Papers by Grant E Daggard
Curation of Wheat Maps to Improve Map Accuracy and QTL Detection
Australian Journal of …, 2005
Three Australian doubled haploid populations were used to illustrate the importance of map curati... more Three Australian doubled haploid populations were used to illustrate the importance of map curation in order to improve the quality of linkage maps and quantative trait locus (QTL) detection. The maps were refined and improved by re-examining the order of markers, inspection of the genetic maps in relation to a consensus map, editing the marker data for double crossovers, and determining estimated recombination fractions for all pairs of markers. The re-ordering of markers and replacing genotypes at double crossovers with missing values resulted in an overall decrease in the length of the maps. Fewer apparent genotyping errors, associated with the presence of double recombinants, were identified with restriction fragment length polymorphisms (RFLPs) than with other types of markers used in this study. The complications that translocations may cause in the ordering of markers and subsequent QTL analysis were investigated. QTL analysis using both the original and revised maps indicated that QTL peaks were more sharply located or had improved log-likelihood (LOD) scores in the revised maps. An accurate indication of the QTL peak and a significant LOD score are both essential for the identification of markers suitable for marker-assisted selection. Recommendations are provided for the improvement of the quality of linkage maps.
A RAPD-PCR genotyping assay which correlates with serotypes of group B streptococci
Letters in Applied Microbiology, 2002
The purpose of this study was to determine if DNA polymorphisms generated by RAPD-PCR could be us... more The purpose of this study was to determine if DNA polymorphisms generated by RAPD-PCR could be used to characterize Group B streptococci (GBS) for epidemiological purposes. 30 unrelated, previously serotyped strains were analysed by RAPD-PCR using two 10-mer primers (5' TGCGAGAGTC 3' and 5' AGAGGGCACA 3'). Both primers generated DNA electropherotype patterns which, on analysis, clustered the isolates within their respective serotypes. A blind test of a further 3 field isolates also defined these strains within their subsequently determined serotypes. The detection of DNA polymorphisms between isolates within a serotype confirmed previous reports of the heterogenous nature of individual GBS serotypes. The RAPD-PCR is a potentially useful assay for the rapid characterization of neonatal infections associated with group B streptococci. The method appears to be more discriminatory than conventional serological assays. The RAPD-PCR assay is faster, more convenient and easier to perform than alternative DNA analytical procedures such as Pulsfield Gel Electrophoresis. We were able to reproduce the same results following re-testing of all isolates some 12 months later which suggests that the assay may be robust enough for use in routine epidemiological investigations.
Late-onset and Recurrent Neonatal Group B Streptococcal Disease Associated with Breast-milk Transmission
Pediatric and Developmental Pathology, 2003
The purpose of the study was to determine the epidemiological relationships in three unrelated ca... more The purpose of the study was to determine the epidemiological relationships in three unrelated cases of neonatal late-onset Group B streptococcal (GBS) disease and maternal breast-milk infection with GBS. All deliveries were by cesarean section; case 1 was at term, and cases 2 and 3 were at 32- and 33-wk gestation, respectively. Case 1 relates to a mother with clinical mastitis and recurrent GBS infection in a 20-day-old male infant. Following antibiotic therapy and cessation of breast-feeding, the infant recovered without sequelae. Case 2 refers to a mother with clinical mastitis and the occurrence of late-onset GBS disease in 5-wk-old male twins. Despite intervention, one infant died and the second became ill. Following antibiotic therapy and cessation of breast-feeding, the surviving infant recovered without sequelae. Case 3 refers to a mother with sub-clinical mastitis and late-onset GBS infection occurring in a 6-day-old female twin. Following intervention, the infant recovered but suffered a bilateral thalamic infarction resulting in developmental delay and a severe seizure disorder. Following recovery of GBS from an inapparent mastitis and cessation of breast-feeding, the second infant remained well. Blood cultures from all affected infants and maternal breast milk were positive for GBS. Epidemiological relationships between neonatal- and maternal-derived GBS isolates were confirmed by a random amplified polymorphic DNA polymerase chain reaction assay (RAPD-PCR). This study is significant in that it has demonstrated that maternal milk (in cases of either clinical or sub-clinical mastitis) can be a potential source of infection resulting in either late-onset or recurrent neonatal GBS disease.
In response to the rapid development of DNA Microarray technology, many classification methods ha... more In response to the rapid development of DNA Microarray technology, many classification methods have been used for Microarray classification. SVMs, decision trees, Bagging, Boosting and Random Forest are commonly used methods. In this paper, we conduct experimental comparison of LibSVMs, C4.5, BaggingC4.5, AdaBoostingC4.5, and Random Forest on seven Microarray cancer data sets. The experimental results show that all ensemble methods outperform C4.5. The experimental results also show that all five methods benefit from data preprocessing, including gene selection and discretization, in classification accuracy. In addition to comparing the average accuracies of ten-fold cross validation tests on seven data sets, we use two statistical tests to validate findings. We observe that Wilcoxon signed rank test is better than sign test for such purpose.
In this paper we propose a clustering algorithm called s-Cluster for analysis of gene expression ... more In this paper we propose a clustering algorithm called s-Cluster for analysis of gene expression data based on pattern-similarity. The algorithm captures the tight clusters exhibiting strong similar expression patterns in Microarray data,and allows a high level of overlap among discovered clusters without completely grouping all genes like other algorithms. This reflects the biological fact that not all functions are turned on in an experiment, and that many genes are co-expressed in multiple groups in response to different stimuli. The experiments have demonstrated that the proposed algorithm successfully groups the genes with strong similar expression patterns and that the found clusters are interpretable.
We investigate the idea of using diversified multiple trees for Microarray data classification. W... more We investigate the idea of using diversified multiple trees for Microarray data classification. We propose an algorithm of Maximally Diversified Multiple Trees (MDMT), which makes use of a set of unique trees in the decision committee. We compare MDMT with some well-known ensemble methods, namely Ad-aBoost, Bagging, and Random Forests. We also compare MDMT with a diversified decision tree algorithm, Cascading and Sharing trees (CS4), which forms the decision committee by using a set of trees with distinct roots. Based on seven Microarray data sets, both MDMT and CS4 are more accurate on average than AdaBoost, Bagging, and Random Forests. Based on a sign test of 95% confidence, both MDMT and CS4 perform better than majority traditional ensemble methods tested. We discuss differences between MDMT and CS4.
In recent years, the rapid development of DNA Microarray technology has made it possible for scie... more In recent years, the rapid development of DNA Microarray technology has made it possible for scientists to monitor the expression level of thousands of genes in a single experiment. As a new technology, Microarray data presents some fresh challenges to scientists since Microarray data contains a large number of genes (around tens thousands) with a small number of samples (around hundreds). Both filter and wrapper gene selection methods aim to select the most informative genes among the massive data in order to reduce the size of the expression database. Gene selection methods are used in both data preprocessing and classification stages. We have conducted some experiments on different existing gene selection methods to preprocess Microarray data for classification by benchmark algorithms SVMs and C4.5. The study suggests that the combination of filter and wrapper methods in general improve the accuracy performance of gene expression Microarray data classification. The study also indicates that not all filter gene selection methods help improve the performance of classification. The experimental results show that among tested gene selection methods, Correlation Coefficient is the best gene selection method for improving the classification accuracy on both SVMs and C4.5 classification algorithms.
Robustness analysis of diversified ensemble decision tree algorithms for Microarray data classification
Ensemble classification methods have shown promise for achieving higher classification accuracy f... more Ensemble classification methods have shown promise for achieving higher classification accuracy for microarray data classification analysis. As noise values do exist in all microarray data even after microarray data preprocessing stage, robustness is therefore another very important criteria in addition to accuracy for evaluating reliable microarray classification algorithms. In this paper, we conduct experimental comparison of our newly developed MDMT with C4.5, BaggingC4.5, Ad-aBoostingC4.5, Random Forest and CS4 on four microarray cancer data sets. We test and evaluate how well a given single or ensemble classifier can tolerate noise data in unseen test datasets, particularly with increasing levels of noise. The experimental results show that MDMT tolerates the noise values in unseen test data sets better than other compared methods do, particularly with increasing levels of noise data. We observe that a random forests is comparable to MDMT in term of resistance to noise. The experimental results also show that ensemble decision tree methods tolerate the noise values better than single tree C4.5 does. We conclude that avoiding overlapping genes exist among the ensemble trees is an intuitive, simple and effective way to achieve higher degree of diversity for ensemble decision tree methods. The algorithm based on this principal is more reliable to deal with microarray data sets with certain level of noise data.
No standardized PCR method is available for the laboratory diagnosis of the pertussis syndrome. C... more No standardized PCR method is available for the laboratory diagnosis of the pertussis syndrome. Consensus recommendations for the use of PCR in the diagnosis of Bordetella pertussis infections have been proposed, and the aim of this study was to develop a method that fulfills all of these criteria. A rapid-cycle shared-primer PCR method with a microwell format and probe hybridization detection step (POR) was developed using novel oligonucleotides targeted to the outer membrane porin gene (Bordetella spp.). In specimens positive for Bordetella spp., B. pertussis was differentiated from Bordetella parapertussis and Bordetella bronchiseptica by hybridization with organism-specific oligonucleotide probes. An internal control was developed using overlap extension PCR and mouse -actin DNA. The analytical specificity was 100%. The analytical sensitivity was comparable to that of nested IS481 and IS1001 PCR (ϳ1 organism per reaction). The clinical sensitivity and specificity were ascertained using 705 specimens (from 705 patients). The results were compared to those of a nested-PCR method targeting the insertion sequences IS481 and IS1001. Fifty-one specimens were positive for B. pertussis by POR and IS481 PCR. Two specimens which fulfilled a clinical definition of pertussis were positive by POR and negative by IS481 PCR. A total of 652 specimens were negative by both methods. B. parapertussis was not detected in any specimens. PCR inhibition was detected in 21 out of 705 specimens (2.98%). Thus, a rapid (4 h, including specimen preparation) PCR method which fulfills all of the consensus recommendations was developed and validated for the detection of B. pertussis.
Journal of Medical Microbiology, 2006
The immunogenicity of P97 adhesin repeat region R1 (P97R1) of Mycoplasma hyopneumoniae, an import... more The immunogenicity of P97 adhesin repeat region R1 (P97R1) of Mycoplasma hyopneumoniae, an important pathogenesis-associated region of P97, was evaluated in mice as a mucosal vaccine. Mice were immunized orally with attenuated Salmonella typhimurium aroA strain CS332 harbouring a eukaryotic or prokaryotic expression vector encoding P97R1. Local and systemic immune responses were analysed by ELISA on mouse sera, lung washes and splenocyte supernatants following splenocyte stimulation with specific antigens in vitro. Although no P97R1-specific antibody responses were detected in serum and lung washes, significant gamma interferon was produced by P97R1-stimulated splenocytes from mice immunized orally with S. typhimurium aroA harbouring either expression system, indicating induction of a cell-mediated immune response. These results suggested that live bacterial vectors carrying DNA vaccines or expressing heterologous antigens preferentially induce a Th1 response. Surprisingly, however, mice immunized with the vaccine carrier S. typhimurium aroA CS332 induced serum IgG, but not mucosal IgA, against P97R1 or S. typhimurium aroA CS332 whole-cell lysate, emphasizing the importance of assessing the suitability of attenuated S. typhimurium antigen-carrier delivery vectors in the mouse model prior to their evaluation as potential vaccines in the target species, which in this instance was pigs.
Journal of Medical Microbiology, 2008
The immunogenicity and protective efficacy of a DNA vaccine encoding a genetically inactivated S1... more The immunogenicity and protective efficacy of a DNA vaccine encoding a genetically inactivated S1 domain of pertussis toxin was evaluated using a murine respiratory challenge model of Bordetella pertussis infection. It was found that mice immunized via the intramuscular route elicited a purely cell-mediated immune response to the DNA vaccine, with high levels of gamma interferon (IFN-c) and interleukin (IL)-2 detected in the S1-stimulated splenocyte supernatants and no serum IgG. Despite the lack of an antibody response, the lungs of DNA-immunized mice were cleared of B. pertussis at a significantly faster rate compared with mock-immunized mice following an aerosol challenge. To gauge the true potential of this S1 DNA vaccine, the immune response and protective efficacy of the commercial diphtheria-tetanus-acellular pertussis (DTaP) vaccine were included as the gold standard. Immunization with DTaP elicited a typically strong T-helper (Th)2-polarized immune response with significantly higher titres of serum IgG than in the DNA vaccine group, but a relatively weak Th1 response with low levels of IFN-c and IL-2 detected in the supernatants of antigen-stimulated splenocytes. DTaP-immunized mice cleared the aerosol challenge more efficiently than DNA-immunized mice, with no detectable pathogen after day 7 post-challenge.
Journal of Cereal Science, 2007
A wheat_maize induced doubled haploid population that segregates at the Awned locus for awned and... more A wheat_maize induced doubled haploid population that segregates at the Awned locus for awned and awnless phenotypes were studied at two field sites using a genetic linkage map. Interval QTL analysis indicated that significant QTLs for wheat flour water absorption and protein content were located on a linkage group associated with the morphological marker, awns. The QTL peak for flour water absorption was located at the Awned locus (B1, 5AL), whilst the QTL peak for protein content was located nearby, 10.1 cm away from the Awned locus. The locations of those QTL were confirmed by analysing data from two independent field trials conducted under different environment conditions. The QTL identified for water absorption controlled 12% and 11% of the observed variance at the two field trials, whilst for flour protein content the QTL explained 7% and 19% of the variance respectively. Variance component analysis indicated that the QTL for water absorption controlled approximately 14.8-25.0% and 13.6-23% of the genetic variance at the two sites studied (Roma and imbour) whilst the QTL for protein content explained between 12.8% and 30.4% of the genetic variance at Roma and 34.7-82.6% at Jimbour. Cross-site analysis with composite interval mapping approach resulted in significant LOD values of 6.12 and 9.94 for water absorption and protein content, respectively. The QTL for water absorption was independent from the hardness locus.
Journal of Chemical Ecology, 2001
A screening was conducted to study the allelopathic potential of Australian-held accessions of Tr... more A screening was conducted to study the allelopathic potential of Australian-held accessions of Triticum speltoides. Of 26 accessions, four were found to inhibit root growth in the indicator species, lettuce (Lactuca sativa). The methanol leaf extracts of these accessions significantly reduced the root length of wild oat (Avena spp.). In all but one case, alellopathic accessions contained higher amounts of DIMBOA than did nonallelopathic accessions. Since some variation in allelopathic response was detected within lines, random amplified polymorphic DNA (RAPD) markers were used to estimate genetic diversity between and within the allelopathic accessions of Triticum speltoides L. The average genetic similarity between all possible pairs of selected accessions was found to be 55% and ranged from 44% to 88%. Comparison of DNA extracted from different single seedlings within the same accession revealed significant intraaccession genetic diversity (4–24%), although this was much less than that observed between accessions tested. This intraaccession diversity has significant implications for the selection of T. speltoides accessions in breeding or screening programs.
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Papers by Grant E Daggard