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48 results for “Endosomes”
A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction - buil and Analysis
<p><strong>Title publication: </strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong><strong> </strong>2018</p> <p><strong>DOI publication: </strong>10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> All scripts, jupyter notebooks, and data files used to building and analyzing systems in the presented in the paper. Also related experimental data.</p>
Barley endosomal MONENSIN SENSITIVITY1 is a target of the powdery mildew effector CSEP0162 and plays a role in plant immunity
<p><span>Encasements formed around haustoria and biotrophic hyphae as well as hypersensitive reaction (HR) cell death are essential plant immune responses to filamentous pathogens. In this study we examine the components that may contribute to the absence of these responses in susceptible barley attacked by the powdery mildew fungus. We find that the effector CSEP0162 from this pathogen targets plant MONENSIN SENSITIVITY1 (MON1), which is important for the fusion of multivesicular bodies to their target membranes. Overexpression of CSEP0162 and silencing of barley MON1 both inhibit encasement formation. We find that the Arabidopsis ecotype No-0 has resistance to powdery mildew, and that this is partially dependent on MON1. Surprisingly, we find the MON1-dependent resistance in No-0 not only includes an encasement response, but also an effective HR. Similarly, silencing of MON1 in barley also blocks Mla3-mediated HR-based powdery mildew resistance. Our results indicate that MON1 is a vital plant immunity component, and we speculate that the barley powdery mildew fungus introduces the effector CSEP0162 to target MON1 and hence reduces encasement formation and HR.</span></p>
ATG9A regulates dissociation of recycling endosomes from microtubules leading to formation of influenza A virus liquid condensates - MAIN FIGURES
<p>Metadata for the manuscript entitled "ATG9A regulates dissociation of recycling endosomes from microtubules leading to formation of influenza A virus liquid inclusions" - MAIN FIGURES</p>
Barley endosomal MONENSIN SENSITIVITY1 is a target of the powdery mildew effector CSEP0162 and plays a role in plant immunity
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Data from: Interactions between TTYH2 and APOE facilitate endosomal lipid transfer
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Dataset related to article "Control of Cytoskeletal Dynamics by β-Arrestin1/Myosin Vb Signaling Regulates Endosomal Sorting and Scavenging Activity of the Atypical Chemokine Receptor ACKR2"
<p>This record contains raw data related to article "Control of Cytoskeletal Dynamics by β-Arrestin1/Myosin Vb Signaling Regulates Endosomal Sorting and Scavenging Activity of the Atypical Chemokine Receptor ACKR2"</p> <p>The atypical chemokine receptor ACKR2, formerly named D6, is a scavenger chemokine receptor with a non-redundant role in the control of inflammation and immunity. The scavenging activity of ACKR2 depends on its trafficking properties, which require actin cytoskeleton rearrangements downstream of a β-arrestin1-Rac1-PAK1-LIMK1-cofilin-dependent signaling pathway. We here demonstrate that in basal conditions, ACKR2 trafficking properties require intact actin and microtubules networks. The dynamic turnover of actin filaments is required to sustain ACKR2 constitutive endocytosis, while both actin and microtubule networks are involved in processes regulating ACKR2 constitutive sorting to rapid, Rab4-dependent and slow, Rab11-dependent recycling pathways, respectively. After chemokine engagement, ACKR2 requires myosin Vb activity to promote its trafficking from Rab11-positive recycling endosomes to the plasma membrane, which sustains its scavenging activity. Other than cofilin phosphorylation, induction of the β-arrestin1-dependent signaling pathway by ACKR2 agonists also leads to the rearrangement of microtubules, which is required to support the myosin Vb-dependent ACKR2 upregulation and its scavenging properties. Disruption of the actin-based cytoskeleton by the apoptosis-inducing agent staurosporine results in impaired ACKR2 internalization and chemokine degradation that is consistent with the emerging scavenging-independent activity of the receptor in apoptotic neutrophils instrumental for promoting efficient efferocytosis during the resolution of inflammation. In conclusion, we provide evidence that ACKR2 activates a β-arrestin1-dependent signaling pathway, triggering both the actin and the microtubule cytoskeletal networks, which control its trafficking and scavenger properties.</p>
Fluorescent Membrane Tension Probes for Early Endosomes
<p><strong>Table of contents</strong></p> <p>1. Synthesis and Characterization</p> <p>1.1. Compounds <strong>1</strong>,<strong> 3</strong>,<strong> 4</strong>,<strong> 6</strong>,<strong> 7</strong>,<strong> 9</strong>,<strong> 10</strong>, <strong>11</strong>,<strong> 12</strong></p> <ul> <li>Lab Book Page</li> <li>NMR</li> <li>LC-MS</li> <li>IR</li> <li>HRMS</li> </ul> <p>1.2. Compounds <strong>15</strong>,<strong> 17</strong>,<strong> 19</strong>,<strong> 24</strong>,<strong> 1’</strong>,<strong> 3’</strong>,<strong> 5’</strong>,<strong> 7’</strong></p> <ul> <li>Lab Book Page</li> <li>NMR</li> <li>LC-MS</li> <li>IR</li> <li>ESI-MS</li> </ul> <p>1.3. Compounds <strong>21</strong>,<strong> 23</strong>,<strong> 26</strong>,<strong> 8’</strong>,<strong> 10’</strong></p> <ul> <li>Lab Book Page</li> <li>NMR</li> <li>LC-MS</li> <li>IR</li> </ul> <p>2. p<em>K</em><sub>a</sub> Determination</p> <p>2.1. Titration of <strong>32</strong>,<strong> 35</strong>,<strong> 36</strong> for the determination of the correction function</p> <ul> <li>Lab Book Page</li> <li>NMR</li> </ul> <p>2.2. Titration of Model Compounds <strong>1’</strong> – <strong>10’</strong></p> <ul> <li>Lab Book Page</li> <li>NMR </li> </ul> <p>3. Co-Localization with EGF</p> <p>4. Automated Microscopy</p> <p>5. FLIM Imaging</p> <p>6. FLIM of Early Endosomes</p>
Spatial snapshots of amyloid precursor protein intramembrane processing via early endosome proteomics
<p>Source datasets for Western blot quantification in Figures S1d and S5a for Park et al. "Spatial snapshots of amyloid precursor protein intramembrane processing via early endosome proteomics". </p>
Interferon-inducible phospholipids govern IFITM3-dependent endosomal antiviral immunity
<p>Raw data from indicated Figures of our work entitled "Interferon-inducible phospholipids govern IFITM3-dependent endosomal antiviral immunity" by Unali et al., published as Open Access in EMBO J.</p> <p> </p> <p> </p>
A molecular view on the escape of lipoplexed DNA from the endosome (no trajectories)
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Data from: Recruitment dynamics of ESCRT-III and Vps4 to endosomes and implications for reverse membrane budding
The ESCRT machinery mediates reverse membrane scission. By quantitative fluorescence lattice light-sheet microscopy, we have shown that ESCRT-III subunits polymerize rapidly on yeast endosomes, together with the recruitment of at least two Vps4 hexamers. During their 3-45 second lifetimes, the ESCRT-III assemblies accumulated 75-200 Snf7 and 15-50 Vps24 molecules. Productive budding events required at least two additional Vps4 hexamers. Membrane budding was associated with continuous, stochastic exchange of Vps4 and ESCRT-III components, rather than steady growth of fixed assemblies, and depended on Vps4 ATPase activity. An all-or-none step led to final release of ESCRT-III and Vps4. Tomographic electron microscopy demonstrated that acute disruption of Vps4 recruitment stalled membrane budding. We propose a model in which multiple Vps4 hexamers (four or more) draw together several ESCRT-III filaments. This process induces cargo crowding and inward membrane buckling, followed by constriction of the nascent bud neck and ultimately ILV generation by vesicle fission.
ATG9A regulates dissociation of recycling endosomes from microtubules leading to formation of influenza A virus liquid condensates - SUPPLEMENTARY FIGURES
<p>Metadata for the manuscript "ATG9A regulates dissociation of recycling endosomes from microtubules leading to formation of influenza A virus liquid condensates" - Supplementary Figures</p>
Data from: Recruitment dynamics of ESCRT-III and Vps4 to endosomes and implications for reverse membrane budding
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PDGFRa signaling regulates Srsf3 transcript binding to affect PI3K signaling and endosomal trafficking (RNA-seq)
GEO Series GSE263169. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
Modulations of mTORC2-GATA3 is by isorhamnetin activates endosomal-lysosomal degradation in J774.1 macrophage-like cell line
GEO Series GSE167010. Mus musculus. 20 samples. Type: Expression profiling by array; Expression profiling by high throughput sequencing.
Human p11-mediated re-direction of phagosomes to the recycling endosome-expulsion pathway by a fungal pathogen
GEO Series GSE217895. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Physiological role of 2’-O-methylation within prokaryotic and eukaryotic tRNA for innate immune activation via endosomal Toll-like receptors
GEO Series GSE125797. Homo sapiens. 24 samples. Type: Expression profiling by array.
A large panel of isogenic APP and PSEN1 mutant human iPSC neurons reveals shared endosomal abnormalities mediated by APP b-CTFs, not Ab [ribosome profiling]
GEO Series GSE128344. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Endosomal trafficking bypassed by RAB5B-CD109 interplay promotes axonogenesis in KRAS-mutant pancreatic cancer
GEO Series GSE251916. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Zeolitic Imidazolate Frameworks Activate Endosomal Toll-like Receptors and Potentiate Immunogenicity of SARS-CoV-2 Spike Protein Trimer
GEO Series GSE246178. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
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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.