Monitoring mosaic biotopes in a marine conservation zone by autonomous underwater vehicle

The number of marine protected areas (MPAs) has increased dramatically in the last decade and poses a major logistic challenge for conservation practitioners in terms of spatial extent and the multiplicity of habitats and biotopes that now require assessment. Photographic assessment by autonomous underwater vehicle (AUV) enables the consistent description of multiple habitats, in our case including mosaics of rock and sediment. As a case study, we used this method to survey the Greater Haig Fras marine conservation zone (Celtic Sea, northeast Atlantic). We distinguished 7 biotopes, detected statistically significant variations in standing stocks, species density, species diversity, and faunal composition, and identified significant indicator species for each habitat. Our results demonstrate that AUV‐based photography can produce robust data for ecological research and practical marine conservation. Standardizing to a minimum number of individuals per sampling unit, rather than to a fixed seafloor area, may be a valuable means of defining an ecologically appropriate sampling unit. Although composite sampling represents a change in standard practice, other users should consider the potential benefits of this approach in conservation studies. It is broadly applicable in the marine environment and has been successfully implemented in deep‐sea conservation and environmental impact studies. Without a cost‐effective method, applicable across habitats, it will be difficult to further a coherent classification of biotopes or to routinely assess their conservation status in the rapidly expanding global extent of MPAs

Dynamic Contrast-Enhanced MRI Assessment of Hyperemic Fractional Microvascular Blood Plasma Volume in Peripheral Arterial Disease: Initial Findings

OBJECTIVES: The aim of the current study was to describe a method that assesses the hyperemic microvascular blood plasma volume of the calf musculature. The reversibly albumin binding contrast agent gadofosveset was used in dynamic contrast-enhanced magnetic resonance imaging (DCE MRI) to assess the microvascular status in patients with peripheral arterial disease (PAD) and healthy controls. In addition, the reproducibility of this method in healthy controls was determined. MATERIALS AND METHODS: Ten PAD patients with intermittent claudication and 10 healthy control subjects were included. Patients underwent contrast-enhanced MR angiography of the peripheral arteries, followed by one DCE MRI examination of the musculature of the calf. Healthy control subjects were examined twice on different days to determine normative values and the interreader and interscan reproducibility of the technique. The MRI protocol comprised dynamic imaging of contrast agent wash-in under reactive hyperemia conditions of the calf musculature. Using pharmacokinetic modeling the hyperemic fractional microvascular blood plasma volume (V(p), unit: %) of the anterior tibial, gastrocnemius and soleus muscles was calculated. RESULTS: V(p) was significantly lower for all muscle groups in PAD patients (4.3±1.6%, 5.0±3.3% and 6.1±3.6% for anterior tibial, gastrocnemius and soleus muscles, respectively) compared to healthy control subjects (9.1±2.0%, 8.9±1.9% and 9.3±2.1%). Differences in V(p) between muscle groups were not significant. The coefficient of variation of V(p) varied from 10-14% and 11-16% at interscan and interreader level, respectively. CONCLUSIONS: Using DCE MRI after contrast-enhanced MR angiography with gadofosveset enables reproducible assessment of hyperemic fractional microvascular blood plasma volume of the calf musculature. V(p) was lower in PAD patients than in healthy controls, which reflects a promising functional (hemodynamic) biomarker for the microvascular impairment of macrovascular lesions

Genome-wide Analyses Identify KIF5A as a Novel ALS Gene

To identify novel genes associated with ALS, we undertook two lines of investigation. We carried out a genome-wide association study comparing 20,806 ALS cases and 59,804 controls. Independently, we performed a rare variant burden analysis comparing 1,138 index familial ALS cases and 19,494 controls. Through both approaches, we identified kinesin family member 5A (KIF5A) as a novel gene associated with ALS. Interestingly, mutations predominantly in the N-terminal motor domain of KIF5A are causative for two neurodegenerative diseases: hereditary spastic paraplegia (SPG10) and Charcot-Marie-Tooth type 2 (CMT2). In contrast, ALS-associated mutations are primarily located at the C-terminal cargo-binding tail domain and patients harboring loss-of-function mutations displayed an extended survival relative to typical ALS cases. Taken together, these results broaden the phenotype spectrum resulting from mutations in KIF5A and strengthen the role of cytoskeletal defects in the pathogenesis of ALS.Peer reviewe

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Eruptive hummocks : building blocks of the upper ocean crust

The spreading axis at many slow-spreading mid-ocean ridges is marked by an axial volcanic ridge. In this study, we use a combination of high-resolution remote sensing methods to elucidate the detailed nature of volcanoes in such a ridge. We find that the “hummocks” described in previous sidescan sonar studies are dome- or cone-shaped edifices, 5–150 m high with diameters of 30–330 m. We estimate they form quickly, in single eruptions, each of which may produce several hummocks. Hummock collapse is common and hummocks of all heights are prone to failure. Collapses generally occur down the regional seafloor slope, suggesting control by local topography. Approximately 33% of hummocks lose ∼40% of their volume by collapse, so ∼12% of all material erupted on the axial volcanic ridge is rapidly converted to talus. The higher porosity of these deposits may increase average upper crustal porosity by several percent, contributing >0.5 km s−1 to seismic velocity decrease in the upper oceanic crust, and may be one of the dominant mechanisms for increasing porosity in upper slow-spreading oceanic crust

The Influence of Subtle Gradient Changes on Deep-Water Gravity Flows: A Case Study From the Moroccan Turbidite System

The Moroccan Turbidite System is unique in that individual gravity-flow deposits can be correlated across distances of several hundred kilometers, both within and between depositional basins. An extensive dataset of shallow sediment cores is analyzed here, in order to investigate the influence of gradient changes on individual siliciclastic gravity flows passing through this system in the last 160,000 years. The largest flows (deposit volumes > 100 km3) are capable of travelling for more than 1000 km across slopes of less than 0.1°. The deposits of these flows display significant lateral heterogeneity as a consequence of changes in seafloor gradient. Increases in gradient can lead to sediment bypass and/or erosion, and unconfined flows may become channelized. Decreases in gradient can lead to significant changes in sand–mud ratio and the deposition of thick mud caps, while small-volume flow deposits may pinch out completely. One of the largest flows shows evidence for multiple transformations as it crossed the Agadir Basin, with the resulting deposits switching laterally from (1) a gravel lag and cut-and-fill scours (representing bypass and erosion across a slope of 0.05°), to (2) a thick linked turbidite–debrite bed containing a muddy sand debrite (in response to a decrease in slope to < 0.01°), to (3) a normally graded turbidite (following a subtle increase in slope to 0.02°). Although the changes in slope angle described here appear remarkably subtle, the relative changes in slope are significant, and clearly exert a major control on flow behavior. Such variations in slope would not be detectable in outcrop or subsurface sequences, yet will generate significant complexity in deep-water reservoirs

Assessment of the Mineral Resource Potential of Atlantic Ferromanganese Crusts Based on Their Growth History, Microstructure, and Texture

The decarbonisation of our energy supply is reliant on new technologies that are raw material intensive and will require a significant increase in the production of metals to sustain them. Ferromanganese (FeMn) crusts are seafloor precipitates, enriched in metals such as cobalt and tellurium, both of which have a predicted future demand above current production rates. In this study, we investigate the texture and composition of FeMn crusts on Tropic Seamount, a typical Atlantic guyot off the coast of western Africa, as a basis for assessing the future mineral resource potential of Atlantic Seamounts. The majority of the summit is flat and covered by FeMn crusts with average thicknesses of 3–4 cm. The crusts are characterized by two dominant textures consisting of either massive pillared growth or more chaotic, cuspate sections of FeMn oxides, with an increased proportion of detrital and organic material. The Fe, Mn, and Co contents in the FeMn oxide layers are not affected by texture. However, detrital material and bioclasts can form about 50% of cuspate areas, and the dilution effect of this entrained material considerably reduces the Fe, Mn, and Co concentrations if the bulk samples are analyzed. Whilst Tropic Seamount meets many of the prerequisites for a crust mining area, the thickness of the crusts and their average metal composition means extraction is unlikely to be viable in the near future. The ability to exploit more difficult terrains or multiple, closely spaced edifices would make economic feasibility more likely

Monitoring mosaic biotopes in a marine conservation zone by autonomous underwater vehicle

The extent of marine protected areas (MPAs) has increased dramatically in the last decade, and poses a major logistic challenge for conservation practitioners in terms of spatial extent and the multiplicity of habitats and biotopes that now require assessment. Here we demonstrate a single field method, photographic assessment by autonomous underwater vehicle (AUV) that enables the consistent description of multiple habitats, in our case including mosaics of rock and sediment. We describe a case study in the Greater Haig Fras marine conservation zone (Celtic Sea, NE Atlantic) where we distinguished seven biotopes, detected statistically significant variations in standing stocks, species density, species diversity, and faunal composition, and identified significant indicator species for each habitat. Our results demonstrate that AUV-based photography can produce robust data for ecological research and practical marine conservation. We note that standardizing to a minimum number of individuals per sampling unit, rather than to a fixed seafloor area, may be a valuable means of defining an ecologically appropriate sampling unit. Although representing a change in ‘standard practise’, we suggest that other users consider the potential benefits of this approach in their own conservation studies. The approach is broadly applicable in the marine environment, and has already been successfully implemented in deep-sea conservation and impact studies. It is clear that without a cost-effective methodology, applicable across habitats, it will be difficult to progress a coherent classification of biotopes, or to routinely assess their conservation status, in the rapidly expanding global extent of MPAs

Conventional and chemical munitions dumpsites in waters >200 m in the OSPAR region (OSPAR, 2005) [28].

<p>Conventional and chemical munitions dumpsites in waters >200 m in the OSPAR region (OSPAR, 2005) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012730#pone.0012730-OSPAR5" target="_blank">[28]</a>.</p

Spatial extent and confidence rating of activities.

<p>Estimates of the spatial extent of six major human activities occurring directly on the sea floor, including structures and artefacts present on the seafloor resulting from past activities, within the OSPAR maritime area of the North East Atlantic in waters >200 m during 2005. Estimates for bottom trawling and marine scientific research are based on 2005 data only.</p><p>wd: water depth;</p>†<p>Confidence ratings indicate whether the spatial extent of each activity is based on data or estimates of location and extent (Eastwood et al., 2007) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012730#pone.0012730-Eastwood1" target="_blank">[19]</a>: 1, estimated location and estimated extent; 2 known location, estimated extent; 3, known location and extent.</p><p>*Carter et al., 2009 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012730#pone.0012730-Carter1" target="_blank">[23]</a>.</p>1<p>Information from NPD and Statoil datasets and Eastwood et al., 2007 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012730#pone.0012730-Eastwood1" target="_blank">[19]</a>.</p>2<p>Overlapping boundaries merged.</p>3<p>SERPENT Project, unpublished data.</p