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Articles by Patrick May
Complementary Mitochondrial and α-Synuclein Signatures Refine Biological Stratification of Parkinson's Disease
We read with interest the Viewpoint by Percetti and colleagues proposing the concept of a biologically defined mitochondrial subtype of Parkinson's disease (PD) (“MitoPD”).1 The authors provide compelling evidence that mitochondrial dysfunction contributes particularly to early-onset and selective genetic forms of PD and advocate for biologically informed disease stratification.
Selective vulnerability of dopaminergic neurons in Parkinson’s disease connects PRKN and differential expression of CHCHD2 and GPNMB
Abstract The mechanism(s) causing selective vulnerability of dopaminergic neurons in Parkinson’s disease (PD) remain largely elusive. To improve our understanding of mitochondrial involvement and related pathways suggested to play a role in this selective vulnerability, we used tyrosine hydroxylase (TH)-mCherry reporter-induced pluripotent stem cells generated by CRISPR/Cas9.
Genetic variation in antidiabetic drug targets: associations with Parkinson’s disease risk and age at onset
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Abstract To investigate whether antidiabetic drugs have a biological basis to be repurposed in PD prevention, we applied a drug target Mendelian randomization framework to assess associations between genetic variation in antidiabetic drug targets and PD risk or age at onset (AAO).
By Katalin Vincze, Alexander Ploner, Robert Karlsson, Xiaoying Kang, Bowen Tang, Chenxi Qin, Cloé Domenighetti, Pierre-Emmanuel Sugier, Claudia Schulte, Patrick May, Dheeraj Reddy Bobbili, Milena Radivojkov-Blagojevic, Peter Lichtner, Andrew Singleton, Dena Hernandez, Connor Edsall, George D. Mellick, Alexander Zimprich, Walter Pirker, Ekaterina Rogaeva, Anthony E Lang, Sulev Kõks, Pille Taba, Suzanne Lesage, Alexis Brice, Jean-Christophe Corvol, Marie-Christine Chartier-Harlin, Eugénie Mutez, Kathrin Brockmann, Angela B. Deutschländer, Lena F. Burbulla, Georges M. Hadjigeorgiou, Efthimos Dardiotis, Leonidas Stefanis, Athina Maria Simitsi, Enza Maria Valente, Simona Petrucci, Letizia Straniero, Anna Zecchinelli, Gianni Pezzoli, Laura Brighina, Carlo Ferrarese, Grazia Annesi, Andrea Quattrone, Monica Gagliardi, Hirotaka Matsuo, Akiyoshi Nakayama, Nobutaka Hattori, Kenya Nishioka, Sun Ju Chung, Yun Joong Kim, Pierre Kolber, Bastiaan R Bloem, Mathias Toft, Lasse Pihlstrøm, Leonor Correia Guedes, Joaquim J Ferreira, Soraya Bardien, Jonathan Carr, Eduardo Tolosa, Mario Ezquerra, Caroline Ran, Andrea C. Belin, Andreas Puschmann, Carl Clarke, Karen Morrison Verified, Manuela MX Tan, Dimitri Krainc, Matt J. Farrer, Zied Landoulsi, Rejko Kruger, Thomas Gasser, Alexis Elbaz, Manu Sharma, Nancy L Pedersen, Sofia Carlsson, Sara Hägg, Karin Wirdefeldt, Agnieszka Szwajda, Bart PC Van de Warrenburg
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Nature
Verified
High-resolution multi-omics enhances prediction and detection of smORF-encoded proteins in the human gut microbiome
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Abstract Small open reading frames (smORFs), which encode proteins under 100 amino acids, represent an underexplored dimension of the human gut microbiome, despite growing evidence of their essential biological roles. Due to small size and poor annotation, smORFs are typically excluded from metagenomic/metaproteomic analyses.
By Megan Davin, Julia Ortis Sunyer, Luis Delgado, Steven Tavis, Zainab Zafar, Rashi Halder, Oskar Hickl, Cédric C Laczny, Etienne Hanslian, Daniela A. Koppold, Nico Steckhan, Sebastian Schade, Jochen Schneider, Brit Mollenhauer, Andreas Michalsen, Patrick May, Robert L. Hettich, Paul Wilmes, Jordan Caussin, Anika Rajput-Khokhar
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Nature
Verified
Genome-wide association study of copy number variations in Parkinson’s disease
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Abstract We investigated the role of copy number variations (CNVs) in Parkinson’s disease (PD) using genotyping data from 10,815 patients (2731 early-onset PD, EOPD) and 8901 controls from the COURAGE-PD consortium. CNVs were analyzed using a sliding window genome-wide association and burden approach.
By Zied Landoulsi, Nicole Kuznetsov, Claudia Schulte, Ludovica Montanucci, Costin Leu, Lisa-Marie Niestroj, Emadeldin Hassanin, Cloé Domenighetti, Pierre-Emmanuel Sugier, Peter Lichtner, Jens Krüger, Dena Hernandez, Cornelis Blauwendraat, George D. Mellick, Alexander Zimprich, Walter Pirker, Manuela MX Tan, Ekaterina Rogaeva, Anthony E Lang, Sulev Kõks, Pille Taba, Suzanne Lesage, Alexis Brice, Jean-Christophe Corvol, Marie-Christine Chartier-Harlin, Eugénie Mutez, Kathrin Brockmann, Angela B. Deutschländer, Leonidas Stefanis, Athina Maria Simitsi, Enza Maria Valente, Simona Petrucci, Letizia Straniero, Anna Zecchinelli, Gianni Pezzoli, Laura Brighina, Carlo Ferrarese, Andrea Quattrone, Monica Gagliardi, Lena F. Burbulla, Hirotaka Matsuo, Akiyoshi Nakayama, Nobutaka Hattori, Kenya Nishioka, Sun Ju Chung, Yun Joong Kim, Lukas Pavelka, Pierre Kolber, Bastiaan R Bloem, Andrew Singleton, Dan M. Vitale, Mathias Toft, Lasse Pihlstrom, Leonor Correia Guedes, Joaquim J Ferreira, Soraya Bardien, Jonathan Carr, Eduardo Tolosa, Mario Ezquerra, Karin Wirdefeldt, Nancy L Pedersen, Caroline Ran, Andrea C. Belin, Andreas Puschmann, Carl Clarke, Karen Morrison Verified, Dimitri Krainc, Dennis Lal, Alexis Elbaz, Thomas Gasser, Rejko Kruger, MANU SHARMA, Patrick May, Dheeraj Reddy Bobbili, Milena Radivojkov-Blagojevic, Connor Edsall, Georges M. Hadjigeorgiou, Efthimos Dardiotis, Grazia Annesi, Matt J. Farrer
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Nature
Verified
Linear predictive coding electroencephalography algorithms predict Parkinson's disease mortality using out-of-sample tests
The authors have declared no competing interest. This study was supported by the National Institutes of Health under grants R01NS100849-01A1 and 1RF1NS127809-01A1. The National Institute of Neurological Disorders and Stroke (NINDS) was not involved in the study's design, data collection, analysis, interpretation, or manuscript preparation. I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.
An Approach to Integrate Metagenomics, Metatranscriptomics and Metaproteomics Data in Public Data Resources
DB database ENA European Nucleotide Archive FAIR findable, accessible, interoperable and reusable FDR false discovery rate IGV integrative genome viewer INSDC International Nucleotide Sequence Database Consortium MAGs metagenome assembled genomes MS mass spectrometry PSMs peptide spectrum matches PUFs proteins of unknown function uHGG unified human gastrointestinal genome 1 Introduction The past two decades have witnessed the increasing application of culture-independent omics methods such as...
Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures - Nature Methods
Abstract Recent advances in AI-based methods have revolutionized the field of structural biology. Concomitantly, high-throughput sequencing and functional genomics have generated genetic variants at an unprecedented scale. However, efficient tools and resources are needed to link disparate data types—to ‘map’ variants onto protein structures, to better understand how the variation causes disease, and thereby design therapeutics.
Gut microbiome is not associated with mild cognitive impairment in Parkinson’s disease - npj Parkinson's Disease
Abstract Gut microbiome differences between people with Parkinson’s disease (PD) and control subjects without Parkinsonism are widely reported, but potential alterations related to PD with mild cognitive impairment (MCI) have yet to be comprehensively explored. We compared gut microbial features of PD with MCI (n = 58) to cognitively unimpaired PD (n = 60) and control subjects (n = 90) with normal cognition. Our results did not support a specific microbiome signature related to MCI in PD.
Author Correction: Accurate long-read sequencing identified GBA1 as major risk factor in the Luxembourgish Parkinson’s study - npj Parkinson's Disease
Correction to: npj Parkinson’s Disease https://doi.org/10.1038/s41531-023-00595-w, published online 23 November 2023 In this article the wrong Table appeared as Table 3.; the Table should have appeared as shown below. The original article has been corrected.
Mechanism-based classification of SARS-CoV-2 Variants by Molecular Dynamics Resembles Phylogenetic Tree
Abstract The COVID-19 pandemics has demonstrated the vulnerability of our societies to viral infectious disease. The mitigation of COVID-19 was complicated by the emergence of Variants of Concern (VOCs) with varying properties including increased transmissibility and immune evasion. Traditional population sequencing proved to be slow and not conducive for timely action.
Accurate long-read sequencing identified GBA1 as major risk factor in the Luxembourgish Parkinson’s study - npj Parkinson's Disease
Abstract Heterozygous variants in the glucocerebrosidase GBA1 gene are an increasingly recognized risk factor for Parkinson’s disease (PD). Due to the GBAP1 pseudogene, which shares 96% sequence homology with the GBA1 coding region, accurate variant calling by array-based or short-read sequencing methods remains a major challenge in understanding the genetic landscape of GBA1-associated PD.
Early-to-mid stage idiopathic Parkinson’s disease shows enhanced cytotoxicity and differentiation in CD8 T-cells in females - Nature Communications
Abstract Neuroinflammation in the brain contributes to the pathogenesis of Parkinson’s disease (PD), but the potential dysregulation of peripheral immunity has not been systematically investigated for idiopathic PD (iPD).
Forecasting the dynamics of a complex microbial community using integrated meta-omics - Nature Ecology & Evolution
Abstract Predicting the behaviour of complex microbial communities is challenging. However, this is essential for complex biotechnological processes such as those in biological wastewater treatment plants (BWWTPs), which require sustainable operation. Here we summarize 14 months of longitudinal meta-omics data from a BWWTP anaerobic tank into 17 temporal signals, explaining 91.1% of the temporal variance, and link those signals to ecological events within the community.
Spatio-functional organization in virocells of small uncultivated archaea from the deep biosphere - The ISME Journal
Abstract Despite important ecological roles posited for virocells (i.e., cells infected with viruses), studying individual cells in situ is technically challenging. We introduce here a novel correlative microscopic approach to study the ecophysiology of virocells.
Functional prediction of proteins from the human gut archaeome
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Functional assignment of gut-specific archaeal proteins in the human gut microbiome
Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website.
UniFuncNet: a flexible network annotation framework
Abstract Summary: Functional annotation is an integral part in the analysis of organisms, as well as of multi-species communities. A common way to integrate such information is using biological networks. However, current data integration network tools are heavily dependent on a single source of information, which might strongly limit the amount of relevant data contained within the network.
Breast and prostate cancer risk: The interplay of polygenic risk, rare pathogenic germline variants, and family history
Abstract Purpose We aimed to investigate to what extent polygenic risk scores (PRS), rare pathogenic germline variants (PVs), and family history jointly influence breast cancer and prostate cancer risk. Methods A total of 200,643 individuals from the UK Biobank were categorized as follows: (1) heterozygotes or nonheterozygotes for PVs in moderate to high-risk cancer genes, (2) PRS strata, and (3) with or without a family history of cancer.
Comprehensive characterization of amino acid positions in protein structures reveals molecular effect of missense variants
Comprehensive characterization of amino acid positions in protein structures reveals molecular effect of missense variants Sumaiya Iqbal, Eduardo Pérez-Palma, Jakob B. Jespersen, Patrick May, David Hoksza, Henrike O. Heyne, Shehab S. Ahmed, Zaara T. Rifat, M. Sohel Rahman, Kasper Lage, Aarno Palotie, Jeffrey R. Cottrell, Florence F. Wagner, Mark J. Daly, Arthur J. Campbell, Dennis Lal Proceedings of the National Academy of Sciences Oct 2020, 202002660; DOI: 10.1073/pnas.2002660117
¿Has pensando en dejar California? Estas ciudades te pagan por mudarte
¿Quién no ha pensado que las rentas en California están por las nubes y que moverse a otro estado suena como una gran idea? Miles de californianos. El buen mercado laboral está empujando a los precios inmobiliarios a las nubes, las autopistas atascadas de tráfico lo que hace que la tarea más cotidiana parezca francamente agotadora.
Rare coding variants in genes encoding GABAA receptors in genetic generalised epilepsies: an exome-based case-control study
Genetic generalised epilepsy is the most common type of inherited epilepsy. Despite a high concordance rate of 80% in monozygotic twins, the genetic background is still poorly understood. We aimed to investigate the burden of rare genetic variants in genetic generalised epilepsy. For this exome-based case-control study, we used three different genetic generalised epilepsy case cohorts and three independent control cohorts, all of European descent.
Natural variation of chronological aging in the Saccharomyces cerevisiae species reveals diet-dependent mechanisms of life span control
Abstract Aging is a complex trait of broad scientific interest, especially because of its intrinsic link with common human diseases. Pioneering work on aging-related mechanisms has been made in Saccharomyces cerevisiae, mainly through the use of deletion collections isogenic to the S288c reference strain. In this study, using a recently published high-throughput approach, we quantified chronological life span (CLS) within a collection of 58 natural strains across seven different conditions.
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