Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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Local fitness landscapes predict yeast evolutionary dynamics in directionally changing environments
Gorter, Florien A. ; Aarts, Mark G.M. ; Zwaan, Bas J. ; Visser, J.A.G.M. de - \ 2018
Genetics 208 (2018)1. - ISSN 0016-6731 - p. 307 - 322.
Experimental evolution - Fitness landscapes - Genotype-environment interaction - Predicting evolution - Saccharomyces cerevisiae
The fitness landscape is a concept that is widely used for understanding and predicting evolutionary adaptation. The topography of the fitness landscape depends critically on the environment, with potentially far-reaching consequences for evolution under changing conditions. However, few studies have assessed directly how empirical fitness landscapes change across conditions, or validated the predicted consequences of such change. We previously evolved replicate yeast populations in the presence of either gradually increasing, or constant high, concentrations of the heavy metals cadmium (Cd), nickel (Ni), and zinc (Zn), and analyzed their phenotypic and genomic changes. Here, we reconstructed the local fitness landscapes underlying adaptation to each metal by deleting all repeatedly mutated genes both by themselves and in combination. Fitness assays revealed that the height, and/or shape, of each local fitness landscape changed considerably across metal concentrations, with distinct qualitative differences between unconditionally (Cd) and conditionally toxic metals (Ni and Zn). This change in topography had particularly crucial consequences in the case of Ni, where a substantial part of the individual mutational fitness effects changed in sign across concentrations. Based on the Ni landscape analyses, we made several predictions about which mutations had been selected when during the evolution experiment. Deep sequencing of population samples from different time points generally confirmed these predictions, demonstrating the power of landscape reconstruction analyses for understanding and ultimately predicting evolutionary dynamics, even under complex scenarios of environmental change.
Genomics of adaptation depends on the rate of environmental change in experimental yeast populations
Gorter, F.A. ; Derks, M.F.L. ; Heuvel, J. van den; Aarts, M.G.M. ; Zwaan, B.J. ; Ridder, D. de; Visser, J.A.G.M. de - \ 2017
Molecular Biology and Evolution 34 (2017)10. - ISSN 0737-4038 - p. 2613 - 2626.
Keywords: Environmental Change, Experimental Evolution, Heavy Metals, Saccharomyces cerevisiae.
The rate of directional environmental change may have profound consequences for evolutionary dynamics and outcomes. Yet, most evolution experiments impose a sudden large change in the environment, after which the environment is kept constant. We previously cultured replicate Saccharomyces cerevisiae populations for 500 generations in the presence of either gradually increasing or constant high concentrations of the heavy metals cadmium, nickel, and zinc. Here, we investigate how each of these treatments affected genomic evolution. Whole genome sequencing of evolved clones revealed that adaptation occurred via a combination of SNPs, small indels, and whole genome duplications and other large-scale structural changes. In contrast to some theoretical predictions, gradual and abrupt environmental change caused similar numbers of genomic changes. For cadmium, which is toxic already at comparatively low concentrations, mutations in the same genes were used for adaptation to both gradual and abrupt increase in concentration. Conversely, for nickel and zinc, which are toxic at high concentrations only, mutations in different genes were used for adaptation depending on the rate of change. Moreover, evolution was more repeatable following a sudden change in the environment, particularly for nickel and zinc. Our results show that the rate of environmental change and the nature of the selection pressure are important drivers of evolutionary dynamics and outcomes, which has implications for a better understanding of societal problems such as climate change and pollution.
Evolution in changing environments : heavy metal adaptation in experimental yeast populations as a case study
Gorter, Florien A. - \ 2017
University. Promotor(en): Bas Zwaan, co-promotor(en): Arjan de Visser; Mark Aarts. - Wageningen : Wageningen University - ISBN 9789463430128 - 184

Directional environmental change in the form of global climate change and human-induced pollution is one of the most pressing problems facing society today. While species can sometimes adapt to such change by means of phenotypic plasticity and range shifts, there is considerable concern that these mechanisms are insufficient for long-term population persistence for at least some species. Evolutionary adaptation could potentially offer a solution, but it is unclear what the potential and limitations of this process are for populations exposed to deteriorating conditions. Specifically, we have limited knowledge about the factors promoting evolutionary population rescue, and we know even less about how directional change affects evolutionary dynamics and outcomes.

In this thesis, I investigated how the rate of directional environmental change affects evolutionary dynamics and outcomes using experimental evolution of heavy metal tolerance in the baker’s yeast Saccharomyces cerevisiae as a model system. Heavy metals are important pollutants that primarily originate from mining and industry and play a key role in both essential biological processes and toxicity due to their highly reactive chemical properties. While some of these metals, such as cadmium (Cd), lead (Pb), and mercury (Hg), are non-essential and have harmful effects even at low concentrations, others, such as manganese (Mn), iron (Fe), nickel (Ni), and zinc (Zn), are essential micronutrients for a wide range of organisms and are harmful only at high concentrations. Baker’s yeast is the most widely studied eukaryote model organism and shares numerous features with both plants and animals. Due to its short generation time, large population sizes, and readily manipulated genetics it is also used extensively in experimental evolution studies. In such studies, organisms are cultured under controlled conditions for many generations, mostly to study fundamental evolutionary questions, but increasingly also to characterize the evolutionary response of an organism to a particular selection pressure and thus increase insight into the genetic architecture of the trait under selection.

I cultured replicate populations of yeast for 500 generations in the presence of either gradually increasing or constant high concentrations of Cd, Ni, and Zn, and analysed the evolutionary response at the fitness (Chapter 2) and genomic (Chapter 3) level. Additionally, I generated several mutants carrying various combinations of mutations based on the genomic information from Chapter 3, and determined their fitness at different metal concentrations (Chapter 4). I used these data to address a number of hypotheses, which were based on a genotype-by-environment (GxE) framework that I developed to aid my thinking about evolution in changing environments. This framework is based on the concept of the fitness landscape, and distinguishes between two general patterns of change in landscape topography across conditions. Magnitude GxE refers to the case where the height of the fitness landscape increases along an environmental gradient, while its shape remains roughly constant. This implies that the fitness ranking of genotypes is the same at all concentrations, but that fitness differences between genotypes are larger at high metal concentrations. This scenario predicts that the same mutations will be selected under gradual and abrupt change, but that adaptation will be delayed under gradual change. By contrast, reranking GxE refers to the case where the shape of the fitness landscape changes along an environmental gradient. This implies that the fitness ranking of genotypes changes across metal concentrations. This scenario predicts that different mutations will be selected under gradual and abrupt change, and that adaptation will be delayed under gradual change. Moreover, it predicts different evolutionary outcomes following gradual and abrupt change, and lower repeatability of evolution under gradual change.

I anticipated that the relative importance of magnitude and reranking GxE would depend on the nature of the stressor. That is, I expected that magnitude GxE would be more important for the non-essential metal Cd, because in that case the same evolutionary solution — minimizing internal Cd concentrations — should be favoured at all concentrations, but more strongly so at high concentrations. This is consistent with directional selection with increasing intensity. On the other hand, for the presumably essential metals Ni and Zn, I expected the reranking GxE scenario to be more important, because in these cases different evolutionary solutions should be favoured at different external metal concentrations to maintain a constant internal metal concentration. This is consistent with stabilizing selection to maintain low, but non-zero intracellular metal concentrations.

My results provide support for these hypotheses at several levels. In Chapter 2, I determined relative fitness of populations isolated at different time points from the evolution experiment in the presence of different concentrations of the selective metal. These phenotypic assays showed that for Cd, the fitness ranking of isolates was the same at all metal concentrations, but that fitness differences were larger at high concentrations. Conversely, for Ni and Zn, the fitness ranking of isolates changed across metal concentrations. For all metals, this resulted in a delay in fitness increase under gradual relative to abrupt change. However, fitness of evolved populations from the final time point of the experiment was the same following gradual and abrupt change.

In Chapter 3, I performed whole-genome sequence analysis on a single clone isolated from each replicate population at the final time point of the evolution experiment. This revealed that adaptation to the selective environments occurred via a complex combination of SNPs, small indels, whole-genome duplications, and other large-scale structural changes. Furthermore, these analyses confirmed the phenotypic results of Chapter 2 and showed that for Cd, mutations in the same genes were selected under gradual and abrupt change, whereas for Ni and Zn, mutations in different genes were selected in response to different rates of environmental change. Additionally, I found that evolution was less repeatable at the genomic level following gradual change in the case of Ni and Zn, as predicted by my GxE framework.

Finally, in Chapter 4, I reconstructed local fitness landscapes for each metal by deleting all repeatedly mutated genes — as identified by whole genome sequencing — both by themselves and in combination. I used deletions because most mutations that I found in the evolved lineages were predicted to result in loss of function. Fitness assays on these landscapes at different metal concentrations were then used to evaluate how the height and shape of each landscape changed as a function of concentration. For Cd, I found that the height, but not the shape, of the landscape changed across concentrations. Conversely, for Ni, the shape of the landscape changed considerably across concentrations, and I made predictions about the consequences that this likely had for the selective dynamics of mutations in my evolution experiment. Deep sequencing of evolved population samples from different time points supported these predictions, demonstrating the power of landscape reconstruction approaches for understanding evolutionary dynamics.

Taken together, this multi-level evidence makes a strong case for the usefulness of my GxE framework for understanding evolution in changing environments. Moreover, my results confirm that the rate of environmental change and the nature of the selection pressure can have crucial consequences for the types and selective dynamics of the mutations that are used for adaptation. These findings imply that if we are to fully understand and anticipate the consequences of important societal problems such as climate change and pollution, we need to take into account not only the total magnitude of the projected change, but also its rate.

My results are explained remarkably well by the GxE framework that I developed, which captures some of the generic principles that determine how local fitness landscapes may change across environments. This framework can be readily extended to other selection pressures and scenarios of change. Therefore, my work provides a potentially useful basis for future studies aimed at understanding evolution in changing environments. Although some of the specifics of my model system and experimental approach preclude a straightforward extrapolation of my results to smaller populations of larger organisms, there are in fact more parallels between evolution under both these settings than may seem obvious. While microbial laboratory evolution experiments make simplifying assumptions about reality, it is exactly for this reason that they capture the essence of adaptation to directionally changing environments in a thus far unmatched manner.

Biofuel policies and the impact of developing countries' policy responses to the 2007-2008 food price boom
Gorter, Harry de; Drabik, D. - \ 2016
Global Food Security 11 (2016). - ISSN 2211-9124 - p. 64 - 71.
Developing countries - Food prices - Biofuel policies - Policy response
Economists have been unanimous that developing countries’ policy responses to high food grain prices in 2007–2008 in restricting exports and promoting imports increased both world food grain price levels and volatility. Furthermore, the literature emphasizes the self-defeating aspects of policy responses: world prices increase even further, thereby raising domestic prices in countries imposing policies to protect domestic consumers. We show that because of the crop-biofuel price linkages that took hold in 2007 caused by biofuel policies, developing countries’ policy responses had little impact on world prices in 2008 and maximum impact in reducing domestic price in developing countries. There is little empirical evidence of a policy responses increasing world prices. Instead, the incidence of those developing countries with policy responses were mostly in reducing domestic prices while those countries that did not respond (including all developed countries) faced high world prices locked onto crude oil prices and unaffected by policy responses. Given that most studies on developing countries’ policy response analyze the impacts on poverty in developing countries, this paper has important policy implications, especially food security analysis which now requires understanding how biofuel policies impact food commodity prices.
Producing biodiesel from soybeans in Zambia : An economic analysis
Drabik, Dusan ; Gorter, Harry de; Timilsina, Govinda R. - \ 2016
Food Policy 59 (2016). - ISSN 0306-9192 - p. 103 - 109.
Biodiesel - Biofuel policy - Biofuels - Soybean - Sub-Saharan Africa - Zambia

Facing a huge fiscal burden due to imports of its entire petroleum demand in the face of ample supply of agricultural land to produce biofuels, Zambia has recently introduced a biofuel mandate. However, a number of questions, particularly those related to the economics of biofuels, have not been fully investigated yet. Using an empirical model, this study analyzes the economics of meeting the biodiesel mandate using soybean oil. The study finds that meeting the biodiesel mandate would reduce social welfare, mainly because of the welfare loss to fuel consumers and net reduction in foreign exchange earnings due to soybean oil imports. However, if Zambia increases its domestic soybean supply, as well as oil yield, soybean-based biodiesel is likely to be welfare-beneficial. The country's welfare is found to be the highest under expanded soybean production and its domestic processing but with no biodiesel mandate.

Dynamics of adaptation in experimental yeast populations exposed to gradual and abrupt change in heavy metal concentration
Gorter, F.A. ; Aarts, M.M.G. ; Zwaan, B.J. ; Visser, Arjan de - \ 2016
American Naturalist 187 (2016)1. - ISSN 0003-0147 - p. 110 - 119.
Environmental change - Experimental evolution - Genotype-environment interaction - Heavy metals - Pleiotropy - Saccharomyces cerevisiae

Directional environmental change is a ubiquitous phe-nomenon that may have profound effects on all living organisms. However, it is unclear how different rates of such change affect the dynamics and outcome of evolution. We studied this question using experimental evolution of heavy metal tolerance in the baker’s yeast Saccharomyces cerevisiae. To this end, we grew replicate lines of yeast for 500 generations in the presence of (1) a constant high concentration of cadmium, nickel, or zinc or (2) a gradually increas-ing concentration of these metals. We found that gradual environ-mental change leads to a delay in fitness increase compared with abrupt change but not necessarily to a different fitness of evolution-ary endpoints. For the nonessential metal cadmium, this delay is due to reduced fitness differences between genotypes at low metal con-centrations, consistent with directional selection to minimize intra-cellular concentrations of this metal. In contrast, for the essential metals nickel and zinc, different genotypes are selected at different concentrations, consistent with stabilizing selection to maintain con-stant intracellular concentrations of these metals. These findings in-dicate diverse fitness consequences of evolved tolerance mechanisms for essential and nonessential metals and imply that the rate of en-vironmental change and the nature of the stressor are crucial deter-minants of evolutionary dynamics.

Dynamics of adaptation in experimental yeast populations exposed to gradual and abrupt change in heavy metal concentration
Gorter, Florien ; Aarts, Mark ; Zwaan, B.J. ; Visser, J.A.G.M. de - \ 2015
adaptation - ecology - evolutionary - microbial - Environmental variability - evolution - fitness - genetics - population - dynamics - fungi - heavy metals - pleiotropy
Directional environmental change is a ubiquitous phenomenon that may have profound effects on all living organisms. However, it is unclear how different rates of such change affect the dynamics and outcome of evolution. We studied this question using experimental evolution of heavy metal tolerance in the baker´s yeast Saccharomyces cerevisiae. To this end, we grew replicate lines of yeast for 500 generations in the presence of (i) a constant high concentration of cadmium, nickel or zinc, or (ii) a gradually increasing concentration of these metals. We found that gradual environmental change leads to a delay in fitness increase compared to abrupt change, but not necessarily to a different fitness of evolutionary endpoints. For the non-essential metal cadmium this delay is due to reduced fitness differences between genotypes at low metal concentrations, consistent with directional selection to minimize intracellular concentrations of this metal. In contrast, for the essential metals nickel and zinc different genotypes are selected at different concentrations, consistent with stabilizing selection to maintain constant intracellular concentrations of these metals. These findings indicate diverse fitness consequences of evolved tolerance mechanisms for essential and non-essential metals, and imply that the rate of environmental change and the nature of the stressor are crucial determinants of evolutionary dynamics.
The distinct economic effects of the ethanol blend wall, RIN prices and ethanol price premium due to the RFS
Gorter, H. de; Drabik, D. - \ 2015
Cornell University (Working paper Dyson School of Applied Economics and Management WP 2015-11) - 40 p.
RIN prices, blend wall, blend mandate price permium, E85 ethanol
The ethanol blend wall and high RIN prices has become a controversial policy issue. We develop a model showing how RIN prices reflect the costs of overcoming the blend wall, namely biodiesel consumed in excess of its mandate and expansion of E85 sales. These costs are very high and are shown to be borne by producers and consumers of ethanol and gasoline. Although RIN prices
reduce consumer prices of ethanol in both the E10 and E85 blends, the net price of E10 rises because obligated parties, who are required to purchase RINs, recoup the cost by passing on higher gasoline prices to blenders. This tax on gasoline production to pay for the subsidy on all ethanol consumption and RIN prices are a means of payment for “excess” RINs that are required to pay for costs overcoming the blend wall.
Burkholder (2015) and EPA (2015) emphasize this first round subsidy that also increases ethanol market prices. But these papers downplay the overall increased costs of fuel to consumers due to RINs taxing gasoline producers, and the separate adverse market effects of a binding blend mandate. The latter has been missing in the debate where it is often implied that the RIN price represents the degree to which the ethanol mandate is binding. We show the RIN price represents the costs of overcoming the blend wall and the ethanol price premium due to the binding blend mandate reflects costs of the RFS itself.
Our model determines RIN prices, the costs of overcoming the blend wall and the relationship with the ethanol price premium due to the binding mandate. We use economic theory consistent with the reality of the RFS and its associated complexities. From our empirical simulations, we find RIN prices went up because of the costs of the blend wall. Increasing the mandate with a blend
wall caused E10 prices and market gasoline prices to increase, along with an increase in ethanol consumption and market prices. But ethanol and market prices would increase far more without a blend wall for the same increase in the mandated volume.
In addition to the costs of overcoming the blend wall, our analysis finds the cost of the mandate price premium for ethanol to fuel consumers is $53.7 billion between 2007 and 2014, and to consumers of crops (including animal agriculture) by $285.4 billion per year worldwide. Our model also obtains the result that the RFS of the 2007 EISA is infeasible with exponentially increasing volume mandates under two situations. First, the E85 price goes to zero with ever
increasing RIN prices. Second, when we assume costs of E85 sales expansion levels off at $2 per gallon with the ethanol price peaking and then slowly declines (with E85 and E10 consumption). This may explain why the EPA scaled back the RFS.
Parasite host range and the evolution of host resistance
Gorter, F.A. ; Hall, A.R. ; A., Buckling ; P.D., Scanlan - \ 2015
Journal of Evolutionary Biology 28 (2015)5. - ISSN 1010-061X - p. 1119 - 1130.
Parasite host range plays a pivotal role in the evolution and ecology of hosts
and the emergence of infectious disease. Although the factors that promote
host range and the epidemiological consequences of variation in host range
are relatively well characterized, the effect of parasite host range on host
resistance evolution is less well understood. In this study, we tested the
impact of parasite host range on host resistance evolution. To do so, we used
the host bacterium Pseudomonas fluorescens SBW25 and a diverse suite of coevolved
viral parasites (lytic bacteriophage Φ2) with variable host ranges
(defined here as the number of host genotypes that can be infected) as our
experimental model organisms. Our results show that resistance evolution
to coevolved phages occurred at a much lower rate than to ancestral phage
(approximately 50% vs. 100%), but the host range of coevolved phages did
not influence the likelihood of resistance evolution. We also show that the
host range of both single parasites and populations of parasites does not
affect the breadth of the resulting resistance range in a na€ıve host but that
hosts that evolve resistance to single parasites are more likely to resist other
(genetically) more closely related parasites as a correlated response. These
findings have important implications for our understanding of resistance
evolution in natural populations of bacteria and viruses and other host–parasite
combinations with similar underlying infection genetics, as well as the
development of phage therapy
The Economics of Biofuel Policies. Impacts on Price Volatility in Grain and Oilseed Markets
Gorter, H. de; Drabik, D. - \ 2015
New York (USA) : Palgrave Macmillan (Palgrave studies in agricultural economics and food policy ) - ISBN 9781137414847
agrarische economie - milieubeleid - biobrandstoffen - bio-energie - biomassa - energie - voedselprijzen - basisproducten - ethanolproductie - suikerriet - vluchtigheid - landbouwprijzen - agricultural economics - environmental policy - biofuels - bioenergy - biomass - energy - food prices - commodities - ethanol production - sugarcane - volatility - agricultural prices
The global food crises of 2008 and 2010 and the increased price volatility revolve around biofuels policies and their interaction with each other, farm policies and between countries. The Economics of Biofuel Policies focuses on the role of biofuel policies in creating turmoil in the world grains and oilseed markets since 2006. This book puts together theory and empirical evidence of how biofuel policies created a link between crop (food grains and oilseeds) and biofuel (ethanol and biodiesel) prices. This combined with biofuel policies role in affecting the link between biofuels and energy (gasoline, diesel and crude oil) prices will form the basis to show how alternative US, EU, and Brazilian biofuel policies have immense impacts on the level and volatility of food grain and oilseed prices.
The Economics of Brazil's Ethanol-Sugar Markets, Mandates, and Tax Exemptions
Drabik, D. ; Gorter, H. de; Just, D.R. ; Timilsina, G.R. - \ 2015
American Journal of Agricultural Economics 97 (2015)5. - ISSN 0002-9092 - p. 1433 - 1450.
Sugarcane in Brazil is processed into sugar and/or ethanol, often in flex plants that can switch between the two products. We develop an economic model of flex plants, export demands, and two domestic fuel demand curves for a blend of ethanol with gasoline consumed by conventional cars, and ethanol consumed only by flex cars. We analyze the market impacts of the following policies: the blend mandate; fixing gasoline prices below world prices; the high gasoline tax; and a higher tax exemption for ethanol blended with gasoline. Because Brazilian and U.S. ethanol prices have become linked, a change in Brazilian ethanol policy or a shock in world sugar markets can now impact U.S. ethanol and corn prices. We show that in theory, each policy analyzed has an ambiguous impact on ethanol and sugar prices. Empirically, however, a low gasoline tax and a high tax exemption for ethanol used in the fuel blend reduce ethanol and sugar prices; this contradicts conventional wisdom. Overall, we find that policy reforms implemented in 2010 offset the ethanol price increase by about 27% due to outward shifts in fuel transportation and sugar export demand curves, and due to a reduced sugarcane supply caused by bad weather. Our model illustrates the importance of Brazil's ethanol policies on world commodity markets; it also provides insight into how the Brazilian government can adjust policies to better control domestic inflation while minimizing impacts on investment.
The Role of Biofuel Policies on Grain and Oilseed Prices
Gorter, H. de; Drabik, D. ; Kliauga, E.M. - \ 2014
In: Trade Policy and Food Security; Improving Access to Food in Developing Countries in the Wake of High World Prices / Gillson, I., Fouad, A., Washington DC, USA : World Bank Group - ISBN 9781464803055 - p. 37 - 63.






Based on forecasts of global population growth, food security will remain an important economic development issue over the next several decades. In addition, real food prices have risen in recent years after decades of decline, bringing the issue of food security even further into the public spotlight. However, there is no global food shortage: the problem is one of moving food, often across borders, from surplus production areas to deficit ones at prices that low-income consumers in developing countries can afford. Trade can be an excellent buffer for domestic fluctuations in food supply. World output of a given food commodity is far less variable than output in individual countries so increased trade integration holds considerable potential to stabilize food prices, boost returns to farmers and reduce the prices faced by consumers. Trade liberalization protects national food markets against domestic shocks by allowing more food to be imported in times of shortage and exported in periods of plenty. Historically, however, most countries have chosen to take the opposite approach by restricting imports of food and discouraging exports to keep domestic markets isolated from international shocks. Food commodity markets, therefore, remain highly distorted despite the wave of liberalization that has swept world trade since the 1980s. In addition to examining the determinants of recent food price spikes, Trade Policy and Food Security explores the impact of food prices on economic welfare, and how the effect of price changes on food security and economic welfare in developing countries can be mitigated through appropriate national policies at the border. It highlights the importance of both the extension and continued application of existing WTO disciplines on trade-distorting agricultural trade policies as a key resolution to the collective action problem witnessed during the recent food price spikes, whereby unilateral border policies—especially export controls—simply exacerbated the initial price increases.
An economic model of the fuel-ethanol-sugar complex in Zimbabwe
Drabik, D. ; Gorter, H. de; Timilsina, G.R. - \ 2014
In: Book of Abstracts of the 18th ICABR Conference. - Nairobi, Kenya : AATF - p. 33 - 33.
An Economic Model of Brazil’s Ethanol-Sugar Markets and Impacts of Fuel Policies
Drabik, D. ; Gorter, H. de; Just, D.R. ; Timilsina, G.R. - \ 2014
We develop an economic model of flex plants, export demands and two domestic fuel demand curves: E25, a 25 percent blend of ethanol with gasoline consumed by conventional cars, and E100, ethanol consumed only by flex cars. This allows us to analyze the market impacts of specific policies, namely the E25 blend mandate, fixing gasoline prices below world prices, the high gasoline tax, and a higher tax exemption for ethanol used in E25. Because Brazilian and U.S. ethanol prices have become linked, a change in Brazilian ethanol policy or a shock in world sugar markets can now impact U.S. ethanol and corn prices. Because of two demand curves, with flex car owners switching between fuels depending on relative prices, and because the mandate is for E25 only, the impact of each Brazilian policy in theory has an ambiguous impact on ethanol and sugar prices. Conventional wisdom is that a higher level of the mandate, gasoline tax exemptions for ethanol and gasoline price, and a lower gasoline tax, all help the ethanol industry. But for two policies, a low gasoline tax and a high tax exemption for ethanol used in E25, our empirical results show ethanol and sugar prices decline. Overall, we find that the package of policy reforms implemented in 2010 offset the ethanol price increase due outward shifts in fuel transportation and sugar export demand curves, and reduced sugarcane supply due to bad weather, by about 27 percent. Our model illustrates the importance of Brazil’s ethanol policies on world commodity markets and provides insights on how the Brazilian government can adjust policies to better control domestic inflation while minimizing impacts on investment.
Socioeconomic Issues and Biofuel Energy
Gorter, H. de; Drabik, D. - \ 2014
In: Our Energy Future: Socioeconomics Implications and Policy Options for Rural America / Albrecht, D.E., New York : Routledge (Routledge Studies in Energy Policy ) - ISBN 9781138784116 - p. 102 - 124.
The effect of biodiesel policies on world biodiesel and oilseed prices
Drabik, D. ; Gorter, H. de; Timilsina, G.R. - \ 2014
Energy Economics 44 (2014). - ISSN 0140-9883 - p. 80 - 88.
biofuels - impacts
A theoretical and empirical model is developed to analyze the effect of a biodiesel mandate, a tax exemption (tax credit) and an exogenous diesel price shock on world soybean and canola markets. The jointness in crushing oil and meal from the oilseed reduces the size of the link between biodiesel and oilseed prices. A diesel price shock with a mandate results in a smaller change in oilseed prices compared with a tax exemption. Higher diesel prices increase biodiesel prices under a tax exemption but lower them with a blend mandate. When both canola and soybeans are used to produce biodiesel, an increase in the diesel price leads to higher canola prices, but the effect on soybean prices is ambiguous and depends on relative elasticities of meal demand and canola supply because canola produces more oil than soybeans.
Brachypodium distachyon line Bd3-1 resistance is elicited by the barley stripe mosaic virus triple gene block 1 movement protein
Lee, M.Y. ; Yan, L.J. ; Gorter, F.A. ; Kim, B.Y.T. ; Cui, Y. ; Hu, Y. ; Yuan, C. ; Grindheim, J. ; Ganesan, U. ; Liu, Z.Y. ; Han, C.G. ; Yu, J.L. ; Li, D.W. ; Jackson, A.O. - \ 2012
Journal of General Virology 93 (2012). - ISSN 0022-1317 - p. 2729 - 2739.
rna-binding - new-model - pathogenicity - determinants - pathogenesis - domain - grass - cdna
Barley stripe mosaic virus North Dakota 18 (ND18), Beijing (BJ), Xinjiang (Xi), Type (TY) and CV21 strains are unable to infect the Brachypodium distachyon Bd3-1 inbred line, which harbours a resistance gene designated Bsr1, but the Norwich (NW) strain is virulent on Bd3-1. Analysis of ND18 and NW genomic RNA reassortants and RNA beta mutants demonstrates that two amino acids within the helicase motif of the triple gene block 1 (TGB1) movement protein have major effects on their Bd3-1 phenotypes. Resistance to ND18 correlates with an arginine residue at TGB1 position 390 (R-390) and a threonine at position 392 (T-392), whereas the virulent NW strain contains lysines (K) at both positions. ND18 TGB1 R390K ((ND)TGB1(R390K)) and (ND)TGB1(T392K) single substitutions, and an (ND)TGB1(R390K,T392K) double mutation resulted in systemic infections of Bd3-1. Reciprocal (ND)TGB1 substitutions into (NW)TGB1 ((NW)TGB1(K390R) and (NW)TGB1(K392T)) failed to affect virulence, implying that K-390 and K-392 compensate for each other. In contrast, an (NW)TGB1(K390R,K392T) double mutant exhibited limited vascular movement in Bd3-1, but developed prominent necrotic streaks that spread from secondary leaf veins. This phenotype, combined with the appearance of necrotic spots in certain ND18 mutants, and necrosis and rapid wilting of Bd3-1 plants after BJ strain ((BJ)TGB1(K390,T392)) inoculations, show that Bd3-1 Bsr1 resistance is elicited by the TGB1 protein and suggest that it involves a hypersensitive response.
Understanding the Common Agricultural Policy
Oskam, A.J. - \ 2012
European Review of Agricultural Economics 39 (2012). - ISSN 0165-1587 - p. 735 - 738.
Can another book on the Common Agricultural Policy (CAP) still be worth reading? The well-known CAP books by Fennell, Ritson and Harvey, and Grant and Ackrill were all published more than 10 years ago: so an update in the UK is not superfluous. Hill's book appeared in November 2011, although the publisher has dated it 2012. It has an unusual structure and is written in an easy, readable style. Nearly all chapter titles start with ‘Understanding’. The author is worried that students read quickly outdated reports, web sites and overviews and advises them to read this book. The first chapter describes the policy process: what determines this process? An excellent idea in theory, but in practice the chapter boils down to explaining only one methodology very similar to the so-called Tinbergen approach: defining problems, identifying targets (or objectives) and searching out best instruments. This approach appeals to me as a Dutchman, since it is still in use in the Netherlands. But it is questionable whether students should learn only this approach in order to understand the CAP. Except in some parts of Chapter 3, public choice/political economy, institutional economics, etc. (De Gorter and Swinnen, 2002; Mueller, 2003) are not mentioned at all in the rest of the book. Problems and policy objectives are handled in Chapter 2. Here, Hill shares with many others the difficulty of working with several rather vague objectives defined in the Treaty of Rome and constantly carried forward to the Treaty of Lisbon (e.g. Senior Nello, 2011: 282). Objectives point in different directions. But that is a typical element of a set of variable multidimensional policy objectives within a Tinbergen framework. Some researchers work with objective functions, others see it as policy process.
Initial mutations direct alternative pathways of protein evolution
Salverda, M.L.M. ; Dellus, E. ; Gorter, F.A. ; Debets, A.J.M. ; Oost, J. van der; Hoekstra, R.F. ; Tawfik, D.S. ; Visser, J.A.G.M. de - \ 2011
Plos Genetics 7 (2011)3. - ISSN 1553-7404 - 11 p.
tem-1 beta-lactamase - empirical fitness landscapes - in-vitro - natural evolution - escherichia-coli - antibiotic-resistance - sequence space - adaptation - epistasis - trajectories
Whether evolution is erratic due to random historical details, or is repeatedly directed along similar paths by certain constraints, remains unclear. Epistasis (i.e. non-additive interaction between mutations that affect fitness) is a mechanism that can contribute to both scenarios. Epistasis can constrain the type and order of selected mutations, but it can also make adaptive trajectories contingent upon the first random substitution. This effect is particularly strong under sign epistasis, when the sign of the fitness effects of a mutation depends on its genetic background. In the current study, we examine how epistatic interactions between mutations determine alternative evolutionary pathways, using in vitro evolution of the antibiotic resistance enzyme TEM-1 ß-lactamase. First, we describe the diversity of adaptive pathways among replicate lines during evolution for resistance to a novel antibiotic (cefotaxime). Consistent with the prediction of epistatic constraints, most lines increased resistance by acquiring three mutations in a fixed order. However, a few lines deviated from this pattern. Next, to test whether negative interactions between alternative initial substitutions drive this divergence, alleles containing initial substitutions from the deviating lines were evolved under identical conditions. Indeed, these alternative initial substitutions consistently led to lower adaptive peaks, involving more and other substitutions than those observed in the common pathway. We found that a combination of decreased enzymatic activity and lower folding cooperativity underlies negative sign epistasis in the clash between key mutations in the common and deviating lines (Gly238Ser and Arg164Ser, respectively). Our results demonstrate that epistasis contributes to contingency in protein evolution by amplifying the selective consequences of random mutations
Bewonersparticipatie in het openbaar groenbeheer : 'State of the art' na vijf jaar zelfbeheer in de wijk EVA-Lanxmeer (Culemborg)
Kruit, J. ; Veer, P. ; Gorter, F. ; Gurp, T. van; Landburg, G. ; Steijven, K. ; Remme, R.P. ; Vermeulen, M.H. ; Trienekens, L. - \ 2011
Wageningen : Wageningen UR Wetenschapswinkel (Rapport / Wageningen UR Wetenschapswinkel 270) - 50
openbaar groen - groenbeheer - bewonersparticipatie - stedelijke gebieden - betuwe - public green areas - management of urban green areas - community participation - urban areas
De wijk EVA-Lanxmeer (1997) is een duurzame woon- en werkwijk in Culemborg, op een grondwaterwingebied van Vitens. Het is een voorbeeldproject op het gebied van duurzame stedenbouw en participatief beleid. Het wordt door gemeenten en groepen burgers in binnen- en buitenland gebruikt om inspiratie, kennis en ervaring op te doen en uit te wisselen op het gebied van innovatief denken binnen de eigen gemeentelijke organisatie. Bewoners onderhouden zelf een belangrijk deel van het wijkgroen op een ecologische wijze. Zij doen dat in samenwerking en overleg met de gemeente Culemborg en Waterwinbedrijf Vitens. De meeste bewoners hebben sterk het gevoel dat het zelfbeheer de kwaliteit en diversiteit van het groen in de wijk verhoogt. De gezamenlijke werkzaamheden maken ongedwongen ontmoetingen met andere bewoners in de wijk mogelijk.
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