Helices at Interfaces

Helically coiled filaments are a frequent motif in nature. In situations commonly encountered in experiments coiled helices are squeezed flat onto two dimensional surfaces. Under such 2-D confinement helices form "squeelices" - peculiar squeezed conformations often resembling looped waves, spirals or circles. Using theory and Monte-Carlo simulations we illuminate here the mechanics and the unusual statistical mechanics of confined helices and show that their fluctuations can be understood in terms of moving and interacting discrete particle-like entities - the "twist-kinks". We show that confined filaments can thermally switch between discrete topological twist quantized states, with some of the states exhibiting dramatically enhanced circularization probability while others displaying surprising hyperflexibility

The use of dynamic landscape metapopulation models for forest management: a case study of the red-backed salamander

Spatial models of population dynamics have been proposed as a useful method for predicting the impacts of environmental change on biodiversity. Here, we demonstrate advances in dynamic landscape metapopulation modelling and its use as a decision support tool for evaluating the impacts of forest management scenarios. This novel modelling framework incorporates both landscape and metapopulation model stochasticity and allows their relative contributions to model output variance to be characterized. It includes a detailed sensitivity analysis, allowing defensible uncertainty bounds and the prioritization of future data gathering to reduce model uncertainties. We demonstrate this framework by modelling the landscape-level impacts of eight forest management scenarios on the red-backed salamander (Plethodon cinereus (Green, 1818)) in the boreal forest of Ontario, Canada, using the RAMAS Landscape package. The 100 year forest management scenarios ranged in intensity of timber harvesting and fire suppression. All scenarios including harvesting predicted decreases in salamander population size and the current style of forest management is predicted to produce a 9%-17% decrease in expected minimum population size compared with scenarios without harvesting. This method is amenable to incorporating many forms of environmental change and allows a meaningful treatment of uncertainty

Dual analysis of host and pathogen transcriptomes in ostreid herpesvirus 1-positive Crassostrea gigas

Ostreid herpesvirus type 1 (OsHV-1) has become a problematic infective agent for the Pacific oyster Crassostrea gigas. In particular, the OsHV-1 \u3bcVar subtype has been associated with severe mortality episodes in oyster spat and juvenile oysters in France and other regions of the world. Factors enhancing the infectivity of the virus and its interactions with susceptible and resistant bivalve hosts are still to be understood, and only few studies have explored the expression of oyster or viral genes during productive infections. In this work, we have performed a dual RNA sequencing analysis on an oyster sample with a high viral load. High sequence coverage allowed us to thoroughly explore the OsHV-1 transcriptome and identify the activated molecular pathways in C.gigas. The identification of several highly induced and defence-related oyster transcripts supports the crucial role played by the innate immune system against the virus and opportunistic microbes possibly contributing to subsequent spat mortality

Reversible protein precipitation to ensure stability during encapsulation within PLGA microspheres

Proteins were precipitated to ensure their stability upon subsequent encapsulation within PLGA microspheres. Spherical, nanosized protein particles were formed by the addition of a salt (sodium chloride) and a water-miscible organic solvent (glycofurol) to protein solutions. Various process parameters were modified to optimize the precipitation efficiency of four model proteins: lysozyme, alpha-chymotrypsin, peroxidase and beta-galactosidase. As monitored by enzymatic activity measurement of the rehydrated particles, conditions to obtain more than 95% of reversible precipitates were defined for each protein. The study of the structure of the rehydrated particles by absorbance spectroscopy, fluorescence spectroscopy and circular dichroism showed an absence of structural-perturbation after precipitation. Protein particles were then microencapsulated within PLGA microspheres using s/o/w technique. The average encapsulation yield was around 80% and no loss of protein activity occurred after the encapsulation step. Additionally, a lysozyme in vitro release study showed that all of the released lysozyme was biologically active. This method of protein precipitation is appropriate for the encapsulation in PLGA microspheres of various proteins without inactivation

An Evolutionary Perspective of Dopachrome Tautomerase Enzymes in Metazoans

Melanin plays a pivotal role in the cellular processes of several metazoans. The final step of the enzymically-regulated melanin biogenesis is the conversion of dopachrome into dihydroxyindoles, a reaction catalyzed by a class of enzymes called dopachrome tautomerases. We traced dopachrome tautomerase (DCT) and dopachrome converting enzyme (DCE) genes throughout metazoans and we could show that only one class is present in most of the phyla. While DCTs are typically found in deuterostomes, DCEs are present in several protostome phyla, including arthropods and mollusks. The respective DCEs belong to the yellow gene family, previously reported to be taxonomically restricted to insects, bacteria and fungi. Mining genomic and transcriptomic data of metazoans, we updated the distribution of DCE/yellow genes, demonstrating their presence and active expression in most of the lophotrochozoan phyla as well as in copepods (Crustacea). We have traced one intronless DCE/yellow gene through most of the analyzed lophotrochozoan genomes and we could show that it was subjected to genomic diversification in some species, while it is conserved in other species. DCE/yellow was expressed in most phyla, although it showed tissue specific expression patterns. In the parasitic copepod Mytilicola intestinalis DCE/yellow even belonged to the 100 most expressed genes. Both tissue specificity and high expression suggests that diverse functions of this gene family also evolved in other phyla apart from insects

Bayesian inference on compact binary inspiral gravitational radiation signals in interferometric data

Presented is a description of a Markov chain Monte Carlo (MCMC) parameter estimation routine for use with interferometric gravitational radiational data in searches for binary neutron star inspiral signals. Five parameters associated with the inspiral can be estimated, and summary statistics are produced. Advanced MCMC methods were implemented, including importance resampling and prior distributions based on detection probability, in order to increase the efficiency of the code. An example is presented from an application using realistic, albeit fictitious, data.Comment: submitted to Classical and Quantum Gravity. 14 pages, 5 figure

Spatial Distribution, Air-Water Fugacity Ratios and Source Apportionment of Polychlorinated Biphenyls in the Lower Great Lakes Basin

Polychlorinated biphenyls (PCBs) continue to be contaminants of concern across the Great Lakes. It is unclear whether current concentrations are driven by ongoing primary emissions from their original uses, or whether ambient PCBs are dominated by their environmental cycling. Freely dissolved PCBs in air and water were measured using polyethylene passive samplers across Lakes Erie and Ontario during summer and fall, 2011, to investigate their spatial distribution, determine and apportion their sources and to asses their air–water exchange gradients. Average gaseous and freely dissolved ∑29 PCB concentrations ranged from 5.0 to 160 pg/m3 and 2.0 to 55 pg/L respectively. Gaseous concentrations were significantly correlated (R2 = 0.80) with the urban area within a 3−20 km radius. Fugacity ratios indicated that the majority of PCBs are volatilizing from the water thus acting as a secondary source for the atmosphere. Dissolved PCBs were probably linked to PCB emissions from contaminated sites and areas of concern. Positive matrix factorization indicated that although volatilized Aroclors (gaseous PCBs) and unaltered Aroclors (dissolved PCBs) dominate in some samples, ongoing non-Aroclor sources such as paints/pigments (PCB 11) and coal/wood combustion showed significant contributions across the lower Great Lakes. Accordingly, control strategies should give further attention to PCBs emitted from current use sources