| 11. |
- Maury, J., et al.
(author)
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Reconstruction of a bacterial isoprenoid biosynthetic pathway in Saccharomyces cerevisiae
- 2008
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In: FEBS Letters. - : Wiley. - 1873-3468 .- 0014-5793. ; 582:29, s. 4032-4038
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Journal article (peer-reviewed)abstract
- A eukaryotic mevalonate pathway transferred and expressed in Escherichia coli, and a mammalian hydrocortisone biosynthetic pathway rebuilt in Saccharomyces cerevisiae are examples showing that transferring metabolic pathways from one organism to another can have a powerful impact on cell properties. In this study, we reconstructed the E. coli isoprenoid biosynthetic pathway in S. cerevisiae. Genes encoding the seven enzymatic steps of the pathway were cloned and expressed in S. cerevisiae. mRNA from the seven genes was detected, and the pathway was shown able to sustain growth of yeast in conditions of inhibition of its constitutive isoprenoid biosynthetic pathway. © 2008 Federation of European Biochemical Societies.
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| 12. |
- Otero, José Manuel, 1979, et al.
(author)
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Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications
- 2010
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In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 11:1, s. 723-
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Journal article (peer-reviewed)abstract
- Background: The need for rapid and efficient microbial cell factory design and construction are possible through the enabling technology, metabolic engineering, which is now being facilitated by systems biology approaches. Metabolic engineering is often complimented by directed evolution, where selective pressure is applied to a partially genetically engineered strain to confer a desirable phenotype. The exact genetic modification or resulting genotype that leads to the improved phenotype is often not identified or understood to enable further metabolic engineering.Results: In this work we performed whole genome high-throughput sequencing and annotation can be used to identify single nucleotide polymorphisms (SNPs) between Saccharomyces cerevisiae strains S288c and CEN.PK113-7D. The yeast strain S288c was the first eukaryote sequenced, serving as the reference genome for the Saccharomyces Genome Database, while CEN.PK113-7D is a preferred laboratory strain for industrial biotechnology research. A total of 13,787 high-quality SNPs were detected between both strains (reference strain: S288c). Considering only metabolic genes (782 of 5,596 annotated genes), a total of 219 metabolism specific SNPs are distributed across 158 metabolic genes, with 85 of the SNPs being nonsynonymous (e. g., encoding amino acid modifications). Amongst metabolic SNPs detected, there was pathway enrichment in the galactose uptake pathway (GAL1, GAL10) and ergosterol biosynthetic pathway (ERG8, ERG9). Physiological characterization confirmed a strong deficiency in galactose uptake and metabolism in S288c compared to CEN.PK113-7D, and similarly, ergosterol content in CEN.PK113-7D was significantly higher in both glucose and galactose supplemented cultivations compared to S288c. Furthermore, DNA microarray profiling of S288c and CEN.PK113-7D in both glucose and galactose batch cultures did not provide a clear hypothesis for major phenotypes observed, suggesting that genotype to phenotype correlations are manifested post-transcriptionally or post-translationally either through protein concentration and/or function.Conclusions: With an intensifying need for microbial cell factories that produce a wide array of target compounds, whole genome high-throughput sequencing and annotation for SNP detection can aid in better reducing and defining the metabolic landscape. This work demonstrates direct correlations between genotype and phenotype that provides clear and high-probability of success metabolic engineering targets. The genome sequence, annotation, and a SNP viewer of CEN.PK113-7D are deposited at http://www.sysbio.se/cenpk.
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| 13. |
- Frieler, Katja, et al.
(author)
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Scenario setup and forcing data for impact model evaluation and impact attribution within the third round of the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP3a)
- 2024
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In: Geoscientific Model Development. - : Copernicus Publications. - 1991-959X .- 1991-9603. ; 17:1, s. 1-51
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Journal article (peer-reviewed)abstract
- This paper describes the rationale and the protocol of the first component of the third simulation round of the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP3a, http://www.isimip.org, last access: 2 November 2023) and the associated set of climate-related and direct human forcing data (CRF and DHF, respectively). The observation-based climate-related forcings for the first time include high-resolution observational climate forcings derived by orographic downscaling, monthly to hourly coastal water levels, and wind fields associated with historical tropical cyclones. The DHFs include land use patterns, population densities, information about water and agricultural management, and fishing intensities. The ISIMIP3a impact model simulations driven by these observation-based climate-related and direct human forcings are designed to test to what degree the impact models can explain observed changes in natural and human systems. In a second set of ISIMIP3a experiments the participating impact models are forced by the same DHFs but a counterfactual set of atmospheric forcings and coastal water levels where observed trends have been removed. These experiments are designed to allow for the attribution of observed changes in natural, human, and managed systems to climate change, rising CH4 and CO2 concentrations, and sea level rise according to the definition of the Working Group II contribution to the IPCC AR6.
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| 14. |
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| 15. |
- Maury, J., et al.
(author)
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Metabolic engineering of isoprenoid production: Reconstruction of multistep heterologous pathways in tractable hosts
- 2013
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In: Isoprenoid Synthesis in Plants and Microorganisms: New Concepts and Experimental Approaches. - New York, NY : Springer New York. - 9781461440635 ; , s. 73-89
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Book chapter (other academic/artistic)abstract
- Isoprenoids represent a wide group of chemically active compounds that can find a wide range of applications as flavors, perfumes, vitamins, nutraceuticals, and pharmaceuticals. Many isoprenoids are naturally produced in very low quantities by plants, which make their use in broader perspectives difficult. Microbial production of plant-originating isoprenoids quickly appeared as an alternative of choice. Metabolic engineering methods were applied and proved successful to improve the supply of precursors to derive toward isoprenoid compounds of interest. Combinations between metabolic engineering and the flourishing field of synthetic biology have also been observed with researchers attempting to reconstruct and optimize complex biosynthetic pathways in well-characterized and tractable microbial hosts. In this chapter, we review recent metabolic engineering studies for isoprenoid production in yeast and try to show, through key examples, that the fields of synthetic biology and metabolic engineering can go hand in hand to establish microbial cell factories for isoprenoid production.
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| 16. |
- Maury, O., et al.
(author)
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A global science-policy partnership for progress toward sustainability of oceanic ecosystems and fisheries
- 2013
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In: Current Opinion in Environmental Sustainability. - : Elsevier BV. - 1877-3435 .- 1877-3443. ; 5:3-4, s. 314-319
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Research review (peer-reviewed)abstract
- Oceanic ecosystems support livelihoods and supply food for hundreds of millions of people. But these ecosystems are deteriorating rapidly and many of the world's oceanic fisheries are in a precarious condition. In addition to well-known and pressing fishery management issues, economic globalization is connecting fisheries beyond the frontiers of the organizations responsible for their management and climate-associated changes are deeply modifying ecosystems, pushing them toward new states and no return situations. The status quo is not a sustainable option, and improved international governance is urgently needed to address this situation. Our proposition consists of an inclusive global science-policy process combining major improvements to the present governance systems, including new incentives for international cooperation and coordination, with an ambitious scientific program to help anticipate threats and opportunities and integrate complex information regarding long-term issues. It would constitute a major step toward sustainability.
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| 18. |
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