TY - JOUR A1 - Hempelmann, Alexander A1 - Hartleb, Laura A1 - van Straaten, Monique A1 - Hashemi, Hamidreza A1 - Zeelen, Johan P. A1 - Bongers, Kevin A1 - Papavasiliou, F. Nina A1 - Engstler, Markus A1 - Stebbins, C. Erec A1 - Jones, Nicola G. T1 - Nanobody-mediated macromolecular crowding induces membrane fission and remodeling in the African trypanosome JF - Cell Reports N2 - The dense variant surface glycoprotein (VSG) coat of African trypanosomes represents the primary host-pathogen interface. Antigenic variation prevents clearing of the pathogen by employing a large repertoire of antigenically distinct VSG genes, thus neutralizing the host’s antibody response. To explore the epitope space of VSGs, we generate anti-VSG nanobodies and combine high-resolution structural analysis of VSG-nanobody complexes with binding assays on living cells, revealing that these camelid antibodies bind deeply inside the coat. One nanobody causes rapid loss of cellular motility, possibly due to blockage of VSG mobility on the coat, whose rapid endocytosis and exocytosis are mechanistically linked to Trypanosoma brucei propulsion and whose density is required for survival. Electron microscopy studies demonstrate that this loss of motility is accompanied by rapid formation and shedding of nanovesicles and nanotubes, suggesting that increased protein crowding on the dense membrane can be a driving force for membrane fission in living cells. KW - African trypanosome KW - host-pathogen interaction KW - variant surface glycoproteins KW - immune epitope mapping KW - structural biology KW - nanovesicle formation KW - nanotube formation KW - protein crowding KW - membrane fission Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-270285 VL - 37 IS - 5 ER - TY - JOUR A1 - Werner, Rudolf A. A1 - Sheikhbahaei, Sara A1 - Jones, Krystyna M. A1 - Javadi, Mehrbod S. A1 - Solnes, Lilja B. A1 - Ross, Ashley E. A1 - Allaf, Mohamad E. A1 - Pienta, Kenneth J. A1 - Lapa, Constantin A1 - Buck, Andreas K. A1 - Higuchi, Takahiro A1 - Pomper, Martin G. A1 - Gorin, Micheal A. A1 - Rowe, Steven P. T1 - Patterns of uptake of prostate-specific membrane antigen (PSMA)-targeted \(^{18}\)F-DCFPyL in peripheral ganglia JF - Annals of Nuclear Medicine N2 - Objective: Radiotracers targeting prostate-specific membrane antigen (PSMA) have increasingly been recognized as showing uptake in a number of normal structures, anatomic variants, and non-prostate-cancer pathologies. We aimed to explore the frequency and degree of uptake in peripheral ganglia in patients undergoing PET with the PSMA-targeted agent \(^{18}\)F-DCFPyL. Methods: A total of 98 patients who underwent \(^{18}\)F-DCFPyL PET/CT imaging were retrospectively analyzed. This included 76 men with prostate cancer (PCa) and 22 patients with renal cell carcinoma (RCC; 13 men, 9 women). Scans were evaluated for uptake in the cervical, stellate, celiac, lumbar and sacral ganglia. Maximum standardized uptake value corrected to body weight (SUV\(_{max}\)), and maximum standardized uptake value corrected to lean body mass (SUL\(_{max}\)) were recorded for all ganglia with visible uptake above background. Ganglia-to-background ratios were calculated by dividing the SUV\(_{max}\) and SUL\(_{max}\) values by the mean uptake in the ascending aorta (Aortamean) and the right gluteus muscle (Gluteusmean). Results: Overall, 95 of 98 (96.9%) patients demonstrated uptake in at least one of the evaluated peripheral ganglia. With regard to the PCa cohort, the most frequent sites of radiotracer accumulation were lumbar ganglia (55/76, 72.4%), followed by the cervical ganglia (51/76, 67.1%). Bilateral uptake was found in the majority of cases [lumbar 44/55 (80%) and cervical 30/51 (58.8%)]. Additionally, discernible radiotracer uptake was recorded in 50/76 (65.8%) of the analyzed stellate ganglia and in 45/76 (59.2%) of the celiac ganglia, whereas only 5/76 (6.6%) of the sacral ganglia demonstrated \(^{18}\)F-DCFPyL accumulation. Similar findings were observed for patients with RCC, with the most frequent locations of radiotracer uptake in both the lumbar (20/22, 90.9%) and cervical ganglia (19/ 22, 86.4%). No laterality preference was found in mean PSMA-ligand uptake for either the PCa or RCC cohorts. Conclusion: As PSMA-targeted agents become more widely disseminated, the patterns of uptake in structures that are not directly relevant to patients’ cancers must be understood. This is the first systematic evaluation of the uptake of \(^{18}\)F-DCFPyL in ganglia demonstrating a general trend with a descending frequency of radiotracer accumulation in lumbar, cervical, stellate, celiac, and sacral ganglia. The underlying biology that leads to variability of PSMA-targeted radiotracers in peripheral ganglia is not currently understood, but may provide opportunities for future research. KW - 18F-DCFPL KW - Positronen-Emissions-Tomografie KW - Prostata KW - PSMA KW - Ganglia KW - Pitfall KW - PET KW - Tracer KW - Radiotracer KW - Imaging pitfalls KW - Prostate Cancer Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-166971 SN - 0914-7187 VL - 31 IS - 9 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 - JOUR A1 - Tacke, Reinhold A1 - Lopez-Mras, A. A1 - Jones, P. G. T1 - Syntheses, crystal structure analyses, and NMR studies of [2-(dimethylammonio)phenyl]bis[glycolato(2-)-O1,O2]silicate and related zwitterionic spirocyclic \(\lambda_5\)Si-silicates N2 - No abstract available KW - Anorganische Chemie Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-64339 ER - TY - JOUR A1 - Tacke, Reinhold A1 - Mühleisen, M. A1 - Jones, P. G. T1 - Das erste zwitterionische, optisch aktive Disilicat mit pentakoordiniertem Silicium N2 - No abstract available KW - Anorganische Chemie Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-64343 ER - TY - JOUR A1 - Tacke, Reinhold A1 - Mühleisen, M. A1 - Jones, P. G. T1 - The first zwitterionic, optically active disilicate with pentacoordinate silicon N2 - No abstract available KW - Anorganische Chemie Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-64358 ER - TY - JOUR A1 - Strohmann, C. A1 - Bauerecker, S. A1 - Cammenga, H. K. A1 - Jones, P. G. A1 - Mutschler, E. A1 - Lambrecht, G. A1 - Tacke, Reinhold T1 - Enantiomers of the muscarinic antagonist 1-cyclohexyl-1-(4-fluorophenyl)-4-piperidino-1-butanol (p-fluoro-hexahydro-difenidol): synthesis, absolute configuration, and enantiomeric purity N2 - The enantiomers of the antimuscarinic agent 1-cyclohexyl-1- (4-fluorophenyl)-4-piperidino-1-butanol [(R)- and (S)-p-fluorohexahydro- difenidol] ((R)- and (S)-2a] and their methiodides (R)- 3 and (S)-3 were prepared with high enantiomeric purity. (R)- 2a and (S)-2a (isolated as hydrochlorides) were obtained by catalytic hydrogenation (Pd/C contact) of the corresponding enantiomers of 1-cyclohexyl-1-( 4-fl uorophen yl)-4-piperidino- 2-butyn-1-ol [(R)- and (S)-4]. Reaction of (R)-2a and (S)-2a with rnethyl iodide led to (R)-3 and (S)-3, respectively. The unsaturated precursors (R)- and (S}-4 (enantiorneric purity ~ 99.80 and ~99.94% e.e.; calorimetric analysis) were prepared by res-sepaolution of rac-4 [available from 4-FC\(_6\)H\(_4\)C(O)C\(_6\)H\(_{11}\) by reaction with LiC ~ CCH\(_2\)NC\(_5\)H\(_{10}\)] using (R)- and (S)-mandelic acid as resolving agents. The absolute configurations of the (R) and (S) enantiomers of 2a, 3, and 4 were determined by an X-ray crystal-structure analysis of (S)-5, the methiodide of (S)-4. (R)- 2a and (R)-3 exhibit a higher affinity for muscarinic M1, M2, M3, and M4 receptors (by up to two orders of magnitude) than their corresponding antipodes (S)-2a and (S)-3, the degree of stereoselectivity depending on the receptor subtype involved. (R)-2a represents a useful tool for rnuscarinic receptor research (affinity profile: M1 ~ M3 ~ M4 > M2). KW - Anorganische Chemie KW - Difenidol KW - p-fluoro-hexahydro- KW - enantiomers of / Muscarinic receptors KW - subtypes of Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-64144 ER -