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2,009 results for “Disruption”
Massively parallel screens to identify splice disruptive variants in human disease genes
<p>Splicing is a critical step in mRNA maturation with roles in gene regulation and proteome diversification. Splice disruptive variants (SDVs) are implicated in diverse human diseases, and 10-33% of exonic variants may disrupt splicing. However, identifying SDVs remains challenging due to the degeneracy and redundancy of the underlying sequence code. Experimental splicing measurements from patient cells or mini-gene assays can detect SDVs but have traditionally been low-throughput. </p> <p>Massively parallel reporter assays (MPSAs) systematically measure splicing impacts at scale and could clarify variant pathogenicity and inform models of splicing regulation. In this assay, complex barcoded libraries of mutant exons are synthesized, cloned into minigene constructs, and transfected into human cells. Splicing outcomes of each mutation are quantified en masse using targeted RNA-seq of minigene-derived transcripts, and I developed custom python package to process the resulting data.</p> <p>In Chapter 2, I apply this assay to the pituitary transcription factor gene <em>POU1F1</em> (in collaboration Dr. Sally Camper’s lab). Mutations in <em>POU1F1</em> cause combined pituitary hormone deficiency (CPHD), a clinically and genetically heterogenous disorder with prevalence ~1:4000. We targeted exon 2, which has two alterative isoforms (alpha and beta) using competing splice acceptors that encode mutually antagonistic proteins. We measured the splicing effects of 1,070 SNVs across the exon and surrounding introns and identified 96 SDVs - 14 of which were synonymous substitutions. Our measurements were concordant with six nearby heterozygous missense and synonymous variants seen in unrelated hypopituitarism patients. This map identifies a putative splice silencer motif that represses the use of the normally lowly expressed beta isoform.</p> <p>In Chapter 3, I apply a MPSA to a critical developmental renal transcription factor gene, <em>WT1</em> (in collaboration with clinical nephrologist Dr. Jen Lai Yee). Mutations in <em>WT1 </em>are implicated in nephrotic syndrome and sexual differentiation phenotypes. I focus on exon 9 which is alternatively spliced at competing donor sites resulting in two isoforms (KTS+ and KTS-). KTS+ and KTS- are normally expressed in ~2:1 ratio, but perturbation of the ratio can lead to Frasier’s syndrome – a rare nephrotic syndrome. We tested 518 SNVs for splicing defects and identified 8 known Frasier’s Syndrome variants as well as 16 additional variants that similarly lowered the KTS ratio. We also detected 19 variants increasing the KTS ratio - two of which have been observed in patients with sexual differentiation phenotypes.</p> <p>Although MPSAs can measure splicing effects of hundreds of variants simultaneously, the current scale of variant discovery via exome and genome sequencing demands efficient and accurate computational approaches to identify splice disruptive variants genome-wide. To evaluate the state of the art within contemporary splice prediction algorithms, in Chapter 4 I employed the results of five high throughput splicing assays and one literature curated variant set. A unique advantage of MPSAs over typical training and validation datasets is that they avoid bias towards essential splice site variants. I found the latest deep learning tools, SpliceAI and Pangolin, were most concordant with the measured splicing effects. However, all tools showed less agreement with exonic splicing outcomes compared to intronic. Some tools’ predictions, like SpliceAI’s, were sensitive to specified annotation files. Thus, there is still room for improvement within the next generation of splice prediction algorithms which future MPSA studies may facilitate.</p>
Disruption of fish gut microbiota composition and holobiont's metabolome during a simulated Microcystis aeruginosa (Cyanobacteria) bloom
<p>This archive contains the R code, QIIME2 script and datasets used to perform the analyses and figures in the manuscript.</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 corresponding to "Disparities in disruptions to public drinking water service in Texas communities during Winter Storm Uri 2021"
<p><strong>Contents:</strong></p> <p><strong>TX_pws_data_uri_zenodo.csv</strong>: This dataset was generated by integrating information on community public water systems (PWSs) from the Texas Commission of Environmental Quality (TCEQ) and Texas Water Development Board's water service boundary viewer, weather data from the National Oceanic and Atmospheric Administration (NOAA), and demographic information from the US Census Bureau's 2010 Decennial Census. More information is available in:<br> Tomko, Brianna, 2022, Public drinking water access in Texas communities during Winter Storm Uri 2021, Bachelor Thesis, The Ohio State University, Columbus. </p> <p><strong>readme_for_TX_pws_data_uri_zenodo.txt</strong>: Explains contents of TX_pws_data_uri_zenodo.csv.</p> <p><strong>WaterOutageSurvey-PeopleOnPublicWaterSystems.xlsx</strong>: This dataset was generated as part of a cross-sectionally survey of people living in Texas during Winter Storm Uri.</p> <p>More information on all datasets is available in:</p> <p>Tomko, B., C.L. Nittrouer, X. Sanchez-Vila, and A.H. Sawyer. (2023) "Disparities in disruptions to public drinking water services in Texas communities during Winter Storm Uri 2021," provisionally accepted at PLOS Water, doi: 10.1371/journal.pwat.0000137.</p>
Early-life sleep disruption impairs subtle social behaviours in prairie voles: a pose-estimation study
<p><span>Early life sleep disruption (ELSD) has been shown to have long-lasting effects on social behaviour in adult prairie voles (Microtus ochrogaster), including impaired expression of pair bonding during partner preference testing. However, due to the limitations of manual behaviour tracking, the effects of ELSD across the time course of pair bonding have not yet been described, hindering our ability to trace mechanisms. Here, we used pose estimation to track prairie voles during opposite-sex cohabitation, the process leading to pair bonding. Male-female pairs were allowed to interact through a mesh divider in the home cage for 72 h, providing variables of body direction, distance-to-divider and locomotion speed. We found that control males displayed periodic patterns of body orientation towards females during cohabitation. In contrast, ELSD males showed reduced duration and ultradian periodicity of these body orientation behaviours towards females. Furthermore, in both sexes, ELSD altered spatial and temporal patterns of locomotion across the light/dark cycles of the 72-h recordings. This study allows a comprehensive behavioural assessment of the effects of ELSD on later life sociality and highlights subtle prairie vole behaviours. Our findings may shed light on neurodevelopmental disorders featuring sleep disruption and social deficits, such as autism spectrum disorders.</span></p>
Disrupt CAD IV With the Shockwave Coronary IVL System
ClinicalTrials.gov study NCT04151628. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Shockwave Coronary Lithoplasty® Study (Disrupt CAD II)
ClinicalTrials.gov study NCT03328949. IPD Sharing: NO. Countries: 9. Publications: 2.
Sleep Disruption Induced Impairments in Bone Formation
ClinicalTrials.gov study NCT03733483. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Oxytocin on Irritability/Emotional Dysregulation of Disruptive Behavior and Mood Disorders
ClinicalTrials.gov study NCT02824627. IPD Sharing: NO. Countries: 1. Publications: 1.
Treatment of Symptomatic Lumbar Internal Disc Disruption (IDD) With the Biostat® System
ClinicalTrials.gov study NCT01011816. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Using MRI-Guided Laser Heat Ablation to Induce Disruption of the Peritumoral Blood Brain Barrier to Enhance Delivery and Efficacy of Treatment of Pediatric Brain Tumors
ClinicalTrials.gov study NCT02372409. IPD Sharing: NO. Countries: 1. Publications: 12.
Disrupt CAD III With the Shockwave Coronary IVL System
ClinicalTrials.gov study NCT03595176. IPD Sharing: Not stated. Countries: 4. Publications: 3.
Shockwave Medical Peripheral Lithoplasty System Study for PAD (Disrupt PAD III)
ClinicalTrials.gov study NCT02923193. IPD Sharing: NO. Countries: 4. Publications: 3.
Disrupt PAD BTK II Study With the Shockwave Peripheral IVL System
ClinicalTrials.gov study NCT05007925. IPD Sharing: Not stated. Countries: 2. Publications: 0.
Mechanisms of Sleep Disruption Hyperalgesia
ClinicalTrials.gov study NCT01794689. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Effects of GSK2798745 on Alveolar Barrier Disruption in a Segmental Lipopolysaccharide (LPS) Challenge Model
ClinicalTrials.gov study NCT03511105. IPD Sharing: YES. Countries: 1. Publications: 1.
Shockwave Coronary Rx Lithoplasty® Study (Disrupt CAD I)
ClinicalTrials.gov study NCT02650128. IPD Sharing: Not stated. Countries: 5. Publications: 2.
A Physical Activity Program to Disrupt Sedentary Time in Older Latinos
ClinicalTrials.gov study NCT04507464. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Functional Melatonin Replacement for Sleep Disruptions in Individuals With Tetraplegia
ClinicalTrials.gov study NCT00507546. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Sleep Disruption in New Mothers: An Intervention Trial
ClinicalTrials.gov study NCT01321710. IPD Sharing: Not stated. Countries: 1. Publications: 4.
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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.