| 1. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 2. |
- Weinstein, John N., et al.
(författare)
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The cancer genome atlas pan-cancer analysis project
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 45:10, s. 1113-1120
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Tidskriftsartikel (refereegranskat)abstract
- The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile. © 2013 Nature America, Inc. All rights reserved.
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| 3. |
- Brady, Mark, et al.
(författare)
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An agent-based approach to modeling impacts of agricultural policy on land use, biodiversity and ecosystem services
- 2012
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Ingår i: Landscape Ecology. - : Springer Science and Business Media LLC. - 1572-9761 .- 0921-2973. ; 27:9, s. 1363-1381
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Tidskriftsartikel (refereegranskat)abstract
- We present extensions to the agent-based agricultural policy simulator (AgriPoliS) model that make it possible to simulate the consequences of agricultural policy reform on farmers' land use decisions and concomitant impacts on landscape mosaic, biodiversity and ecosystem services in a real agricultural region. An observed population of farms is modelled as a multi-agent system where individual farm-agent behaviour and their interactions-principally competition for land-are defined through an optimization framework with land use and landscape impacts resulting as emergent properties of the system. The model is calibrated to real data on the farms and the landscape to be studied. We illustrate the utility of the model by evaluating the potential impacts of three alternative frameworks for the European Union Common Agricultural Policy (CAP) on landscape values in two marginal agricultural regions. Mosaic value was found to be sensitive to the choice of policy scheme in one of the landscapes, whereas significant trade-offs were shown to occur in terms of species richness by habitat and species composition at the landscape scale in both regions. The relationship between food production and other ecosystem services was found to be multifaceted. Thus illustrating the difficulty of achieving landscape goals in a particular region with simple or general land management rules (such as the current rules attached to CAPs direct payments). Given the scarcity of funding for conservation, the level and conditions for allocating direct payments are, potentially, of great importance for preserving landscape values in marginal agricultural regions (subject to levels of other support).
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| 4. |
- Brady, Mark, et al.
(författare)
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Estimating the resilience value of soil biodiversity in agriculture: a stochastic simulation approach
- 2011
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Ingår i: Proceedings EAAE 2011 International Congress, August 30-September 2, 2011, Zurich, Switzerland. ; , s. 1-16
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Konferensbidrag (refereegranskat)abstract
- Abstract in UndeterminedCharacteristic of ecosystems is that different organisms can have similar functions and hence provide similar ecosystem services. Consequently functional diversity can maintain the rate of services despite environmental fluctuations. In this paper we present a method for estimating the resilience value of biodiversity. Central to a resilience perspective on biological conservation is consideration of uncertainty about the future. To do this we propose stochastic simulation as a practical approach for valuing resilience due to the ease of incorporating uncertain variables. We demonstrate the approach by developing a stochastic simulation model for valuing soil biodiversity in agriculture. Our results indicate that the long time frames involved in soil processes create a significant incentive to perpetuate unsustainable farming systems and hence there might be a need for policy intervention. However we also show that investing in soil biodiversity conservation can provide significant risk diversification benefits that are not accounted for in a deterministic evaluation. These benefits can be estimated through stochastic simulation.
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| 5. |
- Brady, Mark
(författare)
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Impact of CAP reform on the environment: some regional results
- 2010
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Introduction of the Single Farm Payment (SPS) in 2005 constitutes perhaps the most radical reform of the Common Agricultural Policy ever. This payment has replaced almost all previous forms of subsidies to farmers and is decoupled, i.e. paid regardless of whether the farmer produces commodities as long as their land is kept in Good Agricultural and Environmental Condition (GAEC). Such a radical reform was expected to have a profound impact on European agriculture; in particular concern was raised about the impacts on historical landscapes and biodiversity. This paper presents the findings of a large EU project, IDEMA, on the potential environmental impacts of the 2003 CAP reform for a selection of case-study regions. Due to the complexity of the issues at hand and the lack of historical data, the assessment was based on dynamic agent-based modelling with the extended AgriPoliS model. Our results indicated small impacts in relatively productive regions, since land use remains largely unchanged. In marginal agricultural regions, however, decoupling was shown to have a negative impact on biodiversity and landscape mosaic because of the homogenisation of land use that results from land being taken out of production. Existing agri-environmental schemes and national support acted however to buffer the full potential impacts of decoupling on landscape values in these regions. The effects of the reform would have been more radical if there was no link between the decoupled payment and land, i.e. via the GAEC obligation. In this case the model results indicated that farmers would leave the sector at a faster rate and average farm size would increase (thereby improving competitiveness). On the other hand, significant areas of agricultural land, primarily grassland, were abandoned in the modelled high-cost or marginal regions. Hence, it might be motivated to strengthen agri-environmental schemes under a Bond-type scheme in affected regions to preserve landscape values (depending on public willingness to pay for landscape preservation)
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| 6. |
- Brady, Mark
(författare)
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Managing Soil Ecosystem Services in Agriculture: a Production Function Approach
- 2014
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Soil natural capital through its delivery of ecosystem services is pivotal for agricultural production. We develop a production-function approach and use data from long-term agricultural field experiments in Europe and the US to show that changes in soil organic carbon (SOC)-through its relation to ecosystem services-can be used to value changes in soil natural capital. Generally, declining SOC reduces both maximum yield and fertilizer use efficiency in the future, thereby depreciating soil natural capital. The depreciation cost will depend on the current state of SOC and the choice of discount rate. Valuing SOC as natural capital makes way for optimising soil ecosystem services in agricultural production.
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| 7. |
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| 8. |
- Brady, Mark
(författare)
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The impact of CAP reform on the environment: some regional results.
- 2011
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Ingår i: Disaggregated Impacts of CAP Reforms: Proceedings of an OECD Workshop. - 9789264097070 ; , s. 215-234
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- This chapter presents the main findings from the IDEMA project on the impact of the single payment scheme on production, prices, trade flows, farm income and structural change at the European Union and regional levels. Three complementary evaluation approaches were used: surveys of farmers' intentions, sector modelling and agent-based models of regional structural change. The findings provide no strong evidence that farmers intend to change their strategic decision to exit agriculture. Instead, structural change is shown to slow down when payments are more decoupled because minimal land management becomes an additional source of income. The reform has increased the market orientation of EU farmers and has reduced trade distortions. The single payment scheme is shown to increase farm incomes, but also land rental prices in most regions. Capitalization of payments into land values over time will, however, erode the ability of the reform to support incomes in the long run as incumbent farmers retire or otherwise leave the sector. The impact of the reform would have been very different if there had been no link between the decoupled payment and land.
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| 9. |
- Brady, Mark, et al.
(författare)
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The impact of decoupling and modulation in the European Union: a sectoral and farm level assessment
- 2010
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Introduction of the Single Payment Scheme (SPS) in 2005 constitutes perhaps the most radical reform of the Common Agricultural Policy ever. This payment has replaced almost all previous forms of subsidies to farmers and is decoupled, i.e., paid regardless of whether the farmer produces or not, as long as land is kept in good agricultural and environmental condition (GAEC). Such a radical reform was expected to have a profound impact on European agriculture. This paper presents a synthesis of the findings of a large EU project, IDEMA. The aim was to assess the potential impacts of decoupling on production, prices, trade flows, farm income, structural change and the environment at the EU and regional levels. Due to the complexity of the issues at hand and the lack of historical data, three complementary evaluation approaches were used: surveys of farmers’ intentions, sector modelling and agent-based models of regional structural change. Surveys and modelling results provide no strong evidence that farmers intend to change their strategic decision to exit agriculture. Instead structural change is shown to slow down when payments are decoupled because minimal land management becomes an additional source of income. Decoupling as a result is also shown to reduce farmers’ off-farm labour supply. In the New Member States the impact of the accession is the dominating effect: the introduction of CAP payments results in larger numbers of farmers remaining in the sector and increased competition for land. Other aims of the reform included boosting farm incomes and improving competitiveness. The reform has also, undoubtedly, increased market orientation of EU farmers and reduced trade distortions. The SPS is shown to increase farm incomes but also land rental prices in most regions. Capitalization of payments in land values over time will, however, erode the ability of the reform to support incomes in the long run as incumbent farmers retire or otherwise leave the sector. The impacts of the reform would have been very different if there was no link between the decoupled payment and land. Without the GAEC obligation model results indicate a strong increase in average farm size as greater numbers of farmers would leave the sector and make their land available to remaining farms (significant areas of land are though shown to be abandoned in the most marginal regions). Due to the significantly lower land (rental) prices and size economies that emerge from this policy, profits per hectare are generally higher. Thus it can be argued that the objective of improving competitiveness has not been achieved due to slower structural change and the higher land prices that follow from the 2003 reform
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| 10. |
- Brady, Mark
(författare)
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What land-use pattern emerges with landscape-scale management? An ecosystem-service perspective
- 2014
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Konferensbidrag (refereegranskat)abstract
- It is argued that landscape-scale management (LSM) of habitat is better than farm-scale management (FSM) when considering the externality of ecosystem services. Given this advantage, how to regulate individual farmers' land-use decisions to achieve the LSM solution is an issue of common concern both for farmers and policymakers. Specifically, it needs to be determined if there exists a dominant land-use pattern that characterizes the LSM solution compared to FSM solution. In addition to the area of habitat, we design a land-use pattern index (LPI) to characterize the configuration of habitat and project itonto the sharing-sparing continuum. We find that the LSM solution is characterized by less intensive farming, and configurations of habitat are closer to land sharing. However, as crop dependency on ecosystem-services declines, the land-use patterns with LSM and FSM converge and the configurations of habitat start to resemble to land sparing. In addition, when habitat quality improves the configurations of habitat on the border farms become important. Finally, the less mobile service-providers are, the more farmers should focus on land-use patterns on their own farms. Our indices of land-use patterns could be integrated into the cross-compliance of CAP (Common Agricultural Policy) to better manage ecosystem-service in the future.
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