Jonathan J. Dennis

Bio: Jonathan J. Dennis is an academic researcher from University of Alberta. The author has contributed to research in topics: Burkholderia cepacia complex & Phage therapy. The author has an hindex of 32, co-authored 82 publications receiving 4959 citations. Previous affiliations of Jonathan J. Dennis include Institute for Infocomm Research Singapore & National Institute for Nanotechnology.

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).

Plasposons : Modular self-cloning minitransposon derivatives for rapid genetic analysis of gram-negative bacterial genomes

Abstract: A series of modular mini-transposon derivatives which permit the rapid cloning and mapping of the DNA flanking the minitransposon's site of insertion has been developed. The basic plasposon, named TnMod, consists of the Tn5 inverted repeats, a conditional origin of replication, rare restriction endonuclease multiple cloning sites, and exchangeable antibiotic resistance cassettes. The broad host range and low target DNA sequence specificity of the Tn5 transposase, in combination with the flexibility afforded by the modular arrangement of TnMod, result in a versatile tool for the mapping of insertional mutations and the rapid recovery of clones from gram-negative bacteria.

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.

Development of Galleria mellonella as an Alternative Infection Model for the Burkholderia cepacia Complex

Abstract: Burkholderia is an important bacterial genus with a complex taxonomy that contains species of both ecological and pathogenic importance, including nine closely related species collectively termed the Burkholderia cepacia complex (BCC). In order to more thoroughly investigate the virulence of this bacterial complex of microorganisms, alternative infection models would be useful. To this end, we have adapted and developed the use of the Galleria mellonella wax moth larvae as a host for examining BCC infections. The experimental conditions affecting the BCC killing of the "wax worm" were optimized. BCC virulence levels were determined using 50% lethal doses, and differences were observed between both species and strains of the BCC. The BCC pathogenicity trends obtained compare favorably with results acquired using other published alternative infection models, as well as mammalian infection models. In addition, BCC killing activity was determined by directly measuring relative bacterial loads in three different BCC strains, thus demonstrating innate differences in BCC strain virulence. Finally, genetically mutated BCC strains were compared to a wild-type BCC strain in order to show concomitant reduction of BCC virulence and increased wax worm survival. For experimentation examining the virulent properties of the BCC, the wax worm has proven to be a useful alternative infection model.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

The Self-Organizing Map

Abstract: An overview of the self-organizing map algorithm, on which the papers in this issue are based, is presented in this article.

PHASTER: a better, faster version of the PHAST phage search tool

Abstract: PHASTER (PHAge Search Tool - Enhanced Release) is a significant upgrade to the popular PHAST web server for the rapid identification and annotation of prophage sequences within bacterial genomes and plasmids. Although the steps in the phage identification pipeline in PHASTER remain largely the same as in the original PHAST, numerous software improvements and significant hardware enhancements have now made PHASTER faster, more efficient, more visually appealing and much more user friendly. In particular, PHASTER is now 4.3× faster than PHAST when analyzing a typical bacterial genome. More specifically, software optimizations have made the backend of PHASTER 2.7X faster than PHAST, while the addition of 80 CPUs to the PHASTER compute cluster are responsible for the remaining speed-up. PHASTER can now process a typical bacterial genome in 3 min from the raw sequence alone, or in 1.5 min when given a pre-annotated GenBank file. A number of other optimizations have also been implemented, including automated algorithms to reduce the size and redundancy of PHASTER's databases, improvements in handling multiple (metagenomic) queries and higher user traffic, along with the ability to perform automated look-ups against 14 000 previously PHAST/PHASTER annotated bacterial genomes (which can lead to complete phage annotations in seconds as opposed to minutes). PHASTER's web interface has also been entirely rewritten. A new graphical genome browser has been added, gene/genome visualization tools have been improved, and the graphical interface is now more modern, robust and user-friendly. PHASTER is available online at www.phaster.ca.

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

Abstract: Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria

Abstract: Disease-suppressive soils are exceptional ecosystems in which crop plants suffer less from specific soil-borne pathogens than expected owing to the activities of other soil microorganisms. For most disease-suppressive soils, the microbes and mechanisms involved in pathogen control are unknown. By coupling PhyloChip-based metagenomics of the rhizosphere microbiome with culture-dependent functional analyses, we identified key bacterial taxa and genes involved in suppression of a fungal root pathogen. More than 33,000 bacterial and archaeal species were detected, with Proteobacteria, Firmicutes, and Actinobacteria consistently associated with disease suppression. Members of the γ-Proteobacteria were shown to have disease-suppressive activity governed by nonribosomal peptide synthetases. Our data indicate that upon attack by a fungal root pathogen, plants can exploit microbial consortia from soil for protection against infections.