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Items: 1 to 50 of 75

1.

Revolutionizing agriculture with synthetic biology.

Wurtzel ET, Vickers CE, Hanson AD, Millar AH, Cooper M, Voss-Fels KP, Nikel PI, Erb TJ.

Nat Plants. 2019 Dec;5(12):1207-1210. doi: 10.1038/s41477-019-0539-0. Epub 2019 Nov 18. Review.

PMID:
31740769
2.

Why Nature Chose Potassium.

Danchin A, Nikel PI.

J Mol Evol. 2019 Dec;87(9-10):271-288. doi: 10.1007/s00239-019-09915-2. Epub 2019 Oct 28. Review.

PMID:
31659374
3.

In silico-guided engineering of Pseudomonas putida towards growth under micro-oxic conditions.

Kampers LFC, van Heck RGA, Donati S, Saccenti E, Volkers RJM, Schaap PJ, Suarez-Diez M, Nikel PI, Martins Dos Santos VAP.

Microb Cell Fact. 2019 Oct 22;18(1):179. doi: 10.1186/s12934-019-1227-5.

4.

Synthesis of Recoded Bacterial Genomes toward Bespoke Biocatalysis.

Nikel PI.

Trends Biotechnol. 2019 Oct;37(10):1036-1038. doi: 10.1016/j.tibtech.2019.07.001. Epub 2019 Jul 13.

PMID:
31311671
5.

Non-invasive, ratiometric determination of intracellular pH in Pseudomonas species using a novel genetically encoded indicator.

Arce-Rodríguez A, Volke DC, Bense S, Häussler S, Nikel PI.

Microb Biotechnol. 2019 Jul;12(4):799-813. doi: 10.1111/1751-7915.13439. Epub 2019 Jun 4.

6.

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

Fernández-Cabezón L, Cros A, Nikel PI.

Biotechnol J. 2019 Sep;14(9):e1800439. doi: 10.1002/biot.201800439. Epub 2019 Jun 12. Review.

PMID:
31070293
7.

Functional implementation of a linear glycolysis for sugar catabolism in Pseudomonas putida.

Sánchez-Pascuala A, Fernández-Cabezón L, de Lorenzo V, Nikel PI.

Metab Eng. 2019 Jul;54:200-211. doi: 10.1016/j.ymben.2019.04.005. Epub 2019 Apr 19.

PMID:
31009747
8.

High-Performance Biocomputing in Synthetic Biology-Integrated Transcriptional and Metabolic Circuits.

Goñi-Moreno A, Nikel PI.

Front Bioeng Biotechnol. 2019 Mar 11;7:40. doi: 10.3389/fbioe.2019.00040. eCollection 2019.

9.

Biochemistry, genetics and biotechnology of glycerol utilization in Pseudomonas species.

Poblete-Castro I, Wittmann C, Nikel PI.

Microb Biotechnol. 2020 Jan;13(1):32-53. doi: 10.1111/1751-7915.13400. Epub 2019 Mar 18. Review.

10.

Physical decoupling of XylS/Pm regulatory elements and conditional proteolysis enable precise control of gene expression in Pseudomonas putida.

Volke DC, Turlin J, Mol V, Nikel PI.

Microb Biotechnol. 2020 Jan;13(1):222-232. doi: 10.1111/1751-7915.13383. Epub 2019 Mar 12.

11.

Accelerated genome engineering of Pseudomonas putida by I-SceI-mediated recombination and CRISPR-Cas9 counterselection.

Wirth NT, Kozaeva E, Nikel PI.

Microb Biotechnol. 2020 Jan;13(1):233-249. doi: 10.1111/1751-7915.13396. Epub 2019 Mar 12.

12.

Breaking the state-of-the-art in the chemical industry with new-to-Nature products via synthetic microbiology.

Martinelli L, Nikel PI.

Microb Biotechnol. 2019 Mar;12(2):187-190. doi: 10.1111/1751-7915.13372. Epub 2019 Jan 31. No abstract available.

13.

The Synthetic Microbiology Caucus: from abstract ideas to turning microbes into cellular machines and back.

Huang WE, Nikel PI.

Microb Biotechnol. 2019 Jan;12(1):5-7. doi: 10.1111/1751-7915.13337. Epub 2018 Nov 20. No abstract available.

14.

The global regulator Crc orchestrates the metabolic robustness underlying oxidative stress resistance in Pseudomonas aeruginosa.

Corona F, Martínez JL, Nikel PI.

Environ Microbiol. 2019 Mar;21(3):898-912. doi: 10.1111/1462-2920.14471. Epub 2018 Dec 16.

PMID:
30411469
15.

Evolving metabolism of 2,4-dinitrotoluene triggers SOS-independent diversification of host cells.

Akkaya Ö, Nikel PI, Pérez-Pantoja D, de Lorenzo V.

Environ Microbiol. 2019 Jan;21(1):314-326. doi: 10.1111/1462-2920.14459. Epub 2018 Dec 3.

PMID:
30362300
16.

A Post-translational Metabolic Switch Enables Complete Decoupling of Bacterial Growth from Biopolymer Production in Engineered Escherichia coli.

Durante-Rodríguez G, de Lorenzo V, Nikel PI.

ACS Synth Biol. 2018 Nov 16;7(11):2686-2697. doi: 10.1021/acssynbio.8b00345. Epub 2018 Oct 22.

PMID:
30346720
17.

The Metabolic Redox Regime of Pseudomonas putida Tunes Its Evolvability toward Novel Xenobiotic Substrates.

Akkaya Ö, Pérez-Pantoja DR, Calles B, Nikel PI, de Lorenzo V.

mBio. 2018 Aug 28;9(4). pii: e01512-18. doi: 10.1128/mBio.01512-18.

18.

Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non-traditional microorganisms.

Calero P, Nikel PI.

Microb Biotechnol. 2019 Jan;12(1):98-124. doi: 10.1111/1751-7915.13292. Epub 2018 Jun 21. Review.

19.

Pseudomonas putida as a functional chassis for industrial biocatalysis: From native biochemistry to trans-metabolism.

Nikel PI, de Lorenzo V.

Metab Eng. 2018 Nov;50:142-155. doi: 10.1016/j.ymben.2018.05.005. Epub 2018 May 16. Review.

20.

Re-Factoring Glycolytic Genes for Targeted Engineering of Catabolism in Gram-Negative Bacteria.

Sánchez-Pascuala A, Nikel PI, de Lorenzo V.

Methods Mol Biol. 2018;1772:3-24. doi: 10.1007/978-1-4939-7795-6_1.

PMID:
29754220
21.

Assessing Carbon Source-Dependent Phenotypic Variability in Pseudomonas putida.

Nikel PI, de Lorenzo V.

Methods Mol Biol. 2018;1745:287-301. doi: 10.1007/978-1-4939-7680-5_16.

PMID:
29476475
22.

Bioremediation 3.0: Engineering pollutant-removing bacteria in the times of systemic biology.

Dvořák P, Nikel PI, Damborský J, de Lorenzo V.

Biotechnol Adv. 2017 Nov 15;35(7):845-866. doi: 10.1016/j.biotechadv.2017.08.001. Epub 2017 Aug 5. Review.

PMID:
28789939
23.

A New Player in the Biorefineries Field: Phasin PhaP Enhances Tolerance to Solvents and Boosts Ethanol and 1,3-Propanediol Synthesis in Escherichia coli.

Mezzina MP, Álvarez DS, Egoburo DE, Díaz Peña R, Nikel PI, Pettinari MJ.

Appl Environ Microbiol. 2017 Jun 30;83(14). pii: e00662-17. doi: 10.1128/AEM.00662-17. Print 2017 Jul 15.

24.

Refactoring the Embden-Meyerhof-Parnas Pathway as a Whole of Portable GlucoBricks for Implantation of Glycolytic Modules in Gram-Negative Bacteria.

Sánchez-Pascuala A, de Lorenzo V, Nikel PI.

ACS Synth Biol. 2017 May 19;6(5):793-805. doi: 10.1021/acssynbio.6b00230. Epub 2017 Feb 9.

25.

A Metabolic Widget Adjusts the Phosphoenolpyruvate-Dependent Fructose Influx in Pseudomonas putida.

Chavarría M, Goñi-Moreno Á, de Lorenzo V, Nikel PI.

mSystems. 2016 Dec 6;1(6). pii: e00154-16. eCollection 2016 Nov-Dec.

26.

Engineering Gram-Negative Microbial Cell Factories Using Transposon Vectors.

Martínez-García E, Aparicio T, de Lorenzo V, Nikel PI.

Methods Mol Biol. 2017;1498:273-293.

PMID:
27709582
27.

Unexpected functions of automatically annotated genes: a lesson learnt from Bacillus subtilis.

Nikel PI.

Environ Microbiol. 2017 Jan;19(1):5-6. doi: 10.1111/1462-2920.13495. Epub 2016 Aug 26. No abstract available.

PMID:
27511628
28.

Pyridine nucleotide transhydrogenases enable redox balance of Pseudomonas putida during biodegradation of aromatic compounds.

Nikel PI, Pérez-Pantoja D, de Lorenzo V.

Environ Microbiol. 2016 Oct;18(10):3565-3582. doi: 10.1111/1462-2920.13434. Epub 2016 Jul 24.

29.

From dirt to industrial applications: Pseudomonas putida as a Synthetic Biology chassis for hosting harsh biochemical reactions.

Nikel PI, Chavarría M, Danchin A, de Lorenzo V.

Curr Opin Chem Biol. 2016 Oct;34:20-29. doi: 10.1016/j.cbpa.2016.05.011. Epub 2016 May 27. Review.

30.

Quantifying the Relative Importance of Phylogeny and Environmental Preferences As Drivers of Gene Content in Prokaryotic Microorganisms.

Tamames J, Sánchez PD, Nikel PI, Pedrós-Alió C.

Front Microbiol. 2016 Mar 31;7:433. doi: 10.3389/fmicb.2016.00433. eCollection 2016.

31.

The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis.

Belda E, van Heck RG, José Lopez-Sanchez M, Cruveiller S, Barbe V, Fraser C, Klenk HP, Petersen J, Morgat A, Nikel PI, Vallenet D, Rouy Z, Sekowska A, Martins Dos Santos VA, de Lorenzo V, Danchin A, Médigue C.

Environ Microbiol. 2016 Oct;18(10):3403-3424. doi: 10.1111/1462-2920.13230. Epub 2016 Apr 28.

PMID:
26913973
32.

Data on the standardization of a cyclohexanone-responsive expression system for Gram-negative bacteria.

Benedetti I, Nikel PI, de Lorenzo V.

Data Brief. 2016 Jan 22;6:738-44. doi: 10.1016/j.dib.2016.01.022. eCollection 2016 Mar.

33.

Exacerbation of substrate toxicity by IPTG in Escherichia coli BL21(DE3) carrying a synthetic metabolic pathway.

Dvorak P, Chrast L, Nikel PI, Fedr R, Soucek K, Sedlackova M, Chaloupkova R, de Lorenzo V, Prokop Z, Damborsky J.

Microb Cell Fact. 2015 Dec 21;14:201. doi: 10.1186/s12934-015-0393-3.

34.

Genetic programming of catalytic Pseudomonas putida biofilms for boosting biodegradation of haloalkanes.

Benedetti I, de Lorenzo V, Nikel PI.

Metab Eng. 2016 Jan;33:109-118. doi: 10.1016/j.ymben.2015.11.004. Epub 2015 Nov 24.

PMID:
26620533
35.

Polyhydroxyalkanoates: Much More than Biodegradable Plastics.

López NI, Pettinari MJ, Nikel PI, Méndez BS.

Adv Appl Microbiol. 2015;93:73-106. doi: 10.1016/bs.aambs.2015.06.001. Epub 2015 Jul 14. Review.

PMID:
26505689
36.

The CreC Regulator of Escherichia coli, a New Target for Metabolic Manipulations.

Godoy MS, Nikel PI, Cabrera Gomez JG, Pettinari MJ.

Appl Environ Microbiol. 2015 Oct 23;82(1):244-54. doi: 10.1128/AEM.02984-15. Print 2016 Jan 1.

37.

Pseudomonas putida mt-2 tolerates reactive oxygen species generated during matric stress by inducing a major oxidative defense response.

Svenningsen NB, Pérez-Pantoja D, Nikel PI, Nicolaisen MH, de Lorenzo V, Nybroe O.

BMC Microbiol. 2015 Oct 6;15:202. doi: 10.1186/s12866-015-0542-1.

38.

The RNA chaperone Hfq enables the environmental stress tolerance super-phenotype of Pseudomonas putida.

Arce-Rodríguez A, Calles B, Nikel PI, de Lorenzo V.

Environ Microbiol. 2016 Oct;18(10):3309-3326. doi: 10.1111/1462-2920.13052. Epub 2015 Dec 2.

PMID:
26373442
39.

Pseudomonas putida KT2440 Strain Metabolizes Glucose through a Cycle Formed by Enzymes of the Entner-Doudoroff, Embden-Meyerhof-Parnas, and Pentose Phosphate Pathways.

Nikel PI, Chavarría M, Fuhrer T, Sauer U, de Lorenzo V.

J Biol Chem. 2015 Oct 23;290(43):25920-32. doi: 10.1074/jbc.M115.687749. Epub 2015 Sep 8.

40.

Genome reduction boosts heterologous gene expression in Pseudomonas putida.

Lieder S, Nikel PI, de Lorenzo V, Takors R.

Microb Cell Fact. 2015 Feb 21;14:23. doi: 10.1186/s12934-015-0207-7.

41.

The glycerol-dependent metabolic persistence of Pseudomonas putida KT2440 reflects the regulatory logic of the GlpR repressor.

Nikel PI, Romero-Campero FJ, Zeidman JA, Goñi-Moreno Á, de Lorenzo V.

mBio. 2015 Mar 31;6(2). pii: e00340-15. doi: 10.1128/mBio.00340-15.

42.

New transposon tools tailored for metabolic engineering of gram-negative microbial cell factories.

Martínez-García E, Aparicio T, de Lorenzo V, Nikel PI.

Front Bioeng Biotechnol. 2014 Oct 28;2:46. doi: 10.3389/fbioe.2014.00046. eCollection 2014.

43.

Pseudomonas 2.0: genetic upgrading of P. putida KT2440 as an enhanced host for heterologous gene expression.

Martínez-García E, Nikel PI, Aparicio T, de Lorenzo V.

Microb Cell Fact. 2014 Nov 11;13:159. doi: 10.1186/s12934-014-0159-3.

44.

Biotechnological domestication of pseudomonads using synthetic biology.

Nikel PI, Martínez-García E, de Lorenzo V.

Nat Rev Microbiol. 2014 May;12(5):368-79. doi: 10.1038/nrmicro3253. Review.

45.

Robustness of Pseudomonas putida KT2440 as a host for ethanol biosynthesis.

Nikel PI, de Lorenzo V.

N Biotechnol. 2014 Dec 25;31(6):562-71. doi: 10.1016/j.nbt.2014.02.006. Epub 2014 Feb 23.

46.

The private life of environmental bacteria: pollutant biodegradation at the single cell level.

Nikel PI, Silva-Rocha R, Benedetti I, de Lorenzo V.

Environ Microbiol. 2014 Mar;16(3):628-42. doi: 10.1111/1462-2920.12360. Epub 2014 Jan 16. Review.

47.

Transcriptomic fingerprinting of Pseudomonas putida under alternative physiological regimes.

Kim J, Oliveros JC, Nikel PI, de Lorenzo V, Silva-Rocha R.

Environ Microbiol Rep. 2013 Dec;5(6):883-91. doi: 10.1111/1758-2229.12090. Epub 2013 Sep 5.

48.

The metabolic cost of flagellar motion in Pseudomonas putida KT2440.

Martínez-García E, Nikel PI, Chavarría M, de Lorenzo V.

Environ Microbiol. 2014 Jan;16(1):291-303. doi: 10.1111/1462-2920.12309. Epub 2013 Nov 18.

49.

Endogenous stress caused by faulty oxidation reactions fosters evolution of 2,4-dinitrotoluene-degrading bacteria.

Pérez-Pantoja D, Nikel PI, Chavarría M, de Lorenzo V.

PLoS Genet. 2013 Aug;9(8):e1003764. doi: 10.1371/journal.pgen.1003764. Epub 2013 Aug 29.

50.

Metabolic and regulatory rearrangements underlying glycerol metabolism in Pseudomonas putida KT2440.

Nikel PI, Kim J, de Lorenzo V.

Environ Microbiol. 2014 Jan;16(1):239-54. doi: 10.1111/1462-2920.12224. Epub 2013 Aug 22.

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