Occurrence of marine litter along abyssal areas of the Gloria Fracture Zone (NE Atlantic).

Marine litter pollution is a recognized form of anthropogenic disturbance that affects widely the marine environment, particularly near the continental margins, although also present at abyssal and bathyal depths. This study reports the occurrence of marine litter distribution and abundance in four abyssal basins along the Gloria fracture zone in the NE Atlantic. Litter items occurrences were analysed using TV-CTD video surveys carried out during the multidisciplinary activities of the R/V Meteor M162 cruise. The surveys reached depths between 3500-4500m and covered 16 km of seafloor, between the Terceira ridge and the Madeira-Tore Rise. Litter items were annotated and categorized by type (i.e., plastic, fishing gear, metal, glass, other unknown items). Results revealed that litter was exclusively found on soft sediment habitats across all areas, i.e. depositional areas, with the overwhelming dominance of plastics items (71%), such as plastic containers, cups and bag fragments. Although less common (6-8%), metal, glass and lost fishing gear were also observed. Litter density was on average 9 times higher in the easternmost area near the Madeira-Tore ridge, when compared to the other areas. Higher litter densities are likely explained due to the proximity to the Madeira-Tore seamount complex targeted by the fishing industry and nearimportant corridors of marine traffic between various Atlantic and Mediterranean locations

Megafauna communities from abyssal sites along the Gloria Fracture Zone (NE Atlantic)

Fracture zones are areas of poorly known abyssal landscapes and benthic faunal communities. During the R/V Meteor M162 cruise several imagery surveys were performed using a TV-CTD guided camera system along four main areas of the Gloria fault system, between the Terceira ridge and the Madeira Tore Rise. Based on these records, we were able to characterize - for the first time - the megafaunal composition, their abundance and diversity along the sub-basin of the Gloria fault at depths between 3500 and 4500m. Quantitative annotations of the observed fauna, as well as evidence of animal traces on the seafloor were explored in relation to topography, substrate type, and geochemical data acquired during surveys. Preliminary observations revealed a total of 121 morphospecies, of which Holothuroidea is the most diverse group, with 12 morphospecies. Deepest transects carried out along the main trace of Gloria Fault system showed the highest similarity among dives, predominantly characterised by soft sediment areas with Elpidiidae holothurians frequently observed. In contrast, the survey carried out at the Terceira ridge showed more diverse communities, which is likely due to a larger variability in substrate and topography. Specifically, soft-sediment sections showed a higher proportion of holothurians, ophiuroids and acorn worms, while unique Anthozoan and Porifera morphospecies were observed in areas with presence of hard substrates. The findings of this study provide unique knowledge of abyssal fauna associated with the Gloria Fault System, including areas inside of national jurisdiction and of relevance for management and conservation actions

GFI1 proteins regulate stem cell formation in the AGM

In vertebrates, the first haematopoietic stem cells (HSCs) with multi-lineage and long-term repopulating potential arise in the AGM (aorta-gonad-mesonephros) region. These HSCs are generated from a rare and transient subset of endothelial cells, called haemogenic endothelium (HE), through an endothelial-to-haematopoietic transition (EHT). Here, we establish the absolute requirement of the transcriptional repressors GFI1 and GFI1B (growth factor independence 1 and 1B) in this unique trans-differentiation process. We first demonstrate that Gfi1 expression specifically defines the rare population of HE that generates emerging HSCs. We further establish that in the absence of GFI1 proteins, HSCs and haematopoietic progenitor cells are not produced in the AGM, revealing the critical requirement for GFI1 proteins in intra-embryonic EHT. Finally, we demonstrate that GFI1 proteins recruit the chromatin-modifying protein LSD1, a member of the CoREST repressive complex, to epigenetically silence the endothelial program in HE and allow the emergence of blood cells.We thank the staff at the Advanced Imaging, animal facility, Molecular Biology Core facilities and Flow Cytometry of CRUK Manchester Institute for technical support and Michael Lie-A-Ling and Elli Marinopoulou for initiating the DamID-PIP bioinformatics project. We thank members of the Stem Cell Biology group, the Stem Cell Haematopoiesis groups and Martin Gering for valuable advice and critical reading of the manuscript. Work in our laboratory is supported by the Leukaemia and Lymphoma Research Foundation (LLR), Cancer Research UK (CRUK) and the Biotechnology and Biological Sciences Research Council (BBSRC). SC is the recipient of an MRC senior fellowship (MR/J009202/1).This is the author accepted manuscript. The final version is available from NPG via http://dx.doi.org/10.1038/ncb327

Exploring subsurface fluid flow and active dewatering along the oceanic plate boundary between Africa and Eurasia (Gloria Fault)

R/V Meteor cruise M162 was conducted as a systematic continuation of ongoing work dedicated to understand if and howfluid flow through crust and sedimentscontinues along transform-type plate boundaries and fracture zones away from mid-ocean ridges and continental margins. Central target was the Gloria Fault in the central Northeast Atlantic. Previous findings along the eastern continuation of the Gloria Fault revealed fault-controlled fluid advection and mud volcanism along strike-slip faults in the Horseshoe Abyssal Plain and the Gulf of Cadiz, where fluid geochemistry revealed the admixture of fluids from deeply buried oceanic crust and oldest sediments on top of it. TheGloria Fault itselfis an old, reactivated, and seismically active oceanic fracture zone. During M162 a systematic survey along the main trace of the Gloria Fault between the Azores Plateau and the Madeira-Tore Rise was carried out, including sub-bottom profiler surveys, heat flow transects, gravity corer sampling, as well as video-guided CTD and multicorer deployments. In accordance to recently recorded seismic activity along the fault, there isevidence for tectonic motion both in sub-bottom profiler records and sediment cores. Heat flow measurements revealed values significantly elevated above the background in many places, predominantly along the main fault trace and other active faults.Ina number of placesfluid geochemistry revealed enhanced diagenetic processes in the sediments, implying the potential relation to upward-directed fluid flow. In summary, cruise M162revealed the first complementary data set on heat flow and fluid geochemistry along an oceanic fault zone, which will further our understanding on themes like the alteration of oceanic lithosphere and crust-ocean element exchange

Resolving early mesoderm diversification through single-cell expression profiling.

In mammals, specification of the three major germ layers occurs during gastrulation, when cells ingressing through the primitive streak differentiate into the precursor cells of major organ systems. However, the molecular mechanisms underlying this process remain unclear, as numbers of gastrulating cells are very limited. In the mouse embryo at embryonic day 6.5, cells located at the junction between the extra-embryonic region and the epiblast on the posterior side of the embryo undergo an epithelial-to-mesenchymal transition and ingress through the primitive streak. Subsequently, cells migrate, either surrounding the prospective ectoderm contributing to the embryo proper, or into the extra-embryonic region to form the yolk sac, umbilical cord and placenta. Fate mapping has shown that mature tissues such as blood and heart originate from specific regions of the pre-gastrula epiblast, but the plasticity of cells within the embryo and the function of key cell-type-specific transcription factors remain unclear. Here we analyse 1,205 cells from the epiblast and nascent Flk1(+) mesoderm of gastrulating mouse embryos using single-cell RNA sequencing, representing the first transcriptome-wide in vivo view of early mesoderm formation during mammalian gastrulation. Additionally, using knockout mice, we study the function of Tal1, a key haematopoietic transcription factor, and demonstrate, contrary to previous studies performed using retrospective assays, that Tal1 knockout does not immediately bias precursor cells towards a cardiac fate.We thank M. de Bruijn, A. Martinez-Arias, J. Nichols and C. Mulas for discussion, the Cambridge Institute for Medical Research Flow Cytometry facility for their expertise in single-cell index sorting, and S. Lorenz from the Sanger Single Cell Genomics Core for supervising purification of Tal1−/− sequencing libraries. ChIP-seq reads were processed by R. Hannah. Research in the authors’ laboratories is supported by the Medical Research Council, Cancer Research UK, the Biotechnology and Biological Sciences Research Council, Bloodwise, the Leukemia and Lymphoma Society, and the Sanger-EBI Single Cell Centre, and by core support grants from the Wellcome Trust to the Cambridge Institute for Medical Research and Wellcome Trust - MRC Cambridge Stem Cell Institute and by core funding from Cancer Research UK and the European Molecular Biology Laboratory. Y.T. was supported by a fellowship from the Japan Society for the Promotion of Science. W.J. is a Wellcome Trust Clinical Research Fellow. A.S. is supported by the Sanger-EBI Single Cell Centre. This work was funded as part of Wellcome Trust Strategic Award 105031/D/14/Z ‘Tracing early mammalian lineage decisions by single-cell genomics’ awarded to W. Reik, S. Teichmann, J. Nichols, B. Simons, T. Voet, S. Srinivas, L. Vallier, B. Göttgens and J. Marioni.This is the author accepted manuscript. The final version is available from Nature Publishing Group via http://dx.doi.org/10.1038/nature1863

Heme Oxygenase-1 Accelerates Cutaneous Wound Healing in Mice

Heme oxygenase-1 (HO-1), a cytoprotective, pro-angiogenic and anti-inflammatory enzyme, is strongly induced in injured tissues. Our aim was to clarify its role in cutaneous wound healing. In wild type mice, maximal expression of HO-1 in the skin was observed on the 2nd and 3rd days after wounding. Inhibition of HO-1 by tin protoporphyrin-IX resulted in retardation of wound closure. Healing was also delayed in HO-1 deficient mice, where lack of HO-1 could lead to complete suppression of reepithelialization and to formation of extensive skin lesions, accompanied by impaired neovascularization. Experiments performed in transgenic mice bearing HO-1 under control of keratin 14 promoter showed that increased level of HO-1 in keratinocytes is enough to improve the neovascularization and hasten the closure of wounds. Importantly, induction of HO-1 in wounded skin was relatively weak and delayed in diabetic (db/db) mice, in which also angiogenesis and wound closure were impaired. In such animals local delivery of HO-1 transgene using adenoviral vectors accelerated the wound healing and increased the vascularization. In summary, induction of HO-1 is necessary for efficient wound closure and neovascularization. Impaired wound healing in diabetic mice may be associated with delayed HO-1 upregulation and can be improved by HO-1 gene transfer

Large-scale exome-wide association analysis identifies loci for White Blood Cell Traits and Pleiotropy with Immune-Mediated Diseases

White blood cells play diverse roles in innate and adaptive immunity. Genetic association analyses of phenotypic variation in circulating white blood cell (WBC) counts from large samples of otherwise healthy individuals can provide insights into genes and biologic pathways involved in production, differentiation, or clearance of particular WBC lineages (myeloid, lymphoid) and also potentially inform the genetic basis of autoimmune, allergic, and blood diseases. We performed an exome array-based meta-analysis of total WBC and subtype counts (neutrophils, monocytes, lymphocytes, basophils, and eosinophils) in a multi-ancestry discovery and replication sample of ∼157,622 individuals from 25 studies. We identified 16 common variants (8 of which were coding variants) associated with one or more WBC traits, the majority of which are pleiotropically associated with autoimmune diseases. Based on functional annotation, these loci included genes encoding surface markers of myeloid, lymphoid, or hematopoietic stem cell differentiation (CD69, CD33, CD87), transcription factors regulating lineage specification during hematopoiesis (ASXL1, IRF8, IKZF1, JMJD1C, ETS2-PSMG1), and molecules involved in neutrophil clearance/apoptosis (C10orf54, LTA), adhesion (TNXB), or centrosome and microtubule structure/function (KIF9, TUBD1). Together with recent reports of somatic ASXL1 mutations among individuals with idiopathic cytopenias or clonal hematopoiesis of undetermined significance, the identification of a common regulatory 3 UTR variant of ASXL1 suggests that both germline and somatic ASXL1 mutations contribute to lower blood counts in otherwise asymptomatic individuals. These association results shed light on genetic mechanisms that regulate circulating WBC counts and suggest a prominent shared genetic architecture with inflammatory and autoimmune diseases

Varying response of bacteria and nematodes to environmental conditions of Sado estuary – implications for estuarine benthic food webs.

Sediment microbiome and benthic nematodes are indispensable in regulating benthic estuarine ecosystems and knowledge on their distribution patterns is essential for understanding of benthic food webs dynamics. However, simultaneous ecological analysis of bacteria and nematodes communities are seldom made, whereas the question if there exist a congruence between both taxonomic groups in their responses to different ecological conditions is largely unresolved. The main goal of this work was to analyze spatial and temporal distributional patterns of bacteria and nematodes in response to different environmental conditions in Sado Estuary, SW Portugal and further establish a link between these results and estuarine food web data generated using stable isotopes. All samples were collected at two distinct sampling occasions (autumn 2019 and Summer 2020) from three contrasting sites with varying sediment characteristics and human impact degrees. The sediment biogeochemical properties and the composition of bacterial and nematode communities were determined. To analyze bacterial communities, total DNA from sediment was extracted using DNeasy Power Soil kit® (MOBIO, Qiagen) and processed for Illumina MiSeq platform sequencing targeting the V3 and V4 region of 16S rRNA gene. Nematode assemblages were morphologically identified until genera level. All bacterial communities were highly diverse (α-diversity) presenting high β-diversity among the three sites and across two seasons. The distributional patterns presented a close concordance with ecological conditions associated to each site and season. Whereas nematode assemblages yielded a less clear distributional patterns suggesting that their response is rather driven by the within site specific factors. These results will be crossed with estuarine food web data generated through stable isotopes to resolve how distribution patterns of bacteria and nematode communities are reflected in the architecture of the estuarine benthic food webs

Spatial distribution patterns of microbiome and free-living benthic nematodes in response to sediment ecological conditions in Sado estuary, Portugal (SW)

Sediment microbiome has an essential role in regulating ecosystem functions, not only regulating primary productivity and nutrient cycling but also shaping trophic interactions with higher trophic levels [1]. While the importance of microbiome in terrestrial soil systems is being highly recognized, its role in marine aquatic environments remains much less studied [2]. Microbiome can be highly affected by bottom up (abiotic factors) and top down (predation by meiofauna) effects [3]. Understanding the interaction effect between abiotic and biotic factors on microbiome communities will be an essential step for future predictions of ecosystem stability. To address this knowledge gap we studied spatial distribution patterns of microbiome communities and nematode assemblages in highly heterogenous Sado Estuary, SW Portugal. The samples were taken from three contrasting sites with varying sediment characteristics and human impact degrees. From each site, three replicate samples for sediment characterization (total organic matter, granulometry, total C and N, chlorophyll a and phaeopigments, contaminants: heavy metals and metalloids, organochlorine pesticides, PAH and PCBs), microbiome (sensu lato) and nematode community were taken. Total DNA from sediment was extracted using DNeasy Power Soil kit® (MOBIO, Qiagen) and processed for Illumina MiSeq platform sequencing targeting the V3 and V4 region of 16S rRNA gene. Sediment characterization indicated heterogeneity between sites with distinct levels of contamination, which resulted in contrasting microbial communities. All sites showed a high α-biodiversity with predominance of Proteobacteria phylum, particularly Woeseiaceae, Desulfobacteraceae and Desulfobulbaceae families. Beside this heterogeneity in microbiome community, β-diversity of microbiome communities was demonstrated to be very high, greatly discriminating among all three sites. Instead, nematode assemblages did not yield clear distributional patterns suggesting that their response is rather driven by the within site specific factors, acting at the smaller spatial scales. Studying the relations between sediment ecological conditions and microbiome and meiobenthic communities greatly advance our understanding on benthic ecosystem functioning