Inclusion of ecological, economic, social, and institutional considerations when setting targets and limits for multispecies fisheries

Targets and limits for long-term management are used in fisheries advice to operationalize the way management reflects societal priorities on ecological, economic, social and institutional aspects. This study reflects on the available published literature as well as new research presented at the international ICES/Myfish symposium on targets and limits for long term fisheries management. We examine the inclusion of ecological, economic, social and institutional objectives in fisheries management, with the aim of progressing towards including all four objectives when setting management targets or limits, or both, for multispecies fisheries. The topics covered include ecological, economic, social and governance objectives in fisheries management, consistent approaches to management, uncertainty and variability, and fisheries governance. We end by identifying ten ways to more effectively include multiple objectives in setting targets and limits in ecosystem based fisheries management

A generic approach to develop a trait-based indicator of trawling-induced disturbance

Biological trait analysis has become a popular tool to infer the vulnerability of benthic species to trawling-induced disturbance. Approaches using multiple traits are being developed, but their generic relevance across faunal components and geographic locations remains poorly tested, and the importance of confounding effects are poorly recognised. This study integrates biological traits of benthic species that are responsive to instantaneous effects of trawling (i.e. sensitivity) and traits expressing recoverability over the longer term (i.e. years). We highlight the functional independence between these 2 components in response to trawling, test the behaviours of single and combined traits and account for potential confounding effects of environment and trawling intensity on benthic communities through variation partitioning. Two case studies are considered: epibenthos from the Bay of Biscay and endobenthos of the Dutch sector of the North Sea. The response to trawling is most pronounced when multiple traits covering different aspects that determine population dynamics (i.e. sensitivity and recoverability) are combined, despite confounding effects between gradients of benthic production and trawling intensity, especially for endobenthos. The integration of traits reflecting both sensitivity and recoverability provides complementary information on the faunal response to trawling, bridging the gap between fishing impact assessments and benthic community status assessment

VMSbase: An R-Package for VMS and Logbook Data Management and Analysis in Fisheries Ecology

VMSbase is an R package devised to manage, process and visualize information about fishing vessels activity (provided by the vessel monitoring system--VMS) and catches/landings (as reported in the logbooks). VMSbase is primarily conceived to be user-friendly; to this end, a suite of state-of-the-art analyses is accessible via a graphical interface. In addition, the package uses a database platform allowing large datasets to be stored, managed and processed vey efficiently. Methodologies include data cleaning, that is removal of redundant or evidently erroneous records, and data enhancing, that is interpolation and merging with external data sources. In particular, VMSbase is able to estimate sea bottom depth for single VMS pings using an on-line connection to the National Oceanic and Atmospheric Administration (NOAA) database. It also allows VMS pings to be assigned to whatever geographic partitioning has been selected by users. Standard analyses comprise: 1) métier identification (using a modified CLARA clustering approach on Logbook data or Artificial Neural Networks on VMS data); 2) linkage between VMS and Logbook records, with the former organized into fishing trips; 3) discrimination between steaming and fishing points; 4) computation of spatial effort with respect to user-selected grids; 5) calculation of standard fishing effort indicators within Data Collection Framework; 6) a variety of mapping tools, including an interface for Google viewer; 7) estimation of trawled area. Here we report a sample workflow for the accessory sample datasets (available with the package) in order to explore the potentialities of VMSbase. In addition, the results of some performance tests on two large datasets (1×10(5) and 1×10(6) VMS signals, respectively) are reported to inform about the time required for the analyses. The results, although merely illustrative, indicate that VMSbase can represent a step forward in extracting and enhancing information from VMS/logbook data for fisheries studies

Proteome-wide Lysine Glutarylation Profiling of the <i>Mycobacterium tuberculosis</i> H37Rv

Lysine glutarylation, a new protein posttranslational modification (PTM), was recently identified and characterized in both prokaryotic and eukaryotic cells. To explore the distribution of lysine glutarylation in <i>Mycobacterium tuberculsosis</i>, by using a comprehensive method combining the immune affinity peptide enrichment by the glutaryl-lysine antibody with LC–MS, we finally identified 41 glutarylation sites in 24 glutarylated proteins from <i>M. tuberculosis</i>. These glutarylated proteins are involved in various cellular functions such as translation and metabolism and exhibit diverse subcellular localizations. Three common glutarylated proteins including 50S ribosomal protein L7/L12, elongation factor Tu, and dihydrolipoamide succinyltransferase are shared between <i>Escherichia coli</i> and <i>M. tuberculosis</i>. Moreover, comparison with other PTMs characterized in <i>M. tuberculosis</i>, 15 glutarylated proteins, are found to be both acetylated and succinylated. Notably, several stress-response-associated proteins including HspX are glutarylated. Our data provide the first analysis of <i>M. tuberculosis</i> lysine glutarylated proteins. Further studies on the role of the glutarylated proteins will unveil the molecular mechanisms of glutarylation underlying <i>M. tuberculosis</i> physiology and pathogenesis