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3. Domestic animal proteomics in the 21st century: A global retrospective and viewpoint analysis

Author

Almeida, André M., Ali, Syed Azmal, Ceciliani, Fabrizio, Eckersall, P. David, Hernández-Castellano, Lorenzo E., Han, Rongwei, Hodnik, Jaka J., Jaswal, Shalini, Lippolis, John D., McLaughlin, Mark, Miller, Ingrid, Mohanty, Ashok Kumar, Mrljak, Vladimir, Nally, Jarlath E., Nanni, Paolo, Plowman, Jeffrey E., Poleti, Mirele D., Ribeiro, David M., Rodrigues, Pedro, Roschitzki, Bernd, Schlapbach, Ralph, Starič, Jože, Yang, Yongxin, and Zachut, Maya

Published
2021
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4. Molecular Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome*

Author

Wang, Xiaorong, Cimermancic, Peter, Yu, Clinton, Schweitzer, Andreas, Chopra, Nikita, Engel, James L, Greenberg, Charles, Huszagh, Alexander S, Beck, Florian, Sakata, Eri, Yang, Yingying, Novitsky, Eric J, Leitner, Alexander, Nanni, Paolo, Kahraman, Abdullah, Guo, Xing, Dixon, Jack E, Rychnovsky, Scott D, Aebersold, Ruedi, Baumeister, Wolfgang, Sali, Andrej, and Huang, Lan

Subjects
Analytical Chemistry, Biochemistry and Cell Biology, Chemical Sciences, Biological Sciences, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Cell Line, Humans, Models, Molecular, Proteasome Endopeptidase Complex, Protein Binding, Protein Interaction Mapping, Protein Interaction Maps, Reproducibility of Results, Tandem Mass Spectrometry, Biochemistry & Molecular Biology
Abstract

The 26S proteasome is the macromolecular machine responsible for ATP/ubiquitin dependent degradation. As aberration in proteasomal degradation has been implicated in many human diseases, structural analysis of the human 26S proteasome complex is essential to advance our understanding of its action and regulation mechanisms. In recent years, cross-linking mass spectrometry (XL-MS) has emerged as a powerful tool for elucidating structural topologies of large protein assemblies, with its unique capability of studying protein complexes in cells. To facilitate the identification of cross-linked peptides, we have previously developed a robust amine reactive sulfoxide-containing MS-cleavable cross-linker, disuccinimidyl sulfoxide (DSSO). To better understand the structure and regulation of the human 26S proteasome, we have established new DSSO-based in vivo and in vitro XL-MS workflows by coupling with HB-tag based affinity purification to comprehensively examine protein-protein interactions within the 26S proteasome. In total, we have identified 447 unique lysine-to-lysine linkages delineating 67 interprotein and 26 intraprotein interactions, representing the largest cross-link dataset for proteasome complexes. In combination with EM maps and computational modeling, the architecture of the 26S proteasome was determined to infer its structural dynamics. In particular, three proteasome subunits Rpn1, Rpn6, and Rpt6 displayed multiple conformations that have not been previously reported. Additionally, cross-links between proteasome subunits and 15 proteasome interacting proteins including 9 known and 6 novel ones have been determined to demonstrate their physical interactions at the amino acid level. Our results have provided new insights on the dynamics of the 26S human proteasome and the methodologies presented here can be applied to study other protein complexes.

Published
2017

5. m-nitrobenzyl alcohol supercharging reagent enhances the chromatographic separation and the charging of disulfide bond linked and His-tag peptides

Author

Lin, Chia-wei; https://orcid.org/0000-0003-4777-2916, Canonica, Fabia; https://orcid.org/0000-0003-4324-3961, Wüthrich, Simone, Fettelschoss-Gabriel, Antonia; https://orcid.org/0000-0002-6189-172X, Schlapbach, Ralph; https://orcid.org/0000-0002-7488-4262, Nanni, Paolo; https://orcid.org/0000-0001-8429-3557, Lin, Chia-wei; https://orcid.org/0000-0003-4777-2916, Canonica, Fabia; https://orcid.org/0000-0003-4324-3961, Wüthrich, Simone, Fettelschoss-Gabriel, Antonia; https://orcid.org/0000-0002-6189-172X, Schlapbach, Ralph; https://orcid.org/0000-0002-7488-4262, and Nanni, Paolo; https://orcid.org/0000-0001-8429-3557

Published
2024

10. Dairy pastoralism sustained eastern Eurasian steppe populations for 5,000 years

Author

Wilkin, Shevan, Ventresca Miller, Alicia, Taylor, William T. T., Miller, Bryan K., Hagan, Richard W., Bleasdale, Madeleine, Scott, Ashley, Gankhuyg, Sumiya, Ramsøe, Abigail, Uliziibayar, S., Trachsel, Christian, Nanni, Paolo, Grossmann, Jonas, Orlando, Ludovic, Horton, Mark, Stockhammer, Philipp W., Myagmar, Erdene, Boivin, Nicole, Warinner, Christina, and Hendy, Jessica

Published
2020
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11. Gel-Free Proteomics

Author

Baiwir, Dominique, Nanni, Paolo, Müller, Susanne, Smargiasso, Nicolas, Morsa, Denis, De Pauw, Edwin, Mazzucchelli, Gabriel, de Almeida, Andre Martinho, editor, Eckersall, David, editor, and Miller, Ingrid, editor

Published
2018
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12. Ancient proteins provide evidence of dairy consumption in eastern Africa

Author

Bleasdale, Madeleine, Richter, Kristine K., Janzen, Anneke, Brown, Samantha, Scott, Ashley, Zech, Jana, Wilkin, Shevan, Wang, Ke, Schiffels, Stephan, Desideri, Jocelyne, Besse, Marie, Reinold, Jacques, Saad, Mohamed, Babiker, Hiba, Power, Robert C., Ndiema, Emmanuel, Ogola, Christine, Manthi, Fredrick K., Zahir, Muhammad, Petraglia, Michael, Trachsel, Christian, Nanni, Paolo, Grossmann, Jonas, Hendy, Jessica, Crowther, Alison, Roberts, Patrick, Goldstein, Steven T., and Boivin, Nicole

Published
2021
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16. Multi-omics Characterization of Response to PD-1 Inhibitors in Advanced Melanoma

Author

Trilla-Fuertes, Lucía, primary, Gámez-Pozo, Angelo, additional, Prado-Vázquez, Guillermo, additional, López-Vacas, Rocío, additional, Soriano, Virtudes, additional, Garicano, Fernando, additional, Lecumberri, M. José, additional, Rodríguez de la Borbolla, María, additional, Majem, Margarita, additional, Pérez-Ruiz, Elisabeth, additional, González-Cao, María, additional, Oramas, Juana, additional, Magdaleno, Alejandra, additional, Fra, Joaquín, additional, Martín-Carnicero, Alfonso, additional, Corral, Mónica, additional, Puértolas, Teresa, additional, Ramos-Ruiz, Ricardo, additional, Dittmann, Antje, additional, Nanni, Paolo, additional, Fresno Vara, Juan Ángel, additional, and Espinosa, Enrique, additional

Published
2023
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22. Figure S2. Threshold analysis of tumor fragmentation in correlation with RFS and OS. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness

Author

Casanova, Ruben, primary, Xia, Daniel, primary, Rulle, Undine, primary, Nanni, Paolo, primary, Grossmann, Jonas, primary, Vrugt, Bart, primary, Wettstein, Reto, primary, Ballester-Ripoll, Rafael, primary, Astolfo, Alberto, primary, Weder, Walter, primary, Moch, Holger, primary, Stampanoni, Marco, primary, Beck, Andrew H., primary, and Soltermann, Alex, primary

Published
2023
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23. Figure S3. Biological processes associated with TF morphotypes from TCGA mRNAseq and WS Mass Spectrometry data. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness

Author

Casanova, Ruben, primary, Xia, Daniel, primary, Rulle, Undine, primary, Nanni, Paolo, primary, Grossmann, Jonas, primary, Vrugt, Bart, primary, Wettstein, Reto, primary, Ballester-Ripoll, Rafael, primary, Astolfo, Alberto, primary, Weder, Walter, primary, Moch, Holger, primary, Stampanoni, Marco, primary, Beck, Andrew H., primary, and Soltermann, Alex, primary

Published
2023
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24. Table S1. Complete list of proteins identifications. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness

Author

Casanova, Ruben, primary, Xia, Daniel, primary, Rulle, Undine, primary, Nanni, Paolo, primary, Grossmann, Jonas, primary, Vrugt, Bart, primary, Wettstein, Reto, primary, Ballester-Ripoll, Rafael, primary, Astolfo, Alberto, primary, Weder, Walter, primary, Moch, Holger, primary, Stampanoni, Marco, primary, Beck, Andrew H., primary, and Soltermann, Alex, primary

Published
2023
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25. Table S3. Association of TF scores with relapse-free survival. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness

Author

Casanova, Ruben, primary, Xia, Daniel, primary, Rulle, Undine, primary, Nanni, Paolo, primary, Grossmann, Jonas, primary, Vrugt, Bart, primary, Wettstein, Reto, primary, Ballester-Ripoll, Rafael, primary, Astolfo, Alberto, primary, Weder, Walter, primary, Moch, Holger, primary, Stampanoni, Marco, primary, Beck, Andrew H., primary, and Soltermann, Alex, primary

Published
2023
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26. Table S4. Association of human-based TF scores with OS and RFS. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness

Author

Casanova, Ruben, primary, Xia, Daniel, primary, Rulle, Undine, primary, Nanni, Paolo, primary, Grossmann, Jonas, primary, Vrugt, Bart, primary, Wettstein, Reto, primary, Ballester-Ripoll, Rafael, primary, Astolfo, Alberto, primary, Weder, Walter, primary, Moch, Holger, primary, Stampanoni, Marco, primary, Beck, Andrew H., primary, and Soltermann, Alex, primary

Published
2023
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27. PRoteomics IDEntifications database from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness

Author

Casanova, Ruben, primary, Xia, Daniel, primary, Rulle, Undine, primary, Nanni, Paolo, primary, Grossmann, Jonas, primary, Vrugt, Bart, primary, Wettstein, Reto, primary, Ballester-Ripoll, Rafael, primary, Astolfo, Alberto, primary, Weder, Walter, primary, Moch, Holger, primary, Stampanoni, Marco, primary, Beck, Andrew H., primary, and Soltermann, Alex, primary

Published
2023
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28. Data from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness

Author

Casanova, Ruben, primary, Xia, Daniel, primary, Rulle, Undine, primary, Nanni, Paolo, primary, Grossmann, Jonas, primary, Vrugt, Bart, primary, Wettstein, Reto, primary, Ballester-Ripoll, Rafael, primary, Astolfo, Alberto, primary, Weder, Walter, primary, Moch, Holger, primary, Stampanoni, Marco, primary, Beck, Andrew H., primary, and Soltermann, Alex, primary

Published
2023
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29. Table S2. Association of tumor fragmentation with clinico-pathological parameters. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness

Author

Casanova, Ruben, primary, Xia, Daniel, primary, Rulle, Undine, primary, Nanni, Paolo, primary, Grossmann, Jonas, primary, Vrugt, Bart, primary, Wettstein, Reto, primary, Ballester-Ripoll, Rafael, primary, Astolfo, Alberto, primary, Weder, Walter, primary, Moch, Holger, primary, Stampanoni, Marco, primary, Beck, Andrew H., primary, and Soltermann, Alex, primary

Published
2023
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30. Table S5. List of proteins associated with tumor fragmentation. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness

Author

Casanova, Ruben, primary, Xia, Daniel, primary, Rulle, Undine, primary, Nanni, Paolo, primary, Grossmann, Jonas, primary, Vrugt, Bart, primary, Wettstein, Reto, primary, Ballester-Ripoll, Rafael, primary, Astolfo, Alberto, primary, Weder, Walter, primary, Moch, Holger, primary, Stampanoni, Marco, primary, Beck, Andrew H., primary, and Soltermann, Alex, primary

Published
2023
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31. Figure S1. Frequency distributions, intra-tumor heterogeneity and inter-observer variability for TF scores. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness

Author

Casanova, Ruben, primary, Xia, Daniel, primary, Rulle, Undine, primary, Nanni, Paolo, primary, Grossmann, Jonas, primary, Vrugt, Bart, primary, Wettstein, Reto, primary, Ballester-Ripoll, Rafael, primary, Astolfo, Alberto, primary, Weder, Walter, primary, Moch, Holger, primary, Stampanoni, Marco, primary, Beck, Andrew H., primary, and Soltermann, Alex, primary

Published
2023
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32. Supplementary Table S1 from PLK1 Phosphorylates PAX3-FOXO1, the Inhibition of Which Triggers Regression of Alveolar Rhabdomyosarcoma

Author

Thalhammer, Verena, primary, Lopez-Garcia, Laura A., primary, Herrero-Martin, David, primary, Hecker, Regina, primary, Laubscher, Dominik, primary, Gierisch, Maria E., primary, Wachtel, Marco, primary, Bode, Peter, primary, Nanni, Paolo, primary, Blank, Bernd, primary, Koscielniak, Ewa, primary, and Schäfer, Beat W., primary

Published
2023
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33. Supplementary Table S7 from Combined Label-Free Quantitative Proteomics and microRNA Expression Analysis of Breast Cancer Unravel Molecular Differences with Clinical Implications

Author

Gámez-Pozo, Angelo, primary, Berges-Soria, Julia, primary, Arevalillo, Jorge M., primary, Nanni, Paolo, primary, López-Vacas, Rocío, primary, Navarro, Hilario, primary, Grossmann, Jonas, primary, Castaneda, Carlos A., primary, Main, Paloma, primary, Díaz-Almirón, Mariana, primary, Espinosa, Enrique, primary, Ciruelos, Eva, primary, and Fresno Vara, Juan Ángel, primary

Published
2023
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34. Supplementary Figures S1-S7 from PLK1 Phosphorylates PAX3-FOXO1, the Inhibition of Which Triggers Regression of Alveolar Rhabdomyosarcoma

Author

Thalhammer, Verena, primary, Lopez-Garcia, Laura A., primary, Herrero-Martin, David, primary, Hecker, Regina, primary, Laubscher, Dominik, primary, Gierisch, Maria E., primary, Wachtel, Marco, primary, Bode, Peter, primary, Nanni, Paolo, primary, Blank, Bernd, primary, Koscielniak, Ewa, primary, and Schäfer, Beat W., primary

Published
2023
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36. Supplementary Figure Legends from PLK1 Phosphorylates PAX3-FOXO1, the Inhibition of Which Triggers Regression of Alveolar Rhabdomyosarcoma

Author

Thalhammer, Verena, primary, Lopez-Garcia, Laura A., primary, Herrero-Martin, David, primary, Hecker, Regina, primary, Laubscher, Dominik, primary, Gierisch, Maria E., primary, Wachtel, Marco, primary, Bode, Peter, primary, Nanni, Paolo, primary, Blank, Bernd, primary, Koscielniak, Ewa, primary, and Schäfer, Beat W., primary

Published
2023
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37. Data from Combined Label-Free Quantitative Proteomics and microRNA Expression Analysis of Breast Cancer Unravel Molecular Differences with Clinical Implications

Author

Gámez-Pozo, Angelo, primary, Berges-Soria, Julia, primary, Arevalillo, Jorge M., primary, Nanni, Paolo, primary, López-Vacas, Rocío, primary, Navarro, Hilario, primary, Grossmann, Jonas, primary, Castaneda, Carlos A., primary, Main, Paloma, primary, Díaz-Almirón, Mariana, primary, Espinosa, Enrique, primary, Ciruelos, Eva, primary, and Fresno Vara, Juan Ángel, primary

Published
2023
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38. Supplementary Figure S2 from Combined Label-Free Quantitative Proteomics and microRNA Expression Analysis of Breast Cancer Unravel Molecular Differences with Clinical Implications

Author

Gámez-Pozo, Angelo, primary, Berges-Soria, Julia, primary, Arevalillo, Jorge M., primary, Nanni, Paolo, primary, López-Vacas, Rocío, primary, Navarro, Hilario, primary, Grossmann, Jonas, primary, Castaneda, Carlos A., primary, Main, Paloma, primary, Díaz-Almirón, Mariana, primary, Espinosa, Enrique, primary, Ciruelos, Eva, primary, and Fresno Vara, Juan Ángel, primary

Published
2023
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39. Supplementary Materials and Methods from PLK1 Phosphorylates PAX3-FOXO1, the Inhibition of Which Triggers Regression of Alveolar Rhabdomyosarcoma

Author

Thalhammer, Verena, primary, Lopez-Garcia, Laura A., primary, Herrero-Martin, David, primary, Hecker, Regina, primary, Laubscher, Dominik, primary, Gierisch, Maria E., primary, Wachtel, Marco, primary, Bode, Peter, primary, Nanni, Paolo, primary, Blank, Bernd, primary, Koscielniak, Ewa, primary, and Schäfer, Beat W., primary

Published
2023
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40. Supplementary Table and Figure Legend from Combined Label-Free Quantitative Proteomics and microRNA Expression Analysis of Breast Cancer Unravel Molecular Differences with Clinical Implications

Author

Gámez-Pozo, Angelo, primary, Berges-Soria, Julia, primary, Arevalillo, Jorge M., primary, Nanni, Paolo, primary, López-Vacas, Rocío, primary, Navarro, Hilario, primary, Grossmann, Jonas, primary, Castaneda, Carlos A., primary, Main, Paloma, primary, Díaz-Almirón, Mariana, primary, Espinosa, Enrique, primary, Ciruelos, Eva, primary, and Fresno Vara, Juan Ángel, primary

Published
2023
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44. Helicase CHD4 is an epigenetic coregulator of PAX3-FOXO1 in alveolar rhabdomyosarcoma

Author

Bohm, Maria, Wachtel, Marco, Marques, Joana G., Streiff, Natalie, Laubscher, Dominik, Nanni, Paolo, Mamchaoui, Kamel, Santoro, Raffaella, and Schafer, Beat W.

Subjects
Gene expression -- Analysis, Rhabdomyosarcoma -- Risk factors -- Care and treatment, Transcription factors -- Analysis, Health care industry
Abstract

A vast number of cancer genes are transcription factors that drive tumorigenesis as oncogenic fusion proteins. Although the direct targeting of transcription factors remains challenging, therapies aimed at oncogenic fusion proteins are attractive as potential treatments for cancer. There is particular interest in targeting the oncogenic PAX3-FOXO1 fusion transcription factor, which induces alveolar rhabdomyosarcoma (aRMS), an aggressive cancer of skeletal muscle cells for which patient outcomes remain dismal. In this work, we have defined the interactome of PAX3-FOXO1 and screened 60 candidate interactors using siRNA-mediated depletion to identify candidates that affect fusion protein activity in aRMS cells. We report that chromodomain helicase DNA binding protein 4 (CHD4), an ATP-dependent chromatin remodeler, acts as crucial coregulator of PAX3-FOXO1 activity. CHD4 interacts with PAX3-FOXO1 via short DNA fragments. Together, they bind to regulatory regions of PAX3-FOXO1 target genes. Gene expression analysis suggested that CHD4 coregulatory activity is essential for a subset of PAX3-FOXO1 target genes. Depletion of CHD4 reduced cell viability of fusion-positive but not of fusion-negative RMS in vitro, which resembled loss of PAX3-FOXO1. It also caused specific regression of fusion-positive xenograft tumors in vivo. Therefore, this work identifies CHD4 as an epigenetic coregulator of PAX3-FOXO1 activity, providing rational evidence for CHD4 as a potential therapeutic target in aRMS., Introduction Rhabdomyosarcoma (RMS) is a heterogeneous family of tumors sharing features with the skeletal muscle lineage. It is the most common soft tissue sarcoma in childhood and can be classified [...]

Published
2016
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47. Pulsed electric field treatment enhances lipid bioaccessibility while preserving oxidative stability in Chlorella vulgaris

Author

Canelli, Greta, Kuster, Isabelle, Jaquenod, Luc, Buchmann, Leandro, Murciano Martínez, Patricia, Rohfritsch, Zhen, Dionisi, Fabiola, Bolten, Christoph J, Nanni, Paolo, Mathys, Alexander, Canelli, Greta, Kuster, Isabelle, Jaquenod, Luc, Buchmann, Leandro, Murciano Martínez, Patricia, Rohfritsch, Zhen, Dionisi, Fabiola, Bolten, Christoph J, Nanni, Paolo, and Mathys, Alexander

Published
2022

48. Paneth Cells Regulate Lymphangiogenesis under Control of Microbial Signals during Experimental Portal Hypertension

Author

Hassan, Mohsin, Juanola, Oriol; https://orcid.org/0000-0001-7432-8808, Keller, Irene, Nanni, Paolo; https://orcid.org/0000-0001-8429-3557, Wolski, Witold, Martínez-López, Sebastián; https://orcid.org/0000-0003-1720-845X, Caparrós, Esther; https://orcid.org/0000-0002-9681-0408, Francés, Rubén; https://orcid.org/0000-0001-5105-1201, Moghadamrad, Sheida; https://orcid.org/0000-0001-7322-4759, Hassan, Mohsin, Juanola, Oriol; https://orcid.org/0000-0001-7432-8808, Keller, Irene, Nanni, Paolo; https://orcid.org/0000-0001-8429-3557, Wolski, Witold, Martínez-López, Sebastián; https://orcid.org/0000-0003-1720-845X, Caparrós, Esther; https://orcid.org/0000-0002-9681-0408, Francés, Rubén; https://orcid.org/0000-0001-5105-1201, and Moghadamrad, Sheida; https://orcid.org/0000-0001-7322-4759

Abstract

Intestinal microbiota can modulate portal hypertension through the regulation of the intestinal vasculature. We have recently demonstrated that bacterial antigens activate Paneth cells (PCs) to secrete products that regulate angiogenesis and portal hypertension. In the present work we hypothesized that Paneth cells regulate the development of lymphatic vessels under the control of intestinal microbiota during experimental portal hypertension. We used a mouse model of inducible PCs depletion (Math1Lox/LoxVilCreERT2) and performed partial portal vein ligation (PPVL) to induce portal hypertension. After 14 days, we performed mRNA sequencing and evaluated the expression of specific lymphangiogenic genes in small intestinal tissue. Intestinal and mesenteric lymphatic vessels proliferation was assessed by immunohistochemistry. Intestinal organoids with or without PCs were exposed to pathogen-associated molecular patterns, and conditioned media (CM) was used to stimulate human lymphatic endothelial cells (LECs). The lymphangiogenic activity of stimulated LECs was assessed by tube formation and wound healing assays. Secretome analysis of CM was performed using label-free proteomics quantification methods. Intestinal immune cell infiltration was evaluated by immunohistochemistry. We observed that the intestinal gene expression pattern was altered by the absence of PCs only in portal hypertensive mice. We found a decreased expression of specific lymphangiogenic genes in the absence of PCs during portal hypertension, resulting in a reduced proliferation of intestinal and mesenteric lymphatic vessels as compared to controls. In vitro analyses demonstrated that lymphatic tube formation and endothelial wound healing responses were reduced significantly in LECs treated with CM from organoids without PCs. Secretome analyses of CM revealed that PCs secrete proteins that are involved in lipid metabolism, cell growth and proliferation. Additionally, intestinal macrophages infiltrated

Published
2022

49. Mass Spectrometry in Proteomics: Technologies, Methods, and Research Applications for the Life Sciences

Author

Nanni, Paolo; https://orcid.org/0000-0001-8429-3557, Gehrig, Peter, Schlapbach, Ralph, Nanni, Paolo; https://orcid.org/0000-0001-8429-3557, Gehrig, Peter, and Schlapbach, Ralph

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.

Published
2022

50. Moderate High-Pressure Superdormancy in $\textit{Bacillus}$ Spores: Properties of Superdormant Spores and Proteins Potentially Influencing Moderate High-Pressure Germination

Author

Dudley, Edward G, Dudley, E G ( Edward G ), Delbrück, Alessia I, Tritten, Yvette, Nanni, Paolo; https://orcid.org/0000-0001-8429-3557, Heydenreich, Rosa, Mathys, Alexander, Dudley, Edward G, Dudley, E G ( Edward G ), Delbrück, Alessia I, Tritten, Yvette, Nanni, Paolo; https://orcid.org/0000-0001-8429-3557, Heydenreich, Rosa, and Mathys, Alexander

Abstract

Resistant bacterial spores are a major concern in industrial decontamination processes. An approach known as pressure-mediated germination-inactivation strategy aims to artificially germinate spores by isostatic pressure to mitigate their resistance to inactivation processes. The successful implementation of such a germination-inactivation strategy relies on the germination of all spores. However, germination is heterogeneous, with some “superdormant” spores germinating extremely slowly or not at all. The present study investigated potential underlying reasons for moderate high-pressure (150 MPa; 37°C) superdormancy of Bacillus subtilis spores. The water and dipicolinic acid content of superdormant spores was compared with that of the initial dormant spore population. The results suggest that water and dipicolinic acid content are not major drivers of moderate high-pressure superdormancy. A proteomic analysis was used to identify proteins that were quantified at significantly different levels in superdormant spores. Subsequent validation of the germination capacity of deletion mutants revealed that the presence of protein YhcN is required for efficient moderate high-pressure germination and that proteins MinC, cse60, and SspK may also play a role, albeit a minor one.

Published
2022

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