Technologies for biological containment of GM and Non-GM crops

International Perspective The development of GM technology continues to expand into increasing numbers of crops and conferred traits. Inevitably, the focus remains on the major field crops of soybean, maize, cotton, oilseed rape and potato with introduced genes conferring herbicide tolerance and/or pest resistance. Although there are comparatively few GM crops that have been commercialised to date, GM versions of 172 plant species have been grown in field trials in 31 countries. European Crops with Containment Issues Of the 20 main crops in the EU there are four for which GM varieties are commercially available (cotton, maize for animal feed and forage, and oilseed rape). Fourteen have GM varieties in field trials (bread wheat, barley, durum wheat, sunflower, oats, potatoes, sugar beet, grapes, alfalfa, olives, field peas, clover, apples, rice) and two have GM varieties still in development (rye, triticale). Many of these crops have hybridisation potential with wild and weedy relatives in the European flora (bread wheat, barley, oilseed rape, durum wheat, oats, sugar beet and grapes), with escapes (sunflower); and all have potential to cross-pollinate fields non-GM crops. Several fodder crops, forestry trees, grasses and ornamentals have varieties in field trials and these too may hybridise with wild relatives in the European flora (alfalfa, clover, lupin, silver birch, sweet chestnut, Norway spruce, Scots pine, poplar, elm, Agrostis canina, A. stolonifera, Festuca arundinacea, Lolium perenne, L. multiflorum, statice and rose). All these crops will require containment strategies to be in place if it is deemed necessary to prevent transgene movement to wild relatives and non-GM crops. Current Containment Strategies A wide variety of GM containment strategies are currently under development, with a particular focus on crops expressing pharmaceutical products. Physical containment in greenhouses and growth rooms is suitable for some crops (tomatoes, lettuce) and for research purposes. Aquatic bioreactors of some non-crop species (algae, moss, and duckweed) expressing pharmaceutical products have been adopted by some biotechnology companies. There are obvious limitations of the scale of physical containment strategies, addressed in part by the development of large underground facilities in the US and Canada. The additional resources required to grow plants underground incurs high costs that in the long term may negate any advantage of GM for commercial productioNatural genetic containment has been adopted by some companies through the selection of either non-food/feed crops (algae, moss, duckweed) as bio-pharming platforms or organisms with no wild relatives present in the local flora (safflower in the Americas). The expression of pharmaceutical products in leafy crops (tobacco, alfalfa, lettuce, spinach) enables growth and harvesting prior to and in the absence of flowering. Transgenically controlled containment strategies range in their approach and degree of development. Plastid transformation is relatively well developed but is not suited to all traits or crops and does not offer complete containment. Male sterility is well developed across a range of plants but has limitations in its application for fruit/seed bearing crops. It has been adopted in some commercial lines of oilseed rape despite not preventing escape via seed. Conditional lethality can be used to prevent flowering or seed development following the application of a chemical inducer, but requires 100% induction of the trait and sufficient application of the inducer to all plants. Equally, inducible expression of the GM trait requires equally stringent application conditions. Such a method will contain the trait but will allow the escape of a non-functioning transgene. Seed lethality (‘terminator’ technology) is the only strategy at present that prevents transgene movement via seed, but due to public opinion against the concept it has never been trialled in the field and is no longer under commercial development. Methods to control flowering and fruit development such as apomixis and cleistogamy will prevent crop-to-wild and wild-to-crop pollination, but in nature both of these strategies are complex and leaky. None of the genes controlling these traits have as yet been identified or characterised and therefore have not been transgenically introduced into crop species. Neither of these strategies will prevent transgene escape via seed and any feral apomicts that form are arguably more likely to become invasives. Transgene mitigation reduces the fitness of initial hybrids and so prevents stable introgression of transgenes into wild populations. However, it does not prevent initial formation of hybrids or spread to non-GM crops. Such strategies could be detrimental to wild populations and have not yet been demonstrated in the field. Similarly, auxotrophy prevents persistence of escapes and hybrids containing the transgene in an uncontrolled environment, but does not prevent transgene movement from the crop. Recoverable block of function, intein trans-splicing and transgene excision all use recombinases to modify the transgene in planta either to induce expression or to prevent it. All require optimal conditions and 100% accuracy to function and none have been tested under field conditions as yet. All will contain the GM trait but all will allow some non-native DNA to escape to wild populations or to non-GM crops. There are particular issues with GM trees and grasses as both are largely undomesticated, wind pollinated and perennial, thus providing many opportunities for hybridisation. Some species of both trees and grass are also capable of vegetative propagation without sexual reproduction. There are additional concerns regarding the weedy nature of many grass species and the long-term stability of GM traits across the life span of trees. Transgene stability and conferred sterility are difficult to trial in trees as most field trials are only conducted during the juvenile phase of tree growth. Bio-pharming of pharmaceutical and industrial compounds in plants Bio-pharming of pharmaceutical and industrial compounds in plants offers an attractive alternative to mammalian-based pharmaceutical and vaccine production. Several plantbased products are already on the market (Prodigene’s avidin, β-glucuronidase, trypsin generated in GM maize; Ventria’s lactoferrin generated in GM rice). Numerous products are in clinical trials (collagen, antibodies against tooth decay and non-Hodgkin’s lymphoma from tobacco; human gastric lipase, therapeutic enzymes, dietary supplements from maize; Hepatitis B and Norwalk virus vaccines from potato; rabies vaccines from spinach; dietary supplements from Arabidopsis). The initial production platforms for plant-based pharmaceuticals were selected from conventional crops, largely because an established knowledge base already existed. Tobacco and other leafy crops such as alfalfa, lettuce and spinach are widely used as leaves can be harvested and no flowering is required. Many of these crops can be grown in contained greenhouses. Potato is also widely used and can also be grown in contained conditions. The introduction of morphological markers may aid in the recognition and traceability of crops expressing pharmaceutical products. Plant cells or plant parts may be transformed and maintained in culture to produce recombinant products in a contained environment. Plant cells in suspension or in vitro, roots, root cells and guttation fluid from leaves may be engineered to secrete proteins that may be harvested in a continuous, non-destructive manner. Most strategies in this category remain developmental and have not been commercially adopted at present. Transient expression produces GM compounds from non-GM plants via the utilisation of bacterial or viral vectors. These vectors introduce the trait into specific tissues of whole plants or plant parts, but do not insert them into the heritable genome. There are some limitations of scale and the field release of such crops will require the regulation of the vector. However, several companies have several transiently expressed products in clinical and pre-clinical trials from crops raised in physical containment.

Reaping the benefits: science and the sustainable intensification of global agriculture

Food security is one of this century’s key global challenges. By 2050 the world will require increased crop production in order to feed its predicted 9 billion people. This must be done in the face of changing consumption patterns, the impacts of climate change and the growing scarcity of water and land. Crop production methods will also have to sustain the environment, preserve natural resources and support livelihoods of farmers and rural populations around the world. There is a pressing need for the ‘sustainable intensifi cation’ of global agriculture in which yields are increased without adverse environmental impact and without the cultivation of more land. Addressing the need to secure a food supply for the whole world requires an urgent international effort with a clear sense of long-term challenges and possibilities. Biological science, especially publicly funded science, must play a vital role in the sustainable intensifi cation of food crop production. The UK has a responsibility and the capacity to take a leading role in providing a range of scientifi c solutions to mitigate potential food shortages. This will require signifi cant funding of cross-disciplinary science for food security. The constraints on food crop production are well understood, but differ widely across regions. The availability of water and good soils are major limiting factors. Signifi cant losses in crop yields occur due to pests, diseases and weed competition. The effects of climate change will further exacerbate the stresses on crop plants, potentially leading to dramatic yield reductions. Maintaining and enhancing the diversity of crop genetic resources is vital to facilitate crop breeding and thereby enhance the resilience of food crop production. Addressing these constraints requires technologies and approaches that are underpinned by good science. Some of these technologies build on existing knowledge, while others are completely radical approaches, drawing on genomics and high-throughput analysis. Novel research methods have the potential to contribute to food crop production through both genetic improvement of crops and new crop and soil management practices. Genetic improvements to crops can occur through breeding or genetic modifi cation to introduce a range of desirable traits. The application of genetic methods has the potential to refi ne existing crops and provide incremental improvements. These methods also have the potential to introduce radical and highly signifi cant improvements to crops by increasing photosynthetic effi ciency, reducing the need for nitrogen or other fertilisers and unlocking some of the unrealised potential of crop genomes. The science of crop management and agricultural practice also needs to be given particular emphasis as part of a food security grand challenge. These approaches can address key constraints in existing crop varieties and can be applied widely. Current approaches to maximising production within agricultural systems are unsustainable; new methodologies that utilise all elements of the agricultural system are needed, including better soil management and enhancement and exploitation of populations of benefi cial soil microbes. Agronomy, soil science and agroecology—the relevant sciences—have been neglected in recent years. Past debates about the use of new technologies for agriculture have tended to adopt an either/or approach, emphasising the merits of particular agricultural systems or technological approaches and the downsides of others. This has been seen most obviously with respect to genetically modifi ed (GM) crops, the use of pesticides and the arguments for and against organic modes of production. These debates have failed to acknowledge that there is no technological panacea for the global challenge of sustainable and secure global food production. There will always be trade-offs and local complexities. This report considers both new crop varieties and appropriate agroecological crop and soil management practices and adopts an inclusive approach. No techniques or technologies should be ruled out. Global agriculture demands a diversity of approaches, specific to crops, localities, cultures and other circumstances. Such diversity demands that the breadth of relevant scientific enquiry is equally diverse, and that science needs to be combined with social, economic and political perspectives. In addition to supporting high-quality science, the UK needs to maintain and build its capacity to innovate, in collaboration with international and national research centres. UK scientists and agronomists have in the past played a leading role in disciplines relevant to agriculture, but training in agricultural sciences and related topics has recently suffered from a lack of policy attention and support. Agricultural extension services, connecting farmers with new innovations, have been similarly neglected in the UK and elsewhere. There is a major need to review the support for and provision of extension services, particularly in developing countries. The governance of innovation for agriculture needs to maximise opportunities for increasing production, while at the same time protecting societies, economies and the environment from negative side effects. Regulatory systems need to improve their assessment of benefits. Horizon scanning will ensure proactive consideration of technological options by governments. Assessment of benefi ts, risks and uncertainties should be seen broadly, and should include the wider impacts of new technologies and practices on economies and societies. Public and stakeholder dialogue—with NGOs, scientists and farmers in particular—needs to be a part of all governance frameworks.

Detection and attribution of climate change: a regional perspective

The Intergovernmental Panel on Climate Change fourth assessment report, published in 2007 came to a more confident assessment of the causes of global temperature change than previous reports and concluded that ‘it is likely that there has been significant anthropogenic warming over the past 50 years averaged over each continent except Antarctica.’ Since then, warming over Antarctica has also been attributed to human influence, and further evidence has accumulated attributing a much wider range of climate changes to human activities. Such changes are broadly consistent with theoretical understanding, and climate model simulations, of how the planet is expected to respond. This paper reviews this evidence from a regional perspective to reflect a growing interest in understanding the regional effects of climate change, which can differ markedly across the globe. We set out the methodological basis for detection and attribution and discuss the spatial scales on which it is possible to make robust attribution statements. We review the evidence showing significant human-induced changes in regional temperatures, and for the effects of external forcings on changes in the hydrological cycle, the cryosphere, circulation changes, oceanic changes, and changes in extremes. We then discuss future challenges for the science of attribution. To better assess the pace of change, and to understand more about the regional changes to which societies need to adapt, we will need to refine our understanding of the effects of external forcing and internal variability

Climate and human influences on global biomass burning over the past two millennia

Large, well-documented wildfires have recently generated worldwide attention, and raised concerns about the impacts of humans and climate change on wildfire regimes. However, comparatively little is known about the patterns and driving forces of global fire activity before the twentieth century. Here we compile sedimentary charcoal records spanning six continents to document trends in both natural and anthropogenic biomass burning for the past two millennia. We find that global biomass burning declined from AD 1 to 1750, before rising sharply between 1750 and 1870. Global burning then declined abruptly after 1870. The early decline in biomass burning occurred in concert with a global cooling trend and despite a rise in the human population. We suggest the subsequent rise was linked to increasing human influences, such as population growth and land-use changes. Our compilation suggests that the final decline occurred despite increasing air temperatures and population. We attribute this reduction in the amount of biomass burned over the past 150 years to the global expansion of intensive grazing, agriculture and fire management.

The influence of ozone precursor emissions from four world regions on tropospheric composition and radiative climate forcing

Ozone (O3) precursor emissions influence regional and global climate and air quality through changes in tropospheric O3 and oxidants, which also influence methane (CH4) and sulfate aerosols (SO42−). We examine changes in the tropospheric composition of O3, CH4, SO42− and global net radiative forcing (RF) for 20% reductions in global CH4 burden and in anthropogenic O3 precursor emissions (NOx, NMVOC, and CO) from four regions (East Asia, Europe and Northern Africa, North America, and South Asia) using the Task Force on Hemispheric Transport of Air Pollution Source-Receptor global chemical transport model (CTM) simulations, assessing uncertainty (mean ± 1 standard deviation) across multiple CTMs. We evaluate steady state O3 responses, including long-term feedbacks via CH4. With a radiative transfer model that includes greenhouse gases and the aerosol direct effect, we find that regional NOx reductions produce global, annually averaged positive net RFs (0.2 ± 0.6 to 1.7 ± 2 mWm−2/Tg N yr−1), with some variation among models. Negative net RFs result from reductions in global CH4 (−162.6 ± 2 mWm−2 for a change from 1760 to 1408 ppbv CH4) and regional NMVOC (−0.4 ± 0.2 to −0.7 ± 0.2 mWm−2/Tg C yr−1) and CO emissions (−0.13 ± 0.02 to −0.15 ± 0.02 mWm−2/Tg CO yr−1). Including the effect of O3 on CO2 uptake by vegetation likely makes these net RFs more negative by −1.9 to −5.2 mWm−2/Tg N yr−1, −0.2 to −0.7 mWm−2/Tg C yr−1, and −0.02 to −0.05 mWm−2/Tg CO yr−1. Net RF impacts reflect the distribution of concentration changes, where RF is affected locally by changes in SO42−, regionally to hemispherically by O3, and globally by CH4. Global annual average SO42− responses to oxidant changes range from 0.4 ± 2.6 to −1.9 ± 1.3 Gg for NOx reductions, 0.1 ± 1.2 to −0.9 ± 0.8 Gg for NMVOC reductions, and −0.09 ± 0.5 to −0.9 ± 0.8 Gg for CO reductions, suggesting additional research is needed. The 100-year global warming potentials (GWP100) are calculated for the global CH4 reduction (20.9 ± 3.7 without stratospheric O3 or water vapor, 24.2 ± 4.2 including those components), and for the regional NOx, NMVOC, and CO reductions (−18.7 ± 25.9 to −1.9 ± 8.7 for NOx, 4.8 ± 1.7 to 8.3 ± 1.9 for NMVOC, and 1.5 ± 0.4 to 1.7 ± 0.5 for CO). Variation in GWP100 for NOx, NMVOC, and CO suggests that regionally specific GWPs may be necessary and could support the inclusion of O3 precursors in future policies that address air quality and climate change simultaneously. Both global net RF and GWP100 are more sensitive to NOx and NMVOC reductions from South Asia than the other three regions.

Review of the formulation of present‐generation stratospheric chemistry‐climate models and associated external forcings

The goal of the Chemistry‐Climate Model Validation (CCMVal) activity is to improve understanding of chemistry‐climate models (CCMs) through process‐oriented evaluation and to provide reliable projections of stratospheric ozone and its impact on climate. An appreciation of the details of model formulations is essential for understanding how models respond to the changing external forcings of greenhouse gases and ozonedepleting substances, and hence for understanding the ozone and climate forecasts produced by the models participating in this activity. Here we introduce and review the models used for the second round (CCMVal‐2) of this intercomparison, regarding the implementation of chemical, transport, radiative, and dynamical processes in these models. In particular, we review the advantages and problems associated with approaches used to model processes of relevance to stratospheric dynamics and chemistry. Furthermore, we state the definitions of the reference simulations performed, and describe the forcing data used in these simulations. We identify some developments in chemistry‐climate modeling that make models more physically based or more comprehensive, including the introduction of an interactive ocean, online photolysis, troposphere‐stratosphere chemistry, and non‐orographic gravity‐wave deposition as linked to tropospheric convection. The relatively new developments indicate that stratospheric CCM modeling is becoming more consistent with our physically based understanding of the atmosphere.

Evidence for a climate signal in trends of global crop yield variability over the past 50 years

Low variability of crop production from year to year is desirable for many reasons, including reduced income risk and stability of supplies. Therefore, it is important to understand the nature of yield variability, whether it is changing through time, and how it varies between crops and regions. Previous studies have shown that national crop yield variability has changed in the past, with the direction and magnitude dependent on crop type and location. Whilst such studies acknowledge the importance of climate variability in determining yield variability, it has been assumed that its magnitude and its effect on crop production have not changed through time and, hence, that changes to yield variability have been due to non-climatic factors. We address this assumption by jointly examining yield and climate variability for three major crops (rice, wheat and maize) over the past 50 years. National yield time series and growing season temperature and precipitation were de-trended and related using multiple linear regression. Yield variability changed significantly in half of the crop–country combinations examined. For several crop–country combinations, changes in yield variability were related to changes in climate variability.

Climate and CO2 controls on global vegetation distribution at the last glacial maximum: analysis based on palaeovegetation data, biome modelling and palaeoclimate simulations.

The global vegetation response to climate and atmospheric CO2 changes between the last glacial maximum and recent times is examined using an equilibrium vegetation model (BIOME4), driven by output from 17 climate simulations from the Palaeoclimate Modelling Intercomparison Project. Features common to all of the simulations include expansion of treeless vegetation in high northern latitudes; southward displacement and fragmentation of boreal and temperate forests; and expansion of drought-tolerant biomes in the tropics. These features are broadly consistent with pollen-based reconstructions of vegetation distribution at the last glacial maximum. Glacial vegetation in high latitudes reflects cold and dry conditions due to the low CO2 concentration and the presence of large continental ice sheets. The extent of drought-tolerant vegetation in tropical and subtropical latitudes reflects a generally drier low-latitude climate. Comparisons of the observations with BIOME4 simulations, with and without consideration of the direct physiological effect of CO2 concentration on C3 photosynthesis, suggest an important additional role of low CO2 concentration in restricting the extent of forests, especially in the tropics. Global forest cover was overestimated by all models when climate change alone was used to drive BIOME4, and estimated more accurately when physiological effects of CO2 concentration were included. This result suggests that both CO2 effects and climate effects were important in determining glacial-interglacial changes in vegetation. More realistic simulations of glacial vegetation and climate will need to take into account the feedback effects of these structural and physiological changes on the climate.

A simple framework for assessing the trade-off between the climate impact of aviation carbon dioxide emissions and contrails for a single flight

Persistent contrails are an important climate impact of aviation which could potentially be reduced by re-routing aircraft to avoid contrailing; however this generally increases both the flight length and its corresponding CO emissions. Here, we provide a simple framework to assess the trade-off between the climate impact of CO emissions and contrails for a single flight, in terms of the absolute global warming potential and absolute global temperature potential metrics for time horizons of 20, 50 and 100 years. We use the framework to illustrate the maximum extra distance (with no altitude changes) that can be added to a flight and still reduce its overall climate impact. Small aircraft can fly up to four times further to avoid contrailing than large aircraft. The results have a strong dependence on the applied metric and time horizon. Applying a conservative estimate of the uncertainty in the contrail radiative forcing and climate efficacy leads to a factor of 20 difference in the maximum extra distance that could be flown to avoid a contrail. The impact of re-routing on other climatically-important aviation emissions could also be considered in this framework.

Evaluating adjusted forcing and model spread for historical and future scenarios in the CMIP5 generation of climate models

We utilize energy budget diagnostics from the Coupled Model Intercomparison Project phase 5 (CMIP5) to evaluate the models' climate forcing since preindustrial times employing an established regression technique. The climate forcing evaluated this way, termed the adjusted forcing (AF), includes a rapid adjustment term associated with cloud changes and other tropospheric and land-surface changes. We estimate a 2010 total anthropogenic and natural AF from CMIP5 models of 1.9 ± 0.9 W m−2 (5–95% range). The projected AF of the Representative Concentration Pathway simulations are lower than their expected radiative forcing (RF) in 2095 but agree well with efficacy weighted forcings from integrated assessment models. The smaller AF, compared to RF, is likely due to cloud adjustment. Multimodel time series of temperature change and AF from 1850 to 2100 have large intermodel spreads throughout the period. The intermodel spread of temperature change is principally driven by forcing differences in the present day and climate feedback differences in 2095, although forcing differences are still important for model spread at 2095. We find no significant relationship between the equilibrium climate sensitivity (ECS) of a model and its 2003 AF, in contrast to that found in older models where higher ECS models generally had less forcing. Given the large present-day model spread, there is no indication of any tendency by modelling groups to adjust their aerosol forcing in order to produce observed trends. Instead, some CMIP5 models have a relatively large positive forcing and overestimate the observed temperature change.

Stochastic climate theory and modeling

Stochastic methods are a crucial area in contemporary climate research and are increasingly being used in comprehensive weather and climate prediction models as well as reduced order climate models. Stochastic methods are used as subgrid-scale parameterizations (SSPs) as well as for model error representation, uncertainty quantification, data assimilation, and ensemble prediction. The need to use stochastic approaches in weather and climate models arises because we still cannot resolve all necessary processes and scales in comprehensive numerical weather and climate prediction models. In many practical applications one is mainly interested in the largest and potentially predictable scales and not necessarily in the small and fast scales. For instance, reduced order models can simulate and predict large-scale modes. Statistical mechanics and dynamical systems theory suggest that in reduced order models the impact of unresolved degrees of freedom can be represented by suitable combinations of deterministic and stochastic components and non-Markovian (memory) terms. Stochastic approaches in numerical weather and climate prediction models also lead to the reduction of model biases. Hence, there is a clear need for systematic stochastic approaches in weather and climate modeling. In this review, we present evidence for stochastic effects in laboratory experiments. Then we provide an overview of stochastic climate theory from an applied mathematics perspective. We also survey the current use of stochastic methods in comprehensive weather and climate prediction models and show that stochastic parameterizations have the potential to remedy many of the current biases in these comprehensive models.

Climate change and infectious disease: time for a new normal?

At present, there is a clarion call for action on climate change across the global health landscape. At the recent WHO-sponsored conference on health and climate (held in Geneva, Switzerland, on Aug 27–29, 2014) and the UN Climate Summit (New York, USA, on Sept 23, 2014), participants were encouraged to act decisively to change the current trajectory of climate disruption. Health inequalities, including those related to infectious diseases, have now been pushed to centre stage. This approach represents a step-change in thinking. But as we are urged toward collective action, is it time to rethink our approach to research, especially in relation to climate change and infectious disease?

Climate change and water in the UK: past changes and future prospects

Climate change is expected to modify rainfall, temperature and catchment hydrological responses across the world, and adapting to these water-related changes is a pressing challenge. This paper reviews the impact of anthropogenic climate change on water in the UK and looks at projections of future change. The natural variability of the UK climate makes change hard to detect; only historical increases in air temperature can be attributed to anthropogenic climate forcing, but over the last 50 years more winter rainfall has been falling in intense events. Future changes in rainfall and evapotranspiration could lead to changed flow regimes and impacts on water quality, aquatic ecosystems and water availability. Summer flows may decrease on average, but floods may become larger and more frequent. River and lake water quality may decline as a result of higher water temperatures, lower river flows and increased algal blooms in summer, and because of higher flows in the winter. In communicating this important work, researchers should pay particular attention to explaining confidence and uncertainty clearly. Much of the relevant research is either global or highly localized: decision-makers would benefit from more studies that address water and climate change at a spatial and temporal scale appropriate for the decisions they make

The climate and environment of Byzantine Anatolia: integrating science, history, and archaeology

The integration of high-resolution archaeological, textual, and environmental data with longer-term, low-resolution data affords greater precision in identifying some of the causal relationships underlying societal change. Regional and microregional case studies about the Byzantine world—in particular, Anatolia, which for several centuries was the heart of that world—reveal many of the difficulties that researchers face when attempting to assess the influence of environmental factors on human society. The Anatolian case challenges a number of assumptions about the impact of climatic factors on socio-political organization and medium-term historical evolution, highlighting the importance of further collaboration between historians, archaeologists, and climate scientists.