Asparaginyl endopeptidases (AEPs) are proteases that have crucial roles in plant defense and seed storage protein maturation. Select plant AEPs, however, do not function as proteases but as ...transpeptidases (ligases) catalyzing the intra-molecular ligation of peptide termini, which leads to peptide cyclization. These ligase-type AEPs have potential biotechnological applications ranging from in vitro peptide engineering to plant molecular farming, but the structural features enabling these enzymes to catalyze peptide ligation/cyclization rather than proteolysis are currently unknown. Here, we compare the sequences, structures, and functions of diverse plant AEPs by combining molecular modeling, sequence space analysis, and functional testing in planta. We find that changes within the substrate-binding pocket and an adjacent loop, here named the "marker of ligase activity", together play a key role for AEP ligase efficiency. Identification of these structural determinants may facilitate the discovery of more ligase-type AEPs and the engineering of AEPs with tailored catalytic properties.
The relative influence of Neogene geomorphological events and Quaternary climatic changes as causal mechanisms on Neotropical diversification remains largely speculative, as most divergence timing ...inferences are based on a single locus and have limited taxonomic or geographic sampling. To investigate these influences, we use a multilocus (two mitochondrial and 11 nuclear genes) range-wide sampling of Phyllopezus pollicaris, a gecko complex widely distributed across the poorly studied South American 'dry diagonal' biomes. Our approach couples traditional and model-based phylogeography with geospatial methods, and demonstrates Miocene diversification and limited influence of Pleistocene climatic fluctuations on P. pollicaris. Phylogeographic structure and distribution models highlight that persistence across multiple isolated regions shaped the diversification of this species complex. Approximate Bayesian computation supports hypotheses of allopatric and ecological/sympatric speciation between lineages that largely coincide with genetic clusters associated with Chaco, Cerrado, and Caatinga, standing for complex diversification between the 'dry diagonal' biomes. We recover extremely high genetic diversity and suggest that eight well-supported clades may be valid species, with direct implications for taxonomy and conservation assessments. These patterns exemplify how low-vagility species complexes, characterized by strong genetic structure and pre-Pleistocene divergence histories, represent ideal radiations to investigate broad biogeographic histories of associated biomes.
Habitat fragmentation is a major cause of biodiversity loss in agricultural landscapes. Studying habitat connectivity in fragmented landscapes is therefore pivotal for better understanding the ...factors that shape faunal communities in anthropogenic landscapes. Amphibians have limited dispersal abilities, strong site fidelity and often perform seasonal movements to reach relatively distant breeding habitats. This calls for a better knowledge of which landscape features might promote dispersal, especially in crops. We applied graph-theoretic network analyses to a set of 35 waterbodies embedded in 10 rice fields in a savanna–rain forest ecotone, Tocantins, Brazil, to assess the importance of landscape features (forest patches, waterbodies) for anuran functional connectivity within the entire network. We used taxonomic, functional and phylogenetic diversity as proxies of anuran functional connectivity (i.e. dispersal ability intrinsic to the taxa), based on previous associations uncovered between species diversity metrics and landscape connectivity. We found that, assuming individuals belonging to each of the 14 amphibian species recorded are unable to disperse over 800 m, forest and waterbody area and abundance are the most important predictors of waterbody importance for connectivity. Hence, pond network connectivity for amphibians in rice crops depends on (1) abundant and large forest patches in the area surrounding waterbodies, and (2) a network of abundant waterbodies.
This review summarizes recent advances in the area of tribology based on the outcome of a Lorentz Center workshop surveying various physical, chemical and mechanical phenomena across scales. Among ...the main themes discussed were those of rough surface representations, the breakdown of continuum theories at the nano- and microscales, as well as multiscale and multiphysics aspects for analytical and computational models relevant to applications spanning a variety of sectors, from automotive to biotribology and nanotechnology. Significant effort is still required to account for complementary nonlinear effects of plasticity, adhesion, friction, wear, lubrication and surface chemistry in tribological models. For each topic, we propose some research directions.
Display omitted
Identification of mechanisms that promote variation in life-history traits is critical to understand the evolution of divergent reproductive strategies. Here we compiled a large life-history data set ...(674 lizard populations, representing 297 species from 263 sites globally) to test a number of hypotheses regarding the evolution of life-history traits in lizards. We found significant phylogenetic signal in most life-history traits, although phylogenetic signal was not particularly high. Climatic variables influenced the evolution of many traits, with clutch frequency being positively related to precipitation and clutches of tropical lizards being smaller than those of temperate species. This result supports the hypothesis that in tropical and less seasonal climates, many lizards tend to reproduce repeatedly throughout the season, producing smaller clutches during each reproductive episode. Our analysis also supported the hypothesis that viviparity has evolved in lizards as a response to cooler climates. Finally, we also found that variation in trait values explained by clade membership is unevenly distributed among lizard clades, with basal clades and a few younger clades showing the most variation. Our global analyses are largely consistent with life-history theory and previous results based on smaller and scattered data sets, suggesting that these patterns are remarkably consistent across geographic and taxonomic scales.
Rates of species formation vary widely across the tree of life and contribute to massive disparities in species richness among clades. This variation can emerge from differences in ...metapopulation-level processes that affect the rates at which lineages diverge, persist, and evolve reproductive barriers and ecological differentiation. For example, populations that evolve reproductive barriers quickly should form new species at faster rates than populations that acquire reproductive barriers more slowly. This expectation implicitly links microevolutionary processes (the evolution of populations) and macroevolutionary patterns (the profound disparity in speciation rate across taxa). Here, leveraging extensive field sampling from the Neotropical Cerrado biome in a biogeographically controlled natural experiment, we test the role of an important microevolutionary process-the propensity for population isolation-as a control on speciation rate in lizards and snakes. By quantifying population genomic structure across a set of codistributed taxa with extensive and phylogenetically independent variation in speciation rate, we show that broad-scale patterns of species formation are decoupled from demographic and genetic processes that promote the formation of population isolates. Population isolation is likely a critical stage of speciation for many taxa, but our results suggest that interspecific variability in the propensity for isolation has little influence on speciation rates. These results suggest that other stages of speciation-including the rate at which reproductive barriers evolve and the extent to which newly formed populations persist-are likely to play a larger role than population isolation in controlling speciation rate variation in squamates.
We present a numerical assessment of the thermal-hydraulic performance of the NbTi bus bars designed for the European DEMO. We consider the CS, TF and PF bus bars, as well as two alternative TF ...options for high-current operations. The main sources of static heat loads are identified and the corresponding thermal budget determined. In addition, the AC losses have been included in the simulations of the CS and PF bus bars, which present a pulsed operation, in contrast with the DC operation of the TF bus bars (and coils). By imposing appropriate pressure drops as boundary conditions, we compute the resulting He mass flow rates and the corresponding temperature margins along each bus bar. Thus, the most critical region of the bus bars in terms of cryogenic stability is identified, as well as the effect of AC losses on the temperature margin is quantified.
Understanding the nature and extent of ecosystem boundaries has important implications for the management and conservation of biodiversity. However, characterizing and establishing such boundary ...limits has been a persistent challenge worldwide. The Cerrado–Amazonia transition (CAT) in Brazil is the world’s largest savanna-forest transition. However, the CAT is represented in official maps used by Brazilian governmental agencies as a simple line separating the two biomes. Here, we demonstrate that the CAT is in fact broad, complex and interdigitating and that its traditional linear representation is not adequate for recognizing and conserving biodiversity in this region. Over the 30 years of our analysis, the CAT suffered more deforestation than the forests and savannas in each individual biomes (Amazonia and Cerrado). The complexity of tropical savanna-forest boundaries has been misunderstood and misrepresented by current maps, severely threatening the complex CAT biota. As a consequence, vegetation losses have reached levels close to collapse in areas of intense human activity.
Context
Deforestation is a major driver of biodiversity loss, mainly due to agriculture. As rice is among the world’s most important crops, determining how agricultural communities are shaped is ...imperative. However, few studies have addressed the factors that alter community assembly in human-modified landscapes. We aim to quantify taxonomic, functional, trait and phylogenetic diversity of an anuran community from rice crops on a biodiversity hotspot.
Objectives
Identify local and landscape characteristics responsible for variations in multiple dimensions of anuran diversity in rice crops.
Methods
This study was performed in Tocantins, Brazil. We chose 36 lentic waterbodies on rice fields for anuran sampling. We quantified taxonomic diversity (TD), functional diversity (FD) and phylogenetic diversity (PD) for each waterbody. We also estimated the mean functional differences among species for each trait separately. To evaluate how local and landscape scale features affect anurans, we performed generalized linear mixed models in 500, 1000 and 1500 m buffers around each waterbody.
Results
We found increased PD and FD in waterbodies closer to many other waterbodies and large forest patches. Anuran biomass decreased with increasing distance to the closest waterbody. Trait diversity varied with waterbody abundance and closeness, percentage of bare ground and marginal vegetation.
Conclusions
Our study emphasizes the importance of waterbody and forest patch networks for maintaining high anuran FD and PD in agricultural landscapes. As both metrics are known to be related to ecosystem resilience, understanding these patterns is pivotal for biodiversity management, especially in the tropics, where agricultural expansion is unrelenting and biodiversity is especially unique.
PDF
