Molecular characterisation of six badnavirus species associated with leaf streak disease of banana in East Africa

Banana leaf streak disease, caused by several species of Banana streak virus (BSV), is widespread in East Africa. We surveyed for this disease in Uganda and Kenya, and used rolling-circle amplification (RCA) to detect the presence of BSV in banana. Six distinct badnavirus sequences, three from Uganda and three from Kenya, were amplified for which only partial sequences were previously available. The complete genomes were sequenced and characterised. The size and organisation of all six sequences was characteristic of other badnaviruses, including conserved functional domains present in the putative polyprotein encoded by open reading frame (ORF) 3. Based on nucleotide sequence analysis within the reverse transcriptase/ribonuclease H-coding region of open reading frame 3, we propose that these sequences be recognised as six new species and be designated as Banana streak UA virus, Banana streak UI virus, Banana streak UL virus, Banana streak UM virus, Banana streak CA virus and Banana streak IM virus. Using PCR and species-specific primers to test for the presence of integrated sequences, we demonstrated that sequences with high similarity to BSIMV only were present in several banana cultivars which had tested negative for episomal BSV sequences.

Application of data mining techniques in the prediction of coronary artery disease : use of anaesthesia time-series and patient risk factor data

The high morbidity and mortality associated with atherosclerotic coronary vascular disease (CVD) and its complications are being lessened by the increased knowledge of risk factors, effective preventative measures and proven therapeutic interventions. However, significant CVD morbidity remains and sudden cardiac death continues to be a presenting feature for some subsequently diagnosed with CVD. Coronary vascular disease is also the leading cause of anaesthesia related complications. Stress electrocardiography/exercise testing is predictive of 10 year risk of CVD events and the cardiovascular variables used to score this test are monitored peri-operatively. Similar physiological time-series datasets are being subjected to data mining methods for the prediction of medical diagnoses and outcomes. This study aims to find predictors of CVD using anaesthesia time-series data and patient risk factor data. Several pre-processing and predictive data mining methods are applied to this data. Physiological time-series data related to anaesthetic procedures are subjected to pre-processing methods for removal of outliers, calculation of moving averages as well as data summarisation and data abstraction methods. Feature selection methods of both wrapper and filter types are applied to derived physiological time-series variable sets alone and to the same variables combined with risk factor variables. The ability of these methods to identify subsets of highly correlated but non-redundant variables is assessed. The major dataset is derived from the entire anaesthesia population and subsets of this population are considered to be at increased anaesthesia risk based on their need for more intensive monitoring (invasive haemodynamic monitoring and additional ECG leads). Because of the unbalanced class distribution in the data, majority class under-sampling and Kappa statistic together with misclassification rate and area under the ROC curve (AUC) are used for evaluation of models generated using different prediction algorithms. The performance based on models derived from feature reduced datasets reveal the filter method, Cfs subset evaluation, to be most consistently effective although Consistency derived subsets tended to slightly increased accuracy but markedly increased complexity. The use of misclassification rate (MR) for model performance evaluation is influenced by class distribution. This could be eliminated by consideration of the AUC or Kappa statistic as well by evaluation of subsets with under-sampled majority class. The noise and outlier removal pre-processing methods produced models with MR ranging from 10.69 to 12.62 with the lowest value being for data from which both outliers and noise were removed (MR 10.69). For the raw time-series dataset, MR is 12.34. Feature selection results in reduction in MR to 9.8 to 10.16 with time segmented summary data (dataset F) MR being 9.8 and raw time-series summary data (dataset A) being 9.92. However, for all time-series only based datasets, the complexity is high. For most pre-processing methods, Cfs could identify a subset of correlated and non-redundant variables from the time-series alone datasets but models derived from these subsets are of one leaf only. MR values are consistent with class distribution in the subset folds evaluated in the n-cross validation method. For models based on Cfs selected time-series derived and risk factor (RF) variables, the MR ranges from 8.83 to 10.36 with dataset RF_A (raw time-series data and RF) being 8.85 and dataset RF_F (time segmented time-series variables and RF) being 9.09. The models based on counts of outliers and counts of data points outside normal range (Dataset RF_E) and derived variables based on time series transformed using Symbolic Aggregate Approximation (SAX) with associated time-series pattern cluster membership (Dataset RF_ G) perform the least well with MR of 10.25 and 10.36 respectively. For coronary vascular disease prediction, nearest neighbour (NNge) and the support vector machine based method, SMO, have the highest MR of 10.1 and 10.28 while logistic regression (LR) and the decision tree (DT) method, J48, have MR of 8.85 and 9.0 respectively. DT rules are most comprehensible and clinically relevant. The predictive accuracy increase achieved by addition of risk factor variables to time-series variable based models is significant. The addition of time-series derived variables to models based on risk factor variables alone is associated with a trend to improved performance. Data mining of feature reduced, anaesthesia time-series variables together with risk factor variables can produce compact and moderately accurate models able to predict coronary vascular disease. Decision tree analysis of time-series data combined with risk factor variables yields rules which are more accurate than models based on time-series data alone. The limited additional value provided by electrocardiographic variables when compared to use of risk factors alone is similar to recent suggestions that exercise electrocardiography (exECG) under standardised conditions has limited additional diagnostic value over risk factor analysis and symptom pattern. The effect of the pre-processing used in this study had limited effect when time-series variables and risk factor variables are used as model input. In the absence of risk factor input, the use of time-series variables after outlier removal and time series variables based on physiological variable values’ being outside the accepted normal range is associated with some improvement in model performance.

The Biology, Epidemiology, and Management of Rice Tungro Disease in Asia

Many farmers in South and Southeast Asia describe rice tungro disease as a cancer disease because of the severe damage it causes and the difficulty of controlling it (121). As the most important of the 14 rice viral diseases, tungro was first recognized as a leafhopper-transmitted virus disease in 1963 (88). However, tungro, which means “degenerated growth” in a Filipino dialect, has a much longer history. It is almost certain that tungro was responsible for a disease outbreak that occurred in 1859 in Indonesia, which was referred to at the time as mentek (83). In the past, a variety of names has been given to tungro, including accep na pula in the Philippines, penyakit merah in Malaysia, and yelloworange leaf in Thailand (83).

Evaluating Two Mass Screening Methods for Tungro Disease Resistance

Tungro is one of the most destructive viral diseases of rice in South and Southeast Asia. It is associated with two viruses---rice tungro bacilliform virus (RTBV) ,and rice tungro spherical virus (RTSV) (Hibino et al 1978). Both viruses are transmitted by the green leafhopper (GLH) Nephotettix virescens (Ling 1979), However, prior acquisition of RTSV is required for Ihe transmission of RTBV alone (Hibino 1983). Plants infected with both viruses show severe stunting and yellowing. Those infected with RTBV alone show mild stunting but no leaf discoloration whereas those infected with RTSV alone do not show any apparent symptoms (Hibino el al 1978). Since the late 1960s, tungro has been mainly managed through varietal resistance (Khush 1989). The instability of resistant varieties in the field (Dahal et .a1 1990) led to a reexamination of the nature of the incorporated sources of resistance and to the adoption of more precise and more accurate screening methods.

Synchrony of planting and proportions of susceptible varieties affect rice tungro disease epidemics in the Philippines.

Surveys were conducted in the Philippines from 1995 to 1997 to examine relationships between production environment variables (agroecosystem, synchrony of planting, and varieties planted) and the occurrence of rice tungro disease epidemics using correspondence analyses. The sites covered were Isabela, Nueva Ecija, North Cotabato, and Bohol provinces as well as Bicol region. Tungro disease incidence in farmers’ fields was assessed visually based on typical symptoms. In addition, leaf samples were collected from each field and indexed serologically by enzyme-linked immunosorbent assay for the presence of Rice tungro bacilliform (RTBV) and Rice tungro spherical (RTSV) viruses. Thus, relationships between the production environment variables and four disease variables — visual incidence and double RTBV and RTSV, single RTSV, and single RTBV infections — were examined. A higher association was observed between site and varieties planted as well as site and synchrony of planting than between site and agroecosystem or site and disease variables (visual incidence, double RTBV and RTSV and single RTSV infections). Disease variables depended on both varieties planted and synchrony of planting and correspondence analysis revealed that the low disease incidence in Nueva Ecija was associated with synchronous planting while the high disease incidence in Isabela was associated with the planting of susceptible varieties and asynchronous planting. Such findings suggest that the relationship between the last two factors at a given site is critical to predicting tungro occurrence. Moreover, correspondence analysis of the relationship among disease variables revealed that tungro incidence is associated with not only double RTBV and RTSV infections but also single RTSV infections. Implications of these results on tungro epidemiology and management are discussed.

Strategies for improved disease resistance in micro-propagated bananas

Bananas (Musa sp) are one of the most important food crops in the world and provide a staple food and source of income in many households especially in Africa. Diseases are a major constraint to production with bunchy top, caused by Banana bunchy top virus (BBTV) generally considered the most important virus disease of bananas worldwide. Of the fungal diseases, Fusarium wilt, caused by the Fusarium oxysporum f.sp cubense (Foc), and black Sigatoka, caused by Mycosphaerella fijiensis, are arguably two of the most important and cause significant yield losses. The low fertility of commercially important banana cultivars has hampered efforts to generate disease resistance using conventional breeding. Possible alternative strategies to generate or increase disease resistance are through genetic engineering or by manipulation of the innate plant defence mechanisms, namely systemic acquired resistance (SAR). The first research component of this thesis describes attempts to generate BBTV-resistant banana plants using a genetic modification approach. The second research component of the thesis focused on the identification of a potential marker gene associated with SAR in banana plants and a comparison of the expression levels of the marker gene in response to biotic and abiotic stresses, and chemical inducers. Previous research at QUT CTCB showed that replication of BBTV DNA components in banana embryogenic cell suspensions (ECS) was abolished following co-bombardment with 1.1mers of mutated BBTV DNA-R. BBTV DNA-R encodes the master replication protein (Rep) and is the only viral protein essential for BBTV replication. In this study, ECS of banana were stably transformed with the same constructs, each containing a different mutation in BBTV DNA-R, namely H41G, Y79F and K187M, to examine the effect on virus replication in stably transformed plants. Cells were also transformed with a construct containing a native BBTV Rep. A total of 16, 16, 11 and five lines of stably transformed banana plants containing the Y79F, H41G, K187M and native Rep constructs, respectively, were generated. Of these, up to nine replicates from Y79F lines, four H41G lines, seven K187M lines and three native Rep lines were inoculated with BBTV by exposure to viruliferous aphids in two separate experiments. At least one replicate from each of the nine Y79F lines developed typical bunchy top symptoms and all tested positive for BBTV using PCR. Of the four H41G lines tested, at least one replicate from three of the lines showed symptoms of bunchy top and tested positive using PCR. However, none of the five replicates of one H41G line (H41G-3) developed symptoms of bunchy top and none of the plants tested positive for BBTV using PCR. Of the seven K187M lines, at least one replicate of all lines except one (K187M-1) developed symptoms of bunchy top and tested positive for BBTV. Importantly, none of the four replicates of line K187M-1 showed symptoms or tested positive for BBTV. At least one replicate from each of the three native Rep lines developed symptoms and tested positive for BBTV. The H41G-3 and K187M-1 lines possibly represent the first transgenic banana plants generated using a mutated Rep strategy. The second research component of this thesis focused on the identification of SAR-associated genes in banana and their expression levels in response to biotic and abiotic stresses and chemical inducers. The impetus for this research was the observation that tissue-cultured (TC) banana plants were more susceptible to Fusarium wilt disease (and possibly bunchy top disease) than plants grown from field-derived suckers, possibly due to decreased levels of SAR gene expression in the former. In this study, the pathogenesis-related protein 1 (PR-1) gene was identified as a potential marker for SAR gene expression in banana. A quantitative real-time PCR assay was developed and optimised in order to determine the expression of PR-1, with polyubiquitin (Ubi-1) found to be the most suitable reference gene to enable relative quantification. The levels of PR-1 expression were subsequently compared in Lady Finger and Cavendish (cv. Williams) banana plants grown under three different environmental conditions, namely in the field, the glass house and in tissue-culture. PR-1 was shown to be expressed in both cultivars growing under different conditions. While PR-1 expression was highest in the field grown bananas and lowest in the TC bananas in Lady Finger cultivar, this was not the case in the Cavendish cultivar with glass house plants exhibiting the lowest PR-1 expression compared with tissue culture and field grown plants. The important outcomes of this work were the establishment of a qPCR-based assay to monitor PR-1 expression levels in banana and a preliminary assessment of the baseline PR-1 expression levels in two banana cultivars under three different growing conditions. After establishing the baseline PR-1 expression levels in Cavendish bananas, a study was done to determine whether PR-1 levels could be increased in these plants by exposure to known banana pathogens and non-pathogens, and a known chemical inducer of SAR. Cavendish banana plants were exposed to pathogenic Foc subtropical race 4 (FocSR4) and non-pathogenic Foc race 1 (Foc1), as well as two putative inducers of resistance, Fusarium lycopersici (Fol) and the chemical, acibenzolar-S-methyl (BION®). Tissue culture bananas were acclimatised under either glass house (TCS) or field (TCH) conditions and treatments were carried out in a randomised complete block design. PR-1 expression was determined using qPCR for both TCS and TCH samples for the period 12-72h post-exposure. Treatment of TCH plants using Foc1 and FocSR4 resulted in 120 and 80 times higher PR-1 expression than baseline levels, respectively. For TCS plants treated with Foc1, PR-1 expression was 30 times higher than baseline levels at 12h post-exposure, while TCS plants treated with FocSR4 showed the highest PR-1 expression (20 times higher than baseline levels) at 72h post-exposure. Interestingly, when TCS plants were treated with Fol there was a marked increase of PR-1 expression at 12 h and 48 h following treatment which was 4 and 8 times higher than the levels observed when TCS plants were treated with Foc1 and FocSR4, respectively. In contrast, when TCH plants were treated with Fol only a slight increase in PR-1 expression was observed at 12 h, which eventually returned to baseline levels. Exposure of both TCS and TCH plants to BION® resulted in no effect on PR-1 expression levels at any time-point. The major outcome of the SAR study was that the glass house acclimatised tissue culture bananas exhibited lower PR-1 gene expression compared to field acclimatised tissue culture plants and the identification of Fol as a good candidate for SAR induction in banana plants exhibiting low PR-1 levels. A number of outcomes that foster understanding of both pathogen-derived and plant innate resistance strategies in order to potentially improve banana resistance to diseases were explored in this study and include identification of potential inducers of systemic acquired resistance and a promising mutated Rep approach for BBTV resistance. The work presented in this thesis is the first report on the generation of potential BBTV resistant bananas using the mutated Rep approach. In addition, this is the first report on the status of SAR in banana grown under different conditions of exposure to the biotic and abiotic environment. Further, a robust qPCR assay for the study of gene expression using banana leaf samples was developed and a potential inducer of SAR in tissue culture bananas identified which could be harnessed to increase resistance in tissue culture bananas.

The effect of olive leaf extract on platelet function

Background Epidemiological studies have shown a reduced incidence of cardiovascular disease in the Mediterranean population attributed to the consumption of dietary olive oil rich in antioxidants. This has lead to increased interest in the antioxidant properties of other phenolic compounds of olive tree products. It has been suggested that olive leaf extract may also have health benefits due to its antioxidant and anti-inflammatory activities. Antioxidants can prevent the effects of oxidative metabolism by scavenging free radicals and decreasing the hyperactivity of platelets associated with the development of occlusive thrombosis. No studies to date have investigated the effects of olive leaf extract on platelet function to our knowledge. Improved understanding of the antioxidant properties of olive leaf extract and its effect on platelet function could lead to improved cardiovascular health. Objective The current study used an olive leaf extract prepared from the Olea europaea L. tree. The aim was to determine if polyphenols in olive leaf extract would reduce platelet activity and, to establish an optimal dose in vitro that would reduce platelet aggregation and ATP release. Design Eleven subjects with normal platelet counts (150–400 x 109/L) were recruited for the current in vitro study. Olive leaf extract was added to citrated whole blood to obtain five concentrations ranging from 5.4 ug/mL to 54.0 ug/mL for a dose response curve. Baseline samples, without olive leaf extract were used as a negative control for each subject. After 2 hours incubation with olive leaf extract samples were analyzed for platelet aggregation and ATP release from platelets stimulated by the addition of collagen. Results Whole blood analysis (n=11) showed a clear dose-dependant reduction in platelet aggregation with the increasing olive leaf extract concentrations (p<0.0001). There was also a similar decrease in ATP release from collagen stimulated platelets (p=0.02). Conclusion In the current study the olive leaf extract obtained from Olea europaea L. inhibited platelet aggregation and ATP release from collagen stimulated platelets in vitro. This study suggests olive leaf extract may prevent occlusive thrombosis by reducing platelet hyperactivity.

Carrot mottle mimic virus (CMoMV): A second umbravirus associated with carrot motley dwarf disease recognised by nucleic acid hybridisation

Carrot mottle umbravirus (CMoV) has always been found co-infecting plants with carrot red leaf luteovirus (CRLV) and in carrot (Daucus carota) these co-infections are associated with carrot motley dwarf disease (CMD). CMD occurs wherever carrots are grown. Hence, CMoV was believed to have a corresponding global distribution. However, little or no hybridisation was detected between cDNA generated from the sequenced Australian isolate of CMoV (CMoV-A) and RNA from the much studied Scottish isolate of CMoV (CMoV-S). A weak hybridisation signal was obtained using cDNA to a conserved part of the RNA-dependent RNA polymerase gene of CMoV-A, but when cDNAs to other parts of the CMoV-A genome were used as probes there was no detectable hybridisation with CMoV-S RNA. This lack of hybridisation suggests that the two virus isolates have relatively divergent genomes and that they should be regarded as distinct virus species. Both viruses are transmitted by Cavariella aegopodii, but only with the help of CRLV, and they yield almost identical double-stranded RNA profiles. For these reasons, we propose that the CMoV isolate from Australia be renamed carrot mottle mimic umbravirus (CMoMV). cDNA to CMoMV RNA hybridised with RNA from an isolate from New Zealand, whereas cDNA to CMoV-S RNA hybridised with RNA from isolates from England and Morocco but not to RNA from the isolate from New Zealand. Although preliminary, these data suggest that CMoV and CMoMV may have different global distributions.

Weather variability, tides, and Barmah Forest Virus Disease in the Gladstone region, Australia

In this study we examined the impact of weather variability and tides on the transmission of Barmah Forest virus (BFV) disease and developed a weather-based forecasting model for BFV disease in the Gladstone region, Australia. We used seasonal autoregressive integrated moving-average (SARIMA) models to determine the contribution of weather variables to BFV transmission after the time-series data of response and explanatory variables were made stationary through seasonal differencing. We obtained data on the monthly counts of BFV cases, weather variables (e.g., mean minimum and maximum temperature, total rainfall, and mean relative humidity), high and low tides, and the population size in the Gladstone region between January 1992 and December 2001 from the Queensland Department of Health, Australian Bureau of Meteorology, Queensland Department of Transport, and Australian Bureau of Statistics, respectively. The SARIMA model shows that the 5-month moving average of minimum temperature (β = 0.15, p-value < 0.001) was statistically significantly and positively associated with BFV disease, whereas high tide in the current month (β = −1.03, p-value = 0.04) was statistically significantly and inversely associated with it. However, no significant association was found for other variables. These results may be applied to forecast the occurrence of BFV disease and to use public health resources in BFV control and prevention.