Thermodynamic phase-field model for microstructure with multiple components and phases: the possibility of metastable phases

A diffuse-interface model for microstructure with an arbitrary number of components and phases was developed from basic thermodynamic and kinetic principles and formalized within a variational framework. The model includes a composition gradient energy to capture solute trapping, and is therefore suited for studying phenomena where the width of the interface plays an important role. Derivation of the inhomogeneous free energy functional from a Taylor expansion of homogeneous free energy reveals how the interfacial properties of each component and phase may be specified under a mass constraint. A diffusion potential for components was defined away from the dilute solution limit, and a multi-obstacle barrier function was used to constrain phase fractions. The model was used to simulate solidification via nucleation, premelting at phase boundaries and triple junctions, the intrinsic instability of small particles, and solutal melting resulting from differing diffusivities in solid and liquid. The shape of metastable free energy surfaces is found to play an important role in microstructure evolution and may explain why some systems premelt at phase boundaries and phase triple junctions while others do not.Comment: 14 pages, 8 figure

Combining genome-wide association mapping and transcriptional networks to identify novel genes controlling glucosinolates in Arabidopsis thaliana.

BackgroundGenome-wide association (GWA) is gaining popularity as a means to study the architecture of complex quantitative traits, partially due to the improvement of high-throughput low-cost genotyping and phenotyping technologies. Glucosinolate (GSL) secondary metabolites within Arabidopsis spp. can serve as a model system to understand the genomic architecture of adaptive quantitative traits. GSL are key anti-herbivory defenses that impart adaptive advantages within field trials. While little is known about how variation in the external or internal environment of an organism may influence the efficiency of GWA, GSL variation is known to be highly dependent upon the external stresses and developmental processes of the plant lending it to be an excellent model for studying conditional GWA.Methodology/principal findingsTo understand how development and environment can influence GWA, we conducted a study using 96 Arabidopsis thaliana accessions, >40 GSL phenotypes across three conditions (one developmental comparison and one environmental comparison) and ∼230,000 SNPs. Developmental stage had dramatic effects on the outcome of GWA, with each stage identifying different loci associated with GSL traits. Further, while the molecular bases of numerous quantitative trait loci (QTL) controlling GSL traits have been identified, there is currently no estimate of how many additional genes may control natural variation in these traits. We developed a novel co-expression network approach to prioritize the thousands of GWA candidates and successfully validated a large number of these genes as influencing GSL accumulation within A. thaliana using single gene isogenic lines.Conclusions/significanceTogether, these results suggest that complex traits imparting environmentally contingent adaptive advantages are likely influenced by up to thousands of loci that are sensitive to fluctuations in the environment or developmental state of the organism. Additionally, while GWA is highly conditional upon genetics, the use of additional genomic information can rapidly identify causal loci en masse

Editorial: Early Avian Evolution

The study of early avian evolution—how birds evolved from dinosaurs and radiated into the most diverse group of amniotes on the planet—is one of the most dynamic areas of research in paleontology, fueled not only by the rapid rate of discovery of new specimens (see Foth et al.; Musser and Clarke; and Xing et al.) and sheer volume of available material (see Zheng et al.) but also by the innovative application of new analytical methods to key evolutionary questions (see Heers et al.; Liu et al.). Also critical to our understanding is the exceptional level of preservation of many Mesozoic and early Cenozoic bird fossils, which not uncommonly preserve soft tissues and other indicators that may provide key insights into the biology of these organisms (see articles by Clark and O’Connor; Foth et al.; Xing et al.; Zheng et al.). In putting together this research topic, our aim was to further expand our understanding of early avian evolution by gathering a body of work highlighting the diversity of research currently being undertaken in this area. As such, articles published in this topic have augmented our understanding of a variety of important areas related to early avian evolution, including the recognition of new taxonomic diversity (see Clark and O’Connor and Musser and Clarke), insights into the evolution of key avian traits such as flight (Heers et al.) and a toothless beak (see Louchart et al. and Zheng et al.), and the piecemeal evolution of crown avian biology (see Atterholt et al. and Heers et al.)

Whole genome resequencing of Botrytis cinerea isolates identifies high levels of standing diversity

How standing genetic variation within a pathogen contributes to diversity in host/pathogen interactions is poorly understood, partly because most studied pathogens are host-specific, clonally reproducing organisms which complicates genetic analysis. In contrast, Botrytis cinerea is a sexually reproducing, true haploid ascomycete that can infect a wide range of diverse plant hosts. While previous work had shown significant genomic variation between two isolates, we proceeded to assess the level and frequency of standing variation in a population of B. cinerea. To begin measuring standing genetic variation in B. cinerea, we re-sequenced the genomes of 13 different isolates and aligned them to the previously sequenced T4 reference genome. In addition one of these isolates was resequenced from four independently repeated cultures. A high level of genetic diversity was found within the 13 isolates. Within this variation, we could identify clusters of genes with major effect polymorphisms, i.e., polymorphisms that lead to a predicted functional knockout, that surrounded genes involved in controlling vegetative incompatibility. The genotype at these loci was able to partially predict the interaction of these isolates in vegetative fusion assays showing that these loci control vegetative incompatibility. This suggests that the vegetative incompatibility loci within B. cinerea are associated with regions of increased genetic diversity. The genome re-sequencing of four clones from the one isolate (Grape) that had been independently propagated over 10 years showed no detectable spontaneous mutation. This suggests that B. cinerea does not display an elevated spontaneous mutation rate. Future work will allow us to test if, and how, this diversity may be contributing to the pathogen's broad host range

The Defense Metabolite, Allyl Glucosinolate, Modulates Arabidopsis thaliana Biomass Dependent upon the Endogenous Glucosinolate Pathway

14 páginas, 8 figuras y 3 tablas.Glucosinolates (GSLs) play an important role in plants as direct mediators of biotic and abiotic stress responses. Recent work is beginning to show that the GSLs can also inducing complex defense and growth networks. However, the physiological significance of these GSL-induced responses and the molecular mechanisms by which GSLs are sensed and/or modulate these responses are not understood. To identify these potential mechanisms within the plant and how they may relate to the endogenous GSLs, we tested the regulatory effect of exogenous allyl GSL application on growth and defense metabolism across sample of Arabidopsis thaliana accessions. We found that application of exogenous allyl GSL had the ability to initiate changes in plant biomass and accumulation of defense metabolites that genetically varied across accessions. This growth effect was related to the allyl GSL side-chain structure. Utilizing this natural variation and mutants in genes within the GSL pathway we could show that the link between allyl GSL and altered growth responses are dependent upon the function of known genes controlling the aliphatic GSL pathway.This work was funded by a Marie Curie International Outgoing Fellowship within the 7th European Community Framework Programme (PIOF-GA-2010-275286), the NSF DBI grant 820580 to DK, the NSF MCB grant 1330337 to DK, the USDA National Institute of Food and Agriculture, Hatch project number CA-D-PLS-7033-H to DK and by the Danish National Research Foundation (DNRF99) grant to DK and MB.Peer reviewe