| 1. |
- Viglione, A., et al.
(författare)
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Insights from socio-hydrology modelling on dealing with flood risk - Roles of collective memory, risk-taking attitude and trust
- 2014
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Ingår i: Journal of Hydrology. - : Elsevier BV. - 0022-1694 .- 1879-2707. ; 518:A, s. 71-82
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Tidskriftsartikel (refereegranskat)abstract
- The risk coping culture of a community plays a major role in the development of urban floodplains. In this paper we analyse, in a conceptual way, the interplay of community risk coping culture, flooding damage and economic growth. We particularly focus on three aspects: (i) collective memory, i.e., the capacity of the community to keep risk awareness high; (ii) risk-taking attitude, i.e., the amount of risk the community is collectively willing to be exposed to; and (iii) trust of the community in risk reduction measures. To this end, we use a dynamic model that represents the feedback between the hydrological and social system components. Model results indicate that, on the one hand, by under perceiving the risk of flooding (because of short collective memory and too much trust in flood protection structures) in combination with a high risk-taking attitude, community development is severely limited because of high damages caused by flooding. On the other hand, overestimation of risk (long memory and lack of trust in flood protection structures) leads to lost economic opportunities and recession. There are many scenarios of favourable development resulting from a trade-off between collective memory and trust in risk reduction measures combined with a low to moderate risk-taking attitude. Interestingly, the model gives rise to situations in which the development of the community in the floodplain is path dependent, i.e., the history of flooding may lead to community growth or recession.
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| 2. |
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| 3. |
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| 4. |
- Di Baldassarre, Giuliano, et al.
(författare)
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Socio-hydrology : conceptualising human-flood interactions
- 2013
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Ingår i: Hydrology and Earth System Sciences. - : Copernicus GmbH. - 1027-5606 .- 1607-7938. ; 17:8, s. 3295-3303
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Tidskriftsartikel (refereegranskat)abstract
- Over history, humankind has tended to settle near streams because of the role of rivers as transportation corridors and the fertility of riparian areas. However, human settlements in floodplains have been threatened by the risk of flooding. Possible responses have been to resettle away and/or modify the river system by building flood control structures. This has led to a complex web of interactions and feedback mechanisms between hydrological and social processes in settled floodplains. This paper is an attempt to conceptualise these interplays for hypothetical human-flood systems. We develop a simple, dynamic model to represent the interactions and feedback loops between hydrological and social processes. The model is then used to explore the dynamics of the human-flood system and the effect of changing individual characteristics, including external forcing such as technological development. The results show that the conceptual model is able to reproduce reciprocal effects between floods and people as well as the emergence of typical patterns. For instance, when levees are built or raised to protect floodplain areas, their presence not only reduces the frequency of flooding, but also exacerbates high water levels. Then, because of this exacerbation, higher flood protection levels are required by society. As a result, more and more flooding events are avoided, but rare and catastrophic events take place.
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| 5. |
- Kuil, Teun, 1993-
(författare)
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Analysis and engineering of central metabolism in Clostridium thermocellum
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- To mitigate climate change, greenhouse gas emissions must be reduced to net-zero in 2050 requiring a drastic transition in today´s energy sector. To achieve this goal, the use of biofuels produced from lignocellulosic feedstocks, including agricultural and forestry residues, is expected to play an important role. The native ability of the anaerobic thermophile Clostridium thermocellum to efficiently degrade lignocellulose makes this microorganism a promising candidate for consolidated bioprocessing of lignocellulosic feedstocks into the biofuel ethanol. However, improvements in ethanol yield, titre, and tolerance are required for industrial implementation. The aim of this thesis was to increase understanding of the central metabolism of C. thermocellum and thereby aid future metabolic engineering and process optimization efforts focused on improving ethanol production from lignocellulosic material. The atypical glycolysis of C. thermocellum uses pyrophosphate (PPi) instead of ATP as phosphoryl donor. This alteration is hypothesized to increase energetic efficiency but simultaneously decrease thermodynamic driving force resulting in lower achievable ethanol titres. As such, improved understanding of the PPi metabolism has both fundamental and applied importance. Knockout studies combined with physiological characterization of four predicted metabolic PPi sources provided valuable insights into the PPi metabolism and demonstrated that the energetic benefits of PPi usage are likely limited. Furthermore, biochemical characterization of the ATP-Pfk from C. thermocellum and other bacteria demonstrated that PPi might be a key allosteric regulator in bacteria with a PPi-dependent glycolysis. The low thermodynamic driving force of the ethanol formation pathway combined with a flexible redox network are key factors that impact ethanol titre, yield, and tolerance in C. thermocellum. Apart from dominant thermodynamic limitations, physiological characterization of wild-type and a non-ethanol producing mutant at various exogenous ethanol concentrations and temperatures demonstrated that biophysical limitations also impact ethanol tolerance. Lowering the cultivation temperature decreased chaotropic effects of ethanol and improved ethanol tolerance. By-product formation and incomplete substrate utilization decrease obtained ethanol yields. To minimize formation of one specific class of by-products, the mechanism behind amino acid secretion in C. thermocellum was investigated. Cellobiose- or ammonium-limited chemostats of wild-type and knockout strains of NADPH-supplying and NADPH-consuming pathways identified catabolic oversupply of NADPH as the main driver behind amino acid secretion. The malate shunt and the ammonium-regulated shift between nitrogen assimilation pathways with differing cofactor specificities were shown to play key roles in NADPH metabolism and amino acid secretion. To improve substrate utilization, laboratory evolution combined with reverse metabolic engineering was used as a tool to provide insights into increased utilization of glucose and fructose. Reproducible and constitutive growth on these hexose sugars was achieved for evolved mutant strains. Additionally, two mutations were identified that are involved in (regulation of) transport or metabolism of these hexose sugars.Together these findings provide valuable insights into the central metabolism of C. thermocellum and aid future optimizations of this organism for consolidated bioprocessing of lignocellulosic feedstocks into fuels and chemicals.
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| 6. |
- Kuil, Teun, et al.
(författare)
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Ethanol tolerance of Clostridium thermocellum : the role of chaotropicity, temperature and pathway thermodynamics on growth and fermentative capacity
- 2022
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Ingår i: Microbial Cell Factories. - : Springer Nature. - 1475-2859 .- 1475-2859. ; 21:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundClostridium thermocellum is a promising candidate for consolidated bioprocessing of lignocellulosic biomass to ethanol. The low ethanol tolerance of this microorganism is one of the remaining obstacles to industrial implementation. Ethanol inhibition can be caused by end-product inhibition and/or chaotropic-induced stress resulting in increased membrane fluidization and disruption of macromolecules. The highly reversible glycolysis of C. thermocellum might be especially sensitive to end-product inhibition. The chaotropic effect of ethanol is known to increase with temperature. This study explores the relative contributions of these two aspects to investigate and possibly mitigate ethanol-induced stress in growing and non-growing C. thermocellum cultures.ResultsTo separate chaotropic from thermodynamic effects of ethanol toxicity, a non-ethanol producing strain AVM062 (P-clo1313_2638::ldh* adhE) was constructed by deleting the bifunctional acetaldehyde/alcohol dehydrogenase gene, adhE, in a lactate-overproducing strain. Exogenously added ethanol lowered the growth rate of both wild-type and the non-ethanol producing mutant. The mutant strain grew quicker than the wild-type at 50 and 55 degrees C for ethanol concentrations >= 10 g L-1 and was able to reach higher maximum OD600 at all ethanol concentrations and temperatures. For the wild-type, the maximum OD600 and relative growth rates were higher at 45 and 50 degrees C, compared to 55 degrees C, for ethanol concentrations >= 15 g L-1. For the mutant strain, no positive effect on growth was observed at lower temperatures. Growth-arrested cells of the wild-type demonstrated improved fermentative capacity over time in the presence of ethanol concentrations up to 40 g L-1 at 45 and 50 degrees C compared to 55 degrees C.ConclusionPositive effects of temperature on ethanol tolerance were limited to wild-type C. thermocellum and are likely related to mechanisms involved in the ethanol-formation pathway and redox cofactor balancing. Lowering the cultivation temperature provides an attractive strategy to improve growth and fermentative capacity at high ethanol titres in high-cellulose loading batch cultivations. Finally, non-ethanol producing strains are useful platform strains to study the effects of chaotropicity and thermodynamics related to ethanol toxicity and allow for deeper understanding of growth and/or fermentation cessation under industrially relevant conditions.
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| 7. |
- Kuil, Teun, et al.
(författare)
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Ethanol tolerance of Clostridium thermocellum: the role of chaotropicity, temperature and pathway thermodynamics on growth and fermentative capacity
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- BACKGROUND Clostridium thermocellum is a promising candidate for consolidated bioprocessing of lignocellulosic biomass to ethanol. The low ethanol tolerance of this microorganism is one of the remaining obstacles to industrial implementation. Ethanol inhibition can be caused by end-product inhibition and/or chaotropicinduced stress resulting in increased membrane uidization and disruption of macromolecules. The highly reversible glycolysis of C. thermocellum might be especially sensitive to end-product inhibition. The chaotropic effect of ethanol is known to increase with temperature. This study explores the relative contributions of these two aspects to investigate and possibly mitigate ethanol-induced stress in growing and non-growing C. thermocellum cultures.RESULTS To separate chaotropic from thermodynamic effects of ethanol toxicity, a non-ethanol producing strain AVM062 (Pclo1313_2638::ldh* ∆adhE) was constructed by deleting the bifunctional acetaldehyde/alcohol dehydrogenase gene, adhE, in a lactate-overproducing strain. Exogenously added ethanol lowered the growth rate of both wild-type and the non-ethanol producing mutant. The mutant strain grew quicker than the wild-type at 50 and 55 °C for ethanol concentrations ≥ 10 g L-1 and was able to reach higher maximum OD600 at all ethanol concentrations and temperatures. For the wild-type, the maximum OD600and relative growth rates were higher at 45 and 50 °C, compared to 55 °C, for ethanol concentrations ≥ 15 g L-1. For the mutant strain, no positive effect on growth was observed at lower temperatures. Growth-arrested cells of the wild-type demonstrated improved fermentative capacity over time in the presence of ethanol concentrations up to 40 g L-1 at 45 and 50 °C compared to 55 °C.CONCLUSION Positive effects of temperature on ethanol tolerance were limited to wild-type C. thermocellum and are likely related to mechanisms involved in the ethanol-formation pathway and redox cofactor balancing. Lowering the cultivation temperature provides an attractive strategy to improve growth and fermentative capacity at high ethanol titres in high-cellulose loading batch cultivations. Finally, non-ethanol producing strains are useful platform strains to study the effects of chaotropicity and thermodynamics related to ethanol toxicity and allow for deeper understanding of growth and/or fermentation cessation under industrially relevant conditions
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| 8. |
- Kuil, Teun, et al.
(författare)
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Functional Analysis of H+-Pumping Membrane-Bound Pyrophosphatase, ADP-Glucose Synthase, and Pyruvate Phosphate Dikinase as Pyrophosphate Sources in Clostridium thermocellum
- 2022
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Ingår i: Applied and Environmental Microbiology. - : American Society for Microbiology. - 0099-2240 .- 1098-5336. ; 88:4
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Tidskriftsartikel (refereegranskat)abstract
- The atypical glycolysis of Clostridium thermocellum is characterized by the use of pyrophosphate (PPi) as a phosphoryl donor for phosphofructokinase (Pfk) and pyruvate phosphate dikinase (Ppdk) reactions. Previously, biosynthetic PPi was calculated to be stoichiometrically insufficient to drive glycolysis. This study investigates the role of a H+-pumping membrane-bound pyrophosphatase, glycogen cycling, a predicted Ppdk-malate shunt cycle, and acetate cycling in generating PPi. Knockout studies and enzyme assays confirmed that clo1313_0823 encodes a membrane-bound pyrophosphatase. Additionally, clo1313_0717-0718 was confirmed to encode ADP-glucose synthase by knockouts, glycogen measurements in C. thermocellum, and heterologous expression in Escherichia coli. Unexpectedly, individually targeted gene deletions of the four putative PPi sources did not have a significant phenotypic effect. Although combinatorial deletion of all four putative PPi sources reduced the growth rate by 22% (0.30 +/- 0.01 h(-1)) and the biomass yield by 38% (0.18 +/- 0.00 g(biomass) g(substrate)-1), this change was much smaller than what would be expected for stoichiometrically essential PPi-supplying mechanisms. Growth-arrested cells of the quadruple knockout readily fermented cellobiose, indicating that the unknown PPi-supplying mechanisms are independent of biosynthesis. An alternative hypothesis that ATP-dependent Pfk activity circumvents a need for PPi altogether was falsified by enzyme assays, heterologous expression of candidate genes, and whole-genome sequencing. As a secondary outcome, enzymatic assays confirmed functional annotation of clo1313_1832 as ATP- and GTP-dependent fructokinase. These results indicate that the four investigated PPi sources individually and combined play no significant PPi-supplying role, and the true source(s) of PPi, or alternative phosphorylating mechanisms, that drive(s) glycolysis in C. thermocellum remain(s) elusive. IMPORTANCE Increased understanding of the central metabolism of C. thermocellum is important from a fundamental as well as from a sustainability and industrial perspective. In addition to showing that H+-pumping membrane-bound PPase, glycogen cycling, a Ppdk-malate shunt cycle, and acetate cycling are not significant sources of PPi supply, this study adds functional annotation of four genes and availability of an updated PP, stoichiometry from biosynthesis to the scientific domain. Together, this aids future metabolic engineering attempts aimed to improve C. thermocellum as a cell factory for sustainable and efficient production of ethanol from lignocellulosic material through consolidated bioprocessing with minimal pretreatment. Getting closer to elucidating the elusive source of PPi or alternative phosphorylating mechanisms, for the atypical glycolysis is itself of fundamental importance. Additionally, the findings of this study directly contribute to investigations into trade-offs between thermodynamic driving force versus energy yield of PPi and ATP-dependent glycolysis.
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| 9. |
- Kuil, Teun, et al.
(författare)
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Pyrophosphate as allosteric regulator of ATP-phosphofructokinase in Clostridium thermocellum and other bacteria with ATP- and PPi-phosphofructokinases
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The phosphofructokinase (Pfk) reaction represents one of the key regulatory points in glycolysis. While most organisms encode for Pfks that use ATP as phosphoryl donor, some organisms also encode for PPi-dependent Pfks. Despite this central role, the biochemical characteristics as well as the physiological role of both Pfks is often not known. Clostridium thermocellum is an example of a microorganism that encodes for both Pfks, however, only PPi-Pfk activity has been detected in cell-free extracts and little is known about the regulation and function of both enzymes. In this study, the ATP- and PPi-Pfk of C. thermocellum were purified and biochemically characterized. No allosteric regulators were found for PPi-Pfk amongst common effectors. With fructose-6-P, PPi, fructose-1,6-bisP, and Pi PPi-Pfk showed high specificity (KM < 0.62 mM) and activity (Vmax > 156 U mgprotein-1). In contrast, ATP-Pfk showed much lower affinity (K0.5 of 9.26 mM) and activity (14.5 U mgprotein-1) with fructose-6-P. In addition to ATP, also GTP, UTP and ITP could be used as phosphoryl donors. The catalytic efficiency with GTP was 7-fold higher than with ATP, suggesting that GTP is the preferred substrate. The enzyme was activated by NH4+, and pronounced inhibition was observed with GDP, FBP, PEP, and especially with PPi (Ki of 0.007 mM). Characterization of purified ATP-Pfks originating from eleven different bacteria, encoding for only ATP-Pfk or for both ATP- and PPi-Pfk, identified that PPi inhibition of ATP-Pfks could be a common phenomenon for organisms with a PPi-dependent glycolysis.
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| 10. |
- Kuil, Teun, et al.
(författare)
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Pyrophosphate as allosteric regulator of ATP-phosphofructokinase in Clostridium thermocellum and other bacteria with ATP- and PPi-phosphofructokinases
- 2023
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Ingår i: Archives of Biochemistry and Biophysics. - : Elsevier BV. - 0003-9861 .- 1096-0384. ; 743
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Tidskriftsartikel (refereegranskat)abstract
- The phosphofructokinase (Pfk) reaction represents one of the key regulatory points in glycolysis. While most organisms encode for Pfks that use ATP as phosphoryl donor, some organisms also encode for PPi-dependent Pfks. Despite this central role, the biochemical characteristics as well as the physiological role of both Pfks is often not known. Clostridium thermocellum is an example of a microorganism that encodes for both Pfks, however, only PPi-Pfk activity has been detected in cell-free extracts and little is known about the regulation and function of both enzymes. In this study, the ATP- and PPi-Pfk of C. thermocellum were purified and biochemically characterized. No allosteric regulators were found for PPi-Pfk amongst common effectors. With fructose-6-P, PPi, fructose-1,6-bisP, and Pi PPi-Pfk showed high specificity (KM < 0.62 mM) and maximum activity (Vmax > 156 U mg-1). In contrast, ATP-Pfk showed much lower affinity (K0.5 of 9.26 mM) and maximum activity (14.5 U mg-1) with fructose-6-P. In addition to ATP, also GTP, UTP and ITP could be used as phosphoryl donors. The catalytic efficiency with GTP was 7-fold higher than with ATP, suggesting that GTP is the preferred substrate. The enzyme was activated by NH4+, and pronounced inhibition was observed with GDP, FBP, PEP, and especially with PPi (Ki of 0.007 mM). Characterization of purified ATP-Pfks originating from eleven different bacteria, encoding for only ATP-Pfk or for both ATP- and PPi-Pfk, identified that PPi inhibition of ATP-Pfks could be a common phenomenon for organisms with a PPi-dependent glycolysis.
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