Modeling biogeomorphological interactions in underwater nourishments

To prevent sandy coastlines from further erosion, nourishments are executed in which sand is usually put underwater at the foreshore. Waves and currents transport the sand on the beach and in this way stabilize the coastal profile. Little is known about the interactions of these so-called shoreface nourishments with the benthic populations inhabiting the coastal strip. Benthos is affected by the nourishments, but benthic populations could in turn affect the morphological evolution of the nourished coast. Monitoring has shown that the benthic community will mainly recovery after ca. 1 year. However, the impact of benthos on the sediment dynamics and hydrodynamics is unknown. In this paper we focus on tube building worms, which have a large abundance in the foreshore, live in patches of several square meters in diameter and protrude several centimeters from the sediment in the water column. Tube building worms are included in a numerical modeling tool (Delft3D), by explicitly accounting for the influence of cylindrical structures on drag and turbulence by an extra source term of friction force in the momentum equation and an extra source term of Total Kinetic Energy (TKE) and turbulent energy dissipation in the k-ε equations respectively. The model is validated against field and flume experiments and it shows a significant influence on flow velocities near the bed, bed shear stress and bed-load transport rates. Moreover, model results reveal that tube building worms are able to stabilize nourishments and slow down the migration of the outer breaker bar. Present model explorations indicate that future research should focus on the measurement of the patchy distribution of bio-engineers in the foreshore and their impact on the sediment dynamics and hydrodynamics. Such knowledge will enable process based modeling of the spatial and temporal variation in biological activity on the morphological development of the coastal profile and also it will lead to validation of the proposed model with field measurements.</jats:p

Vegetation recovery in tidal marshes reveals critical slowing down under increased inundation

A declining rate of recovery following disturbance has been proposed as an important early warning for impending tipping points in complex systems. Despite extensive theoretical and laboratory studies, this \u27critical slowing down\u27 remains largely untested in the complex settings of real-world ecosystems. Here, we provide both observational and experimental support of critical slowing down along natural stress gradients in tidal marsh ecosystems. Time series of aerial images of European marsh development reveal a consistent lengthening of recovery time as inundation stress increases. We corroborate this finding with transplantation experiments in European and North American tidal marshes. In particular, our results emphasize the power of direct observational or experimental measures of recovery over indirect statistical signatures, such as spatial variance or autocorrelation. Our results indicate that the phenomenon of critical slowing down can provide a powerful tool to probe the resilience of natural ecosystems

The implicitome: A resource for rationalizing gene-disease associations

High-throughput experimental methods such as medical sequencing and genome-wide association studies (GWAS) identify increasingly large numbers of potential relations between genetic variants and diseases. Both biological complexity (millions of potential gene-disease associations) and the accelerating rate of data production necessitate computational approaches to prioritize and rationalize potential gene-disease relations. Here, we use concept profile technology to expose from the biomedical literature both explicitly stated gene-disease relations (the explicitome) and a much larger set of implied gene-disease associations (the implicitome). Implicit relations are largely unknown to, or are even unintended by the original authors, but they vastly extend the reach of existing

Association of genetic variation with systolic and diastolic blood pressure among African Americans: the Candidate Gene Association Resource study

The prevalence of hypertension in African Americans (AAs) is higher than in other US groups; yet, few have performed genome-wide association studies (GWASs) in AA. Among people of European descent, GWASs have identified genetic variants at 13 loci that are associated with blood pressure. It is unknown if these variants confer susceptibility in people of African ancestry. Here, we examined genome-wide and candidate gene associations with systolic blood pressure (SBP) and diastolic blood pressure (DBP) using the Candidate Gene Association Resource (CARe) consortium consisting of 8591 AAs. Genotypes included genome-wide single-nucleotide polymorphism (SNP) data utilizing the Affymetrix 6.0 array with imputation to 2.5 million HapMap SNPs and candidate gene SNP data utilizing a 50K cardiovascular gene-centric array (ITMAT-Broad-CARe [IBC] array). For Affymetrix data, the strongest signal for DBP was rs10474346 (P= 3.6 × 10−8) located near GPR98 and ARRDC3. For SBP, the strongest signal was rs2258119 in C21orf91 (P= 4.7 × 10−8). The top IBC association for SBP was rs2012318 (P= 6.4 × 10−6) near SLC25A42 and for DBP was rs2523586 (P= 1.3 × 10−6) near HLA-B. None of the top variants replicated in additional AA (n = 11 882) or European-American (n = 69 899) cohorts. We replicated previously reported European-American blood pressure SNPs in our AA samples (SH2B3, P= 0.009; TBX3-TBX5, P= 0.03; and CSK-ULK3, P= 0.0004). These genetic loci represent the best evidence of genetic influences on SBP and DBP in AAs to date. More broadly, this work supports that notion that blood pressure among AAs is a trait with genetic underpinnings but also with significant complexit

Association of genetic variation with systolic and diastolic blood pressure among African Americans: the Candidate Gene Association Resource study.

The prevalence of hypertension in African Americans (AAs) is higher than in other US groups; yet, few have performed genome-wide association studies (GWASs) in AA. Among people of European descent, GWASs have identified genetic variants at 13 loci that are associated with blood pressure. It is unknown if these variants confer susceptibility in people of African ancestry. Here, we examined genome-wide and candidate gene associations with systolic blood pressure (SBP) and diastolic blood pressure (DBP) using the Candidate Gene Association Resource (CARe) consortium consisting of 8591 AAs. Genotypes included genome-wide single-nucleotide polymorphism (SNP) data utilizing the Affymetrix 6.0 array with imputation to 2.5 million HapMap SNPs and candidate gene SNP data utilizing a 50K cardiovascular gene-centric array (ITMAT-Broad-CARe [IBC] array). For Affymetrix data, the strongest signal for DBP was rs10474346 (P= 3.6 × 10(-8)) located near GPR98 and ARRDC3. For SBP, the strongest signal was rs2258119 in C21orf91 (P= 4.7 × 10(-8)). The top IBC association for SBP was rs2012318 (P= 6.4 × 10(-6)) near SLC25A42 and for DBP was rs2523586 (P= 1.3 × 10(-6)) near HLA-B. None of the top variants replicated in additional AA (n = 11 882) or European-American (n = 69 899) cohorts. We replicated previously reported European-American blood pressure SNPs in our AA samples (SH2B3, P= 0.009; TBX3-TBX5, P= 0.03; and CSK-ULK3, P= 0.0004). These genetic loci represent the best evidence of genetic influences on SBP and DBP in AAs to date. More broadly, this work supports that notion that blood pressure among AAs is a trait with genetic underpinnings but also with significant complexity

Niche dimension differs among life-history stages of Pacific oysters in intertidal environments

Structure-building, autogenic ecosystem engineers are recognized worldwide as potential tools for coastal protection, which depends on long-term sustainability and persistence of their structures. For reef-building oysters, reefs are maintained through accumulation of shell material, which depends on recruitment and growth and which provides substrate for new generations. Knowledge of the fundamental niche of oysters in relation to biotic and abiotic conditions helps define the area where ecosystem engineers grow and survive well and where their structures are likely to persist and be effective for coastal protection. Response curves of different lifehistory stages (larvae, juveniles and adults) of the Pacific oyster Crassostrea gigas were investigated along a tidal emersion gradient in a manipulative field study. Density of juvenile oysters was maximal around 36% tidal emersion. Shell growth of juveniles and adults, condition index (CI) of adults and mortality of adults were negatively related to tidal emersion, whereas mortality of juveniles was positively related to tidal emersion. Tidal emersion had a strong effect on oyster survival and growth, with the most favourable being around 20 to 40% tidal emersion, as indicated by recruit density and the CI of adults. These findings suggest that the area of 20 to 40% tidal emersion is optimal for reef development, which is in line with other investigations of C. gigas and the eastern oyster C. virginica across different systems, supporting a broader geographical application of these findings

Data and analysis of SandMotor benthos

This dataset contains the R scripts, as well as the raw and intermediate data, used in the analysis of changes in the benthic life on and around the Sand Motor between 2010 and 2017