A decade of plant proteomics and mass spectrometry: translation of technical advancements to food security and safety issues

Tremendous progress in plant proteomics driven by mass spectrometry (MS) techniques has been made since 2000 when few proteomics reports were published and plant proteomics was in its infancy. These achievements include the refinement of existing techniques and the search for new techniques to address food security, safety, and health issues. It is projected that in 2050, the world’s population will reach 9–12 billion people demanding a food production increase of 34–70% (FAO, 2009) from today’s food production. Provision of food in a sustainable and environmentally committed manner for such a demand without threatening natural resources, requires that agricultural production increases significantly and that postharvest handling and food manufacturing systems become more efficient requiring lower energy expenditure, a decrease in postharvest losses, less waste generation and food with longer shelf life. There is also a need to look for alternative protein sources to animal based (i.e., plant based) to be able to fulfill the increase in protein demands by 2050. Thus, plant biology has a critical role to play as a science capable of addressing such challenges. In this review, we discuss proteomics especially MS, as a platform, being utilized in plant biology research for the past 10 years having the potential to expedite the process of understanding plant biology for human benefits. The increasing application of proteomics technologies in food security, analysis, and safety is emphasized in this review. But, we are aware that no unique approach/technology is capable to address the global food issues. Proteomics-generated information/resources must be integrated and correlated with other omics-based approaches, information, and conventional programs to ensure sufficient food and resources for human development now and in the future.

Frontline safety: understanding the workplace as a site of regulatory engagement

The concept of frontline safety encapsulates an approach to occupational health and safety that emphasizes the 'other side of the regulatory relationship' – the ways in which safety culture, individual responsibility, organizational citizenship, trust, and compliance are interpreted and experienced at the local level. By exploring theoretical tensions over the most appropriate way of conceptualizing and framing frontline regulatory engagement, we can better identify the ways in which conceptions of individuals (as rational, responsible, economic actors) are constructed and maintained through workplace interactions and decision-making, as part of the fulfilment of the ideological and constitutive needs of neoliberal labor markets.

Running Climate Models On The NERC Cluster Grid Using G-Rex

Compute grids are used widely in many areas of environmental science, but there has been limited uptake of grid computing by the climate modelling community, partly because the characteristics of many climate models make them difficult to use with popular grid middleware systems. In particular, climate models usually produce large volumes of output data, and running them usually involves complicated workflows implemented as shell scripts. For example, NEMO (Smith et al. 2008) is a state-of-the-art ocean model that is used currently for operational ocean forecasting in France, and will soon be used in the UK for both ocean forecasting and climate modelling. On a typical modern cluster, a particular one year global ocean simulation at 1-degree resolution takes about three hours when running on 40 processors, and produces roughly 20 GB of output as 50000 separate files. 50-year simulations are common, during which the model is resubmitted as a new job after each year. Running NEMO relies on a set of complicated shell scripts and command utilities for data pre-processing and post-processing prior to job resubmission. Grid Remote Execution (G-Rex) is a pure Java grid middleware system that allows scientific applications to be deployed as Web services on remote computer systems, and then launched and controlled as if they are running on the user's own computer. Although G-Rex is general purpose middleware it has two key features that make it particularly suitable for remote execution of climate models: (1) Output from the model is transferred back to the user while the run is in progress to prevent it from accumulating on the remote system and to allow the user to monitor the model; (2) The client component is a command-line program that can easily be incorporated into existing model work-flow scripts. G-Rex has a REST (Fielding, 2000) architectural style, which allows client programs to be very simple and lightweight and allows users to interact with model runs using only a basic HTTP client (such as a Web browser or the curl utility) if they wish. This design also allows for new client interfaces to be developed in other programming languages with relatively little effort. The G-Rex server is a standard Web application that runs inside a servlet container such as Apache Tomcat and is therefore easy to install and maintain by system administrators. G-Rex is employed as the middleware for the NERC1 Cluster Grid, a small grid of HPC2 clusters belonging to collaborating NERC research institutes. Currently the NEMO (Smith et al. 2008) and POLCOMS (Holt et al, 2008) ocean models are installed, and there are plans to install the Hadley Centre’s HadCM3 model for use in the decadal climate prediction project GCEP (Haines et al., 2008). The science projects involving NEMO on the Grid have a particular focus on data assimilation (Smith et al. 2008), a technique that involves constraining model simulations with observations. The POLCOMS model will play an important part in the GCOMS project (Holt et al, 2008), which aims to simulate the world’s coastal oceans. A typical use of G-Rex by a scientist to run a climate model on the NERC Cluster Grid proceeds as follows :(1) The scientist prepares input files on his or her local machine. (2) Using information provided by the Grid’s Ganglia3 monitoring system, the scientist selects an appropriate compute resource. (3) The scientist runs the relevant workflow script on his or her local machine. This is unmodified except that calls to run the model (e.g. with “mpirun”) are simply replaced with calls to "GRexRun" (4) The G-Rex middleware automatically handles the uploading of input files to the remote resource, and the downloading of output files back to the user, including their deletion from the remote system, during the run. (5) The scientist monitors the output files, using familiar analysis and visualization tools on his or her own local machine. G-Rex is well suited to climate modelling because it addresses many of the middleware usability issues that have led to limited uptake of grid computing by climate scientists. It is a lightweight, low-impact and easy-to-install solution that is currently designed for use in relatively small grids such as the NERC Cluster Grid. A current topic of research is the use of G-Rex as an easy-to-use front-end to larger-scale Grid resources such as the UK National Grid service.

Analytical functions for the ground state potential surfaces of C3 (X 1 Σ g+) and HCN (X 1 Σ +)

Analytic functions have been obtained to represent the potential energy surfaces of C3 and HCN in their ground electronic states. These functions closely reproduce the available data on the energy, geometry, and force constants in all stable conformations, as well as data on the various dissociation products, and ab initio calculations of the energy at other conformations. The form of the resulting surfaces are portrayed in various ways and discussed briefly.

Nutritional and safety assessments of foods and feeds nutritionally improved through biotechnology: Case studies

During the last 2 decades, the public and private sectors have made substantial international research progress toward improving the nutritional value of a wide range of food and feed crops. Nevertheless, significant numbers of people still suffer from the effects of undernutrition. In addition, the nutritional quality of feed is often a limiting factor in livestock production systems, particularly those in developing countries. As newly developed crops with nutritionally improved traits come closer to being available to producers and consumers, we must ensure that scientifically sound and efficient processes are used to assess the safety and nutritional quality of these crops. Such processes will facilitate deploying these crops to those world areas with large numbers of people who need them. This document describes 5 case studies of crops with improved nutritional value. These case studies examine the principles and recommendations published by the Intl. Life Sciences Inst. (ILSI) in 2004 for the safety and nutritional assessment of foods and feeds derived from nutritionally improved crops (ILSI 2004). One overarching conclusion that spans all 5 case studies is that the comparative safety assessment process is a valid approach. Such a process has been endorsed by many publications and organizations, including the 2004 ILSI publication. The type and extent of data that are appropriate for a scientifically sound comparative safety assessment are presented on a case-by-case basis in a manner that takes into account scientific results published since the 2004 ILSI report. This report will appear in the January issue of Comprehensive Reviews in Food Science and Food Safety.

Pea-barley intercropping for efficient symbiotic N-2-fixation, soil N acquisition and use of other nutrients in European organic cropping systems

Complementarity in acquisition of nitrogen (N) from soil and N-2-fixation within pea and barley intercrops was studied in organic field experiments across Western Europe (Denmark, United Kingdom, France, Germany and Italy). Spring pea and barley were sown either as sole crops, at the recommended plant density (P100 and B100, respectively) or in replacement (P50B50) or additive (P100B50) intercropping designs, in each of three cropping seasons (2003-2005). Irrespective of site and intercrop design, Land Equivalent Ratios (LER) between 1.4 at flowering and 1.3 at maturity showed that total N recovery was greater in the pea-barley intercrops than in the sole Crops Suggesting a high degree of complementarity over a wide range of growing conditions. Complementarity was partly attributed to greater soil mineral N acquisition by barley, forcing pea to rely more on N-2-fixation. At all sites the proportion of total aboveground pea N that was derived from N-2-fixation was greater when intercropped with barley than when grown as a sole crop. No consistent differences were found between the two intercropping designs. Simultaneously, the accumulation Of Phosphorous (P), potassium (K) and sulphur (S) in Danish and German experiments was 20% higher in the intercrop (P50B50) than in the respective sole crops, possibly influencing general crop yields and thereby competitive ability for other resources. Comparing all sites and seasons, the benefits of organic pea-barley intercropping for N acquisition were highly resilient. It is concluded that pea-barley intercropping is a relevant cropping strategy to adopt when trying to optimize N-2-fixation inputs to the cropping system. (C) 2009 Elsevier B.V. All rights reserved.

Pollination and other ecosystem services produced by mobile organisms: a conceptual framework for the effects of land-use change

Many ecosystem services are delivered by organisms that depend on habitats that are segregated spatially or temporally from the location where services are provided. Management of mobile organisms contributing to ecosystem services requires consideration not only of the local scale where services are delivered, but also the distribution of resources at the landscape scale, and the foraging ranges and dispersal movements of the mobile agents. We develop a conceptual model for exploring how one such mobile-agent-based ecosystem service (MABES), pollination, is affected by land-use change, and then generalize the model to other MABES. The model includes interactions and feedbacks among policies affecting land use, market forces and the biology of the organisms involved. Animal-mediated pollination contributes to the production of goods of value to humans such as crops; it also bolsters reproduction of wild plants on which other services or service-providing organisms depend. About one-third of crop production depends on animal pollinators, while 60-90% of plant species require an animal pollinator. The sensitivity of mobile organisms to ecological factors that operate across spatial scales makes the services provided by a given community of mobile agents highly contextual. Services vary, depending on the spatial and temporal distribution of resources surrounding the site, and on biotic interactions occurring locally, such as competition among pollinators for resources, and among plants for pollinators. The value of the resulting goods or services may feed back via market-based forces to influence land-use policies, which in turn influence land management practices that alter local habitat conditions and landscape structure. Developing conceptual models for MABES aids in identifying knowledge gaps, determining research priorities, and targeting interventions that can be applied in an adaptive management context.

Consumer trust, risk and food safety: a review

Consumers' attitudes to trust and risk are key issues in food safety research and attention needs to be focused on clearly defining a framework for analysing consumer behaviour in these terms. In order to achieve this, a detailed review of the recent literature surrounding risk, trust and the relationship between the two must be conducted. This paper aims to collate the current social sciences literature in the fields of food safety, trust and risk. It provides an insight into the economic and other modelling procedures available to measure consumers' attitudes to risk and trust in food safety and specifically notes the need for future research to concentrate on examining risk and trust as inter-related variables rather than two distinct, mutually exclusive concepts. A framework is proposed which it is hoped will assist in devising more effective research to support risk communication to consumers.

Domestically produced food: Consumer perceptions of origin, safety and the issue of trust

It is becoming increasingly difficult for the public to attempt to assess risks using traditional methods such as smell, taste or other physical attributes of food. The existence of extrinsic cues such as the country of origin (COO) of food can help to make food purchase decisions easier for consumers. However, the use of extrinsic cues depends heavily on the extent to which consumers trust such signals to be indicative of quality or safety, which in turn depends on the credibility behind that cue. This paper aims to examine consumers association of domestically produced food with increased food safety standards and the association of COO and food safety information with socio-demographics and other aspects of consumer psychology such as attitudes, risk perception and trust. Using an ordered probit model, domestic production is examined as an extrinsic cue for food safety by looking at the relationship with trust in food safety information provided by national food standards agencies (NFSAs) and other socio-demographic characteristics, based on nationally representative data from 2725 face-to-face interviews across five European countries. Results suggest that domestic production of food is an extrinsic cue for food safety and as consumers place increasing importance on food safety they are more interested in food produced in their own country. This, coupled with consumer trust in a strong, and independent national food standards agency, suggests the potential exists for the increased consumption of domestically produced foods.

Fox-hunting in England and Wales: its contribution to the management of woodland and other habitats

Hunting foxes with hounds has been a countryside pursuit in Britain since the 17th Century, but its effect nationally on habitat management is little understood by the general public. A survey questionnaire was distributed to 163 mounted fox hunts of England and Wales to quantify their management practices in woodland and other habitat. Ninety-two hunts (56%), covering 75,514 km(2), returned details on woodland management motivated by the improvement of their sport. The management details were verified via on-site visits for a sample of 200 woodlands. Following verification, the area of woodlands containing the management was conservatively estimated at 24,053 (+/- 2241) ha, comprising 5.9% of woodland area within the whole of the area hunted by the 92 hunts. Management techniques included: tree planting, coppicing, felling, ride and perimeter management. A case study in five hunt countries in southern England examined, through the use of botanical survey and butterfly counts, the consequences of the hunt management on woodland ground flora and butterflies. Managed areas had, within the last 5 years, been coppiced and rides had been cleared. Vegetation cover in managed and unmanaged sites averaged 86% and 64%, respectively, and managed areas held on average 4 more plant species and a higher plant diversity than unmanaged areas (Shannon index of diversity: 2.25 vs. 1.95). Both the average number of butterfly species (2.2 vs. 0.3) and individuals counted (4.6 vs. 0.3) were higher in the managed than unmanaged sites.

CCL3, acting via the chemokine receptor CCR5, leads to independent activation of Janus kinase 2 (JAK2) and G(i) proteins

The interaction of the chemokine receptor, CCR5, expressed in recombinant cells, with different G proteins was investigated and CCR5 was found to interact with G(i), G(o) and G(q) species. Interaction with Gi leads to G protein activation, whereas G. does not seem to be activated. Additionally, CCR5 activation also leads to phosphorylation of Janus kinase 2 (JAK2). Activation of JAK2 is independent of Gi or Gq activation. Gi protein activation was not prevented by inhibition of JAK, showing that heterotrimeric G protein activation and activation of the JAK/signal transducer and activator of transcription (STAT) pathway are independent of each other. (C) 2004 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.