From HP Lattice Models to Real Proteins: Coordination Number Prediction Using Learning Classifier Systems

Prediction of the coordination number (CN) of residues in proteins based solely on protein sequence has recently received renewed attention. At the same time, simplified protein models such as the HP model have been used to understand protein folding and protein structure prediction. These models represent the sequence of a protein using two residue types: hydrophobic and polar, and restrict the residue locations to those of a lattice. The aim of this paper is to compare CN prediction at three levels of abstraction a) 3D Cubic lattice HP model proteins, b) Real proteins represented by their HP sequence and c) Real proteins using residue sequence alone. For the 3D HP lattice model proteins the CN of each residue is simply the number of neighboring residues on the lattice. For the real proteins, we use a recent real-valued definition of CN proposed by Kinjo et al. To perform the predictions we use GAssist, a recent evolutionary computation based machine learning method belonging to the Learning Classifier System (LCS) family. Its performance was compared against some alternative learning techniques. Predictions using the HP sequence representation with only two residue types were only a little worse than those using a full 20 letter amino acid alphabet (64% vs 68% for two state prediction, 45% vs 50% for three state prediction and 30% vs 33% for five state prediction). That HP sequence information alone can result in predictions accuracies that are within 5% of those obtained using full residue type information indicates that hydrophobicity is a key determinant of CN and further justifies studies of simplified models

Chironomidae (Diptera) and Vegetation in a Created Wetland and Implications for Sampling

Although invertebrate communities are used in the evaluation of created freshwater wetlands, spatial patterns of invertebrate community structure are frequently ignored. Invertebrate distributions are generally associated with plant community distribution in natural aquatic ecosystems. In this study, 180 core samples were collected to examine associations between chironomid (Diptera) genera and emergent vegetation communities in a single created freshwater herbaceous wetland in central Florida. Three of the five common genera were significantly more abundant (p \u3c 0.05, Wilcoxon Rank Sum Test) in areas with greater than 50% cover by emergent vegetation than in open water, but no differences were found between areas dominated by Pontederia cordata and areas dominated by mixed emergent vegetation. Samples from an area of open water and an area with over 80% cover by P. cordata showed significant differences in abundances of all common chironomid genera (P \u3c 0.05, Wilcoxon Rank Sum Test). Results suggest that sampling designs for studies comparing benthic invertebrate communities from natural and created wetlands should consider the possible associations between vegetation and invertebrate communities

Permanent genetic resources added to Molecular Ecology Resources Database 1 August 2011-30 September 2011

This article documents the addition of 299 microsatellite marker loci and nine pairs of single-nucleotide polymorphism (SNP) EPIC primers to the Molecular Ecology Resources (MER) Database. Loci were developed for the following species: Alosa pseudoharengus, Alosa aestivalis, Aphis spiraecola, Argopecten purpuratus, Coreoleuciscus splendidus, Garra gotyla, Hippodamia convergens, Linnaea borealis, Menippe mercenaria, Menippe adina, Parus major, Pinus densiflora, Portunus trituberculatus, Procontarinia mangiferae, Rhynchophorus ferrugineus, Schizothorax richardsonii, Scophthalmus rhombus, Tetraponera aethiops, Thaumetopoea pityocampa, Tuta absoluta and Ugni molinae. These loci were cross-tested on the following species: Barilius bendelisis, Chiromantes haematocheir, Eriocheir sinensis, Eucalyptus camaldulensis, Eucalyptus cladocalix, Eucalyptus globulus, Garra litaninsis vishwanath, Garra para lissorhynchus, Guindilla trinervis, Hemigrapsus sanguineus, Luma chequen. Guayaba, Myrceugenia colchaguensis, Myrceugenia correifolia, Myrceugenia exsucca, Parasesarma plicatum, Parus major, Portunus pelagicus, Psidium guayaba, Schizothorax richardsonii, Scophthalmus maximus, Tetraponera latifrons, Thaumetopoea bonjeani, Thaumetopoea ispartensis, Thaumetopoea libanotica, Thaumetopoea pinivora, Thaumetopoea pityocampa ena clade, Thaumetopoea solitaria, Thaumetopoea wilkinsoni and Tor putitora. This article also documents the addition of nine EPIC primer pairs for Euphaea decorata, Euphaea formosa, Euphaea ornata and Euphaea yayeyamana