RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

This paper is a report of a second round of RNA-Puzzles, a collective and blind experiment in three-dimensional (3D) RNA structure prediction. Three puzzles, Puzzles 5, 6, and 10, represented sequences of three large RNA structures with limited or no homology with previously solved RNA molecules. A lariat-capping ribozyme, as well as riboswitches complexed to adenosylcobalamin and tRNA, were predicted by seven groups using RNAComposer, ModeRNA/SimRNA, Vfold, Rosetta, DMD, MC-Fold, 3dRNA, and AMBER refinement. Some groups derived models using data from state-of-the-art chemical-mapping methods (SHAPE, DMS, CMCT, and mutate-and-map). The comparisons between the predictions and the three subsequently released crystallographic structures, solved at diffraction resolutions of 2.5–3.2 Å, were carried out automatically using various sets of quality indicators. The comparisons clearly demonstrate the state of present-day de novo prediction abilities as well as the limitations of these state-of-the-art methods. All of the best prediction models have similar topologies to the native structures, which suggests that computational methods for RNA structure prediction can already provide useful structural information for biological problems. However, the prediction accuracy for non-Watson–Crick interactions, key to proper folding of RNAs, is low and some predicted models had high Clash Scores. These two difficulties point to some of the continuing bottlenecks in RNA structure prediction. All submitted models are available for download at http://ahsoka.u-strasbg.fr/rnapuzzles/.     

Learning generative models for protein fold families

We introduce a new approach to learning statistical models from multiple sequence alignments (MSA) of proteins. Our method, called GREMLIN (Generative REgularized ModeLs of proteINs), learns an undirected probabilistic graphical model of the amino acid composition within the MSA. The resulting model encodes both the position-specific conservation statistics and the correlated mutation statistics between sequential and long-range pairs of residues. Existing techniques for learning graphical models from MSA either make strong, and often inappropriate assumptions about the conditional independencies within the MSA (e.g., Hidden Markov Models), or else use suboptimal algorithms to learn the parameters of the model. In contrast, GREMLIN makes no a priori assumptions about the conditional independencies within the MSA. We formulate and solve a convex optimization problem, thus guaranteeing that we find a globally optimal model at convergence. The resulting model is also generative, allowing for the design of new protein sequences that have the same statistical properties as those in the MSA. We perform a detailed analysis of covariation statistics on the extensively studied WW and PDZ domains and show that our method out-performs an existing algorithm for learning undirected probabilistic graphical models from MSA. We then apply our approach to 71 additional families from the PFAM database and demonstrate that the resulting models significantly out-perform Hidden Markov Models in terms of predictive accuracy.     

Environmental factors associated with the distribution of floodwater mosquito eggs in irrigated fields in Wrocław,Poland

A survey of distribution patterns of floodwater mosquito eggs related to environmental conditions such as moisture and plant associations was conducted by using soil samples from irrigated fields in Wroc?aw, Poland. Mosquito egg distribution was determined by repeatedly flooding the soil samples with aerated water at a temperature of 25° C. Under laboratory conditions, hatching in installments of Aedes caspius (Pallas) and Aedes vexans (Meigen) were commonly observed. The results show that ～75% of the larvae of Ae. caspius and Ae. vexans hatched after the first flooding under summer‐like conditions, whereas, following the second and third flooding, the numbers of hatched larvae were significantly lower. In our study, within one intermediate flooded field, a total of 66 plant species was identified and classified into six communities. All vegetation types were associated by varied egg densities and showed differences both in richness and Shannon‐Wiener diversity index as well as in ecological indices for moisture, soil reaction, and nutrient level. Small changes in elevation along the slope within the study area showed a large difference in the distribution of mosquito eggs. The highest average egg density was observed in zones with high occurrence of Phalaris arundinacea, usually prevalent in intermediate flooded and fertile areas. Knowledge of the indicators for the distribution of floodwater mosquito eggs in temporary breeding sites may be essential for organizing a successful, integrated mosquito control program with special regard to microbial control agents.     

Butterfly diversity at the ecotone between agricultural and semi‐natural habitats across a climatic gradient

Aim Understanding the response of species to ecotones and habitat edges is essential to designing conservation management, especially in mosaic agricultural landscapes. This study examines how species diversity and composition change with distance from semi‐natural habitats, over ecotones into agricultural fields, and how within‐site patterns of community transition change across a climatic gradient and differ between crop types. Location A total of 19 sites in Israel where semi‐natural habitats border agricultural fields (wheat fields or olive groves) distributed along a sharp climatic gradient ranging between 100 and 800 mm mean annual rainfall. Methods  We performed butterfly surveys in 2006. We analysed species richness (α‐diversity), diversity, community nestedness and species turnover (β‐diversity) within sites and between sites (γ‐diversity). We also assessed where species of conservation concern occurred. Results In wheat sites, richness and diversity declined abruptly from ecotones to fields and remained homogenously poor throughout the fields, regardless of climate. In olive sites, despite the sharp structural boundary, richness and diversity remained high from the semi‐natural habitat to the grove margins and then declined gradually into groves. Species of conservation concern occurred across all habitats at olive sites, but none were found inside wheat fields or at their ecotones. The contrast in community structure between semi‐natural habitats and fields was affected by both climate and field type. Irrigation in arid regions did not augment species diversity. Main conclusions Our results indicate that consideration of crop type, within a climatic context, should receive high priority in biodiversity conservation in agricultural areas. In ‘hostile’ crops, such as wheat, we suggest favouring a combination of high‐intensity management and wide margins over less intensive management without margins, which may merely aid generalist butterfly species. The scarcity of butterflies in arid irrigated fields suggests a need to carefully assess the effects of irrigation and agrochemicals on species’ communities.     

Mechanism of interaction between electromagnetic fields and living organisms

Based on nonlinear phenomena of biophoton emission observed in the past, an interference model concerning with the mechanism of interaction between living organisms and electromagnetic fields was raised. Caused by biological nonlinearly polarizable double layer, destructive interference of incoming and reflected waves establishes in the outside. As a consequence, in the inside constructive interference takes place at the same time. The interference patterns may play an important role in biological self organization and in biological functions. We investigate the boundary conditions necessary for explaining these non-linear optical effects in terms of the phase conjugation. It turns out that there are solutions of the Maxwell equations which satisfy destructive interference of biophotons in agreement with the experimental results. Necessary provisions are nonlinearly polarizable optically active double layers of distances which are small compared to the wavelength of light. In addition, they have to be able to move into the nodal planes of the impinging waves within a small time interval compared to the coherence time. These conditions are likely fulfilled in the optically dense, but ordered and optically excited, highly polarizable living matter.     

Skin temperature increase caused by a mobile phone: a methodological infrared camera study

Mobile phone users often complain about burning sensations or a heating of the ear region. The increase in temperature may be due to thermal insulation by the phone, heating of the mobile phone resulting from its electrical power dissipation, and radio frequency (RF) exposure. The main objective of this study was to use infrared (IR) camera techniques to find how much each of these factors contributes to the increase in skin temperature resulting from the use of one GSM 900 phone. One subject, a healthy male, took part in the study. He was holding the phone in a normal position when the phone was switched off, when it was switched on but with the antenna replaced by a 50 Omega load to eliminate the RF exposure, and when it was transmitting RF fields. The output power could be fixed, and the minimal and the maximal power levels of the phone were used. The study was designed as a double blind experiment. The changes in temperature after 15 and 30 min of mobile phone use were calculated on the exposed side of the head relative to the unexposed side. The insulation and the electrical power dissipation led to statistically significant rises in the skin temperature, while the RF exposure did not.     

Effect of weak, interrupted sinusoidal low frequency magnetic field on neural regeneration in rats: functional evaluation

A study of the effect of weak, interrupted sinusoidal low frequency magnetic field (ISMF) stimulation on regeneration of the rat sciatic nerve was carried out. In the experiment, 60 Wistar rats were used: 24 rats underwent unilateral sciatic nerve transection injury and immediate surgical nerve repair, 24 rats underwent unilateral sciatic nerve crush injury, and the remaining 12 rats underwent a sham surgery. Half of the animals (n = 12) with either sciatic nerve lesion were randomly chosen and exposed between a pair of Helmholtz coils for 3 weeks post-injury, 4 h/day, to an interrupted (active period to pause ratio = 1.4 s/0.8 s) sinusoidal 50 Hz magnetic field of 0.5 mT. The other half of the animals (n = 12) and six rats with sham surgery were used for two separate controls. Functional recovery was followed for 6 weeks for the crush injuries and 7(1/2) months for the transection injuries by video assisted footprint analysis in static conditions and quantified using a recently revised static sciatic index (SSI) formula. We ascertained that the magnetic field influence was weak, but certainly detectable in both injury models. The accuracy of ISMF influence detection, determined by the one-way repeated measures ANOVA test, was better for the crush injury model: F(1, 198) = 9.0144, P = .003, than for the transection injury model: F(1, 198) = 6.4826, P = .012. The Student-Newman-Keuls range test for each response day yielded significant differences (P < .05) between the exposed and control groups early in the beginning of functional recovery and later on from the points adjacent to the beginning of the plateau, or 95% of functional recovery, and the end of observation. These differences probably reflect the ISMF systemic effect on the neuron cell bodies and increased and more efficient reinnervation of the periphery.     

Decreased plasma levels of nitric oxide metabolites, angiotensin II, and aldosterone in spontaneously hypertensive rats exposed to 5 mT static magnetic field

Previously, we found that whole body exposure to static magnetic fields (SMF) at 10 mT (B(max)) and 25 mT (B(max)) for 2-9 weeks suppressed and delayed blood pressure (BP) elevation in young, stroke resistant, spontaneously hypertensive rats (SHR). In this study, we investigated the interrelated antipressor effects of lower field strengths and nitric oxide (NO) metabolites (NO(x) = NO(2)(-) + NO(3)(-)) in SHR. Seven-week-old male rats were exposed to two different ranges of SMF intensity, 0.3-1.0 mT or 1.5-5.0 mT, for 12 weeks. Three experimental groups of 20 animals each were examined: (1) no exposure with intraperitoneal (ip) saline injection (sham-exposed control); (2) 1 mT SMF exposure with ip saline injection (1 mT); (3) 5 mT SMF exposure with ip saline injection (5 mT). Arterial BP, heart rate (HR), skin blood flow (SBF), plasma NO metabolites (NO(x)), and plasma catecholamine levels were monitored. SMF at 5 mT, but not 1 mT, significantly suppressed and retarded the early stage development of hypertension for several weeks, compared with the age matched, unexposed (sham exposed) control. Exposure to 5 mT resulted in reduced plasma NO(x) concentrations together with lower levels of angiotensin II and aldosterone in SHR. These results suggest that SMF may suppress and delay BP elevation via the NO pathways and hormonal regulatory systems.     

WHO health risk assessment process for static fields

The World Health Organization (WHO) has a commitment to helping Member States achieve safe, sustainable and health-enhancing human environments, protected from biological, chemical and physical agents. The latter includes advising on the health impact of electromagnetic fields (EMFs) and radiation.

The results of the WHO/ICNIRP/NRPB workshop on static magnetic fields, published in this volume, provide a valuable and much needed contribution to the health risk assessment of exposure to static electric and magnetic fields, which is currently being coordinated by the WHO's International EMF Project. This WHO health risk assessment will be published as an environmental health criteria (EHC) monograph in early 2005.

This paper briefly gives an overview of the process of developing the WHO static fields EHC monograph, the criteria applied to studies that could contribute to the EHC, along with the ‘weight-of-evidence’ approach to health risk assessment. In addition, there is an increasing awareness of the need to account for uncertainty in the science database. This is traditionally addressed by further research, and the EMF project addresses these needs through the development of a ‘research agenda’. However, research programmes may take several years to complete, and the long latency associated with diseases such as cancer in people may also preclude a rapid outcome in some studies. The issue of current uncertainty is being addressed by the WHO EMF project through the development of a ‘precautionary framework’ in which precautionary measures will be applied to policy recommendations.     

Short-term invasibility patterns in burnt and unburnt experimental Mediterranean grassland communities of varying diversities

This paper reports the findings of a short-term natural invasibility field study in constructed Mediterranean herbaceous communities of varying diversities, under a fire treatment. Three components of invasibility, i.e. species richness, density and biomass of invaders, have been monitored in burnt and unburnt experimental plots with resident diversity ranging from monocultures to 18-species mixtures. In general, species richness, density and biomass of invaders decreased significantly with the increase of resident species richness. Furthermore, the density and biomass of invading species were significantly influenced by the species composition of resident communities. Although aboveground biomass, leaf area index, canopy height and percent bare ground of the resident communities explained a significant part of the variation in the success of invading species, these covariates did not fully explain the effects of resident species richness. Fire mainly influenced invasibility via soil nutrient levels. The effect of fire on observed invasibility patterns seems to be less important than the effects of resident species richness. Our results demonstrate the importance of species richness and composition in controlling the initial stages of plant invasions in Mediterranean grasslands but that there was a lack of interaction with the effects of fire disturbance.