Formalin fixed Paraffin Embedded (FFPE) Tissue preparation for digital pathology quantification using QuPath
By Emma Sherrell onQuPath is an open-source digital pathology analysis software. Here, it is used to quantify various misfolded proteins across anatomical regions. This protocol is appropriate for both human and mouse tissue, and will outline the methods of tissue preparation, digitisation, segmentation, and importing images into QuPath.
Habituation and dishabituation (olfaction test)
By Emma Sherrell onHabituation and dishabituation (olfaction test) for mice.
Raw data associated with each Figure and Supplementary Figures from “Novel green fluorescent polyamines to analyze ATP13A2 and ATP13A3 activity in the mammalian polyamine transport system”
By Emma Sherrell onRaw data associated with each Figure and Supplementary Figures from "Novel green fluorescent polyamines to analyze ATP13A2 and ATP13A3 activity in the mammalian polyamine transport system."
Development and characterization of a non-human primate model of disseminated synucleinopathy
By savannah onIn this study, the performance and biodistribution of the retrogradely-spreading AAV9-SynA53T vector was evaluated in the NHP brain. Conducted intraparenchymal deliveries of viral suspensions in the left putamen gave rise to a disseminated synucleinopathy in a circuit-specific basis.
Neuromelanin accumulation drives endogenous synucleinopathy in non-human primates
By savannah onEvidence has provided showing that intracellular aggregation of endogenous alpha-synuclein is triggered by NMel accumulation, therefore any therapeutic approach intended to decrease NMel levels may provide appealing choices for the successful implementation of novel PD therapeutics.
Polyamines in Parkinson’s Disease: Balancing Between Neurotoxicity and Neuroprotection
By Emma Sherrell onPublished: The authors formulate outstanding research questions regarding the role of polyamines in PD, their potential as PD biomarkers, and possible therapeutic strategies for PD targeting polyamine homeostasis.
ImageJ FIJI code to semi-automatize the morphological analysis of microglia in histological sections
By savannah onImageJ FIJI code to semi-automatize the morphological analysis of microglia in histological sections.
Lyso-IP: Uncovering Pathogenic Mechanisms of Lysosomal Dysfunction
By Emma Sherrell onPublished: Future applications of rapid lysosomal isolation techniques are likely to greatly enhance our understanding of lysosomal dysfunction in rare and common neurodegeneration causes.
Modelling human brain-wide pigmentation in rodents recapitulates age-related multisystem neurodegenerative deficits
By savannah onIn parallel to progressive human-like neuromelanin pigmentation, these animals display age-related neuronal dysfunction and degeneration affecting numerous brain circuits and body tissues, linked to motor and non-motor deficits, reminiscent of early neurodegenerative stages. This model may open new research avenues in the field of brain aging and neurodegeneration.
Adult-specific Reelin expression alters striatal neuronal organization: implications for neuropsychiatric disorders
By savannah onThe authors increased Reelin levels might modulate the numbers of striatal interneurons and the density of the nigrostriatal dopaminergic projections, suggesting that these changes may be involved in the protection of Reelin against neuropsychiatric disorders. View original preprint.
Is Gauchian genotyping of GBA1 variants reliable?
By Emma Sherrell onPreprint: The authors evaluated Gauchian in 90 Sanger-sequenced patients with GD and five GBA1 heterozygotes using the software tool Gauchian to identify GBA1 variants from whole genome sequencing. While Gauchian genotyped most patients correctly, this limits Gauchian's utility in variant screening and precluding its use in diagnostics.
Targeted detection of SNCA CNVs in SOX10+ nuclei from oligodendrocytes containing alpha-synuclein inclusions isolated from human post-mortem brain
By savannah onThe protocol is optimized to detect SOX10, a nuclear oligodendrocyte marker, and alpha-synuclein inclusions, which are frequently retained at the perinucleus in MSA (the so-called Papp-Lantos inclusions). This protocol also describes its use in affected PD and MSA brain regions such as the putamen, substantia nigra (SN), and cerebellum.
Section 3: Libraries quality control (QC)
By savannah onThis protocol details quality control of libraries and should be performed after Section 2: NGS library preparation for sequencing.
Section 2: NGS library preparation for sequencing
By savannah onThis protocol details NGS library preparation for sequencing and should be performed after Section 1: Enzymatic DNA Fragmentation (Manually).
Population fraction of Parkinson’s disease attributable to preventable risk factors
By Emma Sherrell onPublished: The team identified repeated blows to head in sports/combat as a potential new risk factor. 23% of PD cases in females were attributable to pesticides/herbicides exposure, and 30% of PD in males were attributable to pesticides/herbicides, military-related chemical exposures, and repeated blows to the head, and therefore could have potentially been prevented. View original preprint.
Section 1: Enzymatic DNA Fragmentation (Manually)
By savannah onThis protocol details manual enzymatic DNA Fragmentation prior to Section 2: NGS library preparation for sequencing.
Manual isolation of nuclei from human brain using CellRaft device and single nucleus Whole Genome Amplification
By savannah onProtocol for manual nuclear isolation from human brain tissue using Cell Raft device for single cell Whole Genome Amplification Protocol for manual nuclear isolation from human brain tissue using Cell Raft device for single cell Whole Genome Amplification
PyRates—A code-generation tool for modeling dynamical systems in biology and beyond
By Emma Sherrell onPublished: The main purpose of the paper is to demonstrate how these three tools can support the computational/mathematical modeling of neural systems with a variety of numerical methods that are well tested and documented. Thus, the authors present a powerful tool kit for computational/mathematical approaches to studying the dynamics and functions of complex neural systems such as the basal ganglia. View original preprint.
