Mixed siliciclastic-carbonate-evaporite sedimentation in an arid eolian landscape: The Khor Al Adaid tide-dominated coastal embayment, Qatar

The Khor Al Adaid embayment of southern Qatar represents a unique shallow-water mixed siliciclastic‑carbonate coastal depositional system that developed in a hyper-arid climatic setting over the past 6000 years. The embayment, which was formed during the Flandrian transgression as a result of flooding across a partially fault-controlled incised fluvial drainage, is supplied by quartz-rich sands delivered by wind-blown dunes migrating southward across the surface of Qatar. These offshore-migrating eolian-derived sediments are being redistributed by tidal currents in an otherwise low-energy coastal zone, where in situ formation of carbonate mud and a low-diversity skeletal assemblage is ongoing within salinity-restricted environments. Three depositional sectors are delineated: 1) an energetic, linear, fault-controlled Entrance Channel into which the eolian dunes spill directly; 2) a relatively deep (up to 20 m) Outer Lagoon, interpreted to represent a flooded karst-collapse structure; and 3) a sprawling, low-energy, shallow (<2 m) Inner Lagoon occupying low-lying areas between deflated eolian dunes.Physical oceanographic modeling, integrating multi-seasonal current meter and tidal gage measurements, demonstrates tidal current flow velocities are relatively high in both the Entrance Channel and at the constricted entrance to the Inner Lagoon. Associated flow expansion into less confined areas results in deposition of the eolian-derived sands as flood-tidal deltas, one in the Outer, and two in the Inner Lagoon. A weakly-developed ebb-tidal delta occurs where the Entrance Channel debouches into the Arabian Gulf. Flood-tide dominance is also apparent in Entrance Channel deposits, where sand accumulates in seaward-terminating “ebb barbs” along the margins of the flood-dominant thalweg. Such flood-tide dominance of the thalweg is unusual and likely reflects the absence of river discharge. Evidence of significant inverse estuarine circulation (seaward flow of a brine along the embayment floor) is mostly absent in spite of the landward increase of salinity, where concentrations reach more than double normal seawater salinity in the Inner Lagoon. Modeling results show that seaward-flowing brines formed in the Inner Lagoon are trapped in the relatively deep Outer Lagoon, and that mixing by tidal currents in the energetic Entrance Channel precludes the formation of vertical density gradients there. Because siliciclastic mud is essentially absent, and most of the sediment forming the deltas consists of sand, upper intertidal deltaic deposits that would normally consist of mud are absent, resulting in the flood-tide deltas having a pronounced lobate geometry similar to that of fluvial deltas formed predominantly of sand.Away from tidal deltas, low-energy lagoons are floored by carbonate mud of local production, with minor gypsum precipitating in the Inner Lagoon. Wind-generated waves only locally influence sedimentation, forming complex nearshore bars along some lagoonal shorelines. The overall landward increase in salinity is accompanied by a decrease in the diversity of benthic fauna and their skeletal remains. A fairly diverse faunal assemblage is observed in the Entrance Channel near the Arabian Gulf, including colonial corals, whereas the inner lagoon assemblage is dominated gastropods belonging to Pirenella cingulata. The remnants of large eolian dunes are preserved in the low-energy setting of the Inner Lagoon, segmenting the waterbody, and locally increasing restriction. The sedimentology of the arid-zone coastal Khor Al Adaid embayment may serve as an analogue for environmental settings that were perhaps more commonplace in arid zones of flooded continents during greenhouse times

Bacteria-responsive microRNAs regulate plant innate immunity by modulating plant hormone networks

MicroRNAs (miRNAs) are key regulators of gene expression in development and stress responses in most eukaryotes. We globally profiled plant miRNAs in response to infection of bacterial pathogen Pseudomonas syringae pv. tomato (Pst). We sequenced 13 small-RNA libraries constructed from Arabidopsis at 6 and 14 h post infection of non-pathogenic, virulent and avirulent strains of Pst. We identified 15, 27 and 20 miRNA families being differentially expressed upon Pst DC3000 hrcC, Pst DC3000 EV and Pst DC3000 avrRpt2 infections, respectively. In particular, a group of bacteria-regulated miRNAs targets protein-coding genes that are involved in plant hormone biosynthesis and signaling pathways, including those in auxin, abscisic acid, and jasmonic acid pathways. Our results suggest important roles of miRNAs in plant defense signaling by regulating and fine-tuning multiple plant hormone pathways. In addition, we compared the results from sequencing-based profiling of a small set of miRNAs with the results from small RNA Northern blot and that from miRNA quantitative RT-PCR. Our results showed that although the deep-sequencing profiling results are highly reproducible across technical and biological replicates, the results from deep sequencing may not always be consistent with the results from Northern blot or miRNA quantitative RT-PCR. We discussed the procedural differences between these techniques that may cause the inconsistency

Metabolic and miRNA Profiling of TMV Infected Plants Reveals Biphasic Temporal Changes

Plant viral infections induce changes including gene expression and metabolic components. Identification of metabolites and microRNAs (miRNAs) differing in abundance along infection may provide a broad view of the pathways involved in signaling and defense that orchestrate and execute the response in plant-pathogen interactions. We used a systemic approach by applying both liquid and gas chromatography coupled to mass spectrometry to determine the relative level of metabolites across the viral infection, together with a miRs profiling using a micro-array based procedure. Systemic changes in metabolites were characterized by a biphasic response after infection. The first phase, detected at one dpi, evidenced the action of a systemic signal since no virus was detected systemically. Several of the metabolites increased at this stage were hormone-related. miRs profiling after infection also revealed a biphasic alteration, showing miRs alteration at 5 dpi where no virus was detected systemically and a late phase correlating with virus accumulation. Correlation analyses revealed a massive increase in the density of correlation networks after infection indicating a complex reprogramming of the regulatory pathways, either in response to the plant defense mechanism or to the virus infection itself. Our data propose the involvement of a systemic signaling on early miRs alteration

BHPR research: qualitative1. Complex reasoning determines patients' perception of outcome following foot surgery in rheumatoid arhtritis

Background: Foot surgery is common in patients with RA but research into surgical outcomes is limited and conceptually flawed as current outcome measures lack face validity: to date no one has asked patients what is important to them. This study aimed to determine which factors are important to patients when evaluating the success of foot surgery in RA Methods: Semi structured interviews of RA patients who had undergone foot surgery were conducted and transcribed verbatim. Thematic analysis of interviews was conducted to explore issues that were important to patients. Results: 11 RA patients (9 ♂, mean age 59, dis dur = 22yrs, mean of 3 yrs post op) with mixed experiences of foot surgery were interviewed. Patients interpreted outcome in respect to a multitude of factors, frequently positive change in one aspect contrasted with negative opinions about another. Overall, four major themes emerged. Function: Functional ability & participation in valued activities were very important to patients. Walking ability was a key concern but patients interpreted levels of activity in light of other aspects of their disease, reflecting on change in functional ability more than overall level. Positive feelings of improved mobility were often moderated by negative self perception ("I mean, I still walk like a waddling duck”). Appearance: Appearance was important to almost all patients but perhaps the most complex theme of all. Physical appearance, foot shape, and footwear were closely interlinked, yet patients saw these as distinct separate concepts. Patients need to legitimize these feelings was clear and they frequently entered into a defensive repertoire ("it's not cosmetic surgery; it's something that's more important than that, you know?”). Clinician opinion: Surgeons' post operative evaluation of the procedure was very influential. The impact of this appraisal continued to affect patients' lasting impression irrespective of how the outcome compared to their initial goals ("when he'd done it ... he said that hasn't worked as good as he'd wanted to ... but the pain has gone”). Pain: Whilst pain was important to almost all patients, it appeared to be less important than the other themes. Pain was predominately raised when it influenced other themes, such as function; many still felt the need to legitimize their foot pain in order for health professionals to take it seriously ("in the end I went to my GP because it had happened a few times and I went to an orthopaedic surgeon who was quite dismissive of it, it was like what are you complaining about”). Conclusions: Patients interpret the outcome of foot surgery using a multitude of interrelated factors, particularly functional ability, appearance and surgeons' appraisal of the procedure. While pain was often noted, this appeared less important than other factors in the overall outcome of the surgery. Future research into foot surgery should incorporate the complexity of how patients determine their outcome Disclosure statement: All authors have declared no conflicts of interes

SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues

Variability in SARS-CoV-2 susceptibility and COVID-19 disease severity between individuals is partly due to genetic factors. Here, we identify 4 genomic loci with suggestive associations for SARS-CoV-2 susceptibility and 19 for COVID-19 disease severity. Four of these 23 loci likely have an ethnicity-specific component. Genome-wide association study (GWAS) signals in 11 loci colocalize with expression quantitative trait loci (eQTLs) associated with the expression of 20 genes in 62 tissues/cell types (range: 1:43 tissues/gene), including lung, brain, heart, muscle, and skin as well as the digestive system and immune system. We perform genetic fine mapping to compute 99% credible SNP sets, which identify 10 GWAS loci that have eight or fewer SNPs in the credible set, including three loci with one single likely causal SNP. Our study suggests that the diverse symptoms and disease severity of COVID-19 observed between individuals is associated with variants across the genome, affecting gene expression levels in a wide variety of tissue types

A first update on mapping the human genetic architecture of COVID-19

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