Modelling reef hydrodynamics and sediment mobility under sea level rise in atoll reef island systems

This is the author accepted manuscript. The final version is available on open access from Elsevier via the DOI in this record. Low-lying coral reef islands will be significantly impacted by future sea level rise (SLR). It is generally expected that SLR will destabilise reef islands because increasing reef submergence allows larger waves, and therefore greater energy transmission, across reef flats. However, the impact of SLR on altering both reef flat sediment transport and sediment delivery to island shorelines is poorly understood. Here, we use the currents of removal approach (coupling two-dimensional wave modelling with settling velocity data from 186 benthic sediment samples) to model shifts in both reef hydrodynamics and benthic sediment transport under scenarios of mean reef submergence (MRS = +0 m, +0.5 m, +1 m) at two atoll rim reef sites in the Maldives. Under contemporary conditions (MRS = +0 m), we found that benthic sediment transport is likely occurring, consistent with active reef-to-island sediment connectivity. Under conditions of increased MRS, shifts in wave velocities, and in turn sediment potential mobility, were both non-linear and non-uniform. Significant between-site differences were found in the magnitude of projected shifts in sediment mobility under scenarios of increased MRS, which implies that morphological responses to increases in MRS are likely to be diverse, even over local scales. Under increased MRS, the largest increases in sediment mobility were projected on the inner reef flat, whereas lagoonal zones remained as sinks for sediment deposition. We thus hypothesize that while reef islands will persist as sedimentary landforms under projected rates of MRS, lagoonward reef island migration is likely to occur. Findings have implications for predicting the future adaptive capacity of atoll nations. The challenge is to incorporate such potential increases in island mobility and intra-regional diversity in reef system geomorphic responses to sea level rise into national-scale vulnerability assessments.NER

Seagrass meadows are important sources of reef island-building sediment

This is the final version. Available on open access from Nature Research via the DOI in this recordThe future vulnerability of low-lying atoll nations is inextricably linked to the production of island-building carbonate sediments by organisms living in their adjacent marine environments. Seagrass meadows are commonly found adjacent to reef islands, but their potential role as sources of reef island-building sediments has been overlooked. Here, we quantify rates of sediment production by seagrass epibionts in a reef island sediment supply context. Total seagrass epibiont sediment production at our study site (Huvadhoo Atoll, Maldives) was 853,000 ± 90,000 kg CaCO3 yr-1 over an area of 1.1 km2. Of this total sediment production, 541,000 ± 23,000 kg CaCO3 yr-1 was estimated to be suitable to contribute to reef island building (i.e., sand-sized, post-agitation). Our findings highlight a previously unrecognised and highly valuable ecosystem service provided by tropical seagrass meadows as important potential sources of reef island-building sediment. This study, therefore, presents a new and compelling geomorphic argument for seagrass conservation.British Society for Geomorpholog

Astrocytes grown in Alvetex® 3 dimensional scaffolds retain a non-reactive phenotype

yesProtocols which permit the extraction of primary astrocytes from either embryonic or postnatal mice are well established however astrocytes in culture are different to those in the mature CNS. Three dimensional (3D) cultures, using a variety of scaffolds may enable better phenotypic properties to be developed in culture. We present data from embryonic (E15) and postnatal (P4) murine primary cortical astrocytes grown on coated coverslips or a 3D polystyrene scaffold, Alvetex. Growth of both embryonic and postnatal primary astrocytes in the 3D scaffold changed astrocyte morphology to a mature, protoplasmic phenotype. Embryonic-derived astrocytes in 3D expressed markers of mature astrocytes, namely the glutamate transporter GLT-1 with low levels of the chondroitin sulphate proteoglycans, NG2 and SMC3. Embroynic astrocytes derived in 3D show lower levels of markers of reactive astrocytes, namely GFAP and mRNA levels of LCN2, PTX3, Serpina3n and Cx43. Postnatal-derived astrocytes show few protein changes between 2D and 3D conditions. Our data shows that Alvetex is a suitable scaffold for growth of astrocytes, and with appropriate choice of cells allows the maintenance of astrocytes with the properties of mature cells and a non-reactive phenotype.BBSR

CRISPR-Cas orthologues and variants: optimizing the repertoire, specificity and delivery of genome engineering tools

Robust and cost-effective genome editing in a diverse array of cells and model organisms is now possible thanks to the discovery of the RNA-guided endonucleases of the CRISPR-Cas system. The commonly used Cas9 of Streptococcus pyogenes shows high levels of activity but, depending on the application, has been associated with some shortcomings. Firstly, the enzyme has been shown to cause mutagenesis at genomic sequences resembling the target sequence. Secondly, the stringent requirement for a specific motif adjacent to the selected target site can limit the target range of this enzyme. Lastly, the physical size of Cas9 challenges the efficient delivery of genomic engineering tools based on this enzyme as viral particles for potential therapeutic applications. Related and parallel strategies have been employed to address these issues. Taking advantage of the wealth of structural information that is becoming available for CRISPR-Cas effector proteins, Cas9 has been redesigned by mutagenizing key residues contributing to activity and target recognition. The protein has also been shortened and redesigned into component subunits in an attempt to facilitate its efficient delivery. Furthermore, the CRISPR-Cas toolbox has been expanded by exploring the properties of Cas9 orthologues and other related effector proteins from diverse bacterial species, some of which exhibit different target site specificities and reduced molecular size. It is hoped that the improvements in accuracy, target range and efficiency of delivery will facilitate the therapeutic application of these site-specific nucleases

Exploring new physics frontiers through numerical relativity

The demand to obtain answers to highly complex problems within strong-field gravity has been met with significant progress in the numerical solution of Einstein's equations - along with some spectacular results - in various setups. We review techniques for solving Einstein's equations in generic spacetimes, focusing on fully nonlinear evolutions but also on how to benchmark those results with perturbative approaches. The results address problems in high-energy physics, holography, mathematical physics, fundamental physics, astrophysics and cosmology

Antiinflammatory Therapy with Canakinumab for Atherosclerotic Disease

Background: Experimental and clinical data suggest that reducing inflammation without affecting lipid levels may reduce the risk of cardiovascular disease. Yet, the inflammatory hypothesis of atherothrombosis has remained unproved. Methods: We conducted a randomized, double-blind trial of canakinumab, a therapeutic monoclonal antibody targeting interleukin-1β, involving 10,061 patients with previous myocardial infarction and a high-sensitivity C-reactive protein level of 2 mg or more per liter. The trial compared three doses of canakinumab (50 mg, 150 mg, and 300 mg, administered subcutaneously every 3 months) with placebo. The primary efficacy end point was nonfatal myocardial infarction, nonfatal stroke, or cardiovascular death. RESULTS: At 48 months, the median reduction from baseline in the high-sensitivity C-reactive protein level was 26 percentage points greater in the group that received the 50-mg dose of canakinumab, 37 percentage points greater in the 150-mg group, and 41 percentage points greater in the 300-mg group than in the placebo group. Canakinumab did not reduce lipid levels from baseline. At a median follow-up of 3.7 years, the incidence rate for the primary end point was 4.50 events per 100 person-years in the placebo group, 4.11 events per 100 person-years in the 50-mg group, 3.86 events per 100 person-years in the 150-mg group, and 3.90 events per 100 person-years in the 300-mg group. The hazard ratios as compared with placebo were as follows: in the 50-mg group, 0.93 (95% confidence interval [CI], 0.80 to 1.07; P = 0.30); in the 150-mg group, 0.85 (95% CI, 0.74 to 0.98; P = 0.021); and in the 300-mg group, 0.86 (95% CI, 0.75 to 0.99; P = 0.031). The 150-mg dose, but not the other doses, met the prespecified multiplicity-adjusted threshold for statistical significance for the primary end point and the secondary end point that additionally included hospitalization for unstable angina that led to urgent revascularization (hazard ratio vs. placebo, 0.83; 95% CI, 0.73 to 0.95; P = 0.005). Canakinumab was associated with a higher incidence of fatal infection than was placebo. There was no significant difference in all-cause mortality (hazard ratio for all canakinumab doses vs. placebo, 0.94; 95% CI, 0.83 to 1.06; P = 0.31). Conclusions: Antiinflammatory therapy targeting the interleukin-1β innate immunity pathway with canakinumab at a dose of 150 mg every 3 months led to a significantly lower rate of recurrent cardiovascular events than placebo, independent of lipid-level lowering. (Funded by Novartis; CANTOS ClinicalTrials.gov number, NCT01327846.

From Mendel’s discovery on pea to today’s plant genetics and breeding

In 2015, we celebrated the 150th anniversary of the presentation of the seminal work of Gregor Johann Mendel. While Darwin’s theory of evolution was based on differential survival and differential reproductive success, Mendel’s theory of heredity relies on equality and stability throughout all stages of the life cycle. Darwin’s concepts were continuous variation and “soft” heredity; Mendel espoused discontinuous variation and “hard” heredity. Thus, the combination of Mendelian genetics with Darwin’s theory of natural selection was the process that resulted in the modern synthesis of evolutionary biology. Although biology, genetics, and genomics have been revolutionized in recent years, modern genetics will forever rely on simple principles founded on pea breeding using seven single gene characters. Purposeful use of mutants to study gene function is one of the essential tools of modern genetics. Today, over 100 plant species genomes have been sequenced. Mapping populations and their use in segregation of molecular markers and marker–trait association to map and isolate genes, were developed on the basis of Mendel's work. Genome-wide or genomic selection is a recent approach for the development of improved breeding lines. The analysis of complex traits has been enhanced by high-throughput phenotyping and developments in statistical and modeling methods for the analysis of phenotypic data. Introgression of novel alleles from landraces and wild relatives widens genetic diversity and improves traits; transgenic methodologies allow for the introduction of novel genes from diverse sources, and gene editing approaches offer possibilities to manipulate gene in a precise manner

SizeExtractR: A workflow for rapid reproducible extraction of object size metrics from scaled images

1. Size is a biological characteristic that drives ecological processes from microscopic to geographic spatial scales, influencing cellular energetics, species fitness, population dynamics, and ecological interactions. Methods to measure size from images (e.g., proxies of body size, leaf area, and cell area) occur along a gradient from manual approaches to fully automated technologies (e.g., machine learning). These methods differ in terms of time investment, expertise required, and data or resource availability. While manual methods can improve accuracy through human recognition, they can be labor intensive, highlighting the need for semi-automated, and user-friendly software or workflows to increase the efficiency of manual techniques. 2. Here, we present SizeExtractR, an open-source workflow that enables faster extraction of size metrics from scaled images (e.g., each image includes a ruler) using semi-automated protocols. It comprises a set of ImageJ macros to speed up size extraction and annotation, and an R-package for the quality control of annotations, data collation, calibration, and visualization. 3. SizeExtractR extracts seven common size dimensions, including planar area, min/max diameter, and perimeter. Users can record additional categorical variables relating to their own study, for example species ID, by simply adding alphanumeric annotations to individual objects when prompted. Using a population size structure case study for hard corals as an example, we show how SizeExtractR was used to quantify the impact of mass coral bleaching on coral population dynamics. Lastly, the time saving benefit of using SizeExtractR was quantified during a series of timed image analyses, revealing up to a 49% reduction in image analysis time compared to a fully manual approach. 4. SizeExtractR automatically archives results, allowing re-analysis of size extraction and promoting quality control and reproducibility. It has already been employed in marine and terrestrial sciences to assess population dynamics and demography, energy investment in eggs, and growth of nursery reared corals, with potential to be applied to a wide range of other research fields