Overcoming function annotation errors in the Gram-positive pathogen Streptococcus suis by a proteomics-driven approach

Background: Annotation of protein-coding genes is a key step in sequencing projects. Protein functions are mainly assigned on the basis of the amino acid sequence alone by searching of homologous proteins. However, fully automated annotation processes often lead to wrong prediction of protein functions, and therefore time-intensive manual curation is often essential. Here we describe a fast and reliable way to correct function annotation in sequencing projects, focusing on surface proteomes. We use a proteomics approach, previously proven to be very powerful for identifying new vaccine candidates against Gram-positive pathogens. It consists of shaving the surface of intact cells with two proteases, the specific cleavage-site trypsin and the unspecific proteinase K, followed by LC/MS/MS analysis of the resulting peptides. The identified proteins are contrasted by computational analysis and their sequences are inspected to correct possible errors in function prediction. Results: When applied to the zoonotic pathogen Streptococcus suis, of which two strains have been recently sequenced and annotated, we identified a set of surface proteins without cytoplasmic contamination: all the proteins identified had exporting or retention signals towards the outside and/or the cell surface, and viability of protease-treated cells was not affected. The combination of both experimental evidences and computational methods allowed us to determine that two of these proteins are putative extracellular new adhesins that had been previously attributed a wrong cytoplasmic function. One of them is a putative component of the pilus of this bacterium. Conclusion: We illustrate the complementary nature of laboratory-based and computational methods to examine in concert the localization of a set of proteins in the cell, and demonstrate the utility of this proteomics-based strategy to experimentally correct function annotation errors in sequencing projects. This approach also contributes to provide strong experimental evidences that can be used to annotate those proteins for which a Gene Ontology (GO) term has not been assigned so far. Function annotation correction would then improve the identification of surfaceassociated proteins in bacterial pathogens, thus accelerating the discovery of new vaccines in infectious disease research

Green Carbon: Making sustainable agriculture real

The concept of sustainable development has evolved from a mere movement for the protection of the environment, to other multidimensional approaches. Indeed, today it calls for a holistic approach, seeking to preserve and improve not only the environment, but also to achieve social equity and economic sustainability. In Europe, society demands quality and safe products, not only in the industrial sector but also in agriculture. According to FAO, sustainable agriculture development is a key element of the new global challenges to meet human food security needs at 2050. Unsustainable practices based on intensive soil tillage and agro-chemical applications have increased agri-environmental risks. Whereas world’s food needs are expected to increase by 70% by 2050, agricultural land in Europe will also have to face environmental, economic and social challenges related to sustainable agriculture. As a result, in the EU 2020 Strategy, it is expressed that the new Common Agricultural Policy (CAP) is required to contribute to smart, sustainable and inclusive growth, enhancing social well-being, providing ecosystem services, managing resources sustainably while avoiding environmental degradation. There is broad consensus within the scientific sector that human actions generate a large portion of the greenhouse gas (GHG) emissions, causing global warming. Certainly, Kyoto Protocol states it. According to the European Environmental Agency (EEA), there has been a decrease of 17% in GHG emissions between 1990 and 2009. However, EEA also stressed the importance of the agricultural contribution to total emissions (10.3%). The fossil fuel used in agricultural field operations, along with increasing CO2 emissions from soil through tillage, are considered to be one of the main direct sources of GHG emissions from agriculture sector. Increased inputs required to sustain conventional agriculture also adds significantly to total GHG emissions. Therefore, intensification of production through tillage, agro-chemicals and heavy machinery, which characterizes conventional agriculture in Europe, strongly contributes to increased net GHG emissions instead of mitigating global warming. Sustainable agricultural soil management is crucial for mitigating climate change, especially for the restoration of lost soil organic carbon. In fact, "Agricultural soils management" is recognized as one of the 15 most promising technology options for reducing GHG emissions in the COM (2005) 35 final "Winning the battle against global climate change." The Green Carbon Conference aims to show sustainable management of agricultural soils can help to agriculture mitigate and adapt to climate change, being compatible with the objectives of environmental protection, enhancing biodiversity and supporting farmers’ welfare along with many other environmental, economic and social benefits. Over the last decade, Conservation Agriculture has become known as a set of interlinked agricultural practices, of no or minimum mechanical soil disturbance, maintenance of soil mulch cover, and diversified cropping system, capable of: (a) overcoming several of the severe sustainability limitations of conventional agriculture; and (b) raising productivity, enhancing resilience, reducing degradation and increasing the flow of ecosystem services. The discussion around both the Soil Thematic Strategy initiated in 2002, and the JRC SoCo (Soil Conservation) project clearly recognized the potential of Conservation Agriculture in mitigating and even reversing the problems of soil erosion, soil organic matter decline, soil compaction, loss of biodiversity, climate change vulnerability, among others. Whereas Conservation Agriculture is now practiced successfully on more than 125 million hectares worldwide, Europe has shown to be reluctant with regard to its adoption, despite many promising results confirming its suitability in Europe. Therefore, this European Conference on Green Carbon provides an opportunity to take a leap forward in terms of sharing farmers experiences on Conservation Agriculture across Europe, reviewing the recent progress made in knowledge generation regarding Conservation Agriculture, and to disseminate the outcomes of the currently running LIFE+ Agricarbon (LIFE08 ENV/E/000129). The slogan of ‘Green Carbon’ chosen for this Conference attempts to clarify and highlight the indivisible yet vital link between soil organic carbon and the role that soil health plays in the sustainability of agricultural production and in the flow of ecosystem services. Nevertheless, the topics addressed by the Green Carbon Conference are not only related to the importance of soil organic carbon for the overall soil quality and health, but also include other sustainability issues intimately related to the role of soil carbon such as landscape scale ecosystem functions and services, climate change mitigation and carbon offset, and economic aspects. This Conference also seeks to alert and inform EU policy stakeholders and technical officers of the urgent need to adopt sustainable soil and production practices of Conservation Agriculture to contribute to the objectives of Europe 2020, the EU's growth strategy for the coming decades

Mobilizing Greater Crop and Land Potentials Sustainably

The supply side of the food security engine is the way we farm. The current engine of conventional tillage farming is faltering and needs to be replaced. This presentation will address supply side issues of agriculture to meet future agricultural demands for food and industry using the alternate no-till Conservation Agriculture (CA) paradigm (involving no-till farming with mulch soil cover and diversified cropping) that is able to raise productivity sustainably and efficiently, reduce inputs, regenerate degraded land, minimise soil erosion, and harness the flow of ecosystem services. CA is an ecosystems approach to farming capable of enhancing not only the economic and environmental performance of crop production and land management, but also promotes a mindset change for producing ‘more from less’, the key attitude towards sustainable production intensification. CA is now spreading globally in all continents at an annual rate of 10 Mha and covers some 157 Mha of cropland. Today global agriculture produces enough food to feed three times the current population of 7.21 billion. In 1976, when the world population was 4.15 billion, world food production far exceeded the amount necessary to feed that population. However, our urban and industrialised lifestyle leads to wastage of food of some 30%-40%, as well as waste of enormous amount of energy and protein while transforming crop-based food into animal-derived food; we have a higher proportion of people than ever before who are obese; we continue to degrade our ecosystems including much of our agricultural land of which some 400 Mha is reported to be abandoned due to severe soil and land degradation; and yields of staple cereals appear to have stagnated. These are signs of unsustainability at the structural level in the society, and it is at the structural level, for both supply side and demand side, that we need transformed mind sets about production, consumption and distribution. CA not only provides the possibility of increased crop yields for the low input smallholder farmer, it also provides a pro-poor rural and agricultural development model to support agricultural intensification in an affordable manner. For the high output farmer, it offers greater efficiency (productivity) and profit, resilience and stewardship. For farming anywhere, it addresses the root causes of agricultural land degradation, sub-optimal ecological crop and land potentials or yield ceilings, and poor crop phenotypic expressions or yield gaps. As national economies expand and diversify, more people become integrated into the economy and are able to access food. However, for those whose livelihoods continue to depend on agriculture to feed themselves and the rest of the world population, the challenge is for agriculture to produce the needed food and raw material for industry with minimum harm to the environment and the society, and to produce it with maximum efficiency and resilience against abiotic and biotic stresses, including those arising from climate change. There is growing empirical and scientific evidence worldwide that the future global supplies of food and agricultural raw materials can be assured sustainably at much lower environmental and economic cost by shifting away from conventional tillage-based food and agriculture systems to no-till CA-based food and agriculture systems. To achieve this goal will require effective national and global policy and institutional support (including research and education)

Seroprevalencia de las infecciones por el virus Diarrea Vírica Bovina en ganado bovino en Andalucía

Se ha realizado un estudio seroepidemiológico frente al virus de la Diarrea Vírica Bovina (vDVB) en la cabaña bovina andaluza, utilizando para ello un ELISA indirecto para la detección de anticuerpos frente a una proteína altamente conservada (p80). Después de eliminar los animales vacunados, la encuesta se realizó sobre 4.768 individuos pertenecientes a 227 colectivos no vacunados frente al vDVB, mediante muestreo estadístico para un nivel de confianza del 95 por ciento. La seropositividad obtenida ha sido del 42,3 por ciento de los individuos analizados, mientras que la prevalencia estimada de rebaños seropositivos alcanzó el 70,9 por ciento. La proporción de bovinos persistentemente infectados (IP) encontrada en la muestra (0,063 % de los individuos y 1,32 de los colectivos), ha sido más baja de la esperada en función de la alta seroprevalencia detectada, hecho que demuestra que la supervivencia de estos animales lógicamente está condicionada

Making Climate Change Mitigation and Adaptability Real in Africa with Conservation Agriculture

In this report, the authors have gathered essential information on how the agricultural sector can respond to climate change through Conservation Agriculture (CA). This document aims to serve as a basis for decision-making based on science and agricultural experimentation in Africa

Infeccions urinàries en mascotes i bacteris multiresistents : estat de la qüestió a Espanya

Molts dels bacteris que causen infecció del tracte urinari (ITU) en persones i animals de companyia ofereixen resistència a un o varis antibiòtics, fet que suposa un repte per a la medicina veterinària i un problema de salut pública. Per orientar els veterinaris en l'ús més apropiat d'antibiòtics, un estudi liderat per investigadores del Departament de Sanitat i Anatomia Animal de la UAB ha actualitzat les dades sobre els bacteris multiresistents detectats en gossos i gats amb ITU a Espanya. Les autores donen suport a les pautes de tractament aplicades avui dia, tot i que reservant els antibiòtics d'ús crític en humans només per al tractament dels casos més greus, i recomanen extremar pràctiques d'higiene i prevenció per minimitzar la transmissió bacteriana entre mascotes i humans.Muchas de las bacterias que causan infección del tracto urinario (ITU) en personas y animales de compañía ofrecen resistencia a uno o varios antibióticos, lo que supone un reto para la medicina veterinaria y un problema de salud pública. Para orientar a los veterinarios en el uso más apropiado de antibióticos, un estudio liderado por investigadoras del Departamento de Sanidad y Anatomía Animal de la UAB ha actualizado los datos sobre las bacterias multirresistentes detectadas en perros y gatos con ITU en España. Las autoras apoyan las pautas de tratamiento aplicadas hoy día, aunque reservando los antibióticos de uso crítico en humanos sólo para el tratamiento de los casos más graves, y recomiendan extremar prácticas de higiene y prevención para minimizar la transmisión bacteriana entre mascotas y humanos

Challenge of Pigs with Classical Swine Fever Viruses after C-Strain Vaccination Reveals Remarkably Rapid Protection and Insights into Early Immunity

Pre-emptive culling is becoming increasingly questioned as a means of controlling animal diseases, including classical swine fever (CSF). This has prompted discussions on the use of emergency vaccination to control future CSF outbreaks in domestic pigs. Despite a long history of safe use in endemic areas, there is a paucity of data on aspects important to emergency strategies, such as how rapidly CSFV vaccines would protect against transmission, and if this protection is equivalent for all viral genotypes, including highly divergent genotype 3 strains. To evaluate these questions, pigs were vaccinated with the Riemser® C-strain vaccine at 1, 3 and 5 days prior to challenge with genotype 2.1 and 3.3 challenge strains. The vaccine provided equivalent protection against clinical disease caused by for the two challenge strains and, as expected, protection was complete at 5 days post-vaccination. Substantial protection was achieved after 3 days, which was sufficient to prevent transmission of the 3.3 strain to animals in direct contact. Even by one day post-vaccination approximately half the animals were partially protected, and were able to control the infection, indicating that a reduction of the infectious potential is achieved very rapidly after vaccination. There was a close temporal correlation between T cell IFN-γ responses and protection. Interestingly, compared to responses of animals challenged 5 days after vaccination, challenge of animals 3 or 1 days post-vaccination resulted in impaired vaccine-induced T cell responses. This, together with the failure to detect a T cell IFN-γ response in unprotected and unvaccinated animals, indicates that virulent CSFV can inhibit the potent antiviral host defences primed by C-strain in the early period post vaccination

SalK/SalR, a Two-Component Signal Transduction System, Is Essential for Full Virulence of Highly Invasive Streptococcus suis Serotype 2

BACKGROUND: Streptococcus suis serotype 2 (S. suis 2, SS2) has evolved into a highly infectious entity, which caused the two recent large-scale outbreaks of human SS2 epidemic in China, and is characterized by a toxic shock-like syndrome. However, the molecular pathogenesis of this new emerging pathogen is still poorly understood. METHODOLOGY/PRINCIPAL FINDINGS: 89K is a newly predicted pathogenicity island (PAI) which is specific to Chinese epidemic strains isolated from these two SS2 outbreaks. Further bioinformatics analysis revealed a unique two-component signal transduction system (TCSTS) located in the candidate 89K PAI, which is orthologous to the SalK/SalR regulatory system of Streptococcus salivarius. Knockout of salKR eliminated the lethality of SS2 in experimental infection of piglets. Functional complementation of salKR into the isogenic mutant DeltasalKR restored its soaring pathogenicity. Colonization experiments showed that the DeltasalKR mutant could not colonize any susceptible tissue of piglets when administered alone. Bactericidal assays demonstrated that resistance of the mutant to polymorphonuclear leukocyte (PMN)-mediated killing was greatly decreased. Expression microarray analysis exhibited a transcription profile alteration of 26 various genes down-regulated in the DeltasalKR mutant. CONCLUSIONS/SIGNIFICANCE: These findings suggest that SalK/SalR is requisite for the full virulence of ethnic Chinese isolates of highly pathogenic SS2, thus providing experimental evidence for the validity of this bioinformatically predicted PAI