Bacteriophage MS2 displays unreported capsid variability assembling T = 4 and mixed capsids

Bacteriophage MS2 is a positive-sense, single-stranded RNA virus encapsulated in an asymmetric T = 3 pseudo-icosahedral capsid. It infects Escherichia coli through the F-pilus, in which it binds through a maturation protein incorporated into its capsid. Cryogenic electron microscopy has previously shown that its genome is highly ordered within virions, and that it regulates the assembly process of the capsid. In this study, we have assembled recombinant MS2 capsids with non-genomic RNA containing the capsid incorporation sequence, and investigated the structures formed, revealing that T = 3, T = 4 and mixed capsids between these two triangulation numbers are generated, and resolving structures of T = 3 and T = 4 capsids to 4 Å and 6 Å respectively. We conclude that the basic MS2 capsid can form a mix of T = 3 and T = 4 structures, supporting a role for the ordered genome in favouring the formation of functional T = 3 virions.     

Testing the short-term effects of a fish invader on the trophic ecology of a closely related species

The effects of invaders on native species are usually tested using species mean trait values over long time scales. However, considering individual variation over short timescales can help us better understand the interaction between invaders and native species. We compared trophic traits of the non-native guppy (Poecilia reticulata) and the native Brazilian poeciliid Phalloceros harpagos using experiments simulating the early stages of an invasive process. We used short-term mesocosms to simulate an early invasion scenario, where the two species were placed together, and a pre-invasion scenario, where species were kept separated, and analyzed interspecific and intraspecific trophic variability. We also compared the foraging efficiency of species in laboratory experiments. We found no differences on the mean diet of both species between pre and early invasion treatments. At the individual level, in the early invasion scenario, individuals of both species reduced their trophic niche as a probable effect of the presence of the heterospecific. Phalloceros harpagos had higher consumption rates than guppies indicating greater efficiency in feeding on invertebrates. Our results suggest that non-native species were not intrinsically better consumers of high-quality resources. Instead, intraspecific variation might be playing an overlooked role in shaping interactions between species during the early stages of invasion.

     

Assessing the Environmental Impact of Water Consumption by Energy Crops Grown in Spain

The environmental impact of the water consumption of four typical crop rotations grown in Spain, including energy crops, was analyzed and compared against Spanish agricultural and natural reference situations. The life cycle assessment (LCA) methodology was used for the assessment of the potential environmental impact of blue water (withdrawal from water bodies) and green water (uptake of soil moisture) consumption. The latter has so far been disregarded in LCA. To account for green water, two approaches have been applied: the first accounts for the difference in green water demand of the crops and a reference situation. The second is a green water scarcity index, which measures the fraction of the soil‐water plant consumption to the available green water. Our results show that, if the aim is to minimize the environmental impacts of water consumption, the energy crop rotations assessed in this study were most suitable in basins in the northeast of Spain. In contrast, the energy crops grown in basins in the southeast of Spain were associated with the greatest environmental impacts. Further research into the integration of quantitative green water assessment in LCA is crucial in studies of systems with a high dependence on green water resources.     

Society and GMOs—chicken and egg?: The lessons from the GM crops debate in Europe over risk management and communication provide valuable pointers for the upcoming debate on GM animals

The debate about GM crops in Europe holds valuable lessons about risk management and risk communication. These lessons will be helpful for the upcoming debate on GM animals.Biomedical research and biotechnology have grown enormously in the past decades, as nations have heavily invested time and money in these endeavours to reap the benefits of the so-called ‘bioeconomy''. Higher investments on research should increase knowledge, which is expected to translate into applied research and eventually give rise to new products and services that are of economic or social benefit. Many governments have developed ambitious strategies—both economic and political—to accelerate this process and fuel economic growth (http://www.oecd.org/futures/bioeconomy/2030). However, it turns out that social attitudes are a more important factor for translating scientific advances than previously realized; public resistance can effectively slow down or even halt technological progress, and some hoped-for developments have hit roadblocks. Addressing these difficulties has become a major challenge for policy-makers, who have to find the middle ground between promoting innovation and addressing ethical and cultural values.There are many examples of how scientific and technological advances raise broad societal concerns: research that uses human embryonic stem cells, nanotechnology, cloning and genetically modified (GM) organisms are perhaps the most contested ones. The prime example of a promising technology that has failed to reach its full potential owing to ethical, cultural and societal concerns is GM organisms (GMOs); specifically, GM crops. Intense lobbying and communication by ‘anti-GM'' groups, combined with poor public relations from industry and scientists, has turned consumers against GM crops and has largely hampered the application of this technology in most European countries. Despite this negative outcome, however, the decade-long debate has provided important lessons and insight for the management of other controversial technologies: in particular, the use of GM animals.During the early 1990s, ‘anti-GM'' non-governmental organizations (NGOs) and ‘pro-GM'' industry were the main culprits for the irreversible polarization of the GMO debate. Both groups lobbied policy-makers and politicians, but NGOs ultimately proved better at persuading the public, a crucial player in the debate. Nevertheless, the level of public outcry varied significantly, reaching its peak in the European Union (EU). In addition to the values of citizens and effective campaigning by NGOs, the structural organization of the EU had a crucial role in triggering the GMO crisis. Within the EU, the European Commission (EC) is an administrative body the decisions of which have a legal impact on the 27 Member States. The EC is well-aware of its unique position and has compensated its lack of democratic accountability by increasing transparency and making itself accessible to the third sector [1]. This strategy was an important factor in the GMO debate as the EC was willing to listen to the views of environmental groups and consumer organizations.…it turns out that social attitudes are a more important factor for translating scientific advances than previously realized…Environmental NGOs successfully exploited this gap between the European electorate and the EC, and assumed to speak as the vox populi in debates. At the same time, politicians in EU Member States were faced with aggressive anti-GMO campaigns and increasingly polarized debates. To avoid the lobbying pressure and alleviate public concerns, they chose to hide behind science: the result was a proliferation of ‘scientific committees'' charged with assessing the health and environmental risks of GM crops.Scientists soon realized that their so-called ‘expert consultation'' was only a political smoke screen in most cases. Their reports and advice were used as arguments to justify policies—rather than tools for determining policy—that sometimes ignored the actual evidence and scientific results [2,3]. For example, in 2008, French President Nikolas Sarkozy announced that he would not authorize GM pest-resistant MON810 maize for cultivation in France if ‘the experts'' had any concerns over its safety. However, although the scientific committee appointed to assess MON810 concluded that the maize was safe for cultivation, the government''s version of the report eventually claimed that scientists had “serious doubts” on MON810 safety, which was then used as an argument to ban its cultivation. Francoise Hollande''s government has adopted a similar strategy to maintain the ban on MON810 [4].In addition to the values of citizens and effective campaigning by NGOs, the structural organization of the EU had a crucial role in triggering the GMO crisisSuch unilateral decisions by Member States challenged the EC''s authority to approve the cultivation of GM crops in the EU. After intense discussions, the EC and the Member States agreed on a centralized procedure for the approval of GMOs and the distribution of responsibilities for the three stages of the risk management process: risk assessment, risk management and risk communication (Fig 1). The European Food Safety Authority (EFSA) alone would be responsible for carrying out risk assessment, whilst the Member States would deal with risk management through the standard EU comitology procedure, by which policy-makers from Member States reach consensus on existing laws. Finally, both the EC and Member States committed to engage with European citizens in an attempt to gain credibility and promote transparency.Open in a separate windowFigure 1Risk assessment and risk management for GM crops in the EU. The new process for GM crop approval under Regulation (EC) No. 1829/2003, which defines the responsibilities for risk assessment and risk management. EC, European Community; EU, European Union; GM, genetically modified.More than 20 years after this debate, the claims made both for and against GM crops have failed to materialize. GMOs have neither reduced world hunger, nor destroyed entire ecosystems or poisoned humankind, even after widespread cultivation. Most of the negative effects have occurred in international food trade [5], partly owing to a lack of harmonization in international governance. More importantly, given that the EU is the largest commodity market in the world, this is caused by the EU''s chronic resistance to GM crops. The agreed centralized procedure has not been implemented satisfactorily and the blame is laid at the door of risk management (http://ec.europa.eu/food/food/biotechnology/evaluation/index_en.htm). Indeed, the 27 Member States have never reached a consensus on GM crops, which is the only non-functional comitology procedure in the EU [2]. Moreover, even after a GM crop was approved, some member states refused to allow its cultivation, which prompted the USA, Canada and Argentina to file a dispute at the World Trade Organization (WTO) against the EU.The inability to reach agreement through the comitology procedure, has forced the EC to make the final decision for all GMO applications. Given that the EC is an administrative body with no scientific expertise, it has relied heavily on EFSA''s opinion. This has created a peculiar situation in which the EFSA performs both risk assessment and management. Anti-GM groups have therefore focused their efforts on discrediting the EFSA as an expert body. Faced with regular questions related to agricultural management or globalization, EFSA scientists are forced to respond to issues that are more linked to risk management than risk assessment [5]. By repeatedly mixing socio-economic and cultural values with scientific opinions, NGOs have questioned the expertise of EFSA scientists and portrayed them as having vested interests in GMOs.Nevertheless, there is no doubt that science has accumulated enormous knowledge on GM crops, which are the most studied crops in human history [6]. In the EU alone, about 270 million euros have been spent through the Framework Programme to study health and environmental risks [5]. Framework Programme funding is approved by Member State consensus and benefits have never been on the agenda of these studies. Despite this bias in funding, the results show that GM crops do not pose a greater threat to human health and the environment than traditional crops [5,6,7]. In addition, scientists have reached international consensus on the methodology to perform risk assessment of GMOs under the umbrella of the Codex Alimentarius [8]. One might therefore conclude that the scientific risk assessment is solid and, contrary to the views of NGOs, that science has done its homework. However, attention still remains fixed on risk assessment in an attempt to fix risk management. But what about the third stage? Have the EC and Member States done their homework on risk communication?It is generally accepted that risk management in food safety crucially depends on efficient risk communication [9]. However, risk communication has remained the stepchild of the three risk management stages [6]. A review of the GM Food/Feed Regulations noted that public communication by EU authorities had been sparse and sometimes inconsistent between the EC and Member States. Similarly, a review of the EC Directive for the release of GMOs to the environment described the information provided to the public as inadequate because it is highly technical and only published in English (http://ec.europa.eu/food/food/biotechnology/evaluation/index_en.htm). Accordingly, it is not surprising that EU citizens remain averse to GMOs. Moreover, a Eurobarometer poll lists GMOs as one of the top five environmental issues for which EU citizens feel they lack sufficient information [10]. Despite the overwhelming proliferation of scientific evidence, politicians and policy-makers have ignored the most important stakeholder: society. Indeed, the reviews mentioned above recommend that the EC and Member States should improve their risk communication activities.What have we learned from the experience? Is it prudent and realistic to gauge the public''s views on a new technology before it is put into use? Can we move towards a bioeconomy and continue to ignore society? To address these questions, we focus on GM animals, as these organisms are beginning to reach the market, raise many similar issues to GM plants and thus have the potential to re-open the GM debate. GM animals, if brought into use, will involve a similar range and distribution of stakeholders in the EU, with two significant differences: animal welfare organizations will probably take the lead over environmental NGOs in the anti-GM side, and the breeding industry is far more cautious in adopting GM animals than the plant seed industry was to adopt GM crops [11].It is generally accepted that risk management in food safety crucially depends on efficient risk communicationGloFish^®—a GM fish that glows when illuminated with UV light and is being sold as a novelty pet—serves as an illustrative example. GloFish^® was the first GM animal to reach the market and, more importantly, did so without any negative media coverage. It is also a controversial application of GM technology, as animal welfare organizations and scientists alike consider it a frivolous use of GM, describing it as “complete nonsense” [18]. The GloFish^® is not allowed in the EU, but it is commercially available throughout the USA, except in California. One might imagine that consumers in general would not be that interested in GloFish^®, as research indicates that consumer acceptance of a new product is usually higher when there are clear perceived benefits [13,14]. It is difficult to imagine the benefit of GloFish^® beyond its novelty, and yet it has been found illegally in the Netherlands, Germany and the UK [15]. This highlights the futility of predicting the public''s views without consulting them.Consumer attitudes and behaviour—including in regard to GMOs—are complex and change over time [13,14]. During the past years, the perception from academia and governments of the public has moved away from portraying them as a ‘victim'' of industry towards recognizing consumers as an important factor for change. Still, such arguments put citizens at the end of the production chain where they can only exert their influence by choosing to buy or to ignore certain products. Indeed, one of the strongest arguments against GM crops has been that the public never asked for them in the first place.With GM animals, the use of recombinant DNA technologies in animal breeding would rekindle an old battle between animal welfare organizations and the meat industryWith GM animals, the use of recombinant DNA technologies in animal breeding would rekindle an old battle between animal welfare organizations and the meat industry. Animal welfare organizations claim that European consumers demand better treatment for farm animals, whilst industry maintains that price remains one of the most important factors for consumers [12]. Both sides have facts to support their claims: animal welfare issues take a prominent role in the political agenda and animal welfare organizations are growing in both number and influence; industry can demonstrate a competitive disadvantage over countries in which animal welfare regulations are more relaxed and prices are lower, such as Argentina. However, the public is absent in this debate.Consumers have been described as wearing two hats: one that supports animal welfare and one that looks at the price ticket at the supermarket [16]. This situation has an impact on the breeding of livestock and the meat industry, which sees consumer prices decreasing whilst production costs increase. This trend is believed to reflect the increasing detachment of consumers from the food production chain [17]. Higher demands on animal welfare standards, environmental protection and competing international meat producers all influence the final price of meat. To remain competitive, the meat industry has to increase production per unit; it can therefore be argued that one of the main impetuses to develop GM animals was created by the behaviour—not belief—of consumers. This second example illustrates once again that society cannot be ignored when discussing any strategy to move towards the bioeconomy.The EU''s obsession with assessing risk and side-lining benefits has not facilitated an open dialogueIn conclusion, we believe that functional risk management requires all three components, including risk communication. For applications of biotechnology, a disproportionate amount of emphasis has been placed on risk assessment. The result is that the GMO debate has been framed as black and white, as either safe or unsafe, leaving policy-makers with the difficult task of educating the public about the many shades of grey. However, there are a wide range of issues that a citizen will want take into account when deciding about GM, and not all of them can be answered by science. Citizens might trust what scientists say, but “when scientists and politicians are brought together, we may well not trust that the quality of science will remain intact” [18]. By reducing the debate to scientific matters, it is a free card for the misuse of science and has a negative impact on science itself. Whilst scientists publishing pro-GM results have been attacked by NGOs, scientific publications that highlighted potential risks of GM crops came under disproportionate attacks from the scientific community [19].Flexible governance and context need to work hand-in-hand if investments in biotechnology are ultimately to benefit society. The EU''s obsession with assessing risk and side-lining benefits has not facilitated an open dialogue. The GMO experience has also shown that science cannot provide all the answers. Democratically elected governments should therefore take the lead in communicating the risks and benefits of technological advances to their electorate, and should discuss what the bioeconomy really means and the role of new technologies, including GMOs. We need to move the spotlight away from the science alone to take in the bigger picture. Ultimately, do consumers feel that paying a few extra cents for a dozen eggs is worth it if they know the chicken is happy whether it is so-called ‘natural'' or GM?? Open in a separate windowNúria Vàzquez-SalatOpen in a separate windowLouis-Marie Houdebine     

Molecular characterization of methicillin-resistant Panton-valentine leukocidin positive <Emphasis Type="Italic">staphylococcus aureus</Emphasis> clones disseminating in Tunisian hospitals and in the community

Background

The spread of MRSA strains at hospitals as well as in the community are of great concern worldwide. We characterized the MRSA clones isolated at Tunisian hospitals and in the community by comparing them to those isolated in other countries.

Results

We characterized 69 MRSA strains isolated from two Tunisian university hospitals between the years 2004-2008. Twenty-two of 28 (79%) community-associated MRSA (CA-MRSA) strains and 21 of 41 (51%) healthcare-associated MRSA (HA-MRSA) strains were PVL-positive. The PVL-positive strains belonged to predicted founder group (FG) 80 in MLST and carried either type IVc SCCmec or nontypeable SCCmec that harbours the class B mec gene complex. In contrast, very diverse clones were identified in PVL-negative strains: three FGs (5, 15, and 22) for HA-MRSA strains and four FGs (5, 15, 45, and 80) for CA-MRSA strains; and these strains carried the SCCmec element of either type I, III, IVc or was nontypeable. The nucleotide sequencing of phi7401PVL lysogenized in a CA-MRSA strain JCSC7401, revealed that the phage was highly homologous to phiSA2mw, with nucleotide identities of more than 95%. Furthermore, all PVL positive strains were found to carry the same PVL phage, since these strains were positive in two PCR studies, identifying gene linkage between lukS and mtp (major tail protein) and the lysogeny region, both of which are in common with phi7401PVL and phiSa2mw.

Conclusions

Our experiments suggest that FG80 S. aureus strains have changed to be more virulent by acquiring phi7401PVL, and to be resistant to β-lactams by acquiring SCCmec elements. These novel clones might have disseminated in the Tunisian community as well as at the Tunisian hospitals by taking over existing MRSA clones.

     

Lab-Scale Treatability Tests for the Thermal Desorption of Hydrocarbon-Contaminated Soils

Within an integrated management plan for contaminated site remediation at a given territorial scale, the performance of treatability tests could be useful and/or expressly requested by the control authority on a site-specific basis to evaluate the overall feasibility of a given remedial option. The thermal desorption process appears to be a favorable treatment technology for organic contaminants. In this context, a particular lab-scale, indirectly heated desorber for treatability tests was originally developed and first applied to natural soils with different textures (silty sand, loam, silt clay, and clayey silt) that were “ad hoc” highly contaminated with diesel oil at various desorption process conditions (heating temperature in the range of 300–390°C, and reactor retention time in the range of 40–120 min). The Italian soil threshold level for heavy hydrocarbons (C > 12) of 50 mg kg^?1 (dry matter) was assumed to be the successful goal of the treatability studies. In addition to the individuation of the favorable desorption process conditions for each soil, also in terms of a composite evaluation of heating temperature and retention time, the comparative experimental results provided useful indications of the possible influence of soil texture, the reduction of initial soil organic matter, and the evaluation of kinetic rate constants.