysregulation of mTOR signaling mediates common neurite and migration defects in both idiopathic and 16p11.2 deletion autism neural precursor cells
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Data from: Deletion of an sRNA primes development in a multicellular bacterium
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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>
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>
Data from: Two genes, one culprit - a functional candidate validation of a <em>SPATA7</em> deletion in dogs with day blindness/retinal degeneration
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Data from: A SACS deletion variant in Great Pyrenees dogs causes autosomal recessive neuronal degeneration
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Data from: HIF prolyl hydroxylase 2/3 deletion disrupts astrocytic integrity and exacerbates neuroinflammation
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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
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live cell super-resolution data_dual_color_cell_line_SCR_deletion
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live cell super-resolution data_dual_color_cell_line_E15_deletion
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ENDOG_NGS data related to article "Biallelic variants in ENDOG associated with mitochondrial myopathy and multiple mtDNA deletions" submitted to Cells
<p>vcf file of the targeted NGS; csv of the top 50 rare variants from WES prioritized by eVAI software; csv of WES rare variants prioritized by eVAI software using patient's phenotype information.</p>
text-fig. 54. Reduced consensus tree of the pruned data matrix after the deletion of Shuvosaurus, Segisaurus, and Poekilopleuron. Named nodes: 1, Saurischia; 4, Herrerasauridae; 5, Neotheropoda; 6, Coelophysoidea; 8, Coelophysidae; 9, Liliensternus', 12, Ceratosauria; 13, Abelisauroidea; 14, etanurae; 16, Camosauria; 17, Spinosauroidea; 20, Allosauroidea; 24, Coelurosauria; 26, Coeluridae; 27, Compsognathinae; 30, Tyrannosauroidea; 34, Maniraptora; 37, Deinonychosauria. in The interrelationships and evolution of basal theropod dinosaurs
text-fig. 54. Reduced consensus tree of the pruned data matrix after the deletion of Shuvosaurus, Segisaurus, and Poekilopleuron. Named nodes: 1, Saurischia; 4, Herrerasauridae; 5, Neotheropoda; 6, Coelophysoidea; 8, Coelophysidae; 9, Liliensternus', 12, Ceratosauria; 13, Abelisauroidea; 14, etanurae; 16, Camosauria; 17, Spinosauroidea; 20, Allosauroidea; 24, Coelurosauria; 26, Coeluridae; 27, Compsognathinae; 30, Tyrannosauroidea; 34, Maniraptora; 37, Deinonychosauria.
text-fig. 52. wo selected reduced consensus trees from the analysis of the complete data set. a, after deletion of 'Chilantaisaurus' maortuensis. B, after deletion of Proceratosaurus and Xuanhanosaurus. in The interrelationships and evolution of basal theropod dinosaurs
text-fig. 52. wo selected reduced consensus trees from the analysis of the complete data set. a, after deletion of 'Chilantaisaurus' maortuensis. B, after deletion of Proceratosaurus and Xuanhanosaurus.
Data_Tab1_Deletion of the transcription factor Prox-1 specifically in the renal distal convoluted tubule causes hypomagnesemia via reduced expression of TRPM6 and NCC
<p>Data of Tab1 from “Deletion of the transcription factor Prox-1 specifically in the renal distal convoluted tubule causes hypomagnesemia via reduced expression of TRPM6 and NCC”</p> <p>Dataset (doi: 10.1007/s00424-020-02491-1) contains the original publication as PDF-format (10.1007_s00424-020-02491-1.pdf). Corresponding raw data obtained from LC-MS/MS analysis provided as one file in CSV format (31003A-179400_10.1007_s00424-020-02491-1_DW_4-1.csv). All further experiment related information provided as two meta-data-files (31003A-179400_10.1007_s00424-020-02491-1_DW _4-1_M_1.PDF, 31003A-179400_10.1007_s00424-020-02491-1_DW _4-1_M_2.pdf) as PDF format.</p>
Data from: Out of the testis, into the ovary: biased outcomes of gene duplication and deletion in Drosophila
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Data from: Mining for single nucleotide polymorphisms and insertions / deletions in expressed sequence tag libraries of oil palm
The oil palm is a tropical oil bearing tree. Recently EST-derived SNPs and SSRs are a free by-product of the currently expanding EST (Expressed Sequence Tag) data bases. The development of high-throughput methods for the detection of SNPs (Single Nucleotide Polymorphism) and small indels (insertion / deletion) has led to a revolution in their use as molecular markers. Available (5452) Oil palm EST sequences were mined from dbEST of NCBI. CAP3 program was used to assemble EST sequences into contigs. Candidate SNPs and Indel polymorphisms were detected using the perl script auto_snip version 1.0 which has used 576 ESTs for detecting SNPs and Indel sites. We found 1180 SNP sites and 137 indel polymorphisms with frequency 1.36 SNPs / 100 bp. Among the six tissues from which the EST libraries had been generated, mesocarp had high frequency of 2.91 SNPs and indels per 100 bp whereas the zygotic embryos had lowest frequency of 0.15 per 100 bp. We also used the Shannon index to analyze the proportion of ten possible types of SNP/indels. ESTs from tissues of normal apex showed highest values of Shannon index (0.60) whereas abnormal apex had least value (0.02). The present report deals the use of Shannon index for comparing SNP/ indel frequencies mined from ESTlibraries and also confirm that the frequency of SNP occurrence in oil palm to use them as markers for genetic studies.
Data from: Recurrent gene deletions and the evolution of adaptive cyanogenesis polymorphisms in white clover (Trifolium repens L.)
Understanding the molecular evolution of genes that underlie intraspecific polymorphisms can provide insights into the process of adaptive evolution. For adaptive polymorphisms characterized by gene presence/absence (P/A) variation, underlying loci commonly show signatures of long-term balancing selection, with gene-presence and gene-absence alleles maintained as two divergent lineages. We examined the molecular evolution of two unlinked P/A polymorphisms that underlie a well-documented adaptive polymorphism for cyanogenesis (hydrogen cyanide release with tissue damage) in white clover. Both cyanogenic and acyanogenic plants occur in this species, and the ecological forces that maintain this chemical defense polymorphism have been studied for several decades. Using a sample of 65 plants, we investigated the molecular evolution of sequences flanking the two underlying cyanogenesis genes: Ac/ac (controlling the presence/absence of cyanogenic glucosides), and Li/li (controlling the presence/absence of their hydrolyzing enzyme, linamarase). A combination of genome-walking, PCR assays, DNA sequence analysis, and Southern blotting was used to test whether these adaptive P/A polymorphisms show evidence of long-term balancing selection, or whether gene-absence alleles have evolved repeatedly through independent deletion events. For both loci, we detect no signatures of balancing selection in closest flanking genomic sequences. Instead, we find evidence for variation in the size of the deletions characterizing gene-absence alleles. These observations strongly suggest that both of these polymorphisms have been evolving through recurrent gene deletions over time. We discuss the genetic mechanisms that could account for this surprising pattern and the implications of these findings for mechanisms of rapid adaptive evolution in white clover.
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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.