Artist Eduardo R. Miranda was invited to the laboratory of researcher Pablo I. Nikel at the Danish DTU Biosustain as part of the research project SinFonia. Miranda developed a method to converge the enzymes, used to handle fluorine in the cell, into musical composition. This way we can listen how the bacteria incorporates fluorine into its metabolism.


Listen to the musical enzymes created by Eduardo Miranda during his residency at Pablo Nikel's lab.

1. Aldolase: 

2. Fluorinase:

3. Aldehyde dehydrogenase:

4. Isomerase:

5. Kinase:

6. Nucleosidase:


Gurdo N, Taylor Parkins SK, Fricano M, Wulff T, Nielsen LK, Nikel PI. 2023. Protocol for absolute quantification of proteins in Gram-negative bacteria based on QconCAT-based labeled peptides. STAR protocols 4 (1),
Martínez-García E, Fraile S, Algar E, Aparicio T, Velázquez E, Calles B, ... 2023. SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes. Nucleic Acids Research 51 (D1),
N Gurdo, DC Volke, D McCloskey, PI Nikel. 2023. Automating the design-build-test-learn cycle towards next-generation bacterial cell factories. New Biotechnology 74, 1-15. DOI 10.1016/j.nbt.2023.01.002

Wirth NT, Gurdo N, Krink N, Vidal-Verdú À, Donati S, Férnandez-Cabezón L, Wulff T, Nikel PI. 2022. A synthetic C2 auxotroph of Pseudomonas putida for evolutionary engineering of alternative sugar catabolic routes. Metabolic Engineering 74,

Calero P, Gurdo N, Nikel PI. 2022. Role of the CrcB transporter of Pseudomonas putida in the multi-level stress response elicited by mineral fluoride. Environmental Microbiology, 

Orsi E, Claassens NJ, Nikel PI, Lindner SN. 2022. Optimizing microbial networks through metabolic bypasses. Biotechnology advances, 

Volke DC, Martino RA, Kozaeva E, Smania AM, Nikel PI. 2022. Modular (de)construction of complex bacterial phenotypes by CRISPR/nCas9-assisted, multiplex cytidine base-editingNature Communications,

Nikel PI, Welner DH, Cros A, Volke DC. 2022. In vivo fluorine biocatalysis: Six enzymes in search of a cell factory. Chem Catalysis 2 (10),

Volke DC, A Cros, DH Welner, Nikel PI. 2022. Emerging approaches for biocatalysis supporting a sustainable future: Enzymes wanted, dead or alive. Chem Catalysis 2 (10),

Haas R, Nikel PI. 2022. Challenges and opportunities in bringing nonbiological atoms to life with synthetic metabolism. Trends in Biotechnology. Vol 41/1: 27-45


Pardo I, Bednar D, Calero P, Volke DC,  Damborský J, Nikel PI. 2022.A nonconventional archaeal fluorinase identified by in silico mining for enhanced fluorine biocatalysisACS catalysis. Vol 12/11: 6570-6577. DOI 10.1021/acscatal.2c01184


Hernández-Arriaga AM, Campano C, Rivero-Buceta V, Prieto MA. 2022. When microbial biotechnology meets material engineering. Microbial Biotechnology,


Vigasova D, Nemergut M, Liskova B, Damborsky J. 2021 Multi-pathogen infections and Alzheimer's disease. Microbial Cell Factories,

Khan RT, Musil M, Stourac J, Damborsky J, Bednar D. 2021. Fully Automated Ancestral Sequence Reconstruction using FireProtASR. Current Protocols,

Orsi E, Claassens NJ, Nikel PI, Lindner SN. 2021. Growth-coupled selection of synthetic modules to accelerate cell factory development. Nature Communications,

Griffith CM, Walvekar AS, Linster CL. 2021. Approaches for completing metabolic networks through metabolite damage and repair discovery. Current Opinion in Systems Biology,

Cros A, Alfaro-Espinoza G, De Maria A, Wirth NT, Nikel PI. 2021. Synthetic metabolism for biohalogenation. Current Opinion in Biotechnology,

Marques SM, Planas-Iglesias J, Damborsky J. 2021. Web-based tools for computational enzyme design. Current Opinion in Structural Biology,

Musil M, Khan RT, Beier A, Stourac J, Konegger H, Damborsky J, Bednar D. 2021. FireProtASR: A Web Server for Fully Automated Ancestral Sequence Reconstruction. Briefings in Bioinformatics,

Hon J, Marusiak M, Martinek T, Kunka A, Zendulka J, Bednar D, Damborsky J. 2021. SoluProt: Prediction of Soluble Protein Expression in Escherichia coli. Bioinformatics,

Markova K, Kunka A, Chmelova K, Havlasek M, Babkova P, Marques SM, Vasina M, Planas-Iglesias J, Chaloupkova R, Bednar D, Prokop Z, Damborsky J, and Marek M. 2021. Computational Enzyme Stabilization Can Affect Folding Energy Landscapes and Lead to Catalytically Enhanced Domain-Swapped Dimers. ACS Catalysis,

Pinto GP, Vavra O, Marques SM, Filipovic J, Bednar D, Damborsky J. 2021. Screening of world approved drugs against highly dynamical spike glycoprotein of SARS-CoV-2 using CaverDock and machine learning. Computational and Structural Biotechnology Journal,

Pérez-Pantoja D, Nikel PI, Chavarría M, de Lorenzo V. 2021. Transcriptional control of 2,4-dinitrotoluene degradation in Burkholderia sp. R34 bears a regulatory patch that eases pathway evolution. Environmental Microbiology,


Mezzina MP, Manoli MT, Prieto MA, Nikel Pl. 2020. Engineering Native and Synthetic Pathways in Pseudomonas putida for the Production of Tailored Polyhydroxyalkanoates. Biotechnology Journal,

Lammens EM, Nikel PI, Lavigne R. 2020. Exploring the synthetic biology potential of bacteriophages for engineering non-model bacteria. Nature Communications,

Dockalova V, Sanchez-Carnerero EM, Dunajova Z, Palao E, Slanska M, Buryska T, Damborsky J, Klán P, Prokop Z. 2020. Fluorescent substrates for haloalkane dehalogenases: Novel probes for mechanistic studies and protein labeling. Computational and Structural Biotechnology Journal,

Nieto-Domínguez M, Nikel PI. Markova K, Chmelova K, Marques SM, Carpentier P, Bednar D, Damborsky J, Marek M. 2020. Decoding the intricate network of molecular interactions of a hyperstable engineered biocatalyst. Chemical Science,

Marek M, Chaloupkova R, Prudnikova T, Sato Y, Rezacova P, Nagata Y, Kuta Smatanova I, Damborsky J. 2020. Structural and catalytic effects of surface loop-helix transplantation within haloalkane dehalogenase family. Computational and Structural Biotechnology Journal,

Chmelova K, Sebestova E, Liskova V, Beier A, Bednar D, Prokop Z, Chaloupkova R, Damborsky J. A 2020. Haloalkane Dehalogenase from Saccharomonospora viridis Strain DSM 43017, a Compost Bacterium with Unusual Catalytic Residues, Unique (S)-Enantiopreference, and High Thermostability. Applied and Environmental Microbiology,

Markakis K, Lowe PT, Davison-Gates L, O'Hagan D, Rosser SJ, Elfick A. 2020. An Engineered E. coli Strain for Direct in Vivo Fluorination. ChemBioChem,

Calero P, Volke DC, Lowe PT et al. 2020. A fluoride-responsive genetic circuit enables in vivo biofluorination in engineered Pseudomonas putida. Nature Communications,

Nieto-Domínguez M, Nikel PI. 2020. Intersecting Xenobiology and Neometabolism To Bring Novel Chemistries to Life. ChemBioChem,

Babkova P, Dunajova Z, Chaloupkova R, Damborsky J, Bednar D, Marek M. 2020. Structures of hyperstable ancestral haloalkane dehalogenases show restricted conformational dynamics. Computational and Structural Biotechnology Journal,

Batianis C, Kozaeva E, Damalas SG, Martín‐Pascual M, Volke DC, Nikel PI, Martins dos Santos VAP. 2020. An expanded CRISPRi toolbox for tunable control of gene expression in Pseudomonas putida. Microbial Biotechnology,

Schmidt M, Budisa N. 2020. Alternative Biofacts – Life as we don’t (yet) know it.
Chapter in the book "Art as We Don’t Know It". PDF

Volke DC, Friis L, Wirth NT, Turlin J, Nikel PI. 2020. Synthetic control of plasmid replication enables target- and self-curing of vectors and expedites genome engineering of Pseudomonas putida. Metabolic Engineering Communications,

Vavra O, Filipovic J, Plhak J, Bednar D, Marques SM, Brezovsky J, Stourac J, Matyska L, Damborsky J. 2019. CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels. Bioinformatics,

Beier A, Damborsky J, Prokop Z. 2019. Transhalogenation Catalysed by Haloalkane Dehalogenases Engineered to Stop Natural Pathway at Intermediate. Advanced Synthesis and Catalysis,

Demko M, Chrást L, Dvořák P, Damborský J, Šafránek D. 2019. Computational Modelling of Metabolic Burden and Substrate Toxicity in Escherichia coli Carrying a Synthetic Metabolic Pathway. Microorganisms.

Arce‐Rodríguez A, Volke DC,  Bense S,  Häussler S,  Nike PI. 2019. Non‐invasive, ratiometric determination of intracellular pH in Pseudomonas species using a novel genetically encoded indicator. Microbial Biotechnology Vol.12(4): 799-813.

 Evolutionary Approaches for Engineering Industrially Relevant Phenotypes in Bacterial Cell Factories. Biotechnology Journal.

Wirth NT, Kozaeva E, Nikel PI, 2019. Accelerated genome engineering of Pseudomonas putida by I‐SceI―mediated recombination and CRISPR‐Cas9 counterselection.  Microbial Biotechnology.
Volke DC, Turlin J, Mol V, Nikel PI, 2019. Physical decoupling of XylS/Pm regulatory elements and conditional proteolysis enable precise control of gene expression in Pseudomonas putida. Microbial Biotechnology.

Martinelli L, Nikel PI. 2019. Breaking the state‐of‐the‐art in the chemical industry with new‐to‐Nature products via synthetic microbiology. Microbial Biotechnology. Vol. 12(2): 187-190.