The impact of genome defense on mobile elements in Microbotryum

Repeat induced point mutation (RIP), a mechanism causing hypermutation of repetitive DNA sequences in fungi, has been described as a ‘genome defense’ which functions to inactivate mobile elements and inhibit their deleterious effects on genome stability. Here we address the interactions between RIP and transposable elements in the Microbotryum violaceum species complex. Ten strains of M. violaceum, most of which belong to different species of the fungus, were all found to contain intragenomic populations of copia-like retrotransposons. Intragenomic DNA sequence variation among the copia-like elements was analyzed for evidence of RIP. Among species with RIP, there was no significant correlation between the frequency of RIP-induced mutations and inferred transposition rate based on diversity. Two strains of M. violaceum, from two different plant species but belonging to the same fungal lineage, contained copia-like elements with very low diversity, as would result from a high transposition rate, and these were also unique in showing no evidence of the hypermutation patterns indicative of the RIP genome defense. In this species, evidence of RIP was also absent from a Class II helitron-like transposable element. However, unexpectedly the absolute repetitive element load was lower than in other strains.

Effects of biochar and the earthworm Eisenia fetida on the bioavailability of polycyclic aromatic hydrocarbons and potentially toxic elements

Polycyclic aromatic hydrocarbons (PAHs) and potentially toxic elements (PTEs) were monitored over 56 days in calcareous contaminated-soil amended with either or both biochar and Eisenia fetida. Biochar reduced total (449 to 306mgkg(-1)) and bioavailable (cyclodextrin extractable) (276 to 182mgkg(-1)) PAHs, PAH concentrations in E. fetida (up to 45%) but also earthworm weight. Earthworms increased PAH bioavailability by >40%. Combined treatment results were similar to the biochar-only treatment. Earthworms increased water soluble Co (3.4 to 29.2mgkg(-1)), Cu (60.0 to 120.1mgkg(-1)) and Ni (31.7 to 83.0mgkg(-1)) but not As, Cd, Pb or Zn; biochar reduced water soluble Cu (60 to 37mgkg(-1)). Combined treatment results were similar to the biochar-only treatment but gave a greater reduction in As and Cd mobility. Biochar has contaminated land remediation potential, but its long-term impact on contaminants and soil biota needs to be assessed.

Temporal relations of column water vapor and tropical precipitation

Empirical studies using satellite data and radiosondes have shown that precipitation increases with column water vapor (CWV) in the tropics, and that this increase is much steeper above some critical CWV value. Here, eight years of 1-min-resolution microwave radiometer and optical gauge data at Nauru Island are analyzed to better understand the relationships among CWV, column liquid water (CLW), and precipitation at small time scales. CWV is found to have large autocorrelation times compared with CLW and precipitation. Before precipitation events, CWV increases on both a synoptic-scale time period and a subsequent shorter time period consistent with mesoscale convective activity; the latter period is associated with the highest CWV levels. Probabilities of precipitation increase greatly with CWV. Given initial high CWV, this increased probability of precipitation persists at least 10–12 h. Even in periods of high CWV, however, probabilities of initial precipitation in a 5-min period remain low enough that there tends to be a lag before the start of the next precipitation event. This is consistent with precipitation occurring stochastically within environments containing high CWV, with the latter being established by a combination of synoptic-scale and mesoscale forcing.

'The Elements' and Hobbesian moral thinking

It is easy to read Hobbes's moral thinking as a deviant contribution to 'modern' natural law, especially if Leviathan (1651) is read through a lens provided by De Cive (1642). But The Elements of Law (1640) encourages the view that Hobbes's argument is 'physicalist', that is, that it requires no premises beyond those required by his physics of matter in motion. The Elements included a draft De Homine and its argument is intimately connected with De Cive's; it shows how such concepts as 'reason', 'right', 'natural law' and 'obligation' can be understood in physicalist terms. But Hobbes's decision to print the latter work in isolation has led to serious misunderstandings

Moisture vertical structure, column water vapor, and tropical deep convection

The vertical structure of the relationship between water vapor and precipitation is analyzed in 5 yr of radiosonde and precipitation gauge data from the Nauru Atmospheric Radiation Measurement (ARM) site. The first vertical principal component of specific humidity is very highly correlated with column water vapor (CWV) and has a maximum of both total and fractional variance captured in the lower free troposphere (around 800 hPa). Moisture profiles conditionally averaged on precipitation show a strong association between rainfall and moisture variability in the free troposphere and little boundary layer variability. A sharp pickup in precipitation occurs near a critical value of CWV, confirming satellite-based studies. A lag–lead analysis suggests it is unlikely that the increase in water vapor is just a result of the falling precipitation. To investigate mechanisms for the CWV–precipitation relationship, entraining plume buoyancy is examined in sonde data and simplified cases. For several different mixing schemes, higher CWV results in progressively greater plume buoyancies, particularly in the upper troposphere, indicating conditions favorable for deep convection. All other things being equal, higher values of lower-tropospheric humidity, via entrainment, play a major role in this buoyancy increase. A small but significant increase in subcloud layer moisture with increasing CWV also contributes to buoyancy. Entrainment coefficients inversely proportional to distance from the surface, associated with mass flux increase through a deep lower-tropospheric layer, appear promising. These yield a relatively even weighting through the lower troposphere for the contribution of environmental water vapor to midtropospheric buoyancy, explaining the association of CWV and buoyancy available for deep convection.

Replication enhancer elements within the open reading frame of tick-borne encephalitis virus and their evolution within the Flavivirus genus

We provide experimental evidence of a replication enhancer element (REE) within the capsid gene of tick-borne encephalitis virus (TBEV, genus Flavivirus). Thermodynamic and phylogenetic analyses predicted that the REE folds as a long stable stem–loop (designated SL6), conserved among all tick-borne flaviviruses (TBFV). Homologous sequences and potential base pairing were found in the corresponding regions of mosquito-borne flaviviruses, but not in more genetically distant flaviviruses. To investigate the role of SL6, nucleotide substitutions were introduced which changed a conserved hexanucleotide motif, the conformation of the terminal loop and the base-paired dsRNA stacking. Substitutions were made within a TBEV reverse genetic system and recovered mutants were compared for plaque morphology, single-step replication kinetics and cytopathic effect. The greatest phenotypic changes were observed in mutants with a destabilized stem. Point mutations in the conserved hexanucleotide motif of the terminal loop caused moderate virus attenuation. However, all mutants eventually reached the titre of wild-type virus late post-infection. Thus, although not essential for growth in tissue culture, the SL6 REE acts to up-regulate virus replication. We hypothesize that this modulatory role may be important for TBEV survival in nature, where the virus circulates by non-viraemic transmission between infected and non-infected ticks, during co-feeding on local rodents.

Identification and characterisation of five novel miniature inverted-repeat transposable elements (MITEs) in amphioxus (Branchiostoma floridae)

As the sister group to vertebrates, amphioxus is consistently used as a model of genome evolution for understanding the invertebrate/vertebrate transition. The amphioxus genome has not undergone massive duplications like those in the vertebrates or disruptive rearrangements like in the genome of Ciona, a urochordate, making it an ideal evolutionary model. Transposable elements have been linked to many genomic evolutionary changes including increased genome size, modified gene expression, massive gene rearrangements, and possibly intron evolution. Despite their importance in genome evolution, few previous examples of transposable elements have been identified in amphioxus. We report five novel Miniature Inverted-repeat Transposable Elements (MITEs) identified by an analysis of amphioxus DNA sequence, which we have named LanceleTn-1, LanceleTn-2, LanceleTn-3a, LanceleTn-3b and LanceleTn-4. Several of the LanceleTn elements were identified in the amphioxus ParaHox cluster, and we suggest these have had important implications for the evolution of this highly conserved gene cluster. The estimated high copy numbers of these elements implies that MITEs are probably the most abundant type of mobile element in amphioxus, and are thus likely to have been of fundamental importance in shaping the evolution of the amphioxus genome.

A simple column model to explore anticipated problems in variational assimilation of satellite observations

We investigate a simplified form of variational data assimilation in a fully nonlinear framework with the aim of extracting dynamical development information from a sequence of observations over time. Information on the vertical wind profile, w(z ), and profiles of temperature, T (z , t), and total water content, qt (z , t), as functions of height, z , and time, t, are converted to brightness temperatures at a single horizontal location by defining a two-dimensional (vertical and time) variational assimilation testbed. The profiles of T and qt are updated using a vertical advection scheme. A basic cloud scheme is used to obtain the fractional cloud amount and, when combined with the temperature field, this information is converted into a brightness temperature, using a simple radiative transfer scheme. It is shown that our model exhibits realistic behaviour with regard to the prediction of cloud, but the effects of nonlinearity become non-negligible in the variational data assimilation algorithm. A careful analysis of the application of the data assimilation scheme to this nonlinear problem is presented, the salient difficulties are highlighted, and suggestions for further developments are discussed.

Effective elements of cognitive behaviour therapy for psychosis: results of a novel type of subgroup analysis based on principal stratification

Background. Meta-analyses show that cognitive behaviour therapy for psychosis (CBT-P) improves distressing positive symptoms. However, it is a complex intervention involving a range of techniques. No previous study has assessed the delivery of the different elements of treatment and their effect on outcome. Our aim was to assess the differential effect of type of treatment delivered on the effectiveness of CBT-P, using novel statistical methodology. Method. The Psychological Prevention of Relapse in Psychosis (PRP) trial was a multi-centre randomized controlled trial (RCT) that compared CBT-P with treatment as usual (TAU). Therapy was manualized, and detailed evaluations of therapy delivery and client engagement were made. Follow-up assessments were made at 12 and 24 months. In a planned analysis, we applied principal stratification (involving structural equation modelling with finite mixtures) to estimate intention-to-treat (ITT) effects for subgroups of participants, defined by qualitative and quantitative differences in receipt of therapy, while maintaining the constraints of randomization. Results. Consistent delivery of full therapy, including specific cognitive and behavioural techniques, was associated with clinically and statistically significant increases in months in remission, and decreases in psychotic and affective symptoms. Delivery of partial therapy involving engagement and assessment was not effective. Conclusions. Our analyses suggest that CBT-P is of significant benefit on multiple outcomes to patients able to engage in the full range of therapy procedures. The novel statistical methods illustrated in this report have general application to the evaluation of heterogeneity in the effects of treatment.

Sub-agent elements for control methods in multi-agent energy management system

Increased penetration of generation and decentralised control are considered to be feasible and effective solution for reducing cost and emissions and hence efficiency associated with power generation and distribution. Distributed generation in combination with the multi-agent technology are perfect candidates for this solution. Pro-active and autonomous nature of multi-agent systems can provide an effective platform for decentralised control whilst improving reliability and flexibility of the grid.

Separation of astaxanthin from cells of Phaffia rhodozyma using colloidal gas aphrons (CGA) in a flotation column

The aim of this study is to investigate the separation of astaxanthin from the cells of Phaffia rhodozyma using colloidal gas aphrons (CGA), which are surfactant stabilized microbubbles, in a flotation column. It was reported in previous studies that optimum recoveries are achieved at conditions that favor electrostatic interactions. Therefore, in this study, CGA generated from the cationic surfactant hexadecyl trimethyl ammonium bromide (CTAB) were applied to suspensions of cells pretreated with NaOH. The different operation modes (batch or continuous) and the effect of volumetric ratio of CGA to feed, initial concentration of feed, operating height, and flow rate of CGA on the separation of astaxanthin were investigated. The volumetric ratio was found to have a significant effect on the separation of astaxanthin for both batch and continuous experiments. Additionally, the effect of homogenization of the cells on the purity of the recovered fractions was investigated, showing that the homogenization resulted in increased purity. Moreover, different concentrations of surfactant were used for the generation of CGA for the recovery of astaxanthin on batch mode; it was found that recoveries up to 98% could be achieved using CGA generated from a CTAB solution 0.8 mM, which is below the CTAB critical micellar concentration (CMC). These results offer important information for the scale-up of the separation of astaxanthin from the cells of P. rhodozyma using CGA.

Eliciting consumer preferences for certified animal-friendly foods: can elements of the theory of planned behavior improve choice experiment analysis?

Models used in neoclassical economics assume human behaviour to be purely rational. On the other hand, models adopted in social and behavioural psychology are founded on the ‘black box’ of human cognition. In view of these observations, this paper aims at bridging this gap by introducing psychological constructs in the well established microeconomic framework of choice behaviour based on random utility theory. In particular, it combines constructs developed employing Ajzen’s theory of planned behaviour with Lancaster’s theory of consumer demand for product characteristics to explain stated preferences over certified animal-friendly foods. To reach this objective a web survey was administered in the largest five EU-25 countries: France, Germany, Italy, Spain and the UK. Findings identify some salient cross-cultural differences between northern and southern Europe and suggest that psychological constructs developed using the Ajzen model are useful in explaining heterogeneity of preferences. Implications for policy makers and marketers involved with certified animal-friendly foods are discussed.

The effect of nonlinearity on the variational assimilation of satellite observations using a simple column model

Cloud imagery is not currently used in numerical weather prediction (NWP) to extract the type of dynamical information that experienced forecasters have extracted subjectively for many years. For example, rapidly developing mid-latitude cyclones have characteristic signatures in the cloud imagery that are most fully appreciated from a sequence of images rather than from a single image. The Met Office is currently developing a technique to extract dynamical development information from satellite imagery using their full incremental 4D-Var (four-dimensional variational data assimilation) system. We investigate a simplified form of this technique in a fully nonlinear framework. We convert information on the vertical wind field, w(z), and profiles of temperature, T(z, t), and total water content, qt (z, t), as functions of height, z, and time, t, to a single brightness temperature by defining a 2D (vertical and time) variational assimilation testbed. The profiles of w, T and qt are updated using a simple vertical advection scheme. We define a basic cloud scheme to obtain the fractional cloud amount and, when combined with the temperature field, we convert this information into a brightness temperature, having developed a simple radiative transfer scheme. With the exception of some matrix inversion routines, all our code is developed from scratch. Throughout the development process we test all aspects of our 2D assimilation system, and then run identical twin experiments to try and recover information on the vertical velocity, from a sequence of observations of brightness temperature. This thesis contains a comprehensive description of our nonlinear models and assimilation system, and the first experimental results.