Fast integral equation methods for the Laplace-Beltrami equation on the sphere

Integral equation methods for solving the Laplace-Beltrami equation on the unit sphere in the presence of multiple "islands" are presented. The surface of the sphere is first mapped to a multiply-connected region in the complex plane via a stereographic projection. After discretizing the integral equation, the resulting dense linear system is solved iteratively using the fast multipole method for the 2D Coulomb potential in order to calculate the matrix-vector products. This numerical scheme requires only O(N) operations, where $N$ is the number of nodes in the discretization of the boundary. The performance of the method is demonstrated on several examples

Genome of campylobacter coli bacteriophage phiCcoIBB_35

Campylobacter is recognized worldwide as the major etiologic agent in human diarrheoal disease, being Campylobacter jejuni and Campylobacter coli the most prevalent species. Bacteriophages are natural predators of bacteria, ubiquitous in the environment, self-limiting, self- replicating and with a high host-specicity. These make them potentially an important biocontrol agent of foodborne diseases. There are only few reports on Campylobacter bacteriophages, probably due to the fastidious nature of the host Campylobacter which makes the isolation of these phages challenging. Moreover the refractory nature to restriction enzymes digestion of their DNA causes difficulties in characterizing Campylobacter phage genomes by common methods such as restriction fragment length polymorphism. In a previous study Campylobacter phages were isolated from poultry intestinal contents (Carvalho et al., 2010) and one of these phages (phage phiCcoIBB 35) was selected to be genetically sequenced as it showed broad lytic spectra against food and clinical Campylobacter coli and Campylobacter jejuni strains. The PFGE analysis indicates that the genome of phage phiCcoIBB 35 is approximately 204kb. However due to the fact that DNA preparations appeared to contain substances that inhibit Taq and 29 enzymes, the DNA sequence data consists of ve DNA contigs in a total of 172 kb that were not possible to be aligned. Annotation indicates that most of the ORFs are unique and that homology exists with members of the Teequatrovirinae namely for all T4 tail proteins, one head protein (gp23), neck protein (gp20); and baseplate proteins (gp6,gp25, gp48). Moreover homologs were found to T4 proteins involved in morphogenesis, nucleotide metabolism, transcription, DNA replication and recombination. Unique genes involved in the carbohydrate metabolism, pathogenesis and amino acid metabolism were also annotated. Several incidences of gene duplications, split genes with intein and introns and insertion-like sequences were present. To our knowledge this study represents the rst report of the genomic sequence of a lytic Campylobacter phage and therefore is of extreme importance for further comparisons with other phage sequences. Nu

Fast integral equation methods for the modified Helmholtz equation

We present a collection of integral equation methods for the solution to the two-dimensional, modified Helmholtz equation, u(\x) - \alpha^2 \Delta u(\x) = 0, in bounded or unbounded multiply-connected domains. We consider both Dirichlet and Neumann problems. We derive well-conditioned Fredholm integral equations of the second kind, which are discretized using high-order, hybrid Gauss-trapezoid rules. Our fast multipole-based iterative solution procedure requires only O(N) or $O(N\log N)$ operations, where N is the number of nodes in the discretization of the boundary. We demonstrate the performance of the methods on several numerical examples.Comment: Published in Computers & Mathematics with Application

Genome characterization of two valuable therapeutic bacteriophages against Salmonella and Campylobacter

Book of abstracts of the Meeting of the Institute for Biotechnology and Bioengineering, 2, Braga, Portugal, 2010Salmonella and Campylobacter are recognized worldwide as the major foodborne pathogens responsible for human gastrointestinal diseases. The increased resistance of bacteria to antibiotics has encouraged the development of alternatives to control bacterial pathogens. Bacteriophages (phages), as natural predators of bacteria, are considered an appealing option. We report herein the isolation and genome characterisation of two Myoviridae broad lytic spectra Campylobacter (vB_CcoM-IBB35) and Salmonella phages (PVP-SE1) with high potential for therapy. The majority of genes of vB_CcoM-IBB35 are unique although homology exists with members of the Teequatrovirinae. Unique genes involved in pathogenesis, carbohydrate and amino acid metabolism were also observed along with several incidences of gene duplications, split genes with intein and introns and “insertion-like sequences”. From the 244 genes found in PVP-SE1, approximately 46% encode unique proteins and only 22.1% exhibited homology with known proteins. The genome sequence presents high homology (145 gene encoding proteins) with the E.coli bacteriophage rV5, both unrelated to any other known phage, which might suggest that they belong to a new phage genetic group. As conclusion, one can argue that the genomic characterization of both phages did not reveal any factor which could preclude its therapeutic use

Genome sequence and characterization of Streptomyces phage Pablito, representing a new species within the genus Janusvirus

Streptomycetes are ubiquitous soil bacteria. Here we report the complete and annotated genome sequence and characterization of Streptomyces phage Pablito, isolated from a soil sample in Haarlem, the Netherlands using Streptomyces lividans as host. This phage was able to infect a diverse range of Streptomyces strains, but none belonging to the sister genus Kitasatospora. Phage Pablito has doublestranded DNA with a genome length of 49,581 base pairs encoding 76 putative proteins, of which 26 could be predicted. The presence of a serine integrase protein indicated the lysogenic nature of phage Pablito. The phage remained stable over a wide range of temperatures (25–45 °C) and at pH≥ 7.0, but lost infectivity at temperatures above 55 °C or when the pH dropped below 6.0. This newly isolated phage is closely related to Streptomyces phage Janus and Hank144 and considered a new species classifed in the genus Janusvirus, within the subfamily Arquattrovirinae.NWOVI.C.192.002Microbial Biotechnolog

Characterization of a new twortlikevirus infecting Staphylococcus epidermidis that exhibits activity against biofilm and stationary bacterial populations

Staphylococcus epidermidis is a major causative agent of nosocomial infections, mainly associated with the use of indwelling devices, on which this bacterium forms structures known as biofilms. Due to biofilms high tolerance to antibiotics, virulent bacteriophages were previously tested as novel therapeutic agents. However, several staphylococcal bacteriophages were shown to be inefficient against biofilms. Using wastewater treatment plant raw effluents, a novel phage was isolated and characterized. This virus was named phiIBB-SEP1 and TEM micrographs suggested that it belonged to the Twortlikevirus genus. Phage phiIBB-SEP1 is able to infect 41 S. epidermidis clinical isolates used in this study, and contrarily to other polyvalent viruses of the Twortlikevirus genus, phiIBB-SEP1 is highly specific for S. epidermidis strains. The genome of this phage was fully sequenced and presents the typical structure of a member of the Twortlikevirus. However, when compared to other staphylococcal members of this genus, it showed DNA sequence identities no greater than 58.2%, suggesting that phiIBB-SEP1 is a new species within this subfamily. Efficacy studies results showed that phage SEP1 is able to cause a 6 Log CFU per ml reduction of the cell titer in less than 2h for some of the clinical strains in exponential phase; and, in less than 4h for stationary phase cells (using a multiplicity of infection of 1). This phage has also the capacity of reducing, by up to 2 Log CFU per ml, 24h scraped biofilm cells. Besides CFU counting, this cell reduction was confirmed by flow cytometry counting. Additionally, live/dead flow cytometry staining allowed the observation that this phage kills biofilms bacteria in different physiological states including dormant cells. These are promising results, since the rare feature presented by this phage of infecting cells with reduced metabolic activity allied with its high broad host strain range suggest its use for therapy purposes

Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes

<p>Abstract</p> <p>Background</p> <p>Adherent and invasive <it>Escherichia coli </it>(AIEC) are commonly found in ileal lesions of Crohn's Disease (CD) patients, where they adhere to intestinal epithelial cells and invade into and survive in epithelial cells and macrophages, thereby gaining access to a typically restricted host niche. Colonization leads to strong inflammatory responses in the gut suggesting that AIEC could play a role in CD immunopathology. Despite extensive investigation, the genetic determinants accounting for the AIEC phenotype remain poorly defined. To address this, we present the complete genome sequence of an AIEC, revealing the genetic blueprint for this disease-associated <it>E. coli </it>pathotype.</p> <p>Results</p> <p>We sequenced the complete genome of <it>E. coli </it>NRG857c (O83:H1), a clinical isolate of AIEC from the ileum of a Crohn's Disease patient. Our sequence data confirmed a phylogenetic linkage between AIEC and extraintestinal pathogenic <it>E. coli </it>causing urinary tract infections and neonatal meningitis. The comparison of the NRG857c AIEC genome with other pathogenic and commensal <it>E. coli </it>allowed for the identification of unique genetic features of the AIEC pathotype, including 41 genomic islands, and unique genes that are found only in strains exhibiting the adherent and invasive phenotype.</p> <p>Conclusions</p> <p>Up to now, the virulence-like features associated with AIEC are detectable only phenotypically. AIEC genome sequence data will facilitate the identification of genetic determinants implicated in invasion and intracellular growth, as well as enable functional genomic studies of AIEC gene expression during health and disease.</p