The small nuclear genomes of Selaginella are associated with a low rate of genome size evolution

The haploid nuclear genome size (1C DNA) of vascular land plants varies over several orders of magnitude. Much of this observed diversity in genome size is due to the proliferation and deletion of transposable elements. To date, all vascular land plant lineages with extremely small nuclear genomes represent recently derived states, having ancestors with much larger genome sizes. The Selaginellaceae represent an ancient lineage with extremely small genomes. It is unclear how small nuclear genomes evolved in Selaginella We compared the rates of nuclear genome size evolution in Selaginella and major vascular plant clades in a comparative phylogenetic framework. For the analyses, we collected 29 new flow cytometry estimates of haploid genome size in Selaginella to augment publicly available data. Selaginella possess some of the smallest known haploid nuclear genome sizes, as well as the lowest rate of genome size evolution observed across all vascular land plants included in our analyses. Additionally, our analyses provide strong support for a history of haploid nuclear genome size stasis in Selaginella Our results indicate that Selaginella, similar to other early diverging lineages of vascular land plants, has relatively low rates of genome size evolution. Further, our analyses highlight that a rapid transition to a small genome size is only one route to an extremely small genome

Gene duplication, population genomics, and species-level differentiation within a tropical mountain shrub.

Gene duplication leads to paralogy, which complicates the de novo assembly of genotyping-by-sequencing (GBS) data. The issue of paralogous genes is exacerbated in plants, because they are particularly prone to gene duplication events. Paralogs are normally filtered from GBS data before undertaking population genomics or phylogenetic analyses. However, gene duplication plays an important role in the functional diversification of genes and it can also lead to the formation of postzygotic barriers. Using populations and closely related species of a tropical mountain shrub, we examine 1) the genomic differentiation produced by putative orthologs, and 2) the distribution of recent gene duplication among lineages and geography. We find high differentiation among populations from isolated mountain peaks and species-level differentiation within what is morphologically described as a single species. The inferred distribution of paralogs among populations is congruent with taxonomy and shows that GBS could be used to examine recent gene duplication as a source of genomic differentiation of nonmodel species

Sonication-induced modification of carbon nanotubes: Effect on the rheological and thermo-oxidative behaviour of polymer-based nanocomposites

The aim of this work is the investigation of the effect of ultrasound treatment on the structural characteristics of carbon nanotubes (CNTs) and the consequent influence that the shortening induced by sonication exerts on the morphology, rheological behaviour and thermo-oxidative resistance of ultra-high molecular weight polyethylene (UHMWPE)-based nanocomposites. First, CNTs have been subjected to sonication for different time intervals and the performed spectroscopic and morphological analyses reveal that a dramatic decrease of the CNT's original length occurs with increased sonication time. The reduction of the initial length of CNTs strongly affects the nanocomposite rheological behaviour, which progressively changes from solid-like to liquid-like as the CNT sonication time increases. The study of the thermo-oxidative behaviour of the investigated nanocomposites reveals that the CNT sonication has a detrimental effect on the thermo-oxidative stability of nanocomposites, especially for long exposure times. The worsening of the thermo-oxidative resistance of sonicated CNT-containing nanocomposites could be attributed to the lower thermal conductivity of low-aspect-ratio CNTs, which causes the increase of the local temperature at the polymer/nanofillers interphase, with the consequent acceleration of the degradative phenomena

Hybridization Capture Using RAD Probes (hyRAD), a New Tool for Performing Genomic Analyses on Collection Specimens.

In the recent years, many protocols aimed at reproducibly sequencing reduced-genome subsets in non-model organisms have been published. Among them, RAD-sequencing is one of the most widely used. It relies on digesting DNA with specific restriction enzymes and performing size selection on the resulting fragments. Despite its acknowledged utility, this method is of limited use with degraded DNA samples, such as those isolated from museum specimens, as these samples are less likely to harbor fragments long enough to comprise two restriction sites making possible ligation of the adapter sequences (in the case of double-digest RAD) or performing size selection of the resulting fragments (in the case of single-digest RAD). Here, we address these limitations by presenting a novel method called hybridization RAD (hyRAD). In this approach, biotinylated RAD fragments, covering a random fraction of the genome, are used as baits for capturing homologous fragments from genomic shotgun sequencing libraries. This simple and cost-effective approach allows sequencing of orthologous loci even from highly degraded DNA samples, opening new avenues of research in the field of museum genomics. Not relying on the restriction site presence, it improves among-sample loci coverage. In a trial study, hyRAD allowed us to obtain a large set of orthologous loci from fresh and museum samples from a non-model butterfly species, with a high proportion of single nucleotide polymorphisms present in all eight analyzed specimens, including 58-year-old museum samples. The utility of the method was further validated using 49 museum and fresh samples of a Palearctic grasshopper species for which the spatial genetic structure was previously assessed using mtDNA amplicons. The application of the method is eventually discussed in a wider context. As it does not rely on the restriction site presence, it is therefore not sensitive to among-sample loci polymorphisms in the restriction sites that usually causes loci dropout. This should enable the application of hyRAD to analyses at broader evolutionary scales

A multi-layer extension of the stochastic heat equation

Motivated by recent developments on solvable directed polymer models, we define a 'multi-layer' extension of the stochastic heat equation involving non-intersecting Brownian motions.Comment: v4: substantially extended and revised versio

The Ross Sea: In a Sea of Change

The Ross Sea, the most productive region in the Antarctic, reaches farther south than any body of water in the world. While its food web is relatively intact, its oceanography, biogeochemistry, and sea ice coverage have been changing dramatically, and likely will continue to do so in the future. Sea ice cover and persistence have been increasing, in contrast to the Amundsen-Bellingshausen sector, which has resulted in reduced open water duration for its biota. Models predict that as the ozone hole recovers, ice cover will begin to diminish. Currents on the continental shelf will likely change in the coming century, with a projected intensification of flow leading to altered deep ocean ventilation. Such changes in ice and circulation will lead to altered plankton distributions and composition, but it is difficult at present to predict the nature of these changes. Iron and irradiance play central roles in regulating phytoplankton production in the Ross Sea, but the impacts of oceanographic changes on the biogeochemistry of iron are unclear. Unlike other Southern Ocean regions, where continental shelves are very narrow and Antarctic krill dominates the herbivorous fauna, the broad shelf of the Ross Sea is dominated by crystal krill and silverfish, which are the major prey items for higher trophic levels. At present, the Ross Sea is considered to be one of the most species-rich areas of the Southern Ocean and a biodiversity hotspot due to its heterogeneous habitats. Despite being among the best-studied regions in the entire Southern Ocean, accurate predictions of the impacts of climate change on the oceanography and ecology of the Ross Sea remain fraught with uncertainty

Structure-properties relationships of polyhedral oligomeric silsesquioxane (POSS) filled PS nanocomposites

The polyhedral oligomeric silsesquioxane (POSS) additivated polystyrene (PS) based nanocomposites were prepared by melt processing and the structure-properties relationships of the POSS-PS systems were compared to those of the neat PS. In order to investigate the effect of these structural parameters on the final properties of the polymer nanocomposites, five different kinds of POSS samples were used, in particular, POSS with different inorganic cage and with different organic pendent groups. The rheological investigation suggests clearly that the POSS acts as a plasticizer and that the processability of the PS was positively modified. The affinity between the POSS samples and the PS matrix was estimated by the calculated theoretical solubility parameters, considering the Hoy’s method and by morphology analysis. Minor difference between the solubility parameter of POSS and the matrix means better compatibility and no aggregation tendency. Furthermore, the POSS loading leads to a decrease of the rigidity, of the glass transition temperature and of the damping factor of the nanocomposite systems. The loading of different POSS molecules with open cage leads to a more pronounced effect on all the investigated properties that the loading of the POSS molecules with closed cage. Moreover, the melt properties are significantly influenced by the type of inorganic framework, by the type of the pendent organic groups and by the interaction between the POSS organic groups and the host matrix, while, the solid state properties appears to be influenced more by the kind of cage

Application of hydrogen peroxide to improve the microbiological stability of food ice produced in industrial facilities

This work was aimed to produce an “active” food ice to preserve its microbiological safety over time. With this in mind, ice cubes were processed with the addition of H2O2 to water before freezing. Four food ice productions were performed at the industrial level: one control trial without the addition of H2O2 (0OX) and three experimental trials obtained by adding 4, 8, and 12 mg/L of H2 O2 (4OX, 8OX, and 12OX), respectively. After production, all food ice trials were artificially contaminated with 102 CFU/100 mL of water-borne pathogenic bacteria (Escherichia coli ATCC 25922, Enteroccus faecalis ATCC 29212, and Pseudomonas aeruginosa ATCC 27853) inoculated individually. Thawed ice samples were then subjected to microbiological analyses performed by the membrane filtration method and the results indicated that only trial 12OX was able to inactivate all bacteria strains. In conclusion, the addition of 12 mg/L H2O2 represents an optimal cost-effective strategy to preserve the microbiological stability of food ice even when it is improperly handled after production

Role of shelfbreak upwelling in the formation of a massive under-ice bloom in the Chukchi Sea

Author Posting. © The Author(s), 2014. This is the author's version of the work. It is posted here by permission of Elsevier for personal use, not for redistribution. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 105 (2014): 17-29, doi:10.1016/j.dsr2.2014.03.017.In the summer of 2011, an oceanographic survey carried out by the Impacts of Climate on EcoSystems and Chemistry of the Arctic Pacific Environment (ICESCAPE) program revealed the presence of a massive phytoplankton bloom under the ice near the shelfbreak in the central Chukchi Sea. For most of the month preceding the measurements there were relatively strong easterly winds, providing upwelling favorable conditions along the shelfbreak. Analysis of similar hydrographic data from summer 2002, in which there were no persistent easterly winds, found no evidence of upwelling near the shelfbreak. A two-dimensional ocean circulation model is used to show that sufficiently strong winds can result not only in upwelling of high nutrient water from offshore onto the shelf, but it can also transport the water out of the bottom boundary layer into the surface Ekman layer at the shelf edge. The extent of upwelling is determined by the degree of overlap between the surface Ekman layer and the bottom boundary layer on the outer shelf. Once in the Ekman layer, this high nutrient water is further transported to the surface through mechanical mixing driven by the surface stress. Two model tracers, a nutrient tracer and a chlorophyll tracer, reveal distributions very similar to that observed in the data. These results suggest that the biomass maximum near the shelfbreak during the massive bloom in summer 2011 resulted from an enhanced supply of nutrients upwelled from the halocline seaward of the shelf. The decade long trend in summertime surface winds suggest that easterly winds in this region are increasing in strength and that such bloom events will become more common.This study was supported by the National Science Foundation under Grant OCE-0959381 (MAS), and by the Ocean Biology and Biogeochemistry Program and the Cryosphere Science Program of the National Aeronautic and Space Administration under Award NNX10AF42G (RSP;KRA). GWKM was supported by the Natural Sciences and Engineering Research Council of Canada. ETB was supported by the U. S. Navy

Flexible Perfluoropolyethers-Functionalized CNTs-Based UHMWPE Composites: A Study on Hydrogen Evolution, Conductivity and Thermal Stability

Flexible conductive composites based on ultra-high molecular weight polyethylene (UHMWPE) filled with multi-walled carbon nanotubes (CNTs) modified by perfluoropolyethers (PFPEs) were produced. The bonding of PFPE chains, added in 1:1 and 2:1 weight ratios, on CNTs influences the dispersion of nanotubes in the UHMWPE matrix due to the non-polar nature of the polymer, facilitating the formation of nanofillers-rich conductive pathways and improving composites’ electrical conductivity (two to five orders of magnitude more) in comparison to UHMWPE-based nanocomposites obtained with pristine CNTs. Electrochemical atomic force microscopy (EC-AFM) was used to evaluate the morphological changes during cyclic voltammetry (CV). The decrease of the overpotential for hydrogen oxidation peaks in samples containing PFPE-functionalized CNTs and hydrogen production (approximately −1.0 V vs. SHE) suggests that these samples could find application in fuel cell technology as well as in hydrogen storage devices. Carbon black-containing composites were prepared for comparative study with CNTs containing nanocomposites