| 1. |
- Cheon, Seungwoo, et al.
(författare)
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Recent trends in metabolic engineering of microorganisms for the production of advanced biofuels
- 2016
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Ingår i: Current opinion in chemical biology. - : Elsevier. - 1367-5931 .- 1879-0402. ; 35, s. 10-21
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Tidskriftsartikel (refereegranskat)abstract
- As climate change has become one of the major global risks, our heavy dependence on petroleum-derived fuels has received much public attention. To solve such problems, production of sustainable fuels has been intensively studied over the past years. Thanks to recent advances in synthetic biology and metabolic engineering technologies, bio-based platforms for advanced biofuels production have been developed using various microorganisms. The strategies for production of advanced biofuels have converged upon four major metabolic routes: the 2-ketoacid pathway, the fatty acid synthesis (FAS) pathway, the isoprenoid pathway, and the reverse β-oxidation pathway. Additionally, the polyketide synthesis pathway has recently been attracting interest as a promising alternative biofuel production route. In this article, recent trends in advanced biofuels production are reviewed by categorizing them into three types of advanced biofuels: alcohols, biodiesel and jet fuel, and gasoline. Focus is given on the strategies of employing synthetic biology and metabolic engineering for the development of microbial strains producing advanced fuels. Finally, the prospects for future advances needed to achieve much more efficient bio-based production of advanced biofuels are discussed, focusing on designing advanced biofuel production pathways coupled with screening, modifying, and creating novel enzymes.
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| 2. |
- Fink, Michael J., et al.
(författare)
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Redesign of water networks for efficient biocatalysis
- 2017
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Ingår i: Current opinion in chemical biology. - : ELSEVIER SCI LTD. - 1367-5931 .- 1879-0402. ; 37, s. 107-114
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Forskningsöversikt (refereegranskat)abstract
- Herein we highlight recent findings on the importance of water networks in proteins, and their redesign and reconfiguration as a new engineering strategy to generate enzymes with modulated binding affinity and improved catalytic versatility. Traditionally, enzyme engineering and drug design have focused on tailoring direct and favorable interactions between protein surfaces and ligands/transition states to achieve stronger binding, or an accelerated manufacturing of medicines, biofuels, fine chemicals and materials. In contrast, the opportunity to relocate water molecules in solvated binding pockets by protein design to improve overall energetics remains essentially unexplored, and fundamental understanding of the elusive processes involved is poor. Rewiring water networks in protein interiors impacts binding affinity, catalysis and the thermodynamic signature of biochemical processes through dynamic mechanisms, and thus has great potential to enhance binding specificity, accelerate catalysis and provide new reaction mechanisms and chemistry, that were not yet explored in nature.
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| 3. |
- Gabelica, Valérie, et al.
(författare)
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Fundamentals of ion mobility spectrometry
- 2018
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Ingår i: Current opinion in chemical biology. - : Elsevier BV. - 1367-5931 .- 1879-0402. ; 42, s. 51-59
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Forskningsöversikt (refereegranskat)abstract
- Fundamental questions in ion mobility spectrometry have practical implications for analytical applications in general, and omics in particular, in three respects. (1) Understanding how ion mobility and collision cross section values depend on the collision gas, on the electric field and on temperature is crucial to ascertain their transferability across instrumental platforms. (2) Predicting collision cross section values for new analytes is necessary to exploit the full potential of ion mobility in discovery workflows. (3) Finally, understanding the fate of ion structures in the gas phase is essential to infer meaningful information on solution structures based on gas-phase ion mobility measurements. We review here the most recent advances in ion mobility fundamentals, relevant to these three aspects.
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| 4. |
- Mahecic, Dora, et al.
(författare)
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Strategies for increasing the throughput of super-resolution microscopies
- 2019
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Ingår i: Current opinion in chemical biology. - : ELSEVIER SCI LTD. - 1367-5931 .- 1879-0402. ; 51, s. 84-91
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Forskningsöversikt (refereegranskat)abstract
- Fluorescence microscopy methods have been developed to circumvent the diffraction limit by exploiting nonlinearities in the interactions between light and fluorophores. Initially, these methods were up to orders of magnitude slower than standard microscopies. In recent years, a wide array of technological advances have increased the throughput of super-resolution microscopies, through parallelization, smart scanning or data processing, and sample expansion. Here, we review re cent innovations for increased throughput, some applications that have benefitted from them, and how they could be improved in the future.
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| 5. |
- Meehan, Richard R., et al.
(författare)
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DNA methylation as a genomic marker of exposure to chemical and environmental agents
- 2018
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Ingår i: Current opinion in chemical biology. - : ELSEVIER SCI LTD. - 1367-5931 .- 1879-0402. ; 45, s. 48-56
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Forskningsöversikt (refereegranskat)abstract
- Recent progress in interpreting comprehensive genetic and epigenetic profiles for human cellular states has contributed new insights into the developmental origins of disease, elucidated novel signalling pathways and enhanced drug discovery programs. A similar comprehensive approach to decoding the epigenetic readouts from chemical challenges in vivo would yield new paradigms for monitoring and assessing environmental exposure in model systems and humans.
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| 6. |
- Wang, Jinfan, et al.
(författare)
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Ribosomal incorporation of unnatural amino acids : lessons and improvements from fast kinetics studies
- 2018
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Ingår i: Current opinion in chemical biology. - : Elsevier. - 1367-5931 .- 1879-0402. ; 46, s. 180-187
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Forskningsöversikt (refereegranskat)abstract
- Technologies for genetically programming ribosomal incorporation of unnatural amino acids are expanding and have created many exciting applications. However, these applications are generally limited by low efficiencies of the unnatural incorporations. Here we review our current mechanistic understanding of these limitations delineated from in vitro fast kinetics. Rate limitation occurs by different mechanisms, depending on the classes of the unnatural amino acids and the tRNA adaptors. This new understanding has led to several ways of improving the incorporation efficiencies, as well as challenges of dogma on rate-limiting steps in protein synthesis in natural cells.
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| 7. |
- Yung, PYK, et al.
(författare)
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Evolution of epigenetic chromatin states
- 2017
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Ingår i: Current opinion in chemical biology. - : Elsevier BV. - 1879-0402 .- 1367-5931. ; 41, s. 36-42
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Tidskriftsartikel (refereegranskat)
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| 8. |
- Poongavanam, Vasanthanathan, et al.
(författare)
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Opportunities and guidelines for discovery of orally absorbed drugs in beyond rule of 5 space
- 2018
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Ingår i: Current Opinion in Chemical Biology. - : Elsevier BV. - 1367-5931. ; 44, s. 23-29
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Forskningsöversikt (refereegranskat)abstract
- Recent years have seen a dramatic increase in the number of drugs approved in chemical space outside of Lipinski’s rule of 5, that is in what has been termed beyond rule of 5 (bRo5) space. The development of three major classes of oral drugs that treat HIV and HCV infections and the growing evidence that novel, difficult targets can be accessed has prompted research into understanding design of drugs displaying cell permeability, solubility and ultimately oral bioavailability in bRo5 space. Studies have found a consistent outer property limit for a reasonable chance of de novo designing oral bioavailability. In addition, several property-based guidelines, along with incorporation of chameleonic features, have emerged as strategies to aid design in bRo5 space. A more detailed understanding of the complex and environment dependent conformational landscape will likely be the focus of the next generation of guidelines allowing property predictions of ever more complex compounds. By pushing the boundaries of current orally designable chemical space we hope that discoveries will be made for fundamental science and also for discovery of novel therapeutics.
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