Increasing the Reliability of Adaptive Quadrature Using Explicit Interpolants

We present two new adaptive quadrature routines. Both routines differ from previously published algorithms in many aspects, most significantly in how they represent the integrand, how they treat non-numerical values of the integrand, how they deal with improper divergent integrals and how they estimate the integration error. The main focus of these improvements is to increase the reliability of the algorithms without significantly impacting their efficiency. Both algorithms are implemented in Matlab and tested using both the "families" suggested by Lyness and Kaganove and the battery test used by Gander and Gautschi and Kahaner. They are shown to be more reliable, albeit in some cases less efficient, than other commonly-used adaptive integrators.Comment: 32 pages, submitted to ACM Transactions on Mathematical Softwar

Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits

Correct orthology assignment is a critical prerequisite of numerous comparative genomics procedures, such as function prediction, construction of phylogenetic species trees and genome rearrangement analysis. We present an algorithm for the detection of non-orthologs that arise by mistake in current orthology classification methods based on genome-specific best hits, such as the COGs database. The algorithm works with pairwise distance estimates, rather than computationally expensive and error-prone tree-building methods. The accuracy of the algorithm is evaluated through verification of the distribution of predicted cases, case-by-case phylogenetic analysis and comparisons with predictions from other projects using independent methods. Our results show that a very significant fraction of the COG groups include non-orthologs: using conservative parameters, the algorithm detects non-orthology in a third of all COG groups. Consequently, sequence analysis sensitive to correct orthology assignments will greatly benefit from these findings

Bacterial diversity on stainless steel surfaces of egg processing companies and potential of selected isolates to spoil liquid whole egg products

AimsTo assess the bacterial diversity in the French egg processing industry and to explore the adhesion and spoilage potential of selected bacteria.Methods and ResultsSterile stainless steel chips were suspended for 2 months inside the pipelines of seven egg processing companies, before and after the pasteurizer, at warm and cold seasons. After exposure, the bacterial diversity was assessed by 16S rDNA sequencing. The 231 collected isolates were mainly facultative anaerobic Gram positive bacteria, such as Streptococcus, Staphylococcus, Bacillus and Kocuria. Sixty‐five representative isolates were further characterized in vitro regarding the potential for adhesion and egg product spoilage. A high diversity was observed from one genus to another. Kocuria and Rothia isolates showed significantly higher adhesion than the isolates of the other genera. Only the isolates belonging to the genera Bacillus and Lysinibacillus, associated with high enzymatic activities on a solid egg‐based medium, were able to induce spoilage of liquid whole egg.ConclusionsBacteria collected on stainless steel surfaces placed in egg processing industries could be associated to liquid egg product spoilage.Significance and Impact of the StudyThis study provides new insights on the bacterial contamination in egg processing companies and represents a first step for the effective control of undesirable bacteria in liquid egg products

Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequences

BACKGROUND: The estimation of the difference between two evolutionary distances within a triplet of homologs is a common operation that is used for example to determine which of two sequences is closer to a third one. The most accurate method is currently maximum likelihood over the entire triplet. However, this approach is relatively time consuming. RESULTS: We show that an alternative estimator, based on pairwise estimates and therefore much faster to compute, has almost the same statistical power as the maximum likelihood estimator. We also provide a numerical approximation for its variance, which could otherwise only be estimated through an expensive re-sampling approach such as bootstrapping. An extensive simulation demonstrates that the approximation delivers precise confidence intervals. To illustrate the possible applications of these results, we show how they improve the detection of asymmetric evolution, and the identification of the closest relative to a given sequence in a group of homologs. CONCLUSION: The results presented in this paper constitute a basis for large-scale protein cross-comparisons of pairwise evolutionary distances

Shaping Biological Knowledge: Applications in Proteomics

The central dogma of molecular biology has provided a meaningful principle for data integration in the field of genomics. In this context, integration reflects the known transitions from a chromosome to a protein sequence: transcription, intron splicing, exon assembly and translation. There is no such clear principle for integrating proteomics data, since the laws governing protein folding and interactivity are not quite understood. In our effort to bring together independent pieces of information relative to proteins in a biologically meaningful way, we assess the bias of bioinformatics resources and consequent approximations in the framework of small-scale studies. We analyse proteomics data while following both a data-driven (focus on proteins smaller than 10 kDa) and a hypothesis-driven (focus on whole bacterial proteomes) approach. These applications are potentially the source of specialized complements to classical biological ontologies

Genus Hydrangea: diversity of pigments and phenolic compounds

The most important collection of Hydrangea in Europe is located in Angers (France). It consists of over 700 germplasm accessions distributed in 13 species. Originating from Asia and America, they were introduced in Europe in the 18th century for their ornamental interest but medicinal properties may also be found in this genus since extracts from H. macrophylla are already described as exhibiting anti-diabetic [1], lipid lowering and anti-oxidative [2], anti-allergic [3] and antimalarial activities [4]. Management of the collection requires botanical, genetic and biochemical studies allowing good, reliable characterization of species, subspecies and varieties. In this context, the biochemical characterization of the inflorescences was undertaken to evaluate the intra and interspecific diversities of pigments and other phenolic compounds. Inflorescences are generally white, except for three species: H. macrophylla, H. involucrata and H .aspera which exhibit rose or blue flowers. Among them only H. macrophylla was previously studied for sepal color variation [5]. In this study, 80 accessions were analyzed by means of HPLC/DAD, LC-MS/MS and NMR experiments: 46 H. macrophylla, 13 H. aspera, 6 H. involucrata, 5 H. paniculata, 3 H. quercifolia, 2 H. arborescens, 2 H. anomala, 2 H. heteromala, 1 H. scandens, 1 H. seemannii and 1 H. integrifolia. About 50 phenolic derivatives - essentially phenolic acids and flavonols (quercetin and kaempferol) - and 20 anthocyanins could be identified. The contents of pigments and other phenolic compounds appeared as very diverse both qualitatively and quantitatively and some compounds could be identified as chemospecific. On this basis, a statistical study using Principal Component Analysis allowed a clear distinction between both species and subspecies. Besides, different biological evaluations of crude extracts and secondary metabolites isolated from Hydrangea sp will also be discussed

OMA 2011: orthology inference among 1000 complete genomes

OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genomes. Initiated in 2004, the project is at its 11th release. It now includes 1000 genomes, making it one of the largest resources of its kind. Here, we describe recent developments in terms of species covered; the algorithmic pipeline—in particular regarding the treatment of alternative splicing, and new features of the web (OMA Browser) and programming interface (SOAP API). In the second part, we review the various representations provided by OMA and their typical applications. The database is publicly accessible at http://omabrowser.org