TY - JOUR A1 - Kuzkina, Anastasia A1 - Bargar, Connor A1 - Schmitt, Daniela A1 - Rößle, Jonas A1 - Wang, Wen A1 - Schubert, Anna-Lena A1 - Tatsuoka, Curtis A1 - Gunzler, Steven A. A1 - Zou, Wen-Quan A1 - Volkmann, Jens A1 - Sommer, Claudia A1 - Doppler, Kathrin A1 - Chen, Shu G. T1 - Diagnostic value of skin RT-QuIC in Parkinson's disease: a two-laboratory study JF - NPJ Parkinson's Disease N2 - Skin alpha-synuclein deposition is considered a potential biomarker for Parkinson's disease (PD). Real-time quaking-induced conversion (RT-QuIC) is a novel, ultrasensitive, and efficient seeding assay that enables the detection of minute amounts of alpha-synuclein aggregates. We aimed to determine the diagnostic accuracy, reliability, and reproducibility of alpha-synuclein RT-QuIC assay of skin biopsy for diagnosing PD and to explore its correlation with clinical markers of PD in a two-center inter-laboratory comparison study. Patients with clinically diagnosed PD (n = 34), as well as control subjects (n = 30), underwent skin punch biopsy at multiple sites (neck, lower back, thigh, and lower leg). The skin biopsy samples (198 in total) were divided in half to be analyzed by RT-QuIC assay in two independent laboratories. The a-synuclein RT-QuIC assay of multiple skin biopsies supported the clinical diagnosis of PD with a diagnostic accuracy of 88.9% and showed a high degree of inter-rater agreement between the two laboratories (92.2%). Higher alpha-synuclein seeding activity in RT-QuIC was shown in patients with longer disease duration and more advanced disease stage and correlated with the presence of REM sleep behavior disorder, cognitive impairment, and constipation. The alpha-synuclein RT-QuIC assay of minimally invasive skin punch biopsy is a reliable and reproducible biomarker for Parkinson's disease. Moreover, alpha-synuclein RT-QuIC seeding activity in the skin may serve as a potential indicator of progression as it correlates with the disease stage and certain non-motor symptoms. KW - diagnostic markers KW - Parkinson's disease Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-260451 VL - 7 IS - 1 ER - TY - JOUR A1 - Jiang, Yuxiang A1 - Oron, Tal Ronnen A1 - Clark, Wyatt T. A1 - Bankapur, Asma R. A1 - D'Andrea, Daniel A1 - Lepore, Rosalba A1 - Funk, Christopher S. A1 - Kahanda, Indika A1 - Verspoor, Karin M. A1 - Ben-Hur, Asa A1 - Koo, Da Chen Emily A1 - Penfold-Brown, Duncan A1 - Shasha, Dennis A1 - Youngs, Noah A1 - Bonneau, Richard A1 - Lin, Alexandra A1 - Sahraeian, Sayed M. E. A1 - Martelli, Pier Luigi A1 - Profiti, Giuseppe A1 - Casadio, Rita A1 - Cao, Renzhi A1 - Zhong, Zhaolong A1 - Cheng, Jianlin A1 - Altenhoff, Adrian A1 - Skunca, Nives A1 - Dessimoz, Christophe A1 - Dogan, Tunca A1 - Hakala, Kai A1 - Kaewphan, Suwisa A1 - Mehryary, Farrokh A1 - Salakoski, Tapio A1 - Ginter, Filip A1 - Fang, Hai A1 - Smithers, Ben A1 - Oates, Matt A1 - Gough, Julian A1 - Törönen, Petri A1 - Koskinen, Patrik A1 - Holm, Liisa A1 - Chen, Ching-Tai A1 - Hsu, Wen-Lian A1 - Bryson, Kevin A1 - Cozzetto, Domenico A1 - Minneci, Federico A1 - Jones, David T. A1 - Chapman, Samuel A1 - BKC, Dukka A1 - Khan, Ishita K. A1 - Kihara, Daisuke A1 - Ofer, Dan A1 - Rappoport, Nadav A1 - Stern, Amos A1 - Cibrian-Uhalte, Elena A1 - Denny, Paul A1 - Foulger, Rebecca E. A1 - Hieta, Reija A1 - Legge, Duncan A1 - Lovering, Ruth C. A1 - Magrane, Michele A1 - Melidoni, Anna N. A1 - Mutowo-Meullenet, Prudence A1 - Pichler, Klemens A1 - Shypitsyna, Aleksandra A1 - Li, Biao A1 - Zakeri, Pooya A1 - ElShal, Sarah A1 - Tranchevent, Léon-Charles A1 - Das, Sayoni A1 - Dawson, Natalie L. A1 - Lee, David A1 - Lees, Jonathan G. A1 - Sillitoe, Ian A1 - Bhat, Prajwal A1 - Nepusz, Tamás A1 - Romero, Alfonso E. A1 - Sasidharan, Rajkumar A1 - Yang, Haixuan A1 - Paccanaro, Alberto A1 - Gillis, Jesse A1 - Sedeño-Cortés, Adriana E. A1 - Pavlidis, Paul A1 - Feng, Shou A1 - Cejuela, Juan M. A1 - Goldberg, Tatyana A1 - Hamp, Tobias A1 - Richter, Lothar A1 - Salamov, Asaf A1 - Gabaldon, Toni A1 - Marcet-Houben, Marina A1 - Supek, Fran A1 - Gong, Qingtian A1 - Ning, Wei A1 - Zhou, Yuanpeng A1 - Tian, Weidong A1 - Falda, Marco A1 - Fontana, Paolo A1 - Lavezzo, Enrico A1 - Toppo, Stefano A1 - Ferrari, Carlo A1 - Giollo, Manuel A1 - Piovesan, Damiano A1 - Tosatto, Silvio C. E. A1 - del Pozo, Angela A1 - Fernández, José M. A1 - Maietta, Paolo A1 - Valencia, Alfonso A1 - Tress, Michael L. A1 - Benso, Alfredo A1 - Di Carlo, Stefano A1 - Politano, Gianfranco A1 - Savino, Alessandro A1 - Rehman, Hafeez Ur A1 - Re, Matteo A1 - Mesiti, Marco A1 - Valentini, Giorgio A1 - Bargsten, Joachim W. A1 - van Dijk, Aalt D. J. A1 - Gemovic, Branislava A1 - Glisic, Sanja A1 - Perovic, Vladmir A1 - Veljkovic, Veljko A1 - Almeida-e-Silva, Danillo C. A1 - Vencio, Ricardo Z. N. A1 - Sharan, Malvika A1 - Vogel, Jörg A1 - Kansakar, Lakesh A1 - Zhang, Shanshan A1 - Vucetic, Slobodan A1 - Wang, Zheng A1 - Sternberg, Michael J. E. A1 - Wass, Mark N. A1 - Huntley, Rachael P. A1 - Martin, Maria J. A1 - O'Donovan, Claire A1 - Robinson, Peter N. A1 - Moreau, Yves A1 - Tramontano, Anna A1 - Babbitt, Patricia C. A1 - Brenner, Steven E. A1 - Linial, Michal A1 - Orengo, Christine A. A1 - Rost, Burkhard A1 - Greene, Casey S. A1 - Mooney, Sean D. A1 - Friedberg, Iddo A1 - Radivojac, Predrag A1 - Veljkovic, Nevena T1 - An expanded evaluation of protein function prediction methods shows an improvement in accuracy JF - Genome Biology N2 - Background A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent. KW - Protein function prediction KW - Disease gene prioritization Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-166293 VL - 17 IS - 184 ER - TY - BOOK A1 - Wang, Wen T1 - Validation of shRNA clones for gene silencing in 293FT cells N2 - ... N2 - The goal of the project was to establish knock down of mRNA in human mesenchymal stem cells. Since these cells are difficult to transfect, a viral approach is needed to achieve sufficient expression of e. g. shRNA in a high percentage of cells to allow for an efficient silencing of corresponding mRNAs. For this purpose for every gene product of interest, a number of shRNA clones have to be tested to detect an individual shRNA with sufficient efficacy. Lentiviral systems for shRNA approaches have recently become available. The principal advantage of the lentiviral system is that it allows gene silencing in nondividing cells and therefore expands the usefulness of the RNAi-based gene silencing system. Lentivirus-delivered shRNAs are capable of specific, highly stable and functional silencing of gene expression in a variety of cell types. Since the viral transfection of MSCs is a time consuming process that involves transfection of 293 FT cells plus transduction of target cells, for this thesis the following approach was chosen: genes of interest were checked for expression in 293FT cells by RT-PCR. These gene products can be silenced in 293FT cells simply by transfection of shRNA clones and efficacy was subsequently tested by RT-PCR. Beyond this thesis then the project can proceed with effective clones to transduce primary MSCs with individual shRNA clones identified as effective silencing tool in this thesis. KW - shRNA KW - RNAi KW - .................................................................... KW - shRNA KW - RNAi Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-25955 N1 - Aus rechtlichen Gründen wurde der Zugriff auf den Volltext zu diesem Dokument gesperrt. ER -