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High-Throughput, Accurate Mass Metabolome Profiling of Cellular Extracts by Flow Injection–Time-of-Flight Mass Spectrometry

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Institute of Molecular Systems Biology, ETH Zurich, Switzerland
Life Science Zurich PhD Program on Systems Biology, ETH Zurich, Switzerland
E-mail: [email protected]. Address: Wolfgang-Pauli Strasse 16, 8093 Zurich, Switzerland. Phone: +41 44 633 31 41. Fax: +41 44 633 10 51.
Cite this: Anal. Chem. 2011, 83, 18, 7074–7080
Publication Date (Web):August 10, 2011
Copyright © 2011 American Chemical Society

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    Direct injection of samples on high-resolving mass spectrometers is an effective way to maximize analytical throughput and yet allow analyte discrimination in complex samples by mass-to-charge ratio. We present a platform of flow injection electrospray–time-of-flight mass spectrometry to profile small molecules in >1400 biological extracts per day at native mass resolution. We comprehensively benchmark the performance with more than 5000 injections of chemically defined standards and Escherichia coli cellular extracts obtained from miniscale cultivations. For at least 90% of tested compounds, we attain a linear response over 3 decades of concentration, interday coefficient of variation of <20%, and a mass accuracy of <0.001 amu. In polar Escherichia coli fractions, we reproducibly detected >1500 distinct ions in each mode. The accurate mass and correlation analysis enabled one to assign with good confidence 400–800 ions to electrospray derivatives of metabolites listed in the genome-wide reconstruction of Escherichia coli metabolism. Hence, we attain a coverage of about one-quarter of the total number of compounds listed in the reconstruction. Finally, we present an exemplary screen with Escherichia coli deletion mutants to show the exquisite capacity of the platform to identify lesions in primary metabolism at high throughputs.

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    15. Bruno Cuevas-Zuviría, Evrim Fer, Zachary R. Adam, Betül Kaçar. The modular biochemical reaction network structure of cellular translation. npj Systems Biology and Applications 2023, 9 (1)
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    22. Marvin Nathanael Iman, Rifqi Ahmad Riyanto, Sastia Prama Putri. Metabolomics as a Tool for Phenotypic Characterization and Strain Improvement. 2023, 154-172.
    23. Claudia Irene Maushart, Wenfei Sun, Alaa Othman, Adhideb Ghosh, Jaël Rut Senn, Jonas Gabriel William Fischer, Philipp Madoerin, Rahel Catherina Loeliger, Robyn Melanie Benz, Martin Takes, Christoph Johannes Zech, Alin Chirindel, Felix Beuschlein, Martin Reincke, Damian Wild, Oliver Bieri, Nicola Zamboni, Christian Wolfrum, Matthias Johannes Betz. Effect of high-dose glucocorticoid treatment on human brown adipose tissue activity: a randomised, double-blinded, placebo-controlled cross-over trial in healthy men. eBioMedicine 2023, 96 , 104771.
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    25. Godfrey S Temba, Nadira Vadaq, Vesla Kullaya, Tal Pecht, Paolo Lionetti, Duccio Cavalieri, Joachim L Schultze, Reginald Kavishe, Leo AB Joosten, Andre J van der Ven, Blandina T Mmbaga, Mihai G Netea, Quirijn de Mast. Differences in the inflammatory proteome of East African and Western European adults and associations with environmental and dietary factors. eLife 2023, 12
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    27. Sarah A. Berger, Christopher Grimm, Jonathan Nyenhuis, Stefan E. Payer, Isabel Oroz‐Guinea, Joerg H. Schrittwieser, Wolfgang Kroutil. Rapid, Label‐Free Screening of Diverse Biotransformations by Flow‐Injection Mass Spectrometry. ChemBioChem 2023, 24 (11)
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    31. Niklas Farke, Thorben Schramm, Andreas Verhülsdonk, Johanna Rapp, Hannes Link. Systematic analysis of in-source modifications of primary metabolites during flow-injection time-of-flight mass spectrometry. Analytical Biochemistry 2023, 664 , 115036.
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    35. Stella Reichling, Peter F Doubleday, Tomas Germade, Ariane Bergmann, Robbie Loewith, Uwe Sauer, Duncan Holbrook-Smith. . eLife 2023
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    40. Jeremiah Bernier-Latmani, Cristina Mauri, Rachel Marcone, François Renevey, Stephan Durot, Liqun He, Michael Vanlandewijck, Catherine Maclachlan, Suzel Davanture, Nicola Zamboni, Graham W. Knott, Sanjiv A. Luther, Christer Betsholtz, Mauro Delorenzi, Cathrin Brisken, Tatiana V. Petrova. ADAMTS18+ villus tip telocytes maintain a polarized VEGFA signaling domain and fenestrations in nutrient-absorbing intestinal blood vessels. Nature Communications 2022, 13 (1)
    41. Louise E. van Eekeren, Vasiliki Matzaraki, Zhenhua Zhang, Lisa van de Wijer, Marc J. T. Blaauw, Marien I. de Jonge, Linos Vandekerckhove, Wim Trypsteen, Leo A. B. Joosten, Mihai G. Netea, Quirijn de Mast, Hans J. P. M. Koenen, Yang Li, André J. A. M. van der Ven. People with HIV have higher percentages of circulating CCR5+ CD8+ T cells and lower percentages of CCR5+ regulatory T cells. Scientific Reports 2022, 12 (1)
    42. Bahtiyar Yilmaz, Tobias Fuhrer, Deborah Morgenthaler, Niklas Krupka, Daoming Wang, Daniel Spari, Daniel Candinas, Benjamin Misselwitz, Guido Beldi, Uwe Sauer, Andrew J. Macpherson. Plasticity of the adult human small intestinal stoma microbiota. Cell Host & Microbe 2022, 30 (12) , 1773-1787.e6.
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    46. Michelle S. Prew, Utsarga Adhikary, Dong Wook Choi, Erika P. Portero, Joao A. Paulo, Pruthvi Gowda, Amit Budhraja, Joseph T. Opferman, Steven P. Gygi, Nika N. Danial, Loren D. Walensky. MCL-1 is a master regulator of cancer dependency on fatty acid oxidation. Cell Reports 2022, 41 (1) , 111445.
    47. Paula Bellés-Sancho, Yilei Liu, Benjamin Heiniger, Elia von Salis, Leo Eberl, Christian H. Ahrens, Nicola Zamboni, Aurélien Bailly, Gabriella Pessi. A novel function of the key nitrogen-fixation activator NifA in beta-rhizobia: Repression of bacterial auxin synthesis during symbiosis. Frontiers in Plant Science 2022, 13
    48. Valerie A. C. M. Koeken, Cancan Qi, Vera P. Mourits, L. Charlotte J. de Bree, Simone J. C. F. M. Moorlag, Vidhisha Sonawane, Heidi Lemmers, Helga Dijkstra, Leo A. B. Joosten, Arjan van Laarhoven, Cheng-Jian Xu, Reinout van Crevel, Mihai G. Netea, Yang Li, . Plasma metabolome predicts trained immunity responses after antituberculosis BCG vaccination. PLOS Biology 2022, 20 (9) , e3001765.
    49. Eden Yifrach, Duncan Holbrook‐Smith, Jérôme Bürgi, Alaa Othman, Miriam Eisenstein, Carlo WT van Roermund, Wouter Visser, Asa Tirosh, Markus Rudowitz, Chen Bibi, Shahar Galor, Uri Weill, Amir Fadel, Yoav Peleg, Ralf Erdmann, Hans R Waterham, Ronald J A Wanders, Matthias Wilmanns, Nicola Zamboni, Maya Schuldiner, Einat Zalckvar. Systematic multi‐level analysis of an organelle proteome reveals new peroxisomal functions. Molecular Systems Biology 2022, 18 (9)
    50. Karin Ortmayr, Mattia Zampieri. Sorting‐free metabolic profiling uncovers the vulnerability of fatty acid β‐oxidation in in vitro quiescence models. Molecular Systems Biology 2022, 18 (9)
    51. L. Ferreira Azevedo, Mauro Miguel Masiero, S. Cherkaoui, M.F. Hornos Carneiro, F. Barbosa Jr, N. Zamboni. The alternative analog plasticizer BPS displays similar phenotypic and metabolomic responses to BPA in HepG2 and INS-1E cells. Food and Chemical Toxicology 2022, 167 , 113266.
    52. Hyung Jun Kim, Yingying Li, Michael Zimmermann, Yunmi Lee, Hui Wen Lim, Alvin Swee Leong Tan, Inhee Choi, Yoonae Ko, Sangchul Lee, Jeong Jea Seo, Mooyoung Seo, Hee Kyoung Jeon, Jonathan Cechetto, Joey Kuok Hoong Yam, Liang Yang, Uwe Sauer, Soojin Jang, Kevin Pethe. Pharmacological perturbation of thiamine metabolism sensitizes Pseudomonas aeruginosa to multiple antibacterial agents. Cell Chemical Biology 2022, 29 (8) , 1317-1324.e5.
    53. Laszlo A Groh, Dagmar E Verel, Charlotte D C C van der Heijden, Vasiliki Matzaraki, Simone J C F M Moorlag, L Charlotte de Bree, Valerie A C M Koeken, Vera P Mourits, Samuel T Keating, Jelmer H van Puffelen, Leo A B Joosten, Mihai G Netea, Niels P Riksen. Immune modulatory effects of progesterone on oxLDL-induced trained immunity in monocytes. Journal of Leukocyte Biology 2022, 112 (2) , 279-288.
    54. Gianmarco Barberi, Antonio Benedetti, Paloma Diaz-Fernandez, Daniel C. Sévin, Johanna Vappiani, Gary Finka, Fabrizio Bezzo, Massimiliano Barolo, Pierantonio Facco. Integrating metabolome dynamics and process data to guide cell line selection in biopharmaceutical process development. Metabolic Engineering 2022, 72 , 353-364.
    55. Maik Kok, Loes Maton, Marielle van der Peet, Thomas Hankemeier, J. G. Coen van Hasselt. Unraveling antimicrobial resistance using metabolomics. Drug Discovery Today 2022, 27 (6) , 1774-1783.
    56. Jenna I. Wurster, Rachel L. Peterson, Peter Belenky. Streptozotocin-Induced Hyperglycemia Is Associated with Unique Microbiome Metabolomic Signatures in Response to Ciprofloxacin Treatment. Antibiotics 2022, 11 (5) , 585.
    57. Miquel Anglada-Girotto, Gabriel Handschin, Karin Ortmayr, Adrian I. Campos, Ludovic Gillet, Pablo Manfredi, Claire V. Mulholland, Michael Berney, Urs Jenal, Paola Picotti, Mattia Zampieri. Combining CRISPRi and metabolomics for functional annotation of compound libraries. Nature Chemical Biology 2022, 18 (5) , 482-491.
    58. Pau Pérez Escriva, Tobias Fuhrer, Uwe Sauer, . Distinct N and C Cross-Feeding Networks in a Synthetic Mouse Gut Consortium. mSystems 2022, 7 (2)
    59. Sammy Pontrelli, Rachel Szabo, Shaul Pollak, Julia Schwartzman, Daniela Ledezma-Tejeida, Otto X. Cordero, Uwe Sauer. Metabolic cross-feeding structures the assembly of polysaccharide degrading communities. Science Advances 2022, 8 (8)
    60. Duncan Holbrook‐Smith, Stephan Durot, Uwe Sauer. High‐throughput metabolomics predicts drug–target relationships for eukaryotic proteins. Molecular Systems Biology 2022, 18 (2)
    61. Belinda B Garana, Nicholas A Graham. Metabolomics paves the way for improved drug target identification. Molecular Systems Biology 2022, 18 (2)
    62. Julia M. Malinowska, Taina Palosaari, Jukka Sund, Donatella Carpi, Gavin R. Lloyd, Ralf J. M. Weber, Maurice Whelan, Mark R. Viant. Automated Sample Preparation and Data Collection Workflow for High-Throughput In Vitro Metabolomics. Metabolites 2022, 12 (1) , 52.
    63. Julia M. Malinowska, Taina Palosaari, Jukka Sund, Donatella Carpi, Mounir Bouhifd, Ralf J. M. Weber, Maurice Whelan, Mark R. Viant. Integrating in vitro metabolomics with a 96-well high-throughput screening platform. Metabolomics 2022, 18 (1)
    64. Zuhal Eraslan, Marta Cascante, Ulrich L. Günther. Metabolomics in Cell Biology. 2022, 181-207.
    65. Evan G. Williams, Niklas Pfister, Suheeta Roy, Cyril Statzer, Jack Haverty, Jesse Ingels, Casey Bohl, Moaraj Hasan, Jelena Čuklina, Peter Bühlmann, Nicola Zamboni, Lu Lu, Collin Y. Ewald, Robert W. Williams, Ruedi Aebersold. Multiomic profiling of the liver across diets and age in a diverse mouse population. Cell Systems 2022, 13 (1) , 43-57.e6.
    66. Corinne Bischof, Peter Mirtschink, Ting Yuan, Meiqian Wu, Chaonan Zhu, Jaskiran Kaur, Minh Duc Pham, Suam Gonzalez-Gonoggia, Marie Hammer, Eva-Maria Rogg, Rahul Sharma, Katharina Bottermann, Bettina Gercken, Eman Hagag, Corinne Berthonneche, Samuel Sossalla, Sebastian N. Stehr, Joachim Maxeiner, Maria Anna Duda, Mathieu Latreille, Nicola Zamboni, Fabio Martelli, Thierry Pedrazzini, Stefanie Dimmeler, Jaya Krishnan. Mitochondrial–cell cycle cross-talk drives endoreplication in heart disease. Science Translational Medicine 2021, 13 (623)
    67. Martin Stražar, Vera P. Mourits, Valerie A. C. M. Koeken, L. Charlotte J. de Bree, Simone J. C. F. M. Moorlag, Leo A. B. Joosten, Reinout van Crevel, Hera Vlamakis, Mihai G. Netea, Ramnik J. Xavier. The influence of the gut microbiome on BCG-induced trained immunity. Genome Biology 2021, 22 (1)
    68. Zhenhua Zhang, Wim Trypsteen, Marc Blaauw, Xiaojing Chu, Sofie Rutsaert, Linos Vandekerckhove, Wouter van der Heijden, Jéssica Cristina dos Santos, Cheng-Jian Xu, Morris A. Swertz, Andre van der Ven, Yang Li. IRF7 and RNH1 are modifying factors of HIV-1 reservoirs: a genome-wide association analysis. BMC Medicine 2021, 19 (1)
    69. Elise Meeder, Vasiliki Matzaraki, Nadira Vadaq, Lisa van de Wijer, André van der Ven, Arnt Schellekens. Unbiased Metabolomics Links Fatty Acid Pathways to Psychiatric Symptoms in People Living with HIV. Journal of Clinical Medicine 2021, 10 (23) , 5466.
    70. Jen Nguyen, Vicente Fernandez, Sammy Pontrelli, Uwe Sauer, Martin Ackermann, Roman Stocker. A distinct growth physiology enhances bacterial growth under rapid nutrient fluctuations. Nature Communications 2021, 12 (1)
    71. Martin Stražar, Godfrey S. Temba, Hera Vlamakis, Vesla I. Kullaya, Furaha Lyamuya, Blandina T. Mmbaga, Leo A. B. Joosten, Andre J. A. M. van der Ven, Mihai G. Netea, Quirijn de Mast, Ramnik J. Xavier. Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations. Nature Communications 2021, 12 (1)
    72. Evgeniya Schastnaya, Zrinka Raguz Nakic, Christoph H. Gruber, Peter Francis Doubleday, Aarti Krishnan, Nathan I. Johns, Jimin Park, Harris H. Wang, Uwe Sauer. Extensive regulation of enzyme activity by phosphorylation in Escherichia coli. Nature Communications 2021, 12 (1)
    73. Ozren Stojanović, Jordi Altirriba, Dorothée Rigo, Martina Spiljar, Emilien Evrard, Benedek Roska, Salvatore Fabbiano, Nicola Zamboni, Pierre Maechler, Françoise Rohner-Jeanrenaud, Mirko Trajkovski. Dietary excess regulates absorption and surface of gut epithelium through intestinal PPARα. Nature Communications 2021, 12 (1)
    74. Jenna I. Wurster, Rachel L. Peterson, Claire E. Brown, Swathi Penumutchu, Douglas V. Guzior, Kerri Neugebauer, William H. Sano, Manu M. Sebastian, Robert A. Quinn, Peter Belenky. Streptozotocin-induced hyperglycemia alters the cecal metabolome and exacerbates antibiotic-induced dysbiosis. Cell Reports 2021, 37 (11) , 110113.
    75. Laura Surace, Jean-Marc Doisne, Carys A. Croft, Anna Thaller, Pedro Escoll, Solenne Marie, Natalia Petrosemoli, Vincent Guillemot, Valerie Dardalhon, Davide Topazio, Antonia Cama, Carmen Buchrieser, Naomi Taylor, Ido Amit, Olimpia Musumeci, James P. Di Santo. Dichotomous metabolic networks govern human ILC2 proliferation and function. Nature Immunology 2021, 22 (11) , 1367-1374.
    76. Accalia Fu, Lara van Rooyen, Lindsay Evans, Nina Armstrong, Daina Avizonis, Tatsuya Kin, Gregory H. Bird, Anita Reddy, Edward T. Chouchani, Marc Liesa-Roig, Loren D. Walensky, A.M. James Shapiro, Nika N. Danial. Glucose metabolism and pyruvate carboxylase enhance glutathione synthesis and restrict oxidative stress in pancreatic islets. Cell Reports 2021, 37 (8) , 110037.
    77. Johanna Vappiani, Tom Eyster, Keegan Orzechowski, Diana Ritz, Pramthesh Patel, Daniel Sévin, Juan Aon. Exometabolome profiling reveals activation of the carnitine buffering pathway in fed‐batch cultures of CHO cells co‐fed with glucose and lactic acid. Biotechnology Progress 2021, 37 (6)
    78. Ana Montalban-Arques, Egle Katkeviciute, Philipp Busenhart, Anna Bircher, Jakob Wirbel, Georg Zeller, Yasser Morsy, Lubor Borsig, Jesus F. Glaus Garzon, Anne Müller, Isabelle C. Arnold, Mariela Artola-Boran, Michael Krauthammer, Anna Sintsova, Nicola Zamboni, Gabriel E. Leventhal, Laura Berchtold, Tomas de Wouters, Gerhard Rogler, Katharina Baebler, Marlene Schwarzfischer, Larissa Hering, Ivan Olivares-Rivas, Kirstin Atrott, Claudia Gottier, Silvia Lang, Onur Boyman, Ralph Fritsch, Markus G. Manz, Marianne R. Spalinger, Michael Scharl. Commensal Clostridiales strains mediate effective anti-cancer immune response against solid tumors. Cell Host & Microbe 2021, 29 (10) , 1573-1588.e7.
    79. Ksenija Radic Shechter, Eleni Kafkia, Katharina Zirngibl, Sylwia Gawrzak, Ashna Alladin, Daniel Machado, Christian Lüchtenborg, Daniel C Sévin, Britta Brügger, Kiran R Patil, Martin Jechlinger. Metabolic memory underlying minimal residual disease in breast cancer. Molecular Systems Biology 2021, 17 (10)
    80. Martina Klünemann, Sergej Andrejev, Sonja Blasche, Andre Mateus, Prasad Phapale, Saravanan Devendran, Johanna Vappiani, Bernd Simon, Timothy A. Scott, Eleni Kafkia, Dimitrios Konstantinidis, Katharina Zirngibl, Eleonora Mastrorilli, Manuel Banzhaf, Marie-Therese Mackmull, Felix Hövelmann, Leo Nesme, Ana Rita Brochado, Lisa Maier, Thomas Bock, Vinita Periwal, Manjeet Kumar, Yongkyu Kim, Melanie Tramontano, Carsten Schultz, Martin Beck, Janosch Hennig, Michael Zimmermann, Daniel C. Sévin, Filipe Cabreiro, Mikhail M. Savitski, Peer Bork, Athanasios Typas, Kiran R. Patil. Bioaccumulation of therapeutic drugs by human gut bacteria. Nature 2021, 597 (7877) , 533-538.
    81. Laura Brunelli, Annalisa Davin, Giovanna Sestito, Maria Chiara Mimmi, Giulia De Simone, Claudia Balducci, Orietta Pansarasa, Gianluigi Forloni, Cristina Cereda, Roberta Pastorelli, Antonio Guaita, . Plasmatic Hippuric Acid as a Hallmark of Frailty in an Italian Cohort: The Mediation Effect of Fruit–Vegetable Intake. The Journals of Gerontology: Series A 2021, 571
    82. Daniela Rodrigues, Terezinha de Souza, Luke Coyle, Matteo Di Piazza, Bram Herpers, Sofia Ferreira, Mian Zhang, Johanna Vappiani, Daniel C. Sévin, Attila Gabor, Anthony Lynch, Seung-Wook Chung, Julio Saez-Rodriguez, Danyel G. J. Jennen, Jos C. S. Kleinjans, Theo M. de Kok. New insights into the mechanisms underlying 5-fluorouracil-induced intestinal toxicity based on transcriptomic and metabolomic responses in human intestinal organoids. Archives of Toxicology 2021, 95 (8) , 2691-2718.
    83. Silvia Brochet, Andrew Quinn, Ruben AT Mars, Nicolas Neuschwander, Uwe Sauer, Philipp Engel. Niche partitioning facilitates coexistence of closely related honey bee gut bacteria. eLife 2021, 10
    84. Alejandra González-Loyola, Esther Bovay, Jaeryung Kim, Tania Wyss Lozano, Amélie Sabine, Francois Renevey, Silvia Arroz-Madeira, Alexis Rapin, Tomasz P. Wypych, Giorgia Rota, Stephan Durot, Dominique Velin, Benjamin Marsland, Greta Guarda, Mauro Delorenzi, Nicola Zamboni, Sanjiv A. Luther, Tatiana V. Petrova. FOXC2 controls adult lymphatic endothelial specialization, function, and gut lymphatic barrier preventing multiorgan failure. Science Advances 2021, 7 (29)
    85. Muzamil Majid Khan, Daniel Poeckel, Aliaksandr Halavatyi, Joanna Zukowska-Kasprzyk, Frank Stein, Johanna Vappiani, Daniel C. Sevin, Christian Tischer, Nico Zinn, Jessica D. Eley, Natasja Stæhr Gudmann, Thomas Muley, Hauke Winter, Andrew J. Fisher, Carmel B. Nanthakumar, Giovanna Bergamini, Rainer Pepperkok. An integrated multiomic and quantitative label-free microscopy-based approach to study pro-fibrotic signalling in ex vivo human precision-cut lung slices. European Respiratory Journal 2021, 58 (1) , 2000221.
    86. Paula Bellés-Sancho, Martina Lardi, Yilei Liu, Leo Eberl, Nicola Zamboni, Aurélien Bailly, Gabriella Pessi. Metabolomics and Dual RNA-Sequencing on Root Nodules Revealed New Cellular Functions Controlled by Paraburkholderia phymatum NifA. Metabolites 2021, 11 (7) , 455.
    87. Anaisa V. Ferreira, Valerie A. C. M. Koeken, Vasiliki Matzaraki, Sarantos Kostidis, Juan Carlos Alarcon-Barrera, L. Charlotte J. de Bree, Simone J. C. F. M. Moorlag, Vera P. Mourits, Boris Novakovic, Martin A. Giera, Mihai G. Netea, Jorge Domínguez-Andrés. Glutathione Metabolism Contributes to the Induction of Trained Immunity. Cells 2021, 10 (5) , 971.
    88. Alexander Reiter, Laura Herbst, Wolfgang Wiechert, Marco Oldiges. Need for speed: evaluation of dilute and shoot-mass spectrometry for accelerated metabolic phenotyping in bioprocess development. Analytical and Bioanalytical Chemistry 2021, 413 (12) , 3253-3268.
    89. Manuel Hörl, Tobias Fuhrer, Nicola Zamboni, . Bifunctional Malic/Malolactic Enzyme Provides a Novel Mechanism for NADPH-Balancing in Bacillus subtilis. mBio 2021, 12 (2)
    90. Raphael Ledermann, Barbara Emmenegger, Jean-Malo Couzigou, Nicola Zamboni, Patrick Kiefer, Julia A. Vorholt, Hans-Martin Fischer, . Bradyrhizobium diazoefficiens Requires Chemical Chaperones To Cope with Osmotic Stress during Soybean Infection. mBio 2021, 12 (2)
    91. Paula Bellés-Sancho, Martina Lardi, Yilei Liu, Sebastian Hug, Marta Adriana Pinto-Carbó, Nicola Zamboni, Gabriella Pessi. Paraburkholderia phymatum Homocitrate Synthase NifV Plays a Key Role for Nitrogenase Activity during Symbiosis with Papilionoids and in Free-Living Growth Conditions. Cells 2021, 10 (4) , 952.
    92. Birgitta W. van der Kolk, Sina Saari, Alen Lovric, Muhammad Arif, Marcus Alvarez, Arthur Ko, Zong Miao, Navid Sahebekhtiari, Maheswary Muniandy, Sini Heinonen, Ali Oghabian, Riikka Jokinen, Sakari Jukarainen, Antti Hakkarainen, Jesper Lundbom, Juho Kuula, Per-Henrik Groop, Taru Tukiainen, Nina Lundbom, Aila Rissanen, Jaakko Kaprio, Evan G. Williams, Nicola Zamboni, Adil Mardinoglu, Päivi Pajukanta, Kirsi H. Pietiläinen. Molecular pathways behind acquired obesity: Adipose tissue and skeletal muscle multiomics in monozygotic twin pairs discordant for BMI. Cell Reports Medicine 2021, 2 (4) , 100226.
    93. Lianmin Chen, Daoming Wang, Sanzhima Garmaeva, Alexander Kurilshikov, Arnau Vich Vila, Ranko Gacesa, Trishla Sinha, Eran Segal, Rinse K. Weersma, Cisca Wijmenga, Alexandra Zhernakova, Jingyuan Fu. The long-term genetic stability and individual specificity of the human gut microbiome. Cell 2021, 184 (9) , 2302-2315.e12.
    94. Karl Kochanowski, Hiroyuki Okano, Vadim Patsalo, James Williamson, Uwe Sauer, Terence Hwa. Global coordination of metabolic pathways in Escherichia coli by active and passive regulation. Molecular Systems Biology 2021, 17 (4)
    95. Godfrey S. Temba, Vesla Kullaya, Tal Pecht, Blandina T. Mmbaga, Anna C. Aschenbrenner, Thomas Ulas, Gibson Kibiki, Furaha Lyamuya, Collins K. Boahen, Vinod Kumar, Leo A. B. Joosten, Joachim L. Schultze, Andre J. van der Ven, Mihai G. Netea, Quirijn de Mast. Urban living in healthy Tanzanians is associated with an inflammatory status driven by dietary and metabolic changes. Nature Immunology 2021, 22 (3) , 287-300.
    96. Daisuke Yamashita, Joshua D. Bernstock, Galal Elsayed, Hirokazu Sadahiro, Ahmed Mohyeldin, Gustavo Chagoya, Adeel Ilyas, James Mooney, Dagoberto Estevez-Ordonez, Shinobu Yamaguchi, Victoria L. Flanary, James R. Hackney, Krishna P. Bhat, Harley I. Kornblum, Nicola Zamboni, Sung-Hak Kim, E. Antonio Chiocca, Ichiro Nakano. Targeting glioma-initiating cells via the tyrosine metabolic pathway. Journal of Neurosurgery 2021, 134 (3) , 721-732.
    97. Topi Hovinen, Liisa Korkalo, Riitta Freese, Essi Skaffari, Pirjo Isohanni, Mikko Niemi, Jaakko Nevalainen, Helena Gylling, Nicola Zamboni, Maijaliisa Erkkola, Anu Suomalainen. Vegan diet in young children remodels metabolism and challenges the statuses of essential nutrients. EMBO Molecular Medicine 2021, 13 (2)
    98. Bernardo Ribeiro da Cunha, Luís P. Fonseca, Cecília R. C. Calado. Simultaneous elucidation of antibiotic mechanism of action and potency with high-throughput Fourier-transform infrared (FTIR) spectroscopy and machine learning. Applied Microbiology and Biotechnology 2021, 105 (3) , 1269-1286.
    99. Thorben Schramm, Hannes Link. Von der Stöchiometrie zur Kontrolle metabolischer Netzwerke. BIOspektrum 2021, 27 (1) , 34-36.
    100. Sonja Blasche, Yongkyu Kim, Ruben A. T. Mars, Daniel Machado, Maria Maansson, Eleni Kafkia, Alessio Milanese, Georg Zeller, Bas Teusink, Jens Nielsen, Vladimir Benes, Rute Neves, Uwe Sauer, Kiran Raosaheb Patil. Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community. Nature Microbiology 2021, 6 (2) , 196-208.
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