Showing papers by "Jonathan J. Dennis published in 2011"

PHAST: A Fast Phage Search Tool

Abstract: PHAge Search Tool (PHAST) is a web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage ‘cornerstone’ feature identification steps to locate, annotate and display prophage sequences and prophage features. Relative to other prophage identification tools, PHAST is up to 40 times faster and up to 15% more sensitive. It is also able to process and annotate both raw DNA sequence data and Genbank files, provide richly annotated tables on prophage features and prophage ‘quality’ and distinguish between intact and incomplete prophage. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views. PHAST is available at (http://phast.wishartlab.com).

Spectrogram Image Feature for Sound Event Classification in Mismatched Conditions

Abstract: In this letter, we present a novel feature extraction method for sound event classification, based on the visual signature extracted from the sound's time-frequency representation. The motivation stems from the fact that spectrograms form recognisable images, that can be identified by a human reader, with perception enhanced by pseudo-coloration of the image. The signal processing in our method is as follows. 1) The spectrogram is normalised into greyscale with a fixed range. 2) The dynamic range is quantized into regions, each of which is then mapped to form a monochrome image. 3) The monochrome images are partitioned into blocks, and the distribution statistics in each block are extracted to form the feature. The robustness of the proposed method comes from the fact that the noise is normally more diffuse than the signal and therefore the effect of the noise is limited to a particular quantization region, leaving the other regions less changed. The method is tested on a database of 60 sound classes containing a mixture of collision, action and characteristic sounds and shows a significant improvement over other methods in mismatched conditions, without the need for noise reduction.

In vitro lung delivery of bacteriophages KS4-M and ΦKZ using dry powder inhalers for treatment of Burkholderia cepacia complex and Pseudomonas aeruginosa infections in cystic fibrosis.

Abstract: Aims: To determine the feasibility of formulating and aerosolizing powders containing bacteriophages KS4-M and ΦKZ for lung delivery and treatment of pulmonary Burkholderia cepacia complex and Pseudomonas aeruginosa infections. Methods and Results: Endotoxin-removed bacteriophages KS4-M and ΦKZ were lyophilized in lactose/lactoferrin 60 : 40 w/w matrix and deagglomerated in a mixer mill (without beads) to formulate respirable powders. The powders were then aerosolized using an Aerolizer® capsule inhaler. Mass median aerodynamic diameter (MMAD) of this inhalable aerosol was determined using Andersen cascade impactor at 60 l min−1. Measured MMAD for both types of powders was 3·4 μm, and geometric standard deviation was 1·9–2·0. Viability of bacteriophages delivered distal to an idealized mouth-throat replica was determined from bioassays of samples collected on filters placed after the idealized replica. As a percentage of inhaler load, amount of powder delivered distal to the mouth-throat replica, which is a measure of lung delivery, was 33·7 ± 0·3% for KS4-M and 32·7 ± 0·9% for ΦKZ. Titres collected downstream of the mouth throat were (3·4 ± 2·5) × 106 PFU for KS4-M with an Aerolizer capsule load of (9·8 ± 4·8) × 106 and (1·9 ± 0·6) × 107 for ΦKZ with an Aerolizer capsule load of (6·5 ± 1·9) × 107. Conclusions: Bacteriophages KS4-M and ΦKZ can be lyophilized without significant loss of viability in a lactose/lactoferrin 60 : 40 w/w matrix. The resulting powders can be aerosolized to deliver viable bacteriophages to the lungs. Significance and Impact of the Study: Development of lactoferrin-based bacteriophage aerosol powders solidifies the ground for future research on developing novel formulations as an alternative to inhaled antibiotic therapy in patients with cystic fibrosis.

An Antirepressor, SrpR, Is Involved in Transcriptional Regulation of the SrpABC Solvent Tolerance Efflux Pump of Pseudomonas putida S12

Abstract: Organic compounds exhibit various levels of toxicity toward living organisms based upon their ability to insert into biological membranes and disrupt normal membrane function The primary mechanism responsible for organic solvent tolerance in many bacteria is energy-dependent extrusion via efflux pumps One such bacterial strain, Pseudomonas putida S12, is known for its high tolerance to organic solvents as provided through the SrpABC resistance-nodulation-cell division (RND) family efflux pump To determine how two putative regulatory proteins (SrpR and SrpS, encoded directly upstream of the SrpABC structural genes) influence SrpABC efflux pump expression, we conducted transcriptional analysis, β-galactosidase fusion experiments, electrophoretic mobility shift assays, and pulldown analysis Together, the results of these experiments suggest that expression of the srpABC operon can be derepressed by two distinct but complementary mechanisms: direct inhibition of the SrpS repressor by organic solvents and binding of SrpS by its antirepressor SrpR

Image Representation of the Subband Power Distribution for Robust Sound Classification.

Abstract: This paper proposes a robust sound event classification method, based on a selective image feature driven from the novel subband power distribution (SPD), which represents the distribution of power over frequency components. This method is an extension of our previous work, which was motivated by the visual perception of the spectrogram to produce a robust feature for sound classification. Unlike the conventional spectrogram, the proposed SPD representation is invariant to timeshifting and therefore suitable for real scenarios where the detected sound clips are not always balanced. Furthermore, we develop a missing feature classification method, which automatically selects the sparse, representative areas of the signal from the noisy SPD image of the sound clip. The method is tested on a large database containing 50 sound classes, under four different noise environments, varying from clean to severe noise conditions. A significant improvement in performance was obtained in mismatched conditions, producing an average classification accuracy of 87.5% in the 0dB noise condition.