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

The genome and proteome of coliphage T1

AbstractThe genome of enterobacterial phage T1 has been sequenced, revealing that its 50.7-kb terminally redundant, circularly permuted sequence contains 48,836 bp of nonredundant nucleotides. Seventy-seven open reading frames (ORFs) were identified, with a high percentage of small genes located at the termini of the genomes displaying no homology to existing phage or prophage proteins. Of the genes showing homologs (47%), we identified those involved in host DNA degradation (three endonucleases) and T1 replication (DNA helicase, primase, and single-stranded DNA-binding proteins) and recombination (RecE and Erf homologs). While the tail genes showed homology to those from temperate coliphage N15, the capsid biosynthetic genes were unique. Phage proteins were resolved by 2D gel electrophoresis, and mass spectrometry was used to identify several of the spots including the major head, portal, and tail proteins, thus verifying the annotation

Characterization of newly isolated lytic bacteriophages active against Acinetobacter baumannii

Based on genotyping and host range, two newly isolated lytic bacteriophages, myovirus vB_AbaM_Acibel004 and podovirus vB_AbaP_Acibel007, active against Acinetobacter baumannii clinical strains, were selected from a new phage library for further characterization. The complete genomes of the two phages were analyzed. Both phages are characterized by broad host range and essential features of potential therapeutic phages, such as short latent period (27 and 21 min, respectively), high burst size (125 and 145, respectively), stability of activity in liquid culture and low frequency of occurrence of phage-resistant mutant bacterial cells. Genomic analysis showed that while Acibel004 represents a novel bacteriophage with resemblance to some unclassified Pseudomonas aeruginosa phages, Acibel007 belongs to the well-characterized genus of the Phikmvlikevirus. The newly isolated phages can serve as potential candidates for phage cocktails to control A. baumannii infections

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

Complete genome sequence of pseudomonas aeruginosa Phage vB_PaeM_CEB_DP1

vB_PaeM_CEB_DP1 is a Pseudomonas aeruginosa bacteriophage (phage) belonging to the Pbunalikevirus genus of the Myoviridae family of phages. It was isolated from hospital sewage. vB_PaeM_CEB_DP1 is a double-stranded DNA (dsDNA) phage, with a genome of 66,158 bp, containing 89 predicted open reading frames.NIH -National Institutes of Health(1DP2OD008435

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