Bacteria Modulate the CD8+ T Cell Epitope Repertoire of Host Cytosol-Exposed Proteins to Manipulate the Host Immune Response

The main adaptive immune response to bacteria is mediated by B cells and CD4+ T-cells. However, some bacterial proteins reach the cytosol of host cells and are exposed to the host CD8+ T-cells response. Both gram-negative and gram-positive bacteria can translocate proteins to the cytosol through type III and IV secretion and ESX-1 systems, respectively. The translocated proteins are often essential for the bacterium survival. Once injected, these proteins can be degraded and presented on MHC-I molecules to CD8+ T-cells. The CD8+ T-cells, in turn, can induce cell death and destroy the bacteria's habitat. In viruses, escape mutations arise to avoid this detection. The accumulation of escape mutations in bacteria has never been systematically studied. We show for the first time that such mutations are systematically present in most bacteria tested. We combine multiple bioinformatic algorithms to compute CD8+ T-cell epitope libraries of bacteria with secretion systems that translocate proteins to the host cytosol. In all bacteria tested, proteins not translocated to the cytosol show no escape mutations in their CD8+ T-cell epitopes. However, proteins translocated to the cytosol show clear escape mutations and have low epitope densities for most tested HLA alleles. The low epitope densities suggest that bacteria, like viruses, are evolutionarily selected to ensure their survival in the presence of CD8+ T-cells. In contrast with most other translocated proteins examined, Pseudomonas aeruginosa's ExoU, which ultimately induces host cell death, was found to have high epitope density. This finding suggests a novel mechanism for the manipulation of CD8+ T-cells by pathogens. The ExoU effector may have evolved to maintain high epitope density enabling it to efficiently induce CD8+ T-cell mediated cell death. These results were tested using multiple epitope prediction algorithms, and were found to be consistent for most proteins tested

Submarine canyons represent an essential habitat network for krill hotspots in a Large Marine Ecosystem

Submarine canyon systems are ubiquitous features of marine ecosystems, known to support high levels of biodiversity. Canyons may be important to benthic-pelagic ecosystem coupling, but their role in concentrating plankton and structuring pelagic communities is not well known. We hypothesize that at the scale of a large marine ecosystem, canyons provide a critical habitat network, which maintain energy flow and trophic interactions. We evaluate canyon characteristics relative to the distribution and abundance of krill, critically important prey in the California Current Ecosystem. Using a geological database, we conducted a census of canyon locations, evaluated their dimensions, and quantified functional relationships with krill hotspots (i.e., sites of persistently elevated abundance) derived from hydro-acoustic surveys. We found that 76% of krill hotspots occurred within and adjacent to canyons. Most krill hotspots were associated with large shelf-incising canyons. Krill hotspots and canyon dimensions displayed similar coherence as a function of latitude and indicate a potential regional habitat network. The latitudinal migration of many fish, seabirds and mammals may be enhanced by using this canyon-krill network to maintain foraging opportunities. Biogeographic assessments and predictions of krill and krill-predator distributions under climate change may be improved by accounting for canyons in habitat models

(Blue) Growth accounting in small-scale European Union fleets

Fisheries account for one-third of the total jobs in the global ocean economies. Small scale fleets (SSF) fisheries are the main segment from the number of jobs point of view, and in the EU, SSF account for over 40% of employment in the fisheries sector. Given this marine employment source, it is important to analyse SSF's productivity growth. This was done using Total Factor Productivity (TFP), which is dened as the portion of output not explained by the traditionally measured inputs of labour, energy and capital used in production. TFP calculation is relevant to understand the technology evolution in fisheries and as a reference for management assessment. TFP was calculated for SSF in two EU main sea areas, the Mediterranean (FAO area 37) and the North-East Atlantic (FAO area 27). Constant elasticity production functions were used to analyse the intensity of the use of production factors and how these are substituted or complemented when producing. Additionally, TFP was corrected by stock evolution indexes to evaluate the EU conservation policy. Results showed how the TFP presented signs of stagnation when stocks status were considered. This implies a low technological evolution and that the use of production factors is to be reduced in the following years. It was concluded that in the North-East Atlantic the EU conservation policy is obtaining the objective of restoring fish stocks and contributing to maintaining the productivity. In the Mediterranean, the stocks are not being restored, therefore not contributing to growth as a production factor. Finally, it is concluded that in neither areas the conservation policy is enough to provide positive productivity trends.JRC.D.2-Water and Marine Resource

Review of Underwater and In-Air Sounds Emitted by Australian and Antarctic Marine Mammals

The study of marine soundscapes is a growing field of research. Recording hardware is becoming more accessible; there are a number of off-the-shelf autonomous recorders that can be deployed for months at a time; software analysis tools exist as shareware; rawor preprocessed recordings are freely and publicly available. However, what is missing are catalogues of commonly recorded sounds. Sounds related to geophysical events (e.g. earthquakes) and weather (e.g. wind and precipitation), to human activities (e.g. ships) and to marine animals (e.g. crustaceans, fish and marine mammals) commonly occur. Marine mammals are distributed throughout Australia's oceans and significantly contribute to the underwater soundscape. However, due to a lack of concurrent visual and passive acoustic observations, it is often not known which species produces which sounds. To aid in the analysis of Australian and Antarctic marine soundscape recordings, a literature review of the sounds made by marine mammals was undertaken. Frequency, duration and source level measurements are summarised and tabulated. In addition to the literature review, new marine mammal data are presented and include recordings from Australia of Omura's whales (Balaenoptera omurai), dwarf sperm whales (Kogia sima), common dolphins (Delphinus delphis), short-finned pilot whales (Globicephala macrorhynchus), long-finned pilot whales (G. melas), Fraser's dolphins (Lagenodelphis hosei), false killer whales (Pseudorca crassidens), striped dolphins (Stenella coeruleoalba) and spinner dolphins (S. longirostris), as well as the whistles and burst-pulse sounds of Australian pygmy killer whales (Feresa attenuata). To date, this is the most comprehensive acoustic summary for marine mammal species in Australian waters