TRY plant trait database – enhanced coverage and open access

Plant traits—the morphological, anatomical, physiological, biochemical and phenological characteristics of plants—determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits—almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

Genetic determinants of telomere length from 109,122 ancestrally diverse whole-genome sequences in TOPMed

Genetic studies on telomere length are important for understanding age-related diseases. Prior GWASs for leukocyte TL have been limited to European and Asian populations. Here, we report the first sequencing-based association study for TL across ancestrally diverse individuals (European, African, Asian, and Hispanic/Latino) from the NHLBI Trans-Omics for Precision Medicine (TOPMed) program. We used whole-genome sequencing (WGS) of whole blood for variant genotype calling and the bioinformatic estimation of telomere length in n = 109,122 individuals. We identified 59 sentinel variants (p < 5 × 10−9) in 36 loci associated with telomere length, including 20 newly associated loci (13 were replicated in external datasets). There was little evidence of effect size heterogeneity across populations. Fine-mapping at OBFC1 indicated that the independent signals colocalized with cell-type-specific eQTLs for OBFC1 (STN1). Using a multi-variant gene-based approach, we identified two genes newly implicated in telomere length, DCLRE1B (SNM1B) and PARN. In PheWAS, we demonstrated that our TL polygenic trait scores (PTSs) were associated with an increased risk of cancer-related phenotypes

Segregation-induced fingering instabilities in granular free-surface flows

Particle-size segregation can have a significant feedback on the bulk motion of granular avalanches when the larger grains experience greater resistance to motion than the fine grains. When such segregation-mobility feedback effects occur the flow may form digitate lobate fingers or spontaneously self-channelize to form lateral levees that enhance run-out distance. This is particularly important in geophysical mass flows, such as pyroclastic currents, snow avalanches and debris flows, where run-out distance is of crucial importance in hazards assessment. A model for finger formation in a bidisperse granular avalanche is developed by coupling a depth-averaged description of the preferential transport of large particles towards the front with an established avalanche model. The coupling is achieved through a concentration-dependent friction coefficient, which results in a system of non-strictly hyperbolic equations. We compute numerical solutions to the flow of a bidisperse mixture of small mobile particles and larger more resistive grains down an inclined chute. The numerical results demonstrate that our model is able to describe the formation of a front rich in large particles, the instability of this front and the subsequent evolution of elongated fingers bounded by large-rich lateral levees, as observed in small-scale laboratory experiments. However, our numerical results are grid dependent, with the number of fingers increasing as the numerical resolution is increased. We investigate this pathology by examining the linear stability of a steady uniform flow, which shows that arbitrarily small wavelength perturbations grow exponentially quickly. Furthermore, we find that on a curve in parameter space the growth rate is unbounded above as the wavelength of perturbations is decreased and so the system of equations on this curve is ill-posed. This indicates that the model captures the physical mechanisms that drive the instability, but additional dissipation mechanisms, such as those considered in the realm of flow rheology, are required to set the length scale of the fingers that develop

Gene3D: Structural Assignment for Whole Genes and Genomes Using the CATH Domain Structure Database

We present a novel web-based resource, Gene3D, of precalculated structural assignments to gene sequences and whole genomes. This resource assigns structural domains from the CATH database to whole genes and links these to their curated functional and structural annotations within the CATH domain structure database, the functional Dictionary of Homologous Superfamilies (DHS) and PDBsum. Currently Gene3D provides annotation for 36 complete genomes (two eukaryotes, six archaea, and 28 bacteria). On average, between 30% and 40% of the genes of a given genome can be structurally annotated. Matches to structural domains are found using the profile-based method (PSI-BLAST). and a novel protocol, DRange, is used to resolve conflicts in matches involving different homologous superfamilies