Unravelling the scientific potential of high resolution fishery data

Fisheries science and fisheries management advice rely on both scientific and commercial data to estimate the distribution and abundance of marine species. These two data types differ, with scientific data having a broader geographical coverage but less intensity and time coverage compared to commercial data. Here we present a new type of commercial data with high resolution and coverage. To our knowledge, the dataset presented in this study has never been used for scientific purposes. While commercial datasets usually include the total weight by species on per haul basis, the new data also include the commercial size class for the species landed, recorded directly on a haul-by-haul basis. Thus, this dataset has the potential to provide knowledge on landed fish with as high spatio-temporal resolution as when coupling logbooks and sales slips but with the addition of detailed knowledge on the size distribution. Such information may otherwise be obtained through on-board observer programmes but unlike the observers’ data, the dataset presented here is routinely collected on most of the trips of the vessels involved, which means that the coverage of the data for the individual vessel is larger than observers’ data. Furthermore, the risk of changes in fishing behaviour due to the presence of an observer on-board is avoided. This paper describes the coverage and completeness of the dataset, and explores the reliability of the data available. We conclude that the main limitation is the small number of fishing vessels covered by the program, but that the data from those vessels are accurate, detailed, and relatively reliable

Unravelling the scientific potential of high resolution fishery data

Fisheries science and fisheries management advice rely on both scientific and commercial data to estimate the distribution and abundance of marine species. These two data types differ, with scientific data having a broader geographical coverage but less intensity and time coverage compared to commercial data. Here we present a new type of commercial data with high resolution and coverage. To our knowledge, the dataset presented in this study has never been used for scientific purposes. While commercial datasets usually include the total weight by species on per haul basis, the new data also include the commercial size class for the species landed, recorded directly on a haul-by-haul basis. Thus, this dataset has the potential to provide knowledge on landed fish with as high spatio-temporal resolution as when coupling logbooks and sales slips but with the addition of detailed knowledge on the size distribution. Such information may otherwise be obtained through on-board observer programmes but unlike the observers’ data, the dataset presented here is routinely collected on most of the trips of the vessels involved, which means that the coverage of the data for the individual vessel is larger than observers’ data. Furthermore, the risk of changes in fishing behaviour due to the presence of an observer on-board is avoided. This paper describes the coverage and completeness of the dataset, and explores the reliability of the data available. We conclude that the main limitation is the small number of fishing vessels covered by the program, but that the data from those vessels are accurate, detailed, and relatively reliable

Cleavage of the urokinase receptor (uPAR) on oral cancer cells: Regulation by transforming growth factor - beta1 (TGF-beta1) and potential effects on migration and invasion

Source at https://doi.org/10.1186/s12885-017-3349-7 Background: Urokinase plasminogen activator (uPA) receptor (uPAR) is up-regulated at the invasive tumour front of human oral squamous cell carcinoma (OSCC), indicating a role for uPAR in tumour progression. We previously observed elevated expression of uPAR at the tumour-stroma interface in a mouse model for OSCC, which was associated with increased proteolytic activity. The tumour microenvironment regulated uPAR expression, as well as its glycosylation and cleavage. Both full-length- and cleaved uPAR (uPAR (II-III)) are involved in highly regulated processes such as cell signalling, proliferation, migration, stem cell mobilization and invasion. The aim of the current study was to analyse tumour associated factors and their effect on uPAR cleavage, and the potential implications for cell proliferation, migration and invasion. Methods: Mouse uPAR was stably overexpressed in the mouse OSCC cell line AT84. The ratio of full-length versus cleaved uPAR as analysed by Western blotting and its regulation was assessed by addition of different protease inhibitors and transforming growth factor - β 1(TGF- β 1). The role of uPAR cleavage in cell proliferation and migration was analysed using real-time cell analysis and invasion was assessed using the myoma invasion model. Results: We found that when uPAR was overexpressed a proportion of the receptor was cleaved, thus the cells presented both full-length uPAR and uPAR (II-III). Cleavage was mainly performed by serine proteases and urokinase plasminogen activator (uPA) in particular. When the OSCC cells were stimulated with TGF- β 1, the production of the uPA inhibitor PAI-1 was increased, resulting in a reduction of uPAR cleavage. By inhibiting cleavage of uPAR, cell migration was reduced, and by inhibiting uPA activity, invasion was reduced. We could also show that medium containing soluble uPAR (suPAR), and cleaved soluble uPAR (suPAR (II-III)), induced migration in OSCC cells with low endogenous levels of uPAR. Conclusions: These results show that soluble factors in the tumour microenvironment, such as TGF- β 1, PAI-1 and uPA, can influence the ratio of full length and uPAR (II-III) and thereby potentially effect cell migration and invasion. Resolving how uPAR cleavage is controlled is therefore vital for understanding how OSCC progresses and potentially provides new targets for therapy

Estimating seabed pressure from demersal trawls, seines, and dredges based on gear design and dimensions

This study assesses the seabed pressure of towed fishing gears and models the physical impact (area and depth of seabed penetration) from trip-based information of vessel size, gear type, and catch. Traditionally fishing pressures are calculated top-down by making use of large-scale statistics such as logbook data. Here, we take a different approach starting from the gear itself (design and dimensions) to estimate the physical interactions with the seabed at the level of the individual fishing operation. We defined 14 distinct towed gear groups in European waters (eight otter trawl groups, three beam trawl groups, two demersal seine groups, and one dredge group), for which we established gear “footprints”. The footprint of a gear is defined as the relative contribution from individual larger gear components, such as trawl doors, sweeps, and groundgear, to the total area and severity of the gear's impact. An industry-based survey covering 13 countries provided the basis for estimating the relative impact-area contributions from individual gear components, whereas sediment penetration was estimated based on a literature review. For each gear group, a vessel size–gear size relationship was estimated to enable the prediction of gear footprint area and sediment penetration from vessel size. Application of these relationships with average vessel sizes and towing speeds provided hourly swept-area estimates by métier. Scottish seining has the largest overall gear footprint of ∼1.6 km2 h−1 of which 0.08 km2 has an impact at the subsurface level (sediment penetration ≥ 2 cm). Beam trawling for flatfish ranks low when comparing overall footprint size/hour but ranks substantially higher when comparing only impact at the subsurface level (0.19 km2h−1). These results have substantial implications for the definition, estimation, and monitoring of fishing pressure indicators, which are discussed in the context of an ecosystem approach to fisheries managemen

Cleavage of the urokinase receptor (uPAR) on oral cancer cells : regulation by transforming growth factor - beta 1 (TGF-beta 1) and potential effects on migration and invasion

Background: Urokinase plasminogen activator (uPA) receptor (uPAR) is up-regulated at the invasive tumour front of human oral squamous cell carcinoma (OSCC), indicating a role for uPAR in tumour progression. We previously observed elevated expression of uPAR at the tumour-stroma interface in a mouse model for OSCC, which was associated with increased proteolytic activity. The tumour microenvironment regulated uPAR expression, as well as its glycosylation and cleavage. Both full-length- and cleaved uPAR (uPAR (II-III)) are involved in highly regulated processes such as cell signalling, proliferation, migration, stem cell mobilization and invasion. The aim of the current study was to analyse tumour associated factors and their effect on uPAR cleavage, and the potential implications for cell proliferation, migration and invasion. Methods: Mouse uPAR was stably overexpressed in the mouse OSCC cell line AT84. The ratio of full-length versus cleaved uPAR as analysed by Western blotting and its regulation was assessed by addition of different protease inhibitors and transforming growth factor - beta 1 (TGF-beta 1). The role of uPAR cleavage in cell proliferation and migration was analysed using real- time cell analysis and invasion was assessed using the myoma invasion model. Results: We found that when uPAR was overexpressed a proportion of the receptor was cleaved, thus the cells presented both full-length uPAR and uPAR (II-III). Cleavage was mainly performed by serine proteases and urokinase plasminogen activator (uPA) in particular. When the OSCC cells were stimulated with TGF-beta 1, the production of the uPA inhibitor PAI-1 was increased, resulting in a reduction of uPAR cleavage. By inhibiting cleavage of uPAR, cell migration was reduced, and by inhibiting uPA activity, invasion was reduced. We could also show that medium containing soluble uPAR (suPAR), and cleaved soluble uPAR (suPAR (II-III)), induced migration in OSCC cells with low endogenous levels of uPAR. Conclusions: These results show that soluble factors in the tumour microenvironment, such as TGF-beta 1, PAI-1 and uPA, can influence the ratio of full length and uPAR (II-III) and thereby potentially effect cell migration and invasion. Resolving how uPAR cleavage is controlled is therefore vital for understanding how OSCC progresses and potentially provides new targets for therapy.Peer reviewe