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/.     

Responses to nutrients in farm animals: implications for production and quality

It is well known that any quantitative (energy and protein levels) and qualitative (nature of the diet, nutrient dynamic) changes in the feeding of animals affect metabolism. Energy expenditure and feed efficiency at the whole-body level, nutrient partitioning between and within tissues and organs and, ultimately, tissue and organ characteristics are the major regulated traits with consequences on the quality of the meat and milk produced. Recent progress in biology has brought to light important biological mechanisms which explain these observations: for instance, regulation by the nutrients of gene expression or of key metabolic enzyme activity, interaction and sometimes cross-regulation or competition between nutrients to provide free energy (ATP) to living cells, indirect action of nutrients through a complex hormonal action, and, particularly in herbivores, interactions between trans-fatty acids produced in the rumen and tissue metabolism. One of the main targets of this nutritional regulation is a modification of tissue insulin sensitivity and hence of insulin action. In addition, the nutritional control of mitochondrial activity (and hence of nutrient catabolism) is another major mechanism by which nutrients may affect body composition and tissue characteristics. These regulations are of great importance in the most metabolically active tissues (the digestive tract and the liver) and may have undesirable (i.e. diabetes and obesity in humans) or desirable consequences (such as the production of fatty liver by ducks and geese, and the production of fatty and hence tasty meat or milk with an adapted fatty acid profile).     

有机碳质量对黄河三角洲芦苇凋落物分解及其温度敏感性的影响

凋落物分解速率及其温度敏感性Q_(10)能够影响凋落物对土壤的碳归还及其对全球变暖的响应。然而,凋落物有机碳质量对凋落物分解及其温度敏感性的影响研究仍不充分。以黄河三角洲芦苇(Phragmites australi)为例,通过凋落物袋法、室内模拟实验及固态~(13)C核磁共振技术,研究有机碳质量对凋落物分解及其温度敏感性的影响,探讨预测凋落物分解及其温度敏感性的指标。结果表明:(1)随着凋落物分解,易分解碳组分(烷氧碳、双烷氧碳)相对含量逐渐降低,而难分解碳组分(芳香碳)相对含量显著增加,疏水碳/亲水碳、芳香碳/烷氧碳比值逐渐增大,凋落物有机碳更加稳定,凋落物呼吸速率及失重率呈下降趋势。(2)凋落物失重主要受烷基碳、烷氧碳相对含量及C/N的影响,凋落物CO_2累积释放量主要受烷氧碳及双烷氧碳相对含量的影响。羰基碳相对含量可以用来解释Q_(10)的变异。因此,相对于生态化学计量比,烷基碳、烷氧碳、双烷氧碳、羰基碳相对含量是预测凋落物分解及其温度敏感性的敏感性指标。     

Inheritance of alleles for Cgy1 and Gy4 storage protein genes in soybean

Summary A cultivar lacking the glycinin subunit A₅A₄B₃ (Raiden) was crossed with one lacking the -subunit of -conglycinin (Keburi). Analysis of F₂ and F₃ progeny indicated that the missing bands of the A₅A₄B₃ and the -subunit were each controlled by a recessive allele of two independently segregating genes. Gene symbols Gy ₄/gy ₄ and Cgy ₁/cgy ₁ were proposed for the genes which confer the presence or absence of the glycinin and conglycinin subunits, respectively.Cooperative research of USDA-ARS and the Indiana Agric. Exp. Stn., Purdue Univ., West Lafayette, IN 47907, USA. Indiana Agric. Exp. Stn. Journal Article 9675. Financial support from the American Soybean Association Research Foundation is gratefully acknowledged     

Stratospheric ozone reduction and ecosystem processes: enhanced UV-B radiation affects chemical quality and decomposition of leaves of the dune grassland species Calamagrostis epigeios

This study reports changes in the plant's chemical composition and the decomposition of this plant material under enhanced solar UV-B radiation. Calamagrostis epigeios, a dominant grass species in the dune grassland in The Netherlands, was grown outdoor on an experimental field under ambient and enhanced solar UV-B (5 and 7.5 kJ m^-2 day^-1 UV-B_BE, respectively), corresponding to about 15% stratospheric ozone depletion. After one growing season aerial plant parts were harvested. The decomposition of this harvested leaf material was studied in a dune grassland and on the above mentioned experimental field under ambient (5 kJ m^-2 day^-1 UV-B_BE) and enhanced (7.5 kJ m^-2 day^-1 UV-B_BE) radiation, using litter bags. The chemical quality of the leaves grown under enhanced solar UV-B changed. There was an increase in the leaf content of lignin, while no significant changes occurred for the content of -cellulose, hemicellulose and tannins under enhanced UV-B. In the field, the rate of decomposition of leaf material grown under enhanced UV-B (with an increased content of lignin) was reduced. The content of lignin of the decomposing leaf material increased, but less under exposure to enhanced UV-B. The latter may be explained by photodegradation of the lignin. The consequences of enhanced UV-B radiation for carbon fluxes in the dune grassland ecosystem are discussed.     

Ecological aspects of water quality regulation in England and Wales

The paper describes the regulatory functions of a new body set up in England and Wales for the management of water pollution, the National Rivers Authority. It outlines proposals for a new water quality classification scheme incorporating biological monitoring as an integral part, and describes other areas of pollution control where biology could be used with advantage. The derivation of statutory water quality objectives as a new concept in the management of natural waters is described, together with an indication of some of the legal mechanisms available to the NRA to ensure that the objectives are met.     

Image quality assessment of an iterative reconstruction algorithm applied to abdominal CT imaging

PurposeTo compare the noise and accuracy on images of the whole porcine liver acquired with iterative reconstruction (IMR, Philips Healthcare, Cleveland, OH, USA) and filtered back projection (FBP) methods.Materials and methodsWe used non-enhanced porcine liver to simulate the human liver and acquired it 100 times to obtain the average FBP value as the ground-truth. The mean and the standard deviation (“inter-scan SD”) of the pixel values on the 100 image acquisitions were calculated for FBP and for three levels of IMR (L1, L2, and L3). We also calculated the noise power spectrum (NPS) and the normalized NPS for the 100 image acquisitions.ResultsThe spatial SD for the porcine liver parenchyma on these slices was 9.92, 4.37, 3.63, and 2.30 Hounsfield units with FBP, IMR-L1, IMR-L2, and IMR-L3, respectively. The detectability of small faint features was better on single IMR than single FBP images. The inter-scan SD value for IMR-L3 images was 53% larger at the liver edges than at the liver parenchyma; it was only 10% larger on FBP images. Assessment of the normalized NPS showed that the noise on IMR images was comprised primarily of low-frequency components.ConclusionIMR images yield the same structure informations as FBP images and image accuracy is maintained. On level 3 IMR images the image noise is more strongly suppressed than on IMR images of the other levels and on FBP images.     

Floral display size and spatial distribution of potential mates affect pollen deposition and female reproductive success in distylous Pulmonaria officinalis (Boraginaceae)

In animal‐pollinated plants, both the spatial distribution of flowering individuals and the number of flowers that an individual displays affect pollen deposition rates and female reproductive success. Heterostylous species are likely to be particularly sensitive to the contingencies of spatial distribution, as they are reproductively subdivided into distinct mating groups, which usually exhibit self‐ and intra‐morph incompatibility and differ in floral morphology. In this paper, we explore the joint effects of both spatial distribution of potential mates and floral display size on morph‐specific pollen deposition rates and seed set patterns in two natural populations of Pulmonaria officinalis, a distylous species with a weak self‐incompatibility system. Both total stigmatic pollen load and the proportion of legitimate pollen decreased with increasing spatial isolation. Legitimate (intermorph) pollen transfer was, however, asymmetric and decreased more rapidly with decreasing proximity to a compatible legitimate mating partner in the S‐morph than in the L‐morph. Total stigmatic pollen loads per flower increased with increasing floral display size, indicating that large plants are disproportionately more visited than smaller individuals. However, because legitimate pollen deposition decreased with increasing floral display size, these results also suggest that larger numbers of flowers increase the degree of geitonogamous pollination. In both the L‐ and S‐morph, seed set significantly decreased with increasing isolation from a legitimate mating partner, but in the L‐morph seed set was less dependent on the spatial distribution of the S‐morph. In addition, seed set significantly increased with floral display size in the L‐morph, but not in the S‐morph. These findings indicate that the spatial distribution of potential mates and variation in floral display size may cause morph‐specific differences in pollen deposition rates and female reproductive success.     

建鲤和异育银鲫摄食不同质量饲料时的氮收支和能量收支比较

实验探讨了建鲤和异育银鲫摄食低质和高质饲料时氮和能量的收支情况.低质饲料以豆粕为主要蛋白源,饲料蛋白含量为33.91%,高质饲料以鱼粉为主要蛋白源,饲料蛋白含量为45.59%.55d的生长结果显示,氮收支和能量收支受到饲料质量和鱼类种类的显著影响:摄食低质饲料时,建鲤的生长氮和生长能比例显著低于异育银鲫,排泄氮、排泄能和代谢能比例显著高于异育银鲫;摄食高质饲料时,两种鱼的氮收支和能量收支无显著差异;建鲤的氮收支和能量收支受饲料质量的显著影响,摄食低质饲料时,其生长氮和生长能比例均显著低于摄食高质饲料时,而排泄氮、粪能和代谢能比例均显著高于摄食高质饲料时;异育银鲫的氮收支、生长能和代谢能比例不受饲料质量的显著影响.结果表明,在低质饲料条件下,建鲤利用氮和能量的能力弱于异育银鲫,在高质饲料条件下,两种鱼没有显著差异.与异育银鲫相比,建鲤利用氮和能量的能力受饲料质量的影响更为显著.       

Approximation of ground water quality for microbial and chemical contamination

Present study was designed to obtain estimation about ground water quality of Bhimber, Azad Jammu and Kashmir (AJK), Pakistan. A total of 12 water samples were collected from different localities of study area to analyze for various physicochemical and biological parameters i.e. namely temperature, pH, turbidity, color, odor, taste, electric conductivity (EC), total dissolved solids (TDS), total hardness (Calcium + Magnesium), chloride, arsenic, phosphate, lead, ammonium ion, nitrite, Fecal coliform and Escherichia coli. Results exposed that all ground water samples of study area were grossly contaminated with pathogenic microorganisms like E. coli and Fecal coliform except one water sample that was obtained from community filter plant Samahni Chowk site. Besides it, values of some physicochemical water quality determining parameters also deviated from recommended limits of World Health Organization (WHO). Chloride ion concentration was little below the prescribed limits in almost all water samples. It has been proven that consumption of un-safe drinking water is one of the major cause of prevalence of water borne diseases like diarrhea, gastroenteritis, typhoid fever and malaria etc. in study area. Community water supply and sanitation projects should be encouraged; government should provide filter plants in all regions of the country so that people could have easy approach to safe drinking water.