A regional benthic fauna assessment method for the Southern North Sea using Margalef diversity and reference value modelling

The aims of this study are to develop an optimized method for regional benthic fauna assessment of the Southern North Sea which (a) is sensitive and precise (quantified as the slope and the R2 value of the pressure-impact relationships, respectively) for the anthropogenic pressures bottom fishing and organic enrichment, (b) is suitable for estimating and modelling reference values, (c) is transparent, (d) can be efficiently applied using dedicated software; and to apply this method to benthic data from the Southern North Sea. Margalef diversity appeared to be the best performing benthic index regarding these criteria, even better than several Multi-Metric Indices (MMIs) containing e.g. AMBI (AZTI Marine Biotic Index) and ITI (Infaunal Trophic Index). Therefore, this relatively simple and very practical index, including a new reference value estimation and modelling method, and BENMMI software were selected as a common OSPAR (Oslo Paris convention) method for the benthic fauna assessment of the Southern North Sea. This method was applied to benthic fauna data from the Southern North Sea collected during the period 2010–2015. The results in general show lower normalized Margalef values in coastal areas, and higher normalized Margalef values in deeper offshore areas. The following benthic indices were compared in this study: species richness, Margalef diversity, SNA index, Shannon index, PIE index, AMBI, ITI. For each assessment area, the least disturbed benthic dataset was selected as an adjacent 6 year period with, on average, the highest Margalef diversity values. For these datasets, the reference values were primarily set as the 99th percentile values of the respective indices. This procedure results in the highest stable reference values that are not outliers. In addition, a variable percentile method was developed, in which the percentile value is adjusted to the average bottom fishing pressure (according to data from the International Council for the Exploration of the Sea, ICES) in the period 2009–2013. The adjusted percentile values were set by expert judgement, at 75th (low fishing pressure), 95th (medium fishing pressure) and 99th (high fishing pressure) percentile. The estimated reference values for Margalef diversity correlate quite well with the median depth of the assessment areas using a sigmoid model (pseudo-R2 = 0.86). This relationship between depth and Margalef diversity was used to estimate reference values in case an assessment area had insufficient benthic data .For testing the effects of bottom fishing pressure, normalized index values (NIV; index value divided by reference value) were used. The rationale for using NIVs is the assumption that, although a certain level of bottom fishing pressure will have a larger absolute effect on more biodiverse benthic communities in deeper waters than on more robust and less biodiverse coastal benthic communities, the relative effects (tested using NIVs) are comparable. A clear exponentially decreasing relationship (R2 = 0.26–0.27, p 2 cm, respectively) and normalized Margalef diversity values, with an asymptotic normalized Margalef value of 0.45 at a subsurface fishing activity >2.3 sweeps/year. This asymptotic value is predominantly found in coastal waters, and probably shows that the naturally more robust coastal benthic communities have been transformed into resilient benthic communities, which rapidly recover from increasing fishing pressure

Assessing the state of marine biodiversity in the Northeast Atlantic

The Northeast Atlantic, a highly productive maritime area, has been exposed to a wide range of direct human pressures, such as fishing, shipping, coastal development, pollution, and non-indigenous species (NIS) introductions, in addition to anthropogenically-driven global climate change. Nonetheless, this regional sea supports a high diversity of species and habitats, whose functioning provides a variety of ecosystem services, essential for human welfare. In 2017, OSPAR, the Northeast Atlantic Regional Seas Commission, delivered an assessment of marine biodiversity for the Northeast Atlantic. This assessment examined biodiversity indicators separately to identify changes in Northeast Atlantic biodiversity, but stopped short of determining the status of biodiversity for many species and habitats. Here, we expand on this work and for the first time, a semi-quantitative approach is applied to evaluate holistically the state of Northeast Atlantic marine biodiversity across marine food webs, from plankton to top predators, via fish, pelagic and benthic habitats, including xeno-biodiversity (i.e. NIS). Our analysis reveals widespread degradation in marine ecosystems and biodiversity, particularly for marine birds and coastal bottlenose dolphins, as well as for benthic habitats and fish in some regions. The poor biodiversity status of these ecosystem components is likely the result of cumulative effects of human activities, such as habitat destruction or disturbance, overexploitation, eutrophication, the introduction of NIS, and climate change. Bright spots are also revealed, such as recent signs of recovery in some fish and marine bird communities and recovery in harbour and grey seal populations and the condition of coastal benthic communities in some regions. The status of many indicators across all ecosystem components, but particularly for the novel pelagic habitats, food webs and NIS indicators, however, remains uncertain due to gaps in data, unclear pressure-state relationships, and the non-linear influence of some pressures on biodiversity indicators. Improving monitoring and data access and increasing understanding of pressure-state relationships, including those that are non-linear, is therefore a priority for enabling future assessments, as is consistent and stable resourcing for expert involvement

Genetic Evidence Supporting the Association of Protease and Protease Inhibitor Genes with Inflammatory Bowel Disease: A Systematic Review

As part of the European research consortium IBDase, we addressed the role of proteases and protease inhibitors (P/PIs) in inflammatory bowel disease (IBD), characterized by chronic mucosal inflammation of the gastrointestinal tract, which affects 2.2 million people in Europe and 1.4 million people in North America. We systematically reviewed all published genetic studies on populations of European ancestry (67 studies on Crohn's disease [CD] and 37 studies on ulcerative colitis [UC]) to identify critical genomic regions associated with IBD. We developed a computer algorithm to map the 807 P/PI genes with exact genomic locations listed in the MEROPS database of peptidases onto these critical regions and to rank P/PI genes according to the accumulated evidence for their association with CD and UC. 82 P/PI genes (75 coding for proteases and 7 coding for protease inhibitors) were retained for CD based on the accumulated evidence. The cylindromatosis/turban tumor syndrome gene (CYLD) on chromosome 16 ranked highest, followed by acylaminoacyl-peptidase (APEH), dystroglycan (DAG1), macrophage-stimulating protein (MST1) and ubiquitin-specific peptidase 4 (USP4), all located on chromosome 3. For UC, 18 P/PI genes were retained (14 proteases and 4protease inhibitors), with a considerably lower amount of accumulated evidence. The ranking of P/PI genes as established in this systematic review is currently used to guide validation studies of candidate P/PI genes, and their functional characterization in interdisciplinary mechanistic studies in vitro and in vivo as part of IBDase. The approach used here overcomes some of the problems encountered when subjectively selecting genes for further evaluation and could be applied to any complex disease and gene family

Plant mitochondrial DNA evolved rapidly in structure, but slowly in sequence

We examined the tempo and mode of mitochondrial DNA (mtDNA) evolution in six species of crucifers from two genera, Brassica and Raphanus . The six mtDNAs have undergone numerous internal rearrangements and therefore differ dramatically with respect to the sizes of their subgenomic circular chromosomes. Between 3 and 14 inversions must be postulated to account for the structural differences found between any two species. In contrast, these mtDNAs are extremely similar in primary sequence, differing at only 1–8 out of every 1000 bp. The point mutation rate in these plant mtDNAs is roughly 4 times slower than in land plant chloroplast DNA (cpDNA) and 100 times slower than in animal mtDNA. Conversely, the rate of rearrangements is extraordinarily faster in plant mtDNA than in cpDNA and animal mtDNA.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/48042/1/239_2005_Article_BF02143500.pd