14 results on '"Nanni, Paolo"'
Search Results
2. Domestic animal proteomics in the 21st century: A global retrospective and viewpoint analysis
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Almeida, André M, Ali, Syed Azmal, Ceciliani, Fabrizio, Eckersall, P David, et al, Nanni, Paolo, Roschitzki, Bernd, Schlapbach, Ralph, University of Zurich, and Almeida, André M
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1303 Biochemistry ,570 Life sciences ,biology ,610 Medicine & health ,10071 Functional Genomics Center Zurich ,1304 Biophysics - Published
- 2021
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3. Ancient proteins provide evidence of dairy consumption in eastern Africa
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Bleasdale, Madeleine, Richter, Kristine K, Janzen, Anneke, Brown, Samantha, et al, Trachsel, Christian, Nanni, Paolo, Grossmann, Jonas, University of Zurich, and Bleasdale, Madeleine
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1300 General Biochemistry, Genetics and Molecular Biology ,570 Life sciences ,biology ,610 Medicine & health ,10071 Functional Genomics Center Zurich ,1600 General Chemistry ,3100 General Physics and Astronomy - Published
- 2021
4. Paneth cells promote angiogenesis and regulate portal hypertension in response to microbial signals
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Mohsin Hassan, Mohsin Hassan, Moghadamrad, Sheida, Sorribas, Marcel, G. Muntet, Sergi, Kellmann, Philipp, Trentesaux, Coralie, Fraudeau, Marie, Nanni, Paolo, Wolski, Witold, Keller, Irene, Hapfelmeier, Siegfried, Shroyer, Noah F, Wiest, Reiner, Romagnolo, Beatrice, and De Gottardi, Andrea
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610 Medicine & health - Abstract
BACKGROUND & AIMS Paneth cells (PCs) synthesize and secrete antimicrobial peptides that are key mediators of host-microbe interactions, establishing a balance between intestinal microflora and enteric pathogens. We observed that their number increases in experimental portal hypertension and aimed to investigate the mechanisms by which these cells can contribute to the regulation of portal pressure. METHODS We first treated Math1Lox/LoxVilcreERT2 mice with tamoxifen to induce the complete depletion of intestinal PCs. Subsequently, we performed partial portal vein or bile duct ligation. We then studied the effects of these interventions on hemodynamic parameters, proliferation of blood vessels and the expression of genes regulating angiogenesis. Intestinal organoids were cultured and exposed to different microbial products to study the composition of their secreted products (by proteomics) and their effects on the proliferation and tube formation of endothelial cells (ECs). In vivo confocal laser endomicroscopy was used to confirm the findings on blood vessel proliferation. RESULTS Portal hypertension was significantly attenuated in PC-depleted mice compared to control mice and was associated with a decrease in portosystemic shunts. Depletion of PCs also resulted in a significantly decreased density of blood vessels in the intestinal wall and mesentery. Furthermore, we observed reduced expression of intestinal genes regulating angiogenesis in Paneth cell depleted mice using arrays and next generation sequencing. Tube formation and wound healing responses were significantly decreased in ECs treated with conditioned media from PC-depleted intestinal organoids exposed to intestinal microbiota-derived products. Proteomic analysis of conditioned media in the presence of PCs revealed an increase in factors regulating angiogenesis and additional metabolic processes. In vivo endomicroscopy showed decreased vascular proliferation in the absence of PCs. CONCLUSIONS These results suggest that in response to intestinal flora and microbiota-derived factors, PCs secrete not only antimicrobial peptides, but also pro-angiogenic signaling molecules, thereby promoting intestinal and mesenteric angiogenesis and regulating portal hypertension. LAY SUMMARY Paneth cells are present in the lining of the small intestine. They prevent the passage of bacteria from the intestine into the blood circulation by secreting substances to fight bacteria. In this paper, we discovered that these substances not only act against bacteria, but also increase the quantity of blood vessels in the intestine and blood pressure in the portal vein. This is important, because high blood pressure in the portal vein may result in several complications which could be targeted with novel approaches.
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- 2020
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5. Mass Spectrometry in Proteomics: Technologies, Methods, and Research Applications for the Life Sciences
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Nanni, Paolo, Gehrig, Peter, Schlapbach, Ralph, University of Zurich, and Schlapbach, Ralph
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570 Life sciences ,biology ,610 Medicine & health ,10071 Functional Genomics Center Zurich ,1600 General Chemistry ,General Medicine ,General Chemistry - Abstract
Mass spectrometry is a powerful tool in the hand of life science researchers, who constantly develop and apply new methods for the investigation of biomolecules, such as proteins, peptides, metabolites, lipids, and glycans. In this review, we will discuss the importance of mass spectrometry for the life science sector, with a special focus on the most relevant current applications in the field of proteomics. Moreover, we will comment on the factors that research groups should consider when setting up a mass spectrometry laboratory, and on the fundamental role played by academic core facilities and industrial service providers.
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- 2022
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6. Large-Scale Quantitative Proteomics Identifies the Ubiquitin Ligase Nedd4-1 as an Essential Regulator of Liver Regeneration
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Bachofner, Marc, Speicher, Tobias, Bogorad, Roman L, Muzumdar, Sukalp, Derrer, Carina P, Hürlimann, Fabrizio, Böhm, Friederike, Nanni, Paolo, Kockmann, Tobias, Kachaylo, Ekaterina, Meyer, Michael, Padrissa-Altés, Susagna, Graf, Rolf, Anderson, Daniel G, Koteliansky, Victor, Auf dem Keller, Ulrich, Werner, Sabine, University of Zurich, and Werner, Sabine
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1309 Developmental Biology ,1307 Cell Biology ,1300 General Biochemistry, Genetics and Molecular Biology ,1312 Molecular Biology ,570 Life sciences ,biology ,610 Medicine & health ,10071 Functional Genomics Center Zurich ,10217 Clinic for Visceral and Transplantation Surgery - Published
- 2017
7. Morphoproteomic characterization of lung squamous cell carcinoma fragmentation, a histological marker of increased tumor invasiveness
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Casanova, Ruben, Xia, Daniel, Rulle, Undīne, Nanni, Paolo, Grossmann, Jonas, Vrugt, Bart, Wettstein, Reto, Ballester, Rafael, Astolfo, Alberto, Weder, Walter, Moch, Holger, Stampanoni, Marco, Beck, Andrew H, Soltermann, Alex, University of Zurich, and Casanova, Ruben
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10255 Clinic for Thoracic Surgery ,10049 Institute of Pathology and Molecular Pathology ,610 Medicine & health ,2730 Oncology ,1306 Cancer Research - Published
- 2017
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8. The longissimus thoracis muscle proteome in Alentejana bulls as affected by growth path
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Almeida, André M, Nanni, Paolo, Ferreira, Ana M, Fortes, Claudia, Grossmann, Jonas, Bessa, Rui J B, Costa, Paulo, University of Zurich, and Almeida, André M
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1303 Biochemistry ,570 Life sciences ,biology ,610 Medicine & health ,10071 Functional Genomics Center Zurich ,1304 Biophysics - Published
- 2017
9. Helicase CHD4 is an epigenetic coregulator of PAX3-FOXO1 in alveolar rhabdomyosarcoma
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Böhm, Maria, Wachtel, Marco, Marques, Joana G, Streiff, Natalie, Laubscher, Dominik, Nanni, Paolo, Mamchaoui, Kamel, Santoro, Raffaella, Schäfer, Beat W, University of Zurich, and Schäfer, Beat W
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10036 Medical Clinic ,570 Life sciences ,biology ,610 Medicine & health ,10071 Functional Genomics Center Zurich ,2700 General Medicine ,10226 Department of Molecular Mechanisms of Disease - Published
- 2016
10. Comprehensive proteomic analysis of nitrogen-starved mycobacterium smegmatis δpup reveals the impact of pupylation on nitrogen stress response
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Fascellaro, Giuseppina, Petrera, Agnese, Lai, Zon Weng, Nanni, Paolo, Grossmann, Jonas, Burger, Sibylle, Biniossek, Martin L, Gomez-Auli, Alejandro, Schilling, Oliver, Imkamp, Frank, University of Zurich, and Imkamp, Frank
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1303 Biochemistry ,10179 Institute of Medical Microbiology ,570 Life sciences ,biology ,610 Medicine & health ,1600 General Chemistry - Published
- 2016
11. Characterization of the phosphoproteome of mature Arabidopsis pollen
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Mayank, Pururawa, Grossman, Jonas, Wuest, Samuel, Boisson-Dernier, Aurélien, Roschitzki, Bernd, Nanni, Paolo, Nühse, Thomas, Grossniklaus, Ueli, University of Zurich, and Grossniklaus, Ueli
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1307 Cell Biology ,10126 Department of Plant and Microbial Biology ,1311 Genetics ,1110 Plant Science ,570 Life sciences ,biology ,610 Medicine & health ,10071 Functional Genomics Center Zurich ,580 Plants (Botany) - Published
- 2012
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12. Regulation of ABCB1/PGP1-catalysed auxin transport by linker phosphorylation
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Henrichs, Sina, Wang, Bangjun, Fukao, Yoichiro, Zhu, Jinsheng, Charrier, Laurence, Bailly, Aurélien, Oehring, Sophie C, Linnert, Miriam, Weiwad, Matthias, Endler, Anne, Nanni, Paolo, Pollmann, Stephan, Mancuso, Stefano, Schulz, Alexander, Geisler, Markus, University of Zurich, and Geisler, Markus
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inorganic chemicals ,Proteomics ,Arabidopsis ,610 Medicine & health ,10071 Functional Genomics Center Zurich ,Protein Serine-Threonine Kinases ,Article ,Tacrolimus Binding Proteins ,1300 General Biochemistry, Genetics and Molecular Biology ,Gene Expression Regulation, Plant ,2400 General Immunology and Microbiology ,Tobacco ,1312 Molecular Biology ,heterocyclic compounds ,Phosphorylation ,Indoleacetic Acids ,Arabidopsis Proteins ,fungi ,2800 General Neuroscience ,food and beverages ,Biological Transport ,Phosphoproteins ,Plants, Genetically Modified ,enzymes and coenzymes (carbohydrates) ,570 Life sciences ,biology ,ATP-Binding Cassette Transporters ,Quercetin - Abstract
Polar transport of the plant hormone auxin is controlled by PIN- and ABCB/PGP-efflux catalysts. PIN polarity is regulated by the AGC protein kinase, PINOID (PID), while ABCB activity was shown to be dependent on interaction with the FKBP42, TWISTED DWARF1 (TWD1). Using co-immunoprecipitation (co-IP) and shotgun LC–MS/MS analysis, we identified PID as a valid partner in the interaction with TWD1. In-vitro and yeast expression analyses indicated that PID specifically modulates ABCB1-mediated auxin efflux in an action that is dependent on its kinase activity and that is reverted by quercetin binding and thus inhibition of PID autophosphorylation. Triple ABCB1/PID/TWD1 co-transfection in tobacco revealed that PID enhances ABCB1-mediated auxin efflux but blocks ABCB1 in the presence of TWD1. Phospho-proteomic analyses identified S634 as a key residue of the regulatory ABCB1 linker and a very likely target of PID phosphorylation that determines both transporter drug binding and activity. In summary, we provide evidence that PID phosphorylation has a dual, counter-active impact on ABCB1 activity that is coordinated by TWD1–PID interaction.
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- 2011
13. Quality standards in proteomics research facilities
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Paolo Nanni, Teresa Mendes Maia, Mariette Matondo, Eduard Sabidó, Francis Impens, Karl Mechtler, Karel Stejskal, Anna Shevchenko, Damarys Loew, Dominic Helm, Thibaut Douché, Cristina Chiva, Mandy Rettel, Christian Panse, Barcelona Institute of Science and Technology (BIST), Universitat Pompeu Fabra [Barcelona] (UPF), VIB Proteomics Core, Ghent, Belgium, VIB-UGent Center for Medical Biotechnology, Universiteit Gent = Ghent University (UGENT), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL), Functional Genomics Center Zurich, Universität Zürich [Zürich] = University of Zurich (UZH)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences (OeAW), Research Institute of Molecular Pathology (IMP), Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology (UTechS MSBio), Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie [Paris], European Molecular Biology Laboratory [Heidelberg] (EMBL), German Cancer Research Center - Deutsches Krebsforschungszentrum [Heidelberg] (DKFZ), Gregor Mendel Institute (GMI) - Vienna Biocenter (VBC), Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Max-Planck-Gesellschaft, The CRG/UPF Proteomics Unit is part of the Spanish Infrastructure for Omics Technologies (ICTS OmicsTech) and it is a member of the ProteoRed PRB3 consortium which is supported by grant PT17/0019 of the PE I + D+i 2013-2016 from the Instituto de Salud Carlos III (ISCIII) and ERDF. We acknowledge support from the Spanish Ministry of Science, Innovation and Universities, 'Centro de Excelencia Severo Ochoa 2013-2017', SEV-2012- 0208, and 'Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya' (2017SGR595). The VIB Proteomics Core acknowledges support from the VIB Tech Watch Fund and FWO-SBO Project S006617N. Research in the Mechtler lab was supported by the ERA-CAPS I 3686 project of the Austrian Science Fund. We acknowledge support from the European Union's Horizon 2020 research and innovation program under grant agreement No 823839 (EPIC-XS)., European Project: 823839,H2020-INFRAIA-2018-1,EPIC-XS(2019), Universiteit Gent = Ghent University [Belgium] (UGENT), Université de Lausanne (UNIL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)-Universität Zürich [Zürich] = University of Zurich (UZH), Institut Pasteur [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), University of Zurich, Nanni, Paolo, Shevchenko, Anna, and Sabidó, Eduard
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Proteomics ,1303 Biochemistry ,Centres d'investigació ,GeneralLiterature_INTRODUCTORYANDSURVEY ,media_common.quotation_subject ,610 Medicine & health ,10071 Functional Genomics Center Zurich ,Proteòmica ,Biochemistry ,Mass Spectrometry ,03 medical and health sciences ,0302 clinical medicine ,1311 Genetics ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,1312 Molecular Biology ,Genetics ,Quality (business) ,Science & Society ,Molecular Biology ,030304 developmental biology ,media_common ,0303 health sciences ,3. Good health ,Engineering management ,ComputingMethodologies_PATTERNRECOGNITION ,570 Life sciences ,biology ,Business ,030217 neurology & neurosurgery - Abstract
Proteomics research infrastructures and core facilities within the Core for Life alliance advocate for community policies for quality control to ensure high standards in proteomics services. The CRG/UPF Proteomics Unit is a member of the ProteoRed PRB3 consortium which is supported by grant PT17/0019 of the PE I + D+i 2013‐2016 from the Instituto de Salud Carlos III (ISCIII) and ERDF. We acknowledge support from the Spanish Ministry of Science, Innovation and Universities, “Centro de Excelencia Severo Ochoa 2013‐2017”, SEV‐2012‐ 0208, and “Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya” (2017SGR595). The VIB Proteomics Core acknowledges support from the VIB Tech Watch Fund and FWO‐SBO Project S006617N. Research in the Mechtler lab was supported by the ERA‐CAPS I 3686 project of the Austrian Science Fund. We acknowledge support from the European Union's Horizon 2020 research and innovation program under grant agreement No 823839 (EPIC‐XS)
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- 2021
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14. PTM MarkerFinder, a software tool to detect and validate spectra from peptides carrying post-translational modifications
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Christian Panse, Paolo Nanni, Jonas Grossmann, Susanne Mueller, Ralph Schlapbach, Peter Gehrig, University of Zurich, and Nanni, Paolo
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Proteomics ,1303 Biochemistry ,Peptide ,610 Medicine & health ,10071 Functional Genomics Center Zurich ,Mass spectrometry ,Orbitrap ,Biochemistry ,Mass Spectrometry ,Spectral line ,law.invention ,Fragmentation (mass spectrometry) ,law ,1312 Molecular Biology ,Data Mining ,Database search engine ,Molecular Biology ,chemistry.chemical_classification ,Chromatography ,Chemistry ,Glycopeptides ,Reproducibility of Results ,High-Throughput Screening Assays ,Electron-transfer dissociation ,570 Life sciences ,biology ,Oxonium ion ,Protein Processing, Post-Translational ,Software - Abstract
Mass spectrometry (MS) analysis of peptides carrying post-translational modifications is challenging due to the instability of some modifications during MS analysis. However, glycopeptides as well as acetylated, methylated and other modified peptides release specific fragment ions during CID (collision-induced dissociation) and HCD (higher energy collisional dissociation) fragmentation. These fragment ions can be used to validate the presence of the PTM on the peptide. Here, we present PTM MarkerFinder, a software tool that takes advantage of such marker ions. PTM MarkerFinder screens the MS/MS spectra in the output of a database search (i.e., Mascot) for marker ions specific for selected PTMs. Moreover, it reports and annotates the HCD and the corresponding electron transfer dissociation (ETD) spectrum (when present), and summarizes information on the type, number, and ratios of marker ions found in the data set. In the present work, a sample containing enriched N-acetylhexosamine (HexNAc) glycopeptides from yeast has been analyzed by liquid chromatography-mass spectrometry on an LTQ Orbitrap Velos using both HCD and ETD fragmentation techniques. The identification result (Mascot .dat file) was submitted as input to PTM MarkerFinder and screened for HexNAc oxonium ions. The software output has been used for high-throughput validation of the identification results.
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- 2013
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