Declining Coral Skeletal Extension for Forereef Colonies of Siderastrea siderea on the Mesoamerican Barrier Reef System, Southern Belize

BACKGROUND: Natural and anthropogenic stressors are predicted to have increasingly negative impacts on coral reefs. Understanding how these environmental stressors have impacted coral skeletal growth should improve our ability to predict how they may affect coral reefs in the future. We investigated century-scale variations in skeletal extension for the slow-growing massive scleractinian coral Siderastrea siderea inhabiting the forereef, backreef, and nearshore reefs of the Mesoamerican Barrier Reef System (MBRS) in the western Caribbean Sea. METHODOLOGY/PRINCIPAL FINDINGS: Thirteen S. siderea cores were extracted, slabbed, and X-rayed. Annual skeletal extension was estimated from adjacent low- and high-density growth bands. Since the early 1900s, forereef S. siderea colonies have shifted from exhibiting the fastest to the slowest average annual skeletal extension, while values for backreef and nearshore colonies have remained relatively constant. The rates of change in annual skeletal extension were -0.020±0.005, 0.011±0.006, and -0.008±0.006 mm yr⁻¹ per year [mean±SE] for forereef, backreef, and nearshore colonies respectively. These values for forereef and nearshore S. siderea were significantly lower by 0.031±0.008 and by 0.019±0.009 mm yr⁻¹ per year, respectively, than for backreef colonies. However, only forereef S. siderea exhibited a statistically significant decline in annual skeletal extension over the last century. CONCLUSIONS/SIGNIFICANCE: Our results suggest that forereef S. siderea colonies are more susceptible to environmental stress than backreef and nearshore counterparts, which may have historically been exposed to higher natural baseline stressors. Alternatively, sediment plumes, nutrients, and pollution originating from watersheds of Guatemala and Honduras may disproportionately impact the forereef environment of the MBRS. We are presently reconstructing the history of environmental stressors that have impacted the MBRS to constrain the cause(s) of the observed reductions in coral skeletal growth. This should improve our ability to predict and potentially mitigate the effects of future environmental stressors on coral reef ecosystems

Next nearest neighbour Ising models on random graphs

This paper develops results for the next nearest neighbour Ising model on random graphs. Besides being an essential ingredient in classic models for frustrated systems, second neighbour interactions interactions arise naturally in several applications such as the colour diversity problem and graphical games. We demonstrate ensembles of random graphs, including regular connectivity graphs, that have a periodic variation of free energy, with either the ratio of nearest to next nearest couplings, or the mean number of nearest neighbours. When the coupling ratio is integer paramagnetic phases can be found at zero temperature. This is shown to be related to the locked or unlocked nature of the interactions. For anti-ferromagnetic couplings, spin glass phases are demonstrated at low temperature. The interaction structure is formulated as a factor graph, the solution on a tree is developed. The replica symmetric and energetic one-step replica symmetry breaking solution is developed using the cavity method. We calculate within these frameworks the phase diagram and demonstrate the existence of dynamical transitions at zero temperature for cases of anti-ferromagnetic coupling on regular and inhomogeneous random graphs.Comment: 55 pages, 15 figures, version 2 with minor revisions, to be published J. Stat. Mec

A potential role for RNA aminoacylation prior to its role in peptide synthesis

Coded ribosomal peptide synthesis could not have evolved unless its sequence and amino acid–specific aminoacylated tRNA substrates already existed. We therefore wondered whether aminoacylated RNAs might have served some primordial function prior to their role in protein synthesis. Here, we show that specific RNA sequences can be nonenzymatically aminoacylated and ligated to produce amino acid–bridged stem-loop RNAs. We used deep sequencing to identify RNAs that undergo highly efficient glycine aminoacylation followed by loop-closing ligation. The crystal structure of one such glycine-bridged RNA hairpin reveals a compact internally stabilized structure with the same eponymous T-loop architecture that is found in many noncoding RNAs, including the modern tRNA. We demonstrate that the T-loop-assisted amino acid bridging of RNA oligonucleotides enables the rapid template-free assembly of a chimeric version of an aminoacyl-RNA synthetase ribozyme. We suggest that the primordial assembly of amino acid–bridged chimeric ribozymes provides a direct and facile route for the covalent incorporation of amino acids into RNA. A greater functionality of covalently incorporated amino acids could contribute to enhanced ribozyme catalysis, providing a driving force for the evolution of sequence and amino acid–specific aminoacyl-RNA synthetase ribozymes in the RNA World. The synthesis of specifically aminoacylated RNAs, an unlikely prospect for nonenzymatic reactions but a likely one for ribozymes, could have set the stage for the subsequent evolution of coded protein synthesis

Revised Masses and Densities of the Planets around Kepler-10

Determining which small exoplanets have stony-iron compositions is necessary for quantifying the occurrence of such planets and for understanding the physics of planet formation. Kepler-10 hosts the stony-iron world Kepler-10b, and also contains what has been reported to be the largest solid silicate-ice planet, Kepler-10c. Using 220 radial velocities (RVs), including 72 precise RVs from Keck-HIRES of which 20 are new from 2014 to 2015, and 17 quarters of Kepler photometry, we obtain the most complete picture of the Kepler-10 system to date. We find that Kepler-10b (R_p = 1.47 R_⊕) has mass 3.72 ± 0.42 M_⊕ and density 6.46 ± 0.73 g cm^(-3). Modeling the interior of Kepler-10b as an iron core overlaid with a silicate mantle, we find that the iron core constitutes 0.17 ± 0.11 of the planet mass. For Kepler-10c (R_p = 2.35 R_⊕) we measure mass 13.98 ± 1.79 M_⊕ and density 5.94 ± 0.76 g cm^(-3), significantly lower than the mass computed in Dumusque et al. (17.2 ± 1.9 M_⊕). Our mass measurement of Kepler-10c rules out a pure stony-iron composition. Internal compositional modeling reveals that at least 10% of the radius of Kepler-10c is a volatile envelope composed of hydrogen–helium (0.2% of the mass, 16% of the radius) or super-ionic water (28% of the mass, 29% of the radius). However, we note that analysis of only HIRES data yields a higher mass for planet b and a lower mass for planet c than does analysis of the HARPS-N data alone, with the mass estimates for Kepler-10 c being formally inconsistent at the 3σ level. Moreover, dividing the data for each instrument into two parts also leads to somewhat inconsistent measurements for the mass of planet c derived from each observatory. Together, this suggests that time-correlated noise is present and that the uncertainties in the masses of the planets (especially planet c) likely exceed our formal estimates. Transit timing variations (TTVs) of Kepler-10c indicate the likely presence of a third planet in the system, KOI-72.X. The TTVs and RVs are consistent with KOI-72.X having an orbital period of 24, 71, or 101 days, and a mass from 1 to 7 M_⊕

Quantum trajectories for Brownian motion

We present the stochastic Schroedinger equation for the dynamics of a quantum particle coupled to a high temperature environment and apply it the dynamics of a driven, damped, nonlinear quantum oscillator. Apart from an initial slip on the environmental memory time scale, in the mean, our result recovers the solution of the known non-Lindblad quantum Brownian motion master equation. A remarkable feature of our approach is its localization property: individual quantum trajectories remain localized wave packets for all times, even for the classically chaotic system considered here, the localization being stronger the smaller $\hbar$.Comment: 4 pages, 3 eps figure

Cooperative light-induced breathing of soft porous crystals via azobenzene buckling

Although light is a prominent stimulus for smart materials, the application of photoswitches as light-responsive triggers for phase transitions of porous materials remains poorly explored. Here we incorporate an azobenzene photoswitch in the backbone of a metal-organic framework producing light-induced structural contraction of the porous network in parallel to gas adsorption. Light-stimulation enables non-invasive spatiotemporal control over the mechanical properties of the framework, which ultimately leads to pore contraction and subsequent guest release via negative gas adsorption. The complex mechanism of light-gated breathing is established by a series of in situ diffraction and spectroscopic experiments, supported by quantum mechanical and molecular dynamic simulations. Unexpectedly, this study identifies a novel light-induced deformation mechanism of constrained azobenzene photoswitches relevant to the future design of light-responsive materials

Effects of Thyroxine Exposure on Osteogenesis in Mouse Calvarial Pre-Osteoblasts

The incidence of craniosynostosis is one in every 1,800-2500 births. The gene-environment model proposes that if a genetic predisposition is coupled with environmental exposures, the effects can be multiplicative resulting in severely abnormal phenotypes. At present, very little is known about the role of gene-environment interactions in modulating craniosynostosis phenotypes, but prior evidence suggests a role for endocrine factors. Here we provide a report of the effects of thyroid hormone exposure on murine calvaria cells. Murine derived calvaria cells were exposed to critical doses of pharmaceutical thyroxine and analyzed after 3 and 7 days of treatment. Endpoint assays were designed to determine the effects of the hormone exposure on markers of osteogenesis and included, proliferation assay, quantitative ALP activity assay, targeted qPCR for mRNA expression of Runx2, Alp, Ocn, and Twist1, genechip array for 28,853 targets, and targeted osteogenic microarray with qPCR confirmations. Exposure to thyroxine stimulated the cells to express ALP in a dose dependent manner. There were no patterns of difference observed for proliferation. Targeted RNA expression data confirmed expression increases for Alp and Ocn at 7 days in culture. The genechip array suggests substantive expression differences for 46 gene targets and the targeted osteogenesis microarray indicated 23 targets with substantive differences. 11 gene targets were chosen for qPCR confirmation because of their known association with bone or craniosynostosis (Col2a1, Dmp1, Fgf1, 2, Igf1, Mmp9, Phex, Tnf, Htra1, Por, and Dcn). We confirmed substantive increases in mRNA for Phex, FGF1, 2, Tnf, Dmp1, Htra1, Por, Igf1 and Mmp9, and substantive decreases for Dcn. It appears thyroid hormone may exert its effects through increasing osteogenesis. Targets isolated suggest a possible interaction for those gene products associated with calvarial suture growth and homeostasis as well as craniosynostosis. © 2013 Cray et al