Phylogenetic diversity of insecticolous fusaria inferred from multilocus DNA sequence data and their molecular identification via FUSARIUM-ID and Fusarium MLST

We constructed several multilocus DNA sequence datasets to assess the phylogenetic diversity of insecticolous fusaria, especially focusing on those housed at the Agricultural Research Service Collection of Entomopathogenic Fungi (ARSEF), and to aid molecular identifications of unknowns via the FUSARIUM-ID and Fusarium MLST online databases and analysis packages. Analyses of a 190-taxon, two-locus dataset, which included 159 isolates from insects, indicated that: (i) insect-associated fusaria were nested within 10 species complexes spanning the phylogenetic breadth of Fusarium, (ii) novel, putatively unnamed insecticolous species were nested within 8/10 species complexes and (iii) Latin binomials could be applied with confidence to only 18/58 phylogenetically distinct fusaria associated with pest insects. Phylogenetic analyses of an 82-taxon, three-locus dataset nearly fully resolved evolutionary relationships among the 10 clades containing insecticolous fusaria. Multilocus typing of isolates within four species complexes identified surprisingly high genetic diversity in that 63/65 of the fusaria typed represented newly discovered haplotypes. The DNA sequence data, together with corrected ABI sequence chromatograms and alignments, have been uploaded to the following websites dedicated to identifying fusaria: FUSARIUM-ID (http://isolate.fusariumdb.org) a

Cryptococcus neoformans escape From Dictyostelium amoeba by both WASH-mediated constitutive exocytosis and vomocytosis

Cryptococcus neoformans is an environmental yeast that can cause opportunistic infections in humans. As infecting animals does not form part of its normal life-cycle, it has been proposed that the virulence traits that allow cryptococci to resist immune cells were selected through interactions with environmental phagocytes such as amoebae. Here, we investigate the interactions between C. neoformans and the social amoeba Dictyostelium discoideum. We show that like macrophages, D. discoideum is unable to kill C. neoformans upon phagocytosis. Despite this, we find that the yeast pass through the amoebae with an apparently normal phagocytic transit and are released alive by constitutive exocytosis after ~80 min. This is the canonical pathway in amoebae, used to dispose of indigestible material after nutrient extraction. Surprisingly however, we show that upon either genetic or pharmacological blockage of constitutive exocytosis, C. neoformans still escape from D. discoideum by a secondary mechanism. We demonstrate that constitutive exocytosis-independent egress is stochastic and actin-independent. This strongly resembles the non-lytic release of cryptococci by vomocytosis from macrophages, which do not perform constitutive exocytosis and normally retain phagocytosed material. Our data indicate that vomocytosis is functionally redundant for escape from amoebae, which thus may not be the primary driver for its evolutionary selection. Nonetheless, we show that vomocytosis of C. neoformans is mechanistically conserved in hosts ranging from amoebae to man, providing new avenues to understand this poorly-understood but important virulence mechanism

Cryptic photosynthesis, Extrasolar planetary oxygen without a surface biological signature

On the Earth, photosynthetic organisms are responsible for the production of virtually all of the oxygen in the atmosphere. On the land, vegetation reflects in the visible, leading to a red edge that developed about 450 Myr ago and has been proposed as a biosignature for life on extrasolar planets. However, in many regions of the Earth, and particularly where surface conditions are extreme, for example in hot and cold deserts, photosynthetic organisms can be driven into and under substrates where light is still sufficient for photosynthesis. These communities exhibit no detectable surface spectral signature to indicate life. The same is true of the assemblages of photosynthetic organisms at more than a few metres depth in water bodies. These communities are widespread and dominate local photosynthetic productivity. We review known cryptic photosynthetic communities and their productivity. We link geomicrobiology with observational astronomy by calculating the disk-averaged spectra of cryptic habitats and identifying detectable features on an exoplanet dominated by such a biota. The hypothetical cryptic photosynthesis worlds discussed here are Earth-analogs that show detectable atmospheric biomarkers like our own planet, but do not exhibit a discernable biological surface feature in the disc-averaged spectrum.Comment: 23 pages, 2 figures, Astrobiology (TBP) - updated Table 1, typo in detectable O2 correcte

Barcoding and border biosecurity: Identifying cyprinid fishes in the aquarium trade

10.1371/journal.pone.0028381PLoS ONE71

Is the Sgr dSph a dark matter dominated system?

We study the evolution of possible progenitors of Sgr dSph}using several numerical N-body simulations of different dwarf spheroidal galaxies both with and without dark matter, as they orbit the Milky Way. The barionic and dark components of the dwarfs were made obeying a Plummer and NFW potentials of one million particles respectively. The Milky Way was modeled like a tree-component rigid potential and the simulations were performed using a modified Gadget-2 code. We found that none of the simulated galaxies without dark matter reproduced the physical properties observed in Sgr dSph, suggesting that, at the beginning of its evolution, Sgr dSph might have been immersed in a dark matter halo. The simulations of progenitors immersed in dark matter halos suggest that Sgr dSph at its beginning might have been an extended system, i.e. its Plummer radius could have had a value approximated to 1.2 kpc or higher; furthermore, this galaxy could have been immersed in a dark halo with a mass higher than 10^8 solar masses. These results are important for the construction of a model of the formation of Sgr dSph.Comment: 13 pages, 6 figures, New Astronomy - accepte

CHARMM-DYES : Parameterization of fluorescent dyes for use with the CHARMM force field

We present CHARMM-compatible force field parameters for a series of fluorescent dyes from the Alexa, Atto, and Cy families, commonly used in Förster resonance energy transfer (FRET) experiments. These dyes are routinely used in experiments to resolve the dynamics of proteins and nucleic acids at the nanoscale. However, little is known about the accuracy of the theoretical approximations used in determining the dynamics from the spectroscopic data. Molecular dynamics simulations can provide valuable insights into these dynamics at an atomistic level, but this requires accurate parameters for the dyes. The complex structure of the dyes and the importance of this in determining their spectroscopic properties mean that parameters generated by analogy to existing parameters do not give meaningful results. Through validation relative to quantum chemical calculation and experiments, the new parameters are shown to significantly outperform those that can be generated automatically, giving better agreement in both the charge distributions and structural properties. These improvements, in particular with regard to orientation of the dipole moments on the dyes, are vital for accurate simulation of FRET processes

The Information Geometry of the Ising Model on Planar Random Graphs

It has been suggested that an information geometric view of statistical mechanics in which a metric is introduced onto the space of parameters provides an interesting alternative characterisation of the phase structure, particularly in the case where there are two such parameters -- such as the Ising model with inverse temperature $\beta$ and external field $h$. In various two parameter calculable models the scalar curvature ${\cal R}$ of the information metric has been found to diverge at the phase transition point $\beta_c$ and a plausible scaling relation postulated: ${\cal R} \sim |\beta- \beta_c|^{\alpha - 2}$. For spin models the necessity of calculating in non-zero field has limited analytic consideration to 1D, mean-field and Bethe lattice Ising models. In this letter we use the solution in field of the Ising model on an ensemble of planar random graphs (where $\alpha=-1, \beta=1/2, \gamma=2$) to evaluate the scaling behaviour of the scalar curvature, and find ${\cal R} \sim | \beta- \beta_c |^{-2}$. The apparent discrepancy is traced back to the effect of a negative $\alpha$.Comment: Version accepted for publication in PRE, revtex

The importance of long‐term experiments in agriculture: their management to ensure continued crop production and soil fertility; the Rothamsted experience

Summary Long‐term field experiments that test a range of treatments and are intended to assess the sustainability of crop production, and thus food security, must be managed actively to identify any treatment that is failing to maintain or increase yields. Once identified, carefully considered changes can be made to the treatment or management, and if they are successful yields will change. If suitable changes cannot be made to an experiment to ensure its continued relevance to sustainable crop production, then it should be stopped. Long‐term experiments have many other uses. They provide a field resource and samples for research on plant and soil processes and properties, especially those properties where change occurs slowly and affects soil fertility. Archived samples of all inputs and outputs are an invaluable source of material for future research, and data from current and archived samples can be used to develop models to describe soil and plant processes. Such changes and uses in the Rothamsted experiments are described, and demonstrate that with the appropriate crop, soil and management, acceptable yields can be maintained for many years, with either organic manure or inorganic fertilizers. Highlights Long‐term experiments demonstrate sustainability and increases in crop yield when managed to optimize soil fertility. Shifting individual response curves into coincidence increases understanding of the factors involved. Changes in inorganic and organic pollutants in archived crop and soil samples are related to inputs over time. Models describing soil processes are developed from current and archived soil data

The role of beach state and the timing of pre-storm surveys in determining the accuracy of storm impact assessments

Dune erosion principally occurs when water level exceeds the elevation of the beach and predicting erosion is progressively becoming more important for management as coastal populations increase, sea level rises, and storms become more powerful. This study assesses storm impacts using a simple model from Stockdon et al. (2007) configured with oceanographic information from the ADCIRC + SWAN model and frequently collected beach profiles. We applied that model to barrier islands in North Carolina including: Core Banks with a more dissipative beach morphology and Shackleford Banks and Onslow Beach with intermediate beach morphologies. The study periods captured 10 events where wave collision with the dunes and/or overwash were either predicted or observed, including large multiple-day events caused by hurricanes and smaller events caused by onshore winds and high tide. Comparing model output with a time series of beach photographs shows the predictive power and sensitivity of the model was consistently high at the Core Banks Site with its wide and low-gradient beach, high-elevation dunes (2.58 m), and high resistance to overwash. Model predictive power and sensitivity was lowest at the Shackleford Banks Site because frequent and large changes to beach slope and intermediate dune elevation (0.54–1.25 m) caused small variations of modeled total water level to either overpredict or underpredict storm impacts. In addition, storm impacts were always overpredicted during hurricanes at the Shackleford Banks Site, which was likely due to storm waves decreasing the beach slope from what was measured prior to the event and used as model input. Like Shackleford Banks, the beach slope of the Onslow Beach Site was steep and variable, but the low-elevation dunes (0.24–0.28 m) made resistance to overwash low and the predictive power and sensitivity of the model higher than at the Shackleford Banks Site. Results suggest that storm impacts and the associated potential for dune erosion is predicted more accurately at beaches where the threshold for overwash is high or low because total water level during most events will commonly fall short of or exceed the overwash threshold, respectively. The accuracy of predicting the storm impact regime is sensitive to beach slope. The slope of intermediate beaches is more variable than dissipative beaches and requires frequent measurement if it is to be represented accurately in the model, but this can be impractical and costly even using the latest drone-surveying methods. To maximize the accuracy of predicting storm impacts, intermediate beach morphology should be constrained by surveying at seasonal or yearly time scales and used as input to numerical models that estimate beach slope over short time scales (hours during an event or daily), configured with the latest wave and water-level forecasts