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151 results for “Trafficking”
Dataset to the publication "A unique signal sequence of the chemokine receptor CCR7 promotes package into COPII vesicles for efficient receptor trafficking"
<p>This repository accompanies the paper:</p> <p>"A unique signal sequence of the chemokine receptor CCR7 promotes package into COPII vesicles for efficient receptor trafficking".</p> <p>Organized into 14 folders it provides the data allowing the replication of all analyses and the manuscript's figures. For a more convenient download files were zipped.</p> <p>Upon publication of results using this dataset, please cite the following paper:</p> <p>Uetz-von Allmen E, Rippl AV, Farhan H, Legler DF. 2018. A unique signal sequence of the chemokine receptor CCR7 promotes package into COPII vesicles for efficient receptor trafficking. J Leukoc Biol 104(2):375-389.</p>
A data directory to facilitate investigations on worldwide wildlife trafficking
<p>We describe a novel, open-access data directory on wildlife trafficking and a corresponding visualization tool that can be used to identify data for multiple purposes, such as exploring wildlife trafficking hotspots and convergence points with other crime, discovering key drivers or deterrents of wildlife trafficking, and uncovering structural patterns. Keyword searches, expert elicitation, and peer-reviewed publications were used to search for extant sources used by industry and non-profit organizations, as well as those leveraged to publish academic research articles. The open-access data directory is designed to be a living document and searchable according to multiple measures. The directory can be instrumental in the data-driven analysis of unsustainable illegal wildlife trade, supply chain structure via link prediction models, the value of demand and supply reduction initiatives via multi-item knapsack problems, or trafficking behavior and transportation choices via network interdiction problems.</p>
Raw data for "Host-interactor screens of Phytophthora infestans RXLR proteins reveal vesicle trafficking as a major effector-targeted process"
<p>This dataset contains raw and original images, phylogenetic tree files, sequence alignment files used for phylogenetic tree construction and unprocessed data for figures presented in the manuscript titled "Host-interactor screens of <em>Phytophthora infestans</em> RXLR proteins reveal vesicle trafficking as a major effector-targeted process". Each zip file contains raw data for each figure in the manuscript. A version of the manuscript is available on bioRxiv with doi.org/10.1101/2020.09.24.308585.</p>
Trafficking dataset for: A massively parallel assay accurately discriminates between functionally normal and abnormal variants in a hotspot domain of KCNH2
<p><span>Many genes, including <em>KCNH2</em>, contain </span><span>'hotspot' domains associated with a high density of variants associated with disease. This has led to the suggestion that variant location can be used as evidence supporting classification of clinical variants. However, it is not known what proportion of all potential variants in hotspot domains cause loss of function. Here, we have used a massively parallel trafficking assay to characterize all single-nucleotide variants in exon 2 of <em>KCNH2, </em>a known hotspot for variants that cause long QT syndrome type 2 and an increased risk of sudden cardiac death<em>. </em>Forty-two percent of <em>KCNH2</em> exon 2 variants caused at least 50 % reduction in protein trafficking and 65% of these trafficking defective variants exerted a dominant-negative effect when co-expressed with a WT <em>KCNH2</em> allele as assessed using a calibrated patch clamp electrophysiology assay. The massively parallel trafficking assay was more accurate (AUC of 0.94) than bioinformatic prediction tools (REVEL and CardioBoost, AUC of 0.81) in discriminating between functionally normal and abnormal variants. Interestingly, over half of variants in exon 2 were found to be functionally normal, suggesting a nuanced interpretation of variants in this 'hotspot' domain is necessary. Our massively parallel trafficking assay can provide this information prospectively.</span></p>
Doublecortin and JIP3 are neural-specific counteracting regulators of dynein-mediated retrograde trafficking
Mutations in the microtubule (MT)-binding protein doublecortin (DCX) or in the MT-based molecular motor dynein result in lissencephaly. However, a functional link between DCX and dynein has not been defined. Here, we demonstrate that DCX negatively regulates dynein-mediated retrograde transport by reducing dynein's association with MTs and by disrupting the composition of the dynein motor complex. Previous work showed an increased binding of the adaptor protein C-Jun-amino-terminal kinase-interacting protein 3 (JIP3) to dynein in the absence of DCX. Using purified components, we demonstrate that JIP3 forms an active motor complex with dynein and its cofactor dynactin with two dyneins per complex. DCX competes with the binding of the second dynein, resulting in a velocity reduction of the complex. We conclude that DCX negatively regulates dynein-mediated retrograde transport through two critical interactions by regulating dynein binding to MTs and by regulating the association of JIP3 to the dynein motor complex.
N-glycosylation acts as a switch for FGFR1 trafficking between the plasma membrane and nuclear envelope - yet unpublished supplementary data regarding Fig. 1C
<p>Fibroblast growth factor receptor 1 (FGFR1) is a heavily N-glycosylated cell surface receptor tyrosine kinase that transmits signals across the plasma membrane, in response to fibroblast growth factors (FGFs). Balanced FGF/FGFR1 signaling is crucial for the development and homeostasis of the human body, and aberrant FGFR1 is frequently observed in various cancers. In addition to its predominant localization to the plasma membrane, FGFR1 has also been detected inside cells, mainly in the nuclear lumen, where it modulates gene expression. However, the exact mechanism of FGFR1 nuclear transport is still unknown. In this study, we generated a glycosylation-free mutant of FGFR1, FGFR1.GF, and demonstrated that it is localized primarily to the nuclear envelope. We show that reintroducing N-glycans into the D3 domain cannot redirect FGFR1 to the plasma membrane or exclude the receptor from the nuclear envelope. Reestablishment of D2 domain N-glycans largely inhibits FGFR1 accumulation in the nuclear envelope, but the receptor continues to accumulate inside the cell, mainly in the ER. Only the simultaneous presence of N-glycans of the D2 and D3 domains of FGFR1 promotes efficient transport of FGFR1 to the plasma membrane. We demonstrate that while disturbed FGFR1 folding results in partial FGFR1 accumulation in the ER, impaired FGFR1 secretion drives FGFR1 trafficking to the nuclear envelope. Intracellular FGFR1.GF displays a high level of autoactivation, suggesting the presence of nuclear FGFR1 signaling, which is independent of FGF. Using mass spectrometry and proximity ligation assay, we identified novel binding partners of the nuclear envelope-localized FGFR1, providing insights into its cellular functions. Collectively, our data define N-glycosylation of FGFR1 as an important regulator of FGFR1 kinase activity and, most importantly, as a switchable signal for FGFR1 trafficking between the nuclear envelope and plasma membrane, which, due to spatial restrictions, shapes FGFR1 interactome and cellular function.</p> <p> </p> <p>These data are raw data of Fig. 1C generated by Aleksandra Chorążewska. These data are not present in supplementary data od publication</p>
Data from: The fat body cortical actin network regulates Drosophila inter-organ nutrient trafficking, signaling, and adipocyte cell size
<p>Defective nutrient storage and adipocyte enlargement (hypertrophy) are emerging features of metabolic syndrome and type 2 diabetes. How the cytoskeletal network contributes to nutrient uptake, fat storage, and adipocyte size remains poorly understood. Utilizing the <em>Drosophila</em> larval fat body (FB) as a model adipose tissue, we show that a specific actin isoform—Act5C—forms the cortical actin network necessary for inter-organ lipid trafficking. Act5C also promotes FB tissue expansion during larval development so larvae can store sufficient biomass for metamorphosis. We find FB-specific loss of Act5C, but not other <em>Drosophila</em> actins, perturbs FB triglyceride (TG) storage in lipid droplets (LDs), resulting in developmentally delayed larvae that fail to develop into flies. Act5C localizes to the FB cell surface where it intimately contacts peripheral LDs (pLDs), forming a cortical actin network together with spectrins for cell architectural support. While both the cortical actin and spectrin cytoskeletons maintain FB cell surface architecture, we find that only the actin network is required for fat storage. Mechanistically, we show that FBs lacking the Act5C cortical cytoskeleton exhibit a block in lipoprotein (Lpp) secretion from FB cells, and a subsequent disruption of gut:FB inter-organ lipid transport, resulting in mid-gut fat accumulation. Utilizing temporal RNAi-depletion approaches, we also reveal that Act5C is indispensable post-embryogenesis during larval feeding to promote FB cell expansion. Act5C-deficient FBs fail to expand cell sizes, leading to lipodystrophic larvae unable to accrue sufficient biomass for metamorphosis. Collectively, we propose that the Act5C-mediated cortical actin network of <em>Drosophila</em> adipose tissue plays an essential role in post-embryonic inter-organ nutrient transport and FB cell size determination for organismal energy homeostasis and development.</p>
Data for: Plasmodesmal endoplasmic reticulum proteins regulate intercellular trafficking of Cucumber mosaic virus in Arabidopsis
<p>Plasmodesmata (PD) are plasma membrane (PM)-lined cytoplasmic nanochannels that mediate in cell-to-cell communication across the cell wall. A range of proteins are embedded in the PD PM and endoplasmic reticulum (ER) and function in regulating PD-mediated symplasmic trafficking. However, knowledge of the nature and function of the ER-embedded proteins, in the intercellular movement of non-cell-autonomous proteins, is limited. Here, we report the functional characterization of two ER luminal proteins, AtBiP1/2, and two ER integral membrane proteins, AtERdj2A/B, which are located within the PD. These PD proteins were identified as interacting proteins with <em>Cucumber mosaic virus </em>(CMV) movement protein (MP) in coimmunoprecipitation studies, using an Arabidopsis-derived plasmodesmal-enriched cell wall protein preparation (PECP). The AtBiP1/2 PD location was confirmed by transmission electron microscopy-based immunolocalization, and their AtBiP1/2 signal peptides (SPs) function in PD targeting. <em>In vitro</em>/<em>in vivo</em> pull-down assays revealed the association between AtBiP1/2 and CMV MP, mediated by AtERdj2A, through the formation of an AtBiP1/2-AtERdj2-CMV MP complex within PD. The role of this complex in CMV infection was established, as systemic infection was retarded in <em>bip1</em>/<em>bip2w</em> and <em>erdj2b</em> mutants. Our findings provide a model for a mechanism by which the CMV MP mediates in cell-to-cell trafficking of its viral ribonucleoprotein complex.</p>
Plasmablast Trafficking and Antibody Response in Influenza Vaccination (SLVP021 2011-2014)
ClinicalTrials.gov study NCT02141581. IPD Sharing: YES. Countries: 1. Publications: 3.
Pilot Study to Determine Effects of the Btk Inhibitor PCI-32765 on Leukemia Cell Kinetics and Trafficking, Using Heavy Water Labeling in Subjects With CLL and SLL
ClinicalTrials.gov study NCT01752426. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Data for: Plasmodesmal endoplasmic reticulum proteins regulate intercellular trafficking of Cucumber mosaic virus in Arabidopsis
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Data from: The fat body cortical actin network regulates Drosophila inter-organ nutrient trafficking, signaling, and adipocyte cell size
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Trafficking dataset for: A massively parallel assay accurately discriminates between functionally normal and abnormal variants in a hotspot domain of KCNH2
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Identifying cellular RNA-binding proteins during infection uncovers a role for MKRN2 in influenza mRNA trafficking
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Doublecortin and JIP3 are neural-specific counteracting regulators of dynein-mediated retrograde trafficking
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Data from: Finding politically feasible conservation policies: the case of wildlife trafficking
Conservation management is of increasing importance in ecology as most ecosystems nowadays are essentially managed ones. Conservation managers work within a political-ecological system when they develop and attempt to implement a conservation plan that is designed to meet particular conservation goals. In this article, we develop a decision support tool that can identify a conservation policy for a managed wildlife population that is both sustainable and politically feasible. Part of our tool consists of a simulation model composed of interacting influence diagrams. We build, fit, and use our tool on the case of rhino horn trafficking between South Africa and Asia. Using these diagrams, we show how a rhino poacher's belief system can be modified by such a policy and locate it in a perceived risks-benefits space before and after policy implementation. We statistically fit our model to observations on group actions and rhino abundance. We then use this fitted model to compute a politically feasible conservation policy.
Mitochondrial and ER membrane protein trafficking CRISPR screens
<p><span>The trafficking of specific protein cohorts to the correct subcellular location at the correct time is essential for every signaling and regulatory process in biology. Gene perturbation screens could provide a powerful approach to probe the molecular mechanisms of protein trafficking, but only if protein localization or mislocalization can be tied to a simple and robust phenotype for cell selection, such as cell proliferation or FACS. To broadly empower the study of protein trafficking processes with gene perturbation, we developed a genetically-encoded molecular tool named HiLITR. HiLITR converts protein colocalization into proteolytic release of a membrane-anchored transcription factor, which drives the expression of a chosen reporter gene. Using HiLITR in combination with FACS-based CRISPRi screening in human cell lines, we identify genes that influence the trafficking of mitochondrial and ER tail-anchored proteins. </span>We show that loss of the SUMO E1 component SAE1 results in the mislocalization and destabilization of mitochondrial tail-anchored proteins. We also demonstrate a distinct regulatory role for EMC10 in the ER membrane complex, opposing the transmembrane-domain insertion activity of the complex. Through transcriptional integration of complex cellular functions, HiLITR expands the scope of biological processes that can be studied by genetic perturbation screening technologies.</p>
Nanoresolution real-time 3D orbital tracking for studying mitochondrial trafficking in vertebrate axons in vivo - Data Set 2
<p>The data set was analyzed in main figures 2, 3 and supplementary figure 5.</p>
Nanoresolution real-time 3D orbital tracking for studying mitochondrial trafficking in vertebrate axons in vivo - Data Set 1
<p>24.01.2014 fish 5 was analyzed in main figures 1,2 and supplementary figure 4</p> <p>21.03.2014 fish 1 was analyzed in main figures 2,3 and supplementary figure 4</p>
Evolution of ubiquitin, cytoskeleton, and vesicular trafficking machinery in giant viruses
<p>This repository contains genomes, proteins, and alignments used in the study "Evolution of ubiquitin, cytoskeleton, and vesicular trafficking machinery in giant viruses".</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)
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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.