Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions

One of the common methods for assessing energy functions of proteins is selection of native or near-native structures from decoys. This is an efficient but indirect test of the energy functions because decoy structures are typically generated either by sampling procedures or by a separate energy function. As a result, these decoys may not contain the global minimum structure that reflects the true folding accuracy of the energy functions. This paper proposes to assess energy functions by ab initio refolding of fully unfolded terminal segments with secondary structures while keeping the rest of the proteins fixed in their native conformations. Global energy minimization of these short unfolded segments, a challenging yet tractable problem, is a direct test of the energy functions. As an illustrative example, refolding terminal segments is employed to assess two closely related all-atom statistical energy functions, DFIRE (distance-scaled, finite, ideal-gas reference state) and DOPE (discrete optimized protein energy). We found that a simple sequence-position dependence contained in the DOPE energy function leads to an intrinsic bias toward the formation of helical structures. Meanwhile, a finer statistical treatment of short-range interactions yields a significant improvement in the accuracy of segment refolding by DFIRE. The updated DFIRE energy function yields success rates of 100% and 67%, respectively, for its ability to sample and fold fully unfolded terminal segments of 15 proteins to within 3.5 A global root-mean-squared distance from the corresponding native structures. The updated DFIRE energy function is available as DFIRE 2.0 upon request.     

Beyond existence and aiming outside the laboratory: estimating frequency-dependent and pay-off-biased social learning strategies

The existence of social learning has been confirmed in diverse taxa, from apes to guppies. In order to advance our understanding of the consequences of social transmission and evolution of behaviour, however, we require statistical tools that can distinguish among diverse social learning strategies. In this paper, we advance two main ideas. First, social learning is diverse, in the sense that individuals can take advantage of different kinds of information and combine them in different ways. Examining learning strategies for different information conditions illuminates the more detailed design of social learning. We construct and analyse an evolutionary model of diverse social learning heuristics, in order to generate predictions and illustrate the impact of design differences on an organism's fitness. Second, in order to eventually escape the laboratory and apply social learning models to natural behaviour, we require statistical methods that do not depend upon tight experimental control. Therefore, we examine strategic social learning in an experimental setting in which the social information itself is endogenous to the experimental group, as it is in natural settings. We develop statistical models for distinguishing among different strategic uses of social information. The experimental data strongly suggest that most participants employ a hierarchical strategy that uses both average observed pay-offs of options as well as frequency information, the same model predicted by our evolutionary analysis to dominate a wide range of conditions.     

A comparison of MSA tools

Multiple sequence alignment (MSA) is essential in phylogenetic, evolutionary and functional analysis. Several MSA tools are available in the literature. Here, we use several MSA tools such as ClustalX, Align-m, T-Coffee, SAGA, ProbCons, MAFFT, MUSCLE and DIALIGN to illustrate comparative phylogenetic trees analysis for two datasets. Results show that there is no single MSA tool that consistently outperforms the rest in producing reliable phylogenetic trees.     

TransPath: a computational method for locating ion transit pathways through membrane proteins

The finely tuned structures of membrane channel proteins allow selective passage of ions through the available aqueous pores. To understand channel function, it is crucial to locate the pores and study their physical and chemical properties. Here, we propose a new pore-searching algorithm (TransPath), which uses the Configurational Bias Monte Carlo (CBMC) method to generate transmembrane trajectories driven by both geometric and electrostatic features. The trajectories are binned into groups determined by a vector distance criterion. From each group, a representative trajectory is selected based on the Rosenbluth weight, and the geometrically optimal path is obtained by simulated annealing. Candidate ion pathways can then be determined by analysis of the radius and potential profiles. The proposed method and its implementation are illustrated using the bacterial KcsA potassium channel as an example. The procedure is then applied to the more complex structures of the bacterial E. coli chloride channel homolog and a homology model of the ClC-0 channel.     

Evaluation of spectrophotometric methods for screening of green rooibos (Aspalathus linearis) and green honeybush (Cyclopia genistoides) extracts for high levels of Bio-active compounds

The potential of UV spectrophotometry and an aluminium chloride (AlCl(3)) colorimetric method to determine the dihydrochalcone (DHC) and mangiferin contents of green rooibos and honeybush (C. genistoides) extracts, respectively, was investigated. The DHC content of rooibos water extracts, determined using UV spectroscopy, correlated with the sum of the aspalathin and nothofagin contents as quantified using HPLC (r = 0.98). A correlation coefficient of 0.91 was obtained when correlating the mangiferin content of C. genistoides methanol extracts, determined by the AlCl(3) colorimetric method, with the results obtained by HPLC. Using the linear equations from the correlations it was possible to predict the DHC and mangiferin contents of extracts from the respective spectrophotometric measurements to a reasonable accuracy as an alternative to HPLC. The total polyphenol (TP) content of rooibos water extracts can also be determined using UV spectrophotometry and aspalathin as a standard (r = 0.99) as an alternative to the Folin-Ciocalteau method. The TP content of rooibos extracts correlated (r = 0.99) with its total antioxidant activity (TAA) as determined with the ABTS radical cation scavenging assay, but the TP content of C. genistoides water extracts is not a good indication of their TAA (r = 0.27). The aspalathin content of rooibos extracts correlated with their TAA (r = 0.96), but the mangiferin content of honeybush water extracts only gave a moderate correlation with their TAA (r = 0.75).     

Monitoring crayfish using a mark-recapture method: potentials,recommendations, and limitations

Crayfish are regarded as useful indicators of environmental quality and freshwater biodiversity. However, reliable methods for monitoring their populations are needed so that this potential can be fully utilised. We report and discuss methodological aspects of the white-clawed crayfish (Austropotamobius pallipes complex) survey conducted in Piedmont, Italy, with the use of mark-recapture. The results suggest that the method can serve as a convenient tool for estimating the size of crayfish populations and inferring their temporal trends. The two populations investigated appeared closed except for wintertime and July. Consequently, the Robust Design, which is regarded as the most reliable mark-recapture approach, can be easily applied. The minimum effective sampling plan for monitoring purposes should comprise one primary period per year, conducted in the summer–autumn season, and consisting of three capture sessions. If gaining insight into the ecology of the investigated species is the prime objective and sufficient resources are available, the optimal plan should include two primary periods (in spring and the summer–autumn season) of five capture sessions each. Capture sessions need to be separated by roughly 2-week intervals in order to avoid the strong, but short-term, negative effect of capturing crayfish on their recapture chances. As the model without heterogeneity in capture probabilities ensures better estimate precision we recommend that data collected for both sexes are analysed separately. Taking into consideration higher male catchabilities and sex ratio being invariably 1:1, it also seems beneficial to estimate only male numbers and double them to achieve total population sizes.     

Comparison of census methods for black-browed albatrosses breeding at the Ildefonso Archipelago,Chile

A breeding population of black-browed albatrosses has been known to exist at the Ildefonso Archipelago, Chile, for >90 years but the population has never been censused using scientifically defendable methods. To estimate population size, and examine the accuracy and practicality of various census methods, the population was censused in the 2002/2003 breeding season using (a) ground-truthed aerial photography, (b) yacht-based photography, (c) ground counts, (d) quadrat sampling and (e) point-distance sampling. Compared to ground-truthed aerial photography (judged the most accurate) yacht-based photography underestimated population size by 55%, ground counts by 13%, quadrat sampling by 11% and point-distance sampling by 9%. Ground-truthed air photography revealed that in the 2002/2003 breeding season 47,000 pairs of black-browed albatrosses bred at the Ildefonso Archipelago. A repeat aerial census in 2006 suggested the size of the breeding population had not changed in the 4 years between the two censuses. After the Falkland Islands/Islas Malvinas, South Georgia and Diego Ramirez, the Ildefonso Archipelago holds the fourth largest population of black-browed albatrosses in the world.     

Evaluation of a leaf area prediction model proposed for sunflower

Six leaf samplings were conducted in two sunflower (Helianthus annuus L.) hybrids during the 2006 growing season in order to evaluate a simple model proposed for leaf area (LA) estimation. A total of 144 leaves were processed using an image analysis system and LA, maximum leaf width (W) [cm], and midvein length (L) [cm] were measured. Also, LA was estimated using the model proposed by Rouphael et al. (2007). Measured LA was exponentially related with L and W, and the W-LA relationships showed higher r ². Estimated LA was strongly and exponentially related with L. Strong, linear relationships with high r ² between estimated and measured LA confirmed the high predictability of the proposed model.     

Computing an NPMLE for a mixing distribution in two closed heterogeneous population size models

Binomial and geometric mixtures can be used to model data gathered in capture-recapture surveys of animal populations, removal surveys of harvest populations, registrations of disease populations, ecological species census, and so on. To compute a nonparametric maximum likelihood estimator for the mixing distribution of heterogeneous capture probabilities, we consider a conditional approach and use a reliable and fast integrative procedure which combines the EM algorithm to increase the likelihood and the vertex-exchange method to update the number of support points. A convergent Newtonian algorithm is used in the M-step of the EM algorithm.