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Biomedical subjects

David Goode

Publications and source records attributed to David Goode.

6 recordsLinked to original sources
PubMed2004

ArrayPipe: a flexible processing pipeline for microarray data.

A number of microarray analysis software packages exist already; however, none combines the user-friendly features of a web-based interface with potential ability to analyse multiple arrays at once using flexible analysis steps. The ArrayPipe web server (freely available at www.pathogenomics.ca/arraypipe) allows the automated application of complex analyses to microarray data which can range from single slides to large data sets including replicates and dye-swaps. It handles output from most commonly used quantification software packages for dual-labelled arrays. Application features range from quality assessment of slides through various data visualizations to multi-step analyses including normalization, detection of differentially expressed genes, andcomparison and highlighting of gene lists. A highly customizable action set-up facilitates unrestricted arrangement of functions, which can be stored as action profiles. A unique combination of web-based and command-line functionality enables comfortable configuration of processes that can be repeatedly applied to large data sets in high throughput. The output consists of reports formatted as standard web pages and tab-delimited lists of calculated values that can be inserted into other analysis programs. Additional features, such as web-based spreadsheet functionality, auto-parallelization and password protection make this a powerful tool in microarray research for individuals and large groups alike.

Gene Expression Profiling↗
PubMed2004

Dissecting virulence: systematic and functional analyses of a pathogenicity island.

Bacterial pathogenicity islands (PAI) often encode both effector molecules responsible for disease and secretion systems that deliver these effectors to host cells. Human enterohemorrhagic Escherichia coli (EHEC), enteropathogenic E. coli, and the mouse pathogen Citrobacter rodentium (CR) possess the locus of enterocyte effacement (LEE) PAI. We systematically mutagenized all 41 CR LEE genes and functionally characterized these mutants in vitro and in a murine infection model. We identified 33 virulence factors, including two virulence regulators and a hierarchical switch for type III secretion. In addition, 7 potential type III effectors encoded outside the LEE were identified by using a proteomics approach. These non-LEE effectors are encoded by three uncharacterized PAIs in EHEC O157, suggesting that these PAIs act cooperatively with the LEE in pathogenesis. Our findings provide significant insights into bacterial virulence mechanisms and disease.

Animals↗
PubMed2004

Proteomic analysis of the intestinal epithelial cell response to enteropathogenic Escherichia coli.

We present the first large scale proteomic analysis of a human cellular response to a pathogen. Enteropathogenic Escherichia coli (EPEC) is an enteric human pathogen responsible for much childhood morbidity and mortality worldwide. EPEC uses a type III secretion system (TTSS) to inject bacterial proteins into the cytosol of intestinal epithelial cells, resulting in diarrhea. We analyzed the host response to TTSS-delivered EPEC effector proteins by infecting polarized intestinal epithelial monolayers with either wild-type or TTSS-deficient EPEC. Host proteins were isolated and subjected to quantitative profiling using isotope-coded affinity tagging (ICAT) combined with electrospray ionization tandem mass spectrometry. We identified over 2000 unique proteins from infected Caco-2 monolayers, of which approximately 13% are expressed differentially in the presence of TTSS-delivered EPEC effector proteins. We validated these data in silico and through immunoblotting and immunofluorescence microscopy. The identified changes extend cytoskeletal observations made in less relevant cell types and generate testable hypotheses with regard to host proteins potentially involved in EPEC-induced diarrhea. These data provide a framework for future biochemical analyses of host-pathogen interactions.

Biological Transport↗
PubMed2004

Identification and characterization of NleA, a non-LEE-encoded type III translocated virulence factor of enterohaemorrhagic Escherichia coli O157:H7.

Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 uses a specialized protein translocation apparatus, the type III secretion system (TTSS), to deliver bacterial effector proteins into host cells. These effectors interfere with host cytoskeletal pathways and signalling cascades to facilitate bacterial survival and replication and promote disease. The genes encoding the TTSS and all known type III secreted effectors in EHEC are localized in a single pathogenicity island on the bacterial chromosome known as the locus for enterocyte effacement (LEE). In this study, we performed a proteomic analysis of proteins secreted by the LEE-encoded TTSS of EHEC. In addition to known LEE-encoded type III secreted proteins, such as EspA, EspB and Tir, a novel protein, NleA (non-LEE-encoded effector A), was identified. NleA is encoded in a prophage-associated pathogenicity island within the EHEC genome, distinct from the LEE. The LEE-encoded TTSS directs translocation of NleA into host cells, where it localizes to the Golgi apparatus. In a panel of strains examined by Southern blot and database analyses, nleA was found to be present in all other LEE-containing pathogens examined, including enteropathogenic E. coli and Citrobacter rodentium, and was absent from non-pathogenic strains of E. coli and non-LEE-containing pathogens. NleA was determined to play a key role in virulence of C. rodentium in a mouse infection model.

Amino Acid Sequence↗
PubMed2003

Influence of axial length of normal eyes on PERG.

The influence of the axial length (AL) of the eye on flash electroretinogram (ERG) responses has been well established in the literature, suggesting an association between ERG abnormalities with myopia (AL > 25 mm). The aim of our present study was to determine whether the AL of normal eyes can also influence the pattern electroretinogram (PERG) on normal subjects. Thirty-nine normal volunteers were subjected to PERG measurements following the standard set by the International Society for Clinical Electrophysiology of Vision (ISCEV). The AL of the eyeball was measured using a TOMEY ultrasonic A scanner. Each volunteer had a complete ophthalmic examination including visual acuity, refraction, intraocular pressure, visual field, colour vision, orthoptic assessment and retinal photographs and had a best corrected visual acuity of 6/9 or better. Only one eye from each of the 39 normal volunteers was included in the statistical analysis of the results. The normal volunteer group had a mean P50 amplitude of 3.8 +/- 1.1 SD microV. The range of AL was between 21.8 and 25.7 mm (mean = 23.8 +/- 1.0 SD mm). Overall findings obtained from this investigation indicate a significant correlation between the AL of normal eyes and the PERG P50 amplitude (Spearman rank correlation coefficient r = -0.413, p < 0.01). The correlation accounts for 17% of the variance observed in the 39 amplitude values. This confirms the current hypothesis that the PERG amplitude is inversely related to axial length and means that AL should be considered when interpreting PERG amplitudes.

Adolescent↗