The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder.

BACKGROUND: Increasing evidence connects the gut microbiota and the onset and/or phenotype of Parkinson's disease (PD). Differences in the abundances of specific bacterial taxa have been reported in PD patients. It is, however, unknown whether these differences can be observed in individuals at high risk, for example, with idiopathic rapid eye movement sleep behavior disorder, a prodromal condition of alpha-synuclein aggregation disorders including PD. OBJECTIVES: To compare microbiota in carefully preserved nasal wash and stool samples of subjects with idiopathic rapid eye movement sleep behavior disorder, manifest PD, and healthy individuals. METHODS: Microbiota of flash-frozen stool and nasal wash samples from 76 PD patients, 21 idiopathic rapid eye movement sleep behavior disorder patients, and 78 healthy controls were assessed by 16S and 18S ribosomal RNA amplicon sequencing. Seventy variables, related to demographics, clinical parameters including nonmotor symptoms, and sample processing, were analyzed in relation to microbiome variability and controlled differential analyses were performed. RESULTS: Differentially abundant gut microbes, such as Akkermansia, were observed in PD, but no strong differences in nasal microbiota. Eighty percent of the differential gut microbes in PD versus healthy controls showed similar trends in idiopathic rapid eye movement sleep behavior disorder, for example, Anaerotruncus and several Bacteroides spp., and correlated with nonmotor symptoms. Metagenomic sequencing of select samples enabled the reconstruction of genomes of so far uncharacterized differentially abundant organisms. CONCLUSION: Our study reveals differential abundances of gut microbial taxa in PD and its prodrome idiopathic rapid eye movement sleep behavior disorder in comparison to the healthy controls, and highlights the potential of metagenomics to identify and characterize microbial taxa, which are enriched or depleted in PD and/or idiopathic rapid eye movement sleep behavior disorder. (c) 2017 International Parkinson and Movement Disorder Society

Postendocytic Sorting of Constitutively Internalized Dopamine Transporter in Cell Lines and Dopaminergic Neurons*

The dopamine transporter (DAT) mediates reuptake of released dopamine and is the target for psychostimulants, such as cocaine and amphetamine. DAT undergoes marked constitutive endocytosis, but little is known about the fate and sorting of the endocytosed transporter. To study DAT sorting in cells lines, we fused the one-transmembrane segment protein Tac to DAT, thereby generating a transporter (TacDAT) with an extracellular antibody epitope suited for trafficking studies. TacDAT was functional and endocytosed constitutively in HEK293 cells. According to an ELISA-based assay, TacDAT intracellular accumulation was increased by the lysosomal protease inhibitor leupeptin and by monensin, an inhibitor of lysosomal degradation and recycling. Monensin also reduced TacDAT surface expression consistent with partial recycling. In both HEK293 cells and in the dopaminergic cell line 1Rb3An27, constitutively internalized TacDAT displayed primary co-localization with the late endosomal marker Rab7, less co-localization with the “short loop” recycling marker Rab4, and little co-localization with the marker of “long loop” recycling endosomes, Rab11. Removal by mutation of N-terminal ubiquitination sites did not affect this sorting pattern. The sorting pattern was distinct from a bona fide recycling membrane protein, the β2-adrenergic receptor, that co-localized primarily with Rab11 and Rab4. Constitutively internalized wild type DAT probed with the fluorescently tagged cocaine analogue JHC 1-64, exhibited the same co-localization pattern as TacDAT in 1Rb3An27 cells and in cultured midbrain dopaminergic neurons. We conclude that DAT is constitutively internalized and sorted in a ubiquitination-independent manner to late endosomes/lysosomes and in part to a Rab4 positive short loop recycling pathway

Chapter 13 Surface Adsorption

© 2017 Elsevier Inc. All rights reserved. Practical aspects are considered that users need to know in choosing computational methods and conceptual ideas for understanding surface adsorption embodying some degree of van der Waals dispersive attractions. Emphasized is the unique chemistry that results when these forces are strong and mix with traditional covalent or ionic bonding mechanisms to control chemical outcomes. Indeed, many methods are being developed to provide accurate descriptions of surface adsorption, including those based on ab initio and density-functional-theory (DFT) approaches. Accurate methods like coupled-cluster theory (CC), the random-phase approximation (RPA), and time-dependent DFT (TDDFT) are demanded when the critical interactions are weak, but these methods are computationally expensive, scaling formally at least as order n6 in system size (though efficient modern algorithms can reduce that to, e.g., order n4logn or even to linear scaling). How such methods can be applied to large systems is discussed, but more focus is given to more approximate, faster approaches, especially: the empirical pairwise additive D3 correction of Grimme et al., the van der Waals density functional approach of Dion et al. (vdW-DF), and the new semiempirical many-body dispersion (MBD) method of Tkatchenko et al. Fundamental understanding of all methods is provided by describing the way they behave in the very short range (unified atom) and very long range asymptotic limits, using Dobson's classification scheme. How simple computational methods can give realistic adsorption energies and structures for close-contact interactions whilst providing very poor descriptions of these asymptotic limits is examined. Four strong-interaction test systems are considered: the adsorption of benzene on coinage metals, the adsorption of 1,10-phenanthroline (PHEN) on Au(111), the adsorption of large tetraalkylporphyrin molecules on graphite from organic solution, and the nature of the Au-S bonds found on gold surfaces and nanoparticles protected by sulfur compounds. For adsorption energies, the vdW-DF method is found to be cumbersome and unreliable, the MBD method to be accurate but often prohibitively expensive, and the D3 method to be computationally efficient and, for the considered examples, highly reliable. Alternatively, neglect of dispersion interactions is found to lead to poor understanding of all important chemical properties