Relative size underlies alternative morph development in a salamander

Size thresholds commonly underlie the induction of alternative morphological states. However, the respective importance of absolute and relative size to such thresholds remains uncertain. If absolute size governs expression, morph frequency should differ among environments that influence absolute sizes (e.g. resources, competition), and individuals of the same morph should have similar average sizes across environments. If relative size determines expression, the frequency of each morph may not differ among environments, but morphs within each environment should differ in size relative to one another. We tested these predictions in a salamander (Ambystoma talpoideum) that develops into either a terrestrial metamorph or an aquatic paedomorph. To generate size variation within and among environments, we reared individuals in mesocosm ponds across three conspecific densities. We found that morph frequency did not differ among density treatments, and the morphs were not similarly sized within each density treatment. Instead, within each environment, relatively larger individuals became metamorphs and relatively smaller individuals became paedomorphs. Relative size therefore determined morph development, highlighting the importance of an individual’s social context to size-dependent morph induction

Gene content evolution in the arthropods

Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods. Using 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception. These analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity

A New Paradigm for Large Earthquakes in Stable Continental Plate Interiors

Large earthquakes within stable continental regions (SCR) show that significant amounts of elastic strain can be released on geological structures far from plate boundary faults, where the vast majority of the Earth's seismic activity takes place. SCR earthquakes show spatial and temporal patterns that differ from those at plate boundaries and occur in regions where tectonic loading rates are negligible. However, in the absence of a more appropriate model, they are traditionally viewed as analogous to their plate boundary counterparts, occuring when the accrual of tectonic stress localized at long-lived active faults reaches failure threshold. Here we argue that SCR earthquakes are better explained by transient perturbations of local stress or fault strength that release elastic energy from a pre-stressed lithosphere. As a result, SCR earthquakes can occur in regions with no previous seismicity and no surface evidence for strain accumulation. They need not repeat, since the tectonic loading rate is close to zero. Therefore, concepts of recurrence time or fault slip rate do not apply. As a consequence, seismic hazard in SCRs is likely more spatially distributed than indicated by paleoearthquakes, current seismicity, or geodetic strain rates

Synthesis of a square-planar rhodium alkylidene N-heterocyclic carbene complex and its reactivity toward alkenes

The first rhodium alkylidene square-planar complex stabilized by an N-heterocyclic carbene ligand, RhCl(-CHPh)(IPr)PPh3 (2; IPr = 1,3-bis(2,6-diisopropylphenyl)imidazol-2-carbene), has been prepared by reaction of RhCl(IPr)(PPh3)2 (1) with phenyldiazomethane and its dynamic behavior in solution studied. Treatment of 2 with alkenes results in the formation of the ¿2-olefin complexes RhCl(¿2-CH2-CHR)(IPr)PPh3 (3, R = H; 4, R = Ph; 5, R = OEt) and new olefins arising from the coupling of the alkylidene with the alkenes, likely via a metallacyclobutane intermediate

Effect of logging wounds on diameter growth of beech (Fagus orientalis Lipsky) trees following selection cutting in Caspian forests of Iran

Background Logging damage to residual trees during selection cutting may lead to serious economic losses in terms of both timber quality and diameter growth reduction. In this study, we investigated the effect of logging operations on residual tree damage and the consequence of injuries on diameter growth in an uneven-aged mixed forest dominated by beech (Fagus orientalis Lipsky)

Travelling and splitting of a wave of hedgehog expression involved in spider-head segmentation

During development segmentation is a process that generates a spatial periodic pattern. Peak splitting of waves of gene expression is a mathematically predicted, simple strategy accounting for this type of process, but it has not been well characterized biologically. Here we show temporally repeated splitting of gene expression into stripes that is associated with head axis growth in the spider Achaearanea embryo. Preceding segmentation, a wave of hedgehog homologue gene expression is observed to travel posteriorly during development stage 6. This stripe, co-expressing an orthodenticle homologue, undergoes two cycles of splitting and shifting accompanied by convergent extension, serving as a generative zone for the head segments. The two orthodenticle and odd-paired homologues are identified as targets of Hedgehog signalling, and evidence suggests that their activities mediate feedback to maintain the head generative zone and to promote stripe splitting in this zone. We propose that the 'stripe-splitting' strategy employs genetic components shared with Drosophila blastoderm subdivision, which are required for participation in an autoregulatory signalling network

Mechanism of Protein Kinetic Stabilization by Engineered Disulfide Crosslinks

The impact of disulfide bonds on protein stability goes beyond simple equilibrium thermodynamics effects associated with the conformational entropy of the unfolded state. Indeed, disulfide crosslinks may play a role in the prevention of dysfunctional association and strongly affect the rates of irreversible enzyme inactivation, highly relevant in biotechnological applications. While these kinetic-stability effects remain poorly understood, by analogy with proposed mechanisms for processes of protein aggregation and fibrillogenesis, we propose that they may be determined by the properties of sparsely-populated, partially-unfolded intermediates. Here we report the successful design, on the basis of high temperature molecular-dynamics simulations, of six thermodynamically and kinetically stabilized variants of phytase from Citrobacter braakii (a biotechnologically important enzyme) with one, two or three engineered disulfides. Activity measurements and 3D crystal structure determination demonstrate that the engineered crosslinks do not cause dramatic alterations in the native structure. The inactivation kinetics for all the variants displays a strongly non-Arrhenius temperature dependence, with the time-scale for the irreversible denaturation process reaching a minimum at a given temperature within the range of the denaturation transition. We show this striking feature to be a signature of a key role played by a partially unfolded, intermediate state/ensemble. Energetic and mutational analyses confirm that the intermediate is highly unfolded (akin to a proposed critical intermediate in the misfolding of the prion protein), a result that explains the observed kinetic stabilization. Our results provide a rationale for the kinetic-stability consequences of disulfide-crosslink engineering and an experimental methodology to arrive at energetic/structural descriptions of the sparsely populated and elusive intermediates that play key roles in irreversible protein denaturation.This work was supported by grants BIO2009-09562, CSD2009-00088 from the Spanish Ministry of Science and Innovation, and FEDER Funds (JMS-R)

Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins

Cotranslational protein folding can facilitate rapid formation of functional structures. However, it might also cause premature assembly of protein complexes, if two interacting nascent chains are in close proximity. By analyzing known protein structures, we show that homomeric protein contacts are enriched towards the C-termini of polypeptide chains across diverse proteomes. We hypothesize that this is the result of evolutionary constraints for folding to occur prior to assembly. Using high-throughput imaging of protein homomers in vivo in E. coli and engineered protein constructs with N- and C-terminal oligomerization domains, we show that, indeed, proteins with C-terminal homomeric interface residues consistently assemble more efficiently than those with N-terminal interface residues. Using in vivo, in vitro and in silico experiments, we identify features that govern successful assembly of homomers, which have implications for protein design and expression optimization