Coral Reefs, Fisheries, and Food Security: Integrated Approaches to Addressing Multiple Challenges in the Coral Triangle

The Coral Triangle is the most biologically and economically valuable marine ecosystem on the planet. Covering just three percent of the globe, the region represents more than half of the world's reefs and boasts 76 percent of its known coral species. Sustaining more than 130 million people who rely directly on the marine ecosystems for their livelihoods and food, the marine habitats of the Coral Triangle contribute billions of dollars each year toward the economies of the region.Although the environmental imperative for preserving this area of incredible value and biodiversity is obvious, the growing pressures and threats from widespread poverty, rapid development, and global demands continue to place enormous strain on the natural marine resources of the Coral Triangle

Kinetics of the reaction of nitric oxide with hydrogen

Mixtures of NO and H2 diluted in argon or krypton were heated by incident shock waves, and the infrared emission from the fundamental vibration-rotation band of NO at 5.3 microns was used to monitor the time-varying NO concentration. The reaction kinetics were studied in the temperature range 2400-4500 K using a shock-tube technique. The decomposition of nitric oxide behind the shock was found to be modeled well by a fifteen-reaction system. A principle result of the study was the determination of the rate constant for the reaction H + NO yields N + OH, which may be the rate-limiting step for NO removal in some combustion systems. Experimental values of k sub 1 were obtained for each test through comparisons of measured and numerically predicted NO profiles

Decomposition of NO studied by infrared emission and CO laser absorption

A diagnostic technique for monitoring the concentration of NO using absorption of CO laser radiation was developed and applied in a study of the decomposition kinetics of NO. Simultaneous measurements of infrared emission by NO at 5.3 microns were also made to validate the laser absorption technique. The data were obtained behind incident shocks in NO-N2O-Ar (or Kr) mixtures, with temperatures in the range 2400-4100 K. Rate constants for dominant reactions were inferred from comparisons with computer simulations of the reactive flow

Empirical prediction of peptide octanol-water partition coefficients

Peptides are of great therapeutic potential as vaccines and drugs. Knowledge of physicochemical descriptors, including the partition coefficient P (commonly expressed in logarithm form: logP), is useful for screening out unsuitable molecules and also for the development of predictive Quantitative Structure-Activity Relationships (QSARs). In this paper we develop a new approach to the prediction of LogP values for peptides based on an empirical relationship between global molecular properties and measured physical properties. Our method was successful in terms of peptide prediction (total r2 = 0.641). The final model consisted of 5 physicochemical descriptors (molecular weight, number of single bonds, 2D-VDW volume, 2D-VSA hydrophobic and 2D-VSA polar). The approach is peptide specific and its predictive accuracy was high. Overall, 67% of the peptides were able to be predicted within +/-0.5 log units from the experimental values. Our method thus represents a novel prediction method with proven predictive ability

The Great Eruption of Eta Carinae

During the years 1838-1858, the very massive star {\eta} Carinae became the prototype supernova impostor: it released nearly as much light as a supernova explosion and shed an impressive amount of mass, but survived as a star.1 Based on a light-echo spectrum of that event, Rest et al.2 conclude that "a new physical mechanism" is required to explain it, because the gas outflow appears cooler than theoretical expectations. Here we note that (1) theory predicted a substantially lower temperature than they quoted, and (2) their inferred observational value is quite uncertain. Therefore, analyses so far do not reveal any significant contradiction between the observed spectrum and most previous discussions of the Great Eruption and its physics.Comment: To appear in Nature, a brief communication arising in response to Rest et al. 2012. Submitted to Nature February 17, 201

A statistical physics perspective on alignment-independent protein sequence comparison.

Motivation: Within bioinformatics, the textual alignment of amino acid sequences has long dominated the determination of similarity between proteins, with all that implies for shared structure, function, and evolutionary descent. Despite the relative success of modern-day sequence alignment algorithms, so-called alignment-free approaches offer a complementary means of determining and expressing similarity, with potential benefits in certain key applications, such as regression analysis of protein structure-function studies, where alignment-base similarity has performed poorly. Results: Here, we offer a fresh, statistical physics-based perspective focusing on the question of alignment-free comparison, in the process adapting results from “first passage probability distribution” to summarize statistics of ensemble averaged amino acid propensity values. In this paper, we introduce and elaborate this approach

Combining algorithms to predict bacterial protein sub-cellular location: Parallel versus concurrent implementations

We describe a novel and potentially important tool for candidate subunit vaccine selection through in silico reverse-vaccinology. A set of Bayesian networks able to make individual predictions for specific subcellular locations is implemented in three pipelines with different architectures: a parallel implementation with a confidence level-based decision engine and two serial implementations with a hierarchical decision structure, one initially rooted by prediction between membrane types and another rooted by soluble versus membrane prediction. The parallel pipeline outperformed the serial pipeline, but took twice as long to execute. The soluble-rooted serial pipeline outperformed the membrane-rooted predictor. Assessment using genomic test sets was more equivocal, as many more predictions are made by the parallel pipeline, yet the serial pipeline identifies 22 more of the 74 proteins of known location

Toward bacterial protein sub-cellular location prediction: single-class discrimminant models for all gram- and gram+ compartments

Based on Bayesian Networks, methods were created that address protein sequence-based bacterial subcellular location prediction. Distinct predictive algorithms for the eight bacterial subcellular locations were created. Several variant methods were explored. These variations included differences in the number of residues considered within the query sequence - which ranged from the N-terminal 10 residues to the whole sequence - and residue representation - which took the form of amino acid composition, percentage amino acid composition, or normalised amino acid composition. The accuracies of the best performing networks were then compared to PSORTB. All individual location methods outperform PSORTB except for the Gram+ cytoplasmic protein predictor, for which accuracies were essentially equal, and for outer membrane protein prediction, where PSORTB outperforms the binary predictor. The method described here is an important new approach to method development for subcellular location prediction. It is also a new, potentially valuable tool for candidate subunit vaccine selection

Multi-class subcellular location prediction for bacterial proteins

Two algorithms, based on Bayesian Networks (BNs), for bacterial subcellular location prediction, are explored in this paper: one predicts all locations for Gram+ bacteria and the other all locations for Gram- bacteria. Methods were evaluated using different numbers of residues (from the N-terminal 10 residues to the whole sequence) and residue representation (amino acid-composition, percentage amino acid-composition or normalised amino acid-composition). The accuracy of the best resulting BN was compared to PSORTB. The accuracy of this multi-location BN was roughly comparable to PSORTB; the difference in predictions is low, often less than 2%. The BN method thus represents both an important new avenue of methodological development for subcellular location prediction and a potentially value new tool of true utilitarian value for candidate subunit vaccine selection