The Aeromonas salmonicida subsp. salmonicida exoproteome: global analysis, moonlighting proteins and putative antigens for vaccination against furunculosis

BACKGROUND Aeromonas salmonicida subsp. salmonicida, the etiologic agent of furunculosis, is a major pathogen of fisheries worldwide. Despite the identification of several virulence factors the pathogenesis is still poorly understood. We have used high-throughput proteomics to display the differences between in vitro secretome of A. salmonicida wild-type (wt, hypervirulent, JF5054) and T3SS-deficient (isogenic ΔascV, extremely low-virulent, JF2747) strains in exponential (GP) and stationary (SP) phases of growth. RESULTS Among the different experimental conditions we obtained semi-quantitative values for a total of 2136 A. salmonicida proteins. Proteins of specific A. salmonicida species were proportionally less detected than proteins common to the Aeromonas genus or those shared with other Aeromonas species, suggesting that in vitro growth did not induce the expression of these genes. Four detected proteins which are unidentified in the genome of reference strains of A. salmonicida were homologous to components of the conjugative T4SS of A. hydrophila pRA1 plasmid. Polypeptides of three proteins which are specific to the 01-B526 strain were also discovered. In supernatants (SNs), the number of detected proteins was higher in SP (326 for wt vs 329 for mutant) than in GP (275 for wt vs 263 for mutant). In pellets, the number of identified proteins (a total of 1536) was approximately the same between GP and SP. Numerous highly conserved cytoplasmic proteins were present in A. salmonicida SNs (mainly EF-Tu, EF-G, EF-P, EF-Ts, TypA, AlaS, ribosomal proteins, HtpG, DnaK, peptidyl-prolyl cis-trans isomerases, GAPDH, Enolase, FbaA, TpiA, Pgk, TktA, AckA, AcnB, Mdh, AhpC, Tpx, SodB and PNPase), and several evidences support the theory that their extracellular localization was not the result of cell lysis. According to the Cluster of Orthologous Groups classification, 29% of excreted proteins in A. salmonicida SNs were currently poorly characterized. CONCLUSIONS In this part of our work we elucidated the whole in vitro exoproteome of hypervirulent A. salmonicida subsp. salmonicida and showed the secretion of several highly conserved cytoplasmic proteins with putative moonlighting functions and roles in virulence. All together, our results offer new information about the pathogenesis of furunculosis and point out potential candidates for vaccine development.

Global lymphoid tissue remodeling during a viral infection is orchestrated by a B cell-lymphotoxin-dependent pathway

Adaptive immune responses are characterized by substantial restructuring of secondary lymphoid organs. The molecular and cellular factors responsible for virus-induced lymphoid remodeling are not well known to date. Here we applied optical projection tomography, a mesoscopic imaging technique, for a global analysis of the entire 3-dimensional structure of mouse peripheral lymph nodes (PLNs), focusing on B-cell areas and high endothelial venule (HEV) networks. Structural homeostasis of PLNs was characterized by a strict correlation between total PLN volume, B-cell volume, B-cell follicle number, and HEV length. After infection with lymphocytic choriomeningitis virus, we observed a substantial, lymphotoxin (LT) beta-receptor-dependent reorganization of the PLN microarchitecture, in which an initial B-cell influx was followed by 3-fold increases in PLN volume and HEV network length on day 8 after infection. Adoptive transfer experiments revealed that virus-induced PLN and HEV network remodeling required LTalpha(1)beta(2)-expressing B cells, whereas the inhibition of vascular endothelial growth factor-A signaling pathways had no significant effect on PLN expansion. In summary, lymphocytic choriomeningitis virus-induced PLN growth depends on a vascular endothelial growth factor-A-independent, LT- and B cell-dependent morphogenic pathway, as revealed by an in-depth mesoscopic analysis of the global PLN structure.

The Chemical Space of Flavours

The flavour of foods is determined by the interaction of taste molecules with receptors in the mouth, and fragrances or aroma with receptors in the upper part of the nose. Here, we discuss the properties of taste and fragrance molecules, from the public databases Superscent, Flavornet, SuperSweet and BitterDB, taken collectively as flavours, in the perspective of the chemical space. We survey simple descriptor profiles in comparison with the public collections ChEMBL (bioactive small molecules), ZINC (commercial drug-like molecules) and GDB-13 (all possible organic molecules up to 13 atoms of C, N, O, S, Cl). A global analysis of the chemical space of flavours is also presented based on molecular quantum numbers (MQN) and SMILES fingerprints (SMIfp). While taste molecules span a very broad property range, fragrances occupy a narrow area of the chemical space consisting of generally very small and relatively nonpolar molecules distinct of standard drug molecules. Proximity searching in the chemical space is exemplified as a simple method to facilitate the search for new fragrances.

CODE ultra-rapid product series for the IGS

CODE, the Center for Orbit Determination in Europe, is a joint venture of the following four institutions: Astronomical Institute, University of Bern (AIUB), Bern, Switzerland; Federal Office of Topography swisstopo, Wabern, Switzerland; Federal Agency of Cartography and Geodesy (BKG), Frankfurt a. M., Germany; Institut für Astronomische und Physikalische Geodäsie, Technische Universität München (IAPG, TUM), Munich, Germany. It acts as a global analysis center of the International GNSS Service (IGS). The operational computations are performed at AIUB using the latest development version of the Bernese GNSS Software. In this context an ultra-rapid solution series is generated considering GPS and GLONASS satellites. It is updated several times per day and contains 24 hours of observed and 24 hours of predicted orbit interval. More details are available in: Lutz, S., G. Beutler, S. Schaer, R. Dach, A. Jäggi; 2014: CODE's new ultra-rapid orbit and ERP products for the IGS. GPS Solutions. DOI 10.1007/s10291-014-0432-2

CODE repro2 product series for the IGS

CODE, the Center for Orbit Determination in Europe, is a joint venture of the following four institutions: • Astronomical Institute, University of Bern (AIUB), Bern, Switzerland • Federal Office of Topography swisstopo, Wabern, Switzerland • Federal Agency of Cartography and Geodesy (BKG), Frankfurt a. M., Germany • Institut für Astronomische und Physikalische Geodäsie, Technische Universität München (IAPG, TUM), Munich, Germany It acts as a global analysis center of the International GNSS Service (IGS, Dow et al, 2009). The operational computations are performed at AIUB using the latest development version of the Bernese GNSS Software (Dach et al., 2015). In this context the contribution to the IGS repro02 effort is generated considering only the GPS satellites between 1994 and 2001 as well as the GPS and GLONASS satellites from 2002 to the end of 2013.

CODE rapid product series for the IGS

CODE, the Center for Orbit Determination in Europe, is a joint venture of the following four institutions: Astronomical Institute, University of Bern (AIUB), Bern, Switzerland;Federal Office of Topography swisstopo, Wabern, Switzerland; Federal Agency of Cartography and Geodesy (BKG), Frankfurt a. M., Germany; Institut für Astronomische und Physikalische Geodäsie, Technische Universität München (IAPG, TUM), Munich, Germany. It acts as a global analysis center of the International GNSS Service (IGS). The operational computations are performed at AIUB using the latest development version of the Bernese GNSS Software (Dach et al., 2015). In this context a rapid solution series is generated considering all active GPS and GLONASS satellites. It contains 24 hours of observed orbits and published at the day after the observations.

CODE final product series for the IGS

CODE, the Center for Orbit Determination in Europe, is a joint venture of the following four institutions:Astronomical Institute, University of Bern (AIUB), Bern, Switzerland; Federal Office of Topography swisstopo, Wabern, Switzerland; Federal Agency of Cartography and Geodesy (BKG), Frankfurt a. M., Germany; Institut für Astronomische und Physikalische Geodäsie, Technische Universität München (IAPG, TUM), Munich, Germany. It acts as a global analysis center of the International GNSS Service (IGS). The operational computations are performed at AIUB using the latest development version of the Bernese GNSS Software. In this context a final solution series is generated considering all active GPS and GLONASS satellites. It is published in daily files with a delay of about two weeks.

CODE product series for the IGS-MGEX project

CODE, the Center for Orbit Determination in Europe, is a joint venture of the following four institutions: Astronomical Institute, University of Bern (AIUB), Bern, Switzerland; Federal Office of Topography swisstopo, Wabern, Switzerland; Federal Agency of Cartography and Geodesy (BKG), Frankfurt a. M., Germany; Institut für Astronomische und Physikalische Geodäsie, Technische Universität München (IAPG, TUM), Munich, Germany. It acts as a global analysis center of the International GNSS Service (IGS). The operational computations are performed at AIUB using the latest development version of the Bernese GNSS Software. In this context a multi-GNSS solution is generated considering all active GPS, GLONASS, Galileo, BeiDou (expect for GEOs), and QZSS satellites as a contribution to the IGS-MGEX project. The results are published with a delay of about two weeks.

The CODE MGEX orbit and clock solution

The Center for Orbit Determination in Europe (CODE) is contributing as a global Analysis center to the International GNSS Service (IGS) since many years. The processing of GPS and GLONASS data is well established in CODE’s ultra-rapid, rapid, and final product lines. With the introduction of new signals for the established and new GNSS, new challenges and opportunities are arising for the GNSS data management and processing. The IGS started the Multi-GNSS-EXperiment (MGEX) in 2012 in order to gain first experience with the new data formats and to develop new strategies for making optimal use of these additional measurements. CODE has started to contribute to IGS MGEX with a consistent, rigorously combined triple-system orbit solution (GPS, GLONASS, and Galileo). SLR residuals for the computed Galileo satellite orbits are of the order of 10 cm. Furthermore CODE established a GPS and Galileo clock solution. A quality assessment shows that these experimental orbit and clock products allow even a Galileo-only precise point positioning (PPP) with accuracies on the decimeter- (static PPP) to meter-level (kinematic PPP) for selected stations.

Imaging the South Pole-Aitken basin in backscattered neutral hydrogen atoms

The lunar surface is very efficient in reflecting impinging solar wind ions as energetic neutral atoms (ENAs). A global analysis of lunar hydrogen ENAs showed that on average 16% of the solar wind protons are reflected, and that the reflected fraction can range from less than 8% to more than 24%, depending on location. It is established that magnetic anomalies reduce the flux of backscattered hydrogen ENAs by screening-off a fraction of the impinging solar wind. The effects of the surface properties, such as porosity, roughness, chemical composition, and extent of weathering, were not known. In this paper, we conduct an in-depth analysis of ENA observations of the South Pole-Aitken basin to determine which of the surface properties might be responsible for the observed variation in the integral ENA flux. The South Pole-Aitken basin with its highly variable surface properties is an ideal object for such studies. It is very deep, possesses strikingly elevated concentrations in iron and thorium, has a low albedo and coincides with a cluster of strong magnetic anomalies located on the northern rim of the basin. Our analysis shows that whereas, as expected, the magnetic anomalies can account well for the observed ENA depletion at the South Pole-Aitken basin, none of the other surface properties seem to influence the ENA reflection efficiency. Therefore, the integral flux of backscattered hydrogen ENAs is mainly determined by the impinging plasma flux and ENA imaging of backscattered hydrogen captures the electrodynamics of the plasma at the surface. We cannot exclude minor effects by surface features. (C) 2015 Elsevier Ltd. All rights reserved.

CODE final product series for the IGS

CODE, the Center for Orbit Determination in Europe, is a joint venture of the following four institutions:Astronomical Institute, University of Bern (AIUB), Bern, Switzerland; Federal Office of Topography swisstopo, Wabern, Switzerland; Federal Agency of Cartography and Geodesy (BKG), Frankfurt a. M., Germany; Institut für Astronomische und Physikalische Geodäsie, Technische Universität München (IAPG, TUM), Munich, Germany. It acts as a global analysis center of the International GNSS Service (IGS). The operational computations are performed at AIUB using the latest development version of the Bernese GNSS Software. In this context a final solution series is generated considering all active GPS and GLONASS satellites. It is published in daily files with a delay of about two weeks.

Combining spatial-temporal and phylogenetic analysis approaches for improved understanding on global H5N1 transmission

Background Since late 2003, the highly pathogenic influenza A H5N1 had initiated several outbreak waves that swept across the Eurasia and Africa continents. Getting prepared for reassortment or mutation of H5N1 viruses has become a global priority. Although the spreading mechanism of H5N1 has been studied from different perspectives, its main transmission agents and spread route problems remain unsolved. Methodology/Principal Findings Based on a compilation of the time and location of global H5N1 outbreaks from November 2003 to December 2006, we report an interdisciplinary effort that combines the geospatial informatics approach with a bioinformatics approach to form an improved understanding on the transmission mechanisms of H5N1 virus. Through a spherical coordinate based analysis, which is not conventionally done in geographical analyses, we reveal obvious spatial and temporal clusters of global H5N1 cases on different scales, which we consider to be associated with two different transmission modes of H5N1 viruses. Then through an interdisciplinary study of both geographic and phylogenetic analysis, we obtain a H5N1 spreading route map. Our results provide insight on competing hypotheses as to which avian hosts are responsible for the spread of H5N1. Conclusions/Significance We found that although South China and Southeast Asia may be the virus pool of avian flu, East Siberia may be the source of the H5N1 epidemic. The concentration of migratory birds from different places increases the possibility of gene mutation. Special attention should be paid to East Siberia, Middle Siberia and South China for improved surveillance of H5N1 viruses and monitoring of migratory birds.

Challenges for Participatory Conservation in Times of Global Change: Lessons from a Comparative Analysis and New Developments

Participatory approaches to conservation have been applied worldwide by governments and non-governmental organisations. However, results from a comparative analysis of the impacts of global change on management issues in 13 protected areas in Africa, Latin America, Asia, and Europe show that in many cases the involvement of local people has remained limited, and economic gains for local livelihoods have been limited or non-existent. Viewed from a ‘new institutionalist’ perspective and focusing on power relations and ideologies, the results of this study carried out within the framework of the Swiss National Centre of Competence in Research (NCCR) North-South show that in African cases local people do not feel part of the process and, therefore, become disengaged. In Asia, and even more so in Latin America, local indigenous peoples and their leaders support protected areas as a means to gain political rights over areas threatened by immigration. The European (Swiss) case is the only one where political rights and economic incentives present a context in which participation is of direct interest to local people. Meanwhile, recent debates on new global conservation developments in the context of climate change policy indicate a growing tendency to treat conservation as a commodity. We argue that this can have problematical effects on efforts to devolve power to the local level in the context of conservation.