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  • Determination of free and protein-bound DA and NE and their metabolites and oxidation products by UPLC-MS/MS method

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    Protocol for the determination of free and protein-bound DA and NE and their metabolites and oxidation products by UPLC-MS/MS method.

  • Endogenous tagging of the YIPF4 gene with mNEON Green and imaging of these cells by microscopy

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    Protocol for tagging YIPF4 gene with mNEON in cells using CRISPR. Method involves editing N-terminus of YIPF4 in WT and FIP200-/- HEK293T cells. Imaging mNEON-YIPF4 in Golgi with GOLGB1 marker is also detailed.

  • powereQTL – An R shiny application for calculating sample size and power of bulk tissue and single-cell eQTL analysis

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    Easy-to-use web application for calculating sample size and power of bulk tissue and single-cell eQTL analysis

  • Confocal imaging on Nikon AXR confocal microscope

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    A step by step protocol to acquire images on Nikon AXR confocal set-up.

  • pGEX4T1-TEV-HsFBXO7 (129-398)/Skp1

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    Plasmid for expression of FBXO7/SKP1 in bacteria

  • Mito and Glycolysis Stress Tests for Enteroendocrine Cells – Hutu-80

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    Mito and glycolysis stress tests for enteroendocrine cells - Hutu-80

  • Organelle isolation from mouse tissues expressing organelle tags

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    The organelles purified using this method are highly enriched, intact, largely contaminant-free and can be used for various downstream applications, including immunoblotting analysis and proteomic analysis, but also lipidomic or metabolomic analysis.

  • Image processing to investigate mitophagy in HelaM and neurons

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    This is a method for imaging cells and quantifying subcellular structures in the resulting data. We developed this protocol for assessing clearance of mitochondria involving OPTN and TBK1, however the method could be used for other applications.

  • Microfluidic Chip Production v1.1 V.2

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    Protocol for producing microfluidic chips used in HyDrop experiment. Visit for more info

  • α-Synuclein expression in response to bacterial ligands and metabolites in gut enteroendocrine cells – an in vitro proof of concept study

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    Caudo-rostral migration of pathological forms of α-synuclein from the gut to the brain is proposed as an early feature in Parkinson disease pathogenesis, but the underlying mechanisms remain unknown. Intestinal epithelial enteroendocrine cells sense and respond to numerous luminal signals, including bacterial factors, and transmit this information to the brain via the enteric nervous system and vagus nerve. There is evidence that gut bacteria composition and their metabolites change in Parkinson disease patients and these alterations can trigger α-synuclein pathology in animal models of the disorder. Here we investigated the effect of toll-like receptor and free fatty acid receptor agonists on the intracellular level of α-synuclein and its release using mouse secretin tumour cell line 1 enteroendocrine cells. Secretin tumour cell line 1 enteroendocrine cells were treated for 24 or 48 hours with toll-like receptor agonists (toll-like receptor 4 selective lipopolysaccharide; toll-like receptor 2 selective Pam3CysSerLys4) and the free fatty acid receptor 2/3 agonists butyrate, propionate and acetate. The effect of selective receptor antagonists on the agonists effects after 24 hours was also investigated. The level of α-synuclein protein was measured in cell lysates and cell culture media by western blot and enzyme-linked immunosorbent assay. The level of α-synuclein and tumour necrosis factor messenger RNA was measured by quantitative reverse transcription real time polymerase chain reaction. Stimulation of secretin tumour cell line 1 enteroendocrine cells for 24 and 48 hours with toll-like receptor and free fatty acid receptor agonists significantly increased the amount of intracellular α-synuclein and the release of α-synuclein from the cells into the culture medium. Both effects were significantly reduced by antagonists selective for each receptor. toll-like receptor and free fatty acid receptor agonists also significantly increased tumour necrosis factor transcription and this was effectively inhibited by corresponding antagonists. Elevated intracellular α-synuclein increases the likelihood of aggregation and conversion to toxic forms. Factors derived from bacteria induce α-synuclein accumulation in secretin tumour cell line 1 enteroendocrine cells. Here we provide support for a mechanism by which exposure of enteroendocrine cells to specific bacterial factors found in Parkinson disease gut dysbiosis might facilitate accumulation of α-synuclein pathology in the gut.

  • NDP52 and OPTN S177D S473D: expression and purification

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    This protocol describes how to express and purify human NDP52 and OPTN S177D S473D. The same procedure can be applied to purify wild type OPTN.

  • pCMV-DNAJC5-ΔC10 (D189–198)

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    Mammalian expression of DNAJC5-ΔC10 (Δ189-198)

  • Virus Production

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    Lentiviral production protocol.

  • SINTBAD-GFP: expression and purification

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    This protocol describes how to express and purify human SINTBAD tagged C-terminally with eGFP.

  • 2BT-His-TEV-cs-ATG3_C264S

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    DISCONTINUED - Plasmid for bacterial Expression of human ATG3 C264S.

  • Immunological detection of autophagy and mTORC1-related proteins

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    A general protocol for immunological detection by Western blotting MTOR, MTOR (pS2448), ULK1, ULK1 (pS757), p70S6K, p70S6K (pT389), SQSTM1, CALCOCO2, MAP1LC3B, GABARAP, TFEB, TFE3, PGRN, HSP90, and PCNA.

  • pCMV-DNAJC5-L116Δ

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    Mammalian expression of DNAJC5 L116Δ

  • Headplate surgery protocol for in vivo electrophysiological and optogenetic manipulation of basal ganglia neurons in awake head-fixed mice

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    Step by step protocol for headplate surgery for in vivo electrophysiological and optogenetic manipulation of basal ganglia neurons in awake mice.

  • pCAG-BECN1

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    Plasmid for Mammalian expression of BECN1.

  • Evaluation of a novel method for spectral analysis of neurophysiology data

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    This code implements a novel method for correcting a distortion effect that is present in the power spectra of neuronal spike trains.

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