Palaeoenvironment and taphonomy of a Late Jurassic (Late Tithonian) Lagerstätte from central Poland

A rich assemblage of exceptionally preserved marine and terrestrial fossils occurs in fine‐grained limestones in the upper part of the Late Tithonian (Middle Volgian) shallowing upward carbonate sequence in Central Poland. The richest horizon, a deposit known locally as the Corbulomima horizon, is named after the shallow burrowing suspension feeding bivalve Corbulomima obscura, moulds of which occur in densities of up to 500 per square metre on some bedding planes. The fauna in this bed also includes organic and phosphatic remains of a wide range of other creatures including the exuviae of limulids and decapods, disarticulated fish skeletons and rare isolated pterosaur bones and teeth. There are also perfectly preserved dragonfly wings and beetle exoskeletons. The average stable carbon and oxygen isotope values for ostracod shells and fine‐grained sediment from this horizon suggest precipitation of the calcium carbonate from warm seawater of normal marine salinity. The carbonate sediments overlying the fossiliferous horizon have been interpreted as nearshore to shoreface facies. These pass abruptly into coarse reworked intraclastic sediments interpreted as possible tsunami or storm surge over‐wash deposits. The clasts in this deposit have more positive oxygen isotope values than those in the underlying limestone, which may indicate that they were lithified in a slightly more evaporative, perhaps intertidal, setting. The succession terminates with silicified fine‐grained limestones likely to have formed in extremely shallow lagoonal environments. In contrast with the Solnhofen limestones of Lower Tithonian age in south‐central Germany the Corbulomima horizon is interpreted as a transitional deposit formed in a shallow marine setting by rapid burial with elements of both Konservat‐ and Konzentrat‐Lagerstätte preservation. □Konzentrat and Konservat‐Lagerstätte, Taphonomy, Palaeoenvironment, Paleogeography, Late Jurassic, Poland.     

Synthesis and Characterization of Templated Mesoporous Materials Using Molecular Simulation

Abstract

Lattice Monte Carlo simulations are used to calculate equilibrium properties of surfactant-solvent-silica liquid-crystal systems under no-polymerization conditions. The formation of a high-surfactant high-silica concentration phase in equilibrium with a dilute phase is observed when the surfactant-silica interactions are stronger than the surfactant-solvent interactions. Different silica structures that are similar to the M41 family are observed, depending on the overall concentration of the system. The formation of a hexagonal phase is favored at a surfactant/silica ratio of 0.2, whereas a lamellar phase is observed a surfactant/silica ratio of 1.

Argon adsorption properties on a model porous structure of the MCM-41 type prepared using this mimetic simulation protocol are calculated using grand canonical Monte Carlo simulation. Heats of adsorption are calculated from fluctuations in the energy and number of molecules [1] following the work of Nicholson and Parsonage [Computer Simulation and the Statistical Mechanics of Adsorption (Academic Press, London), 1982, p 97 8 pp]. A decrease in the heats of adsorption for coverage less than one statistical monolayer is evidence of surface heterogeneity. The results are in qualitative agreement with experimental measurements for argon on MCM-41.     

Computer Simulation of Isothermal Mass Transport in Graphite Slit Pores

Abstract

Results are presented from a simulation study of the mass transport of oxygen and nitrogen through graphite slit pores. The work is motivated by an attempt to understand the molecular origins of the kinetic selectivity displayed when air is separated into its major components using pressure swing adsorption. A combination of non-equilibrium molecular dynamics (NEMD), equilibrium molecular dynamics (EMD) and grand canonical Monte Carlo methods has been employed in our study to extract the maximum information. Transport diffusivities, self-diffusivities, permeabilities and Darken thermodynamic factors have been calculated as a function of pore width and temperature for pure component oxygen and nitrogen. In addition, new EMD simulation data for an 80:20 mixture of nitrogen and oxygen is reported, including a direct calculation of the Stefan-Maxwell coefficients. The results are discussed in terms of the oxygen selectivity and the possible mechanisms, which increase or decrease this quantity.

We find that the pore width behaviour of the diffusion coefficients consists of three distinct regimes: a regime at larger pore widths in which single component diffusion coefficients are largely independent of pore width, an optimum pore width at which both diffusivities increase substantially but the slit pore is selective towards nitrogen, and a regime at very low pore widths at which the diffusivities decrease sharply, but the slits are selective towards oxygen. The mechanism behind each of these regimes is discussed in terms of “entropic” effects and potential barrier heights.

We have also found that permeability selectivity is substantially reduced in a mixture of the two gases with a composition similar to that of air. Cross diffusion coefficients in the mixture have been calculated and shown to be non-negligible.     

Molecular Simulations of Phase Transitions in Pores

Abstract

Methods for simulating phase transitions in narrow pores are reviewed, and the advantages and disadvantages of different techniques are discussed. Examples are given of applications to vapor-liquid, liquid-liquid, melting and freezing, solid-solid and layering transitions. While there has been a considerable body of simulation work on vapor-liquid, wetting and layering transitions for simple fluids and pore geometries, much remains to be done on more complex geometries and network effects, on heterogeneous surfaces, and on liquid-liquid, melting and solid-solid transitions in pores.     

Implicating Culicoides Biting Midges as Vectors of Schmallenberg Virus Using Semi-Quantitative RT-PCR

Background

The recent unprecedented emergence of arboviruses transmitted by Culicoides biting midges in northern Europe has necessitated the development of techniques to differentiate competent vector species. At present these techniques are entirely reliant upon interpretation of semi-quantitative RT-PCR (sqPCR) data in the form of C_q values used to infer the presence of viral RNA in samples.

Methodology/Principal Findings

This study investigates the advantages and limitations of sqPCR in this role by comparing infection and dissemination rates of Schmallenberg virus (SBV) in two colony lines of Culicoides. Through the use of these behaviorally malleable lines we provide tools for demarcating arbovirus infection and dissemination rates in Culicoides which to date have prevented clear implication of primary vector species in northern Europe. The study demonstrates biological transmission of SBV in an arthropod vector, supporting the conclusions from field-caught Culicoides and provides a general framework for future assessment of vector competence of Culicoides for arboviruses using sqPCR.

Conclusions/Significance

When adopting novel diagnostic technologies, correctly implicating vectors of arboviral pathogens requires a coherent laboratory framework to fully understand the implications of results produced in the field. This study illustrates these difficulties and provides a full examination of sqPCR in this role for the Culicoides-arbovirus system.     

Evidence for Transmission of Bluetongue Virus Serotype 26 through Direct Contact

The aim of this study was to assess the mechanisms of transmission of bluetongue virus serotype 26 (BTV-26) in goats. A previous study, which investigated the pathogenicity and infection kinetics of BTV-26 in goats, unexpectedly revealed that one control goat may have been infected through a direct contact transmission route. To investigate the transmission mechanisms of BTV-26 in more detail an experimental infection study was carried out in which three goats were infected with BTV-26, three goats were kept uninfected, but were housed in direct contact with the infected goats, and an additional four goats were kept in indirect contact separated from infected goats by metal gates. This barrier allowed the goats to have occasional face-to-face contact in the same airspace, but feeding, watering, sampling and environmental cleaning was carried out separately. The three experimentally infected goats did not show clinical signs of BTV, however high levels of viral RNA were detected and virus was isolated from their blood. At 21 dpi viral RNA was detected in, and virus was isolated from the blood of the three direct contact goats, which also seroconverted. The four indirect barrier contact goats remained uninfected throughout the duration of the experiment. In order to assess replication in a laboratory model species of Culicoides biting midge, more than 300 Culicoides sonorensis were fed a BTV-26 spiked blood meal and incubated for 7 days. The dissemination of BTV-26 in individual C. sonorensis was inferred from the quantity of virus RNA and indicated that none of the insects processed at day 7 possessed transmissible infections. This study shows that BTV-26 is easily transmitted through direct contact transmission between goats, and the strain does not seem to replicate in C. sonorensis midges using standard incubation conditions.     

An integrative bioinformatic approach for studying escape mutations in human immunodeficiency virus type 1 gag in the Pumwani Sex Worker Cohort

Human immunodeficiency virus type 1 (HIV-1) is able to evade the host cytotoxic T-lymphocyte (CTL) response through a variety of escape avenues. Epitopes that are presented to CTLs are first processed in the presenting cell in several steps, including proteasomal cleavage, transport to the endoplasmic reticulum, binding by the HLA molecule, and finally presentation to the T-cell receptor. An understanding of the potential of the virus to escape CTL responses can aid in designing an effective vaccine. To investigate such a potential, we analyzed HIV-1 gag from 468 HIV-1-positive Kenyan women by using several bioinformatic approaches that allowed the identification of positively selected amino acids in the HIV-1 gag region and study of the effects that these mutations could have on the various stages of antigen processing. Correlations between positively selected residues and mean CD4 counts also allowed study of the effect of mutation on HIV disease progression. A number of mutations that could create or destroy proteasomal cleavage sites or reduce binding affinity of the transport antigen processing protein, effectively hindering epitope presentation, were identified. Many mutations correlated with the presence of specific HLA alleles and with lower or higher CD4 counts. For instance, the mutation V190I in subtype A1-infected individuals is associated with HLA-B*5802 (P = 4.73 x 10(-4)), a rapid-progression allele according to other studies, and also to a decreased mean CD4 count (P = 0.019). Thus, V190I is a possible HLA escape mutant. This method classifies many positively selected mutations across the entire gag region according to their potential for immune escape and their effect on disease progression.     

Geographic and topographic determinants of local FMD transmission applied to the 2001 UK FMD epidemic

Background

Models of Foot and Mouth Disease (FMD) transmission have assumed a homogeneous landscape across which Euclidean distance is a suitable measure of the spatial dependency of transmission. This paper investigated features of the landscape and their impact on transmission during the period of predominantly local spread which followed the implementation of the national movement ban during the 2001 UK FMD epidemic. In this study 113 farms diagnosed with FMD which had a known source of infection within 3 km (cases) were matched to 188 control farms which were either uninfected or infected at a later timepoint. Cases were matched to controls by Euclidean distance to the source of infection and farm size. Intervening geographical features and connectivity between the source of infection and case and controls were compared.

Results

Road distance between holdings, access to holdings, presence of forest, elevation change between holdings and the presence of intervening roads had no impact on the risk of local FMD transmission (p > 0.2). However the presence of linear features in the form of rivers and railways acted as barriers to FMD transmission (odds ratio = 0.507, 95% CIs = 0.297,0.887, p = 0.018).

Conclusion

This paper demonstrated that although FMD spread can generally be modelled using Euclidean distance and numbers of animals on susceptible holdings, the presence of rivers and railways has an additional protective effect reducing the probability of transmission between holdings.

     

Epidemiological Characteristics of Classical Scrapie Outbreaks in 30 Sheep Flocks in the United Kingdom

Background

Most previous analyses of scrapie outbreaks have focused on flocks run by research institutes, which may not reflect the field situation. Within this study, we attempt to rectify this deficit by describing the epidemiological characteristics of 30 sheep flocks naturally-infected with classical scrapie, and by exploring possible underlying causes of variation in the characteristics between flocks, including flock-level prion protein (PrP) genotype profile. In total, the study involved PrP genotype data for nearly 8600 animals and over 400 scrapie cases.

Methodology/Principal Findings

We found that most scrapie cases were restricted to just two PrP genotypes (ARQ/VRQ and VRQ/VRQ), though two flocks had markedly different affected genotypes, despite having similar underlying genotype profiles to other flocks of the same breed; we identified differences amongst flocks in the age of cases of certain PrP genotypes; we found that the age-at-onset of clinical signs depended on peak incidence and flock type; we found evidence that purchasing infected animals is an important means of introducing scrapie to a flock; we found some evidence that flock-level PrP genotype profile and flock size account for variation in outbreak characteristics; identified seasonality in cases associated with lambing time in certain flocks; and we identified one case that was homozygous for phenylalanine at codon 141, a polymorphism associated with a very high risk of atypical scrapie, and 28 cases that were heterozygous at this codon.

Conclusions/Significance

This paper presents the largest study to date on commercially-run sheep flocks naturally-infected with classical scrapie, involving 30 study flocks, more than 400 scrapie cases and over 8500 PrP genotypes. We show that some of the observed variation in epidemiological characteristics between farms is related to differences in their PrP genotype profile; although much remains unexplained and may instead be attributed to the stochastic nature of scrapie dynamics.     

Invasion and persistence of plant parasites in a spatially structured host population

Spatial structure is of central importance in the dynamics of plant-parasite interactions and is imposed by the growth habit and distribution of host plants and by parasite dispersal which is frequently restricted. To investigate the effects of spatial heterogeneity on the dynamics of plant parasites we introduce a simple model for epidemic development within a spatially structured host population. Here the host population is subdivided into a number of patches which are linked to allow for transmission from one patch to another with the connections defining the spatial structure of the host population. Three key parameters are identified that play a critical role in the ability of the parasite to invade and persist within the host population: the within-patch parasite basic reproductive number which characterises the infection dynamics at the local spatial scale; and the neighbourhood of interaction which describes which patches interact with which and the strength of coupling between patches within the neighbourhood which together characterise the spread of the parasite over larger spatial scales. Using both deterministic and stochastic formulations of the model, we investigate how the thresholds and probabilities of invasion and persistence are affected by these parameters, by demographic stochasticity and by differences in the initial level of infection.