Characterisation of the tritrophic interactions between tobacco yellow dwarf virus, its vector and host-plants

Tobacco yellow dwarf virus (TbYDV, family Geminiviridae, genus Mastrevirus) is an economically important pathogen causing summer death and yellow dwarf disease in bean (Phaseolus vulgaris L.) and tobacco (Nicotiana tabacum L.), respectively. Prior to the commencement of this project, little was known about the epidemiology of TbYDV, its vector and host-plant range. As a result, disease control strategies have been restricted to regular poorly timed insecticide applications which are largely ineffective, environmentally hazardous and expensive. In an effort to address this problem, this PhD project was carried out in order to better understand the epidemiology of TbYDV, to identify its host-plant and vectors as well as to characterise the population dynamics and feeding physiology of the main insect vector and other possible vectors. The host-plants and possible leafhopper vectors of TbYDV were assessed over three consecutive growing seasons at seven field sites in the Ovens Valley, Northeastern Victoria, in commercial tobacco and bean growing properties. Leafhoppers and plants were collected and tested for the presence of TbYDV by PCR. Using sweep nets, twenty-three leafhopper species were identified at the seven sites with Orosius orientalis the predominant leafhopper. Of the 23 leafhopper species screened for TbYDV, only Orosius orientalis and Anzygina zealandica tested positive. Forty-two different plant species were also identified at the seven sites and tested. Of these, TbYDV was only detected in four dicotyledonous species, Amaranthus retroflexus, Phaseolus vulgaris, Nicotiana tabacum and Raphanus raphanistrum. Using a quadrat survey, the temporal distribution and diversity of vegetation at four of the field sites was monitored in order to assess the presence of, and changes in, potential host-plants for the leafhopper vector(s) and the virus. These surveys showed that plant composition and the climatic conditions at each site were the major influences on vector numbers, virus presence and the subsequent occurrence of tobacco yellow dwarf and bean summer death diseases. Forty-two plant species were identified from all sites and it was found that sites with the lowest incidence of disease had the highest proportion of monocotyledonous plants that are non hosts for both vector and the virus. In contrast, the sites with the highest disease incidence had more host-plant species for both vector and virus, and experienced higher temperatures and less rainfall. It is likely that these climatic conditions forced the leafhopper to move into the irrigated commercial tobacco and bean crop resulting in disease. In an attempt to understand leafhopper species diversity and abundance, in and around the field borders of commercially grown tobacco crops, leafhoppers were collected from four field sites using three different sampling techniques, namely pan trap, sticky trap and sweep net. Over 51000 leafhopper samples were collected, which comprised 57 species from 11 subfamilies and 19 tribes. Twentythree leafhopper species were recorded for the first time in Victoria in addition to several economically important pest species of crops other than tobacco and bean. The highest number and greatest diversity of leafhoppers were collected in yellow pan traps follow by sticky trap and sweep nets. Orosius orientalis was found to be the most abundant leafhopper collected from all sites with greatest numbers of this leafhopper also caught using the yellow pan trap. Using the three sampling methods mentioned above, the seasonal distribution and population dynamics of O. orientalis was studied at four field sites over three successive growing seasons. The population dynamics of the leafhopper was characterised by trimodal peaks of activity, occurring in the spring and summer months. Although O. orientalis was present in large numbers early in the growing season (September-October), TbYDV was only detected in these leafhoppers between late November and the end of January. The peak in the detection of TbYDV in O. orientalis correlated with the observation of disease symptoms in tobacco and bean and was also associated with warmer temperatures and lower rainfall. To understand the feeding requirements of Orosius orientalis and to enable screening of potential control agents, a chemically-defined artificial diet (designated PT-07) and feeding system was developed. This novel diet formulation allowed survival for O. orientalis for up to 46 days including complete development from first instar through to adulthood. The effect of three selected plant derived proteins, cowpea trypsin inhibitor (CpTi), Galanthus nivalis agglutinin (GNA) and wheat germ agglutinin (WGA), on leafhopper survival and development was assessed. Both GNA and WGA were shown to reduce leafhopper survival and development significantly when incorporated at a 0.1% (w/v) concentration. In contrast, CpTi at the same concentration did not exhibit significant antimetabolic properties. Based on these results, GNA and WGA are potentially useful antimetabolic agents for expression in genetically modified crops to improve the management of O. orientalis, TbYDV and the other pathogens it vectors. Finally, an electrical penetration graph (EPG) was used to study the feeding behaviour of O. orientalis to provide insights into TbYDV acquisition and transmission. Waveforms representing different feeding activity were acquired by EPG from adult O. orientalis feeding on two plant species, Phaseolus vulgaris and Nicotiana tabacum and a simple sucrose-based artificial diet. Five waveforms (designated O1-O5) were observed when O. orientalis fed on P. vulgaris, while only four (O1-O4) and three (O1-O3) waveforms were observed during feeding on N. tabacum and the artificial diet, respectively. The mean duration of each waveform and the waveform type differed markedly depending on the food source. This is the first detailed study on the tritrophic interactions between TbYDV, its leafhopper vector, O. orientalis, and host-plants. The results of this research have provided important fundamental information which can be used to develop more effective control strategies not only for O. orientalis, but also for TbYDV and other pathogens vectored by the leafhopper.

Situation Review of Barley Yellow Dwarf Virus in West Asia and North Africa

Symptoms of barley yellow dwarf (BYD) have been observed on cereals in nearly all countries of West Asia and North Africa. Its incidence. however, has varied during the last 15 years. Observations from field surveys are summarized. Since symptoms of barley yellow dwarf virus (BYDV) are of low diagnostic value, especially in wheat (Triticum aestivum L.), more precise qualitative and quantitative detection was derived by vector transmission and serology. In 1985 and 1986. preliminary surveys by enzyme-linked immunosorbent assay (ELlS A) indicated that BYDV incidence in the regions surveyed in Syria, Morocco, and Tunisia was around 7. 22. and 24%. respectively. By vector transmission PAV-, RPV-, and RMV-like isolates ofBYDV were identified in Morocco and the PAV-like isolate in Syria. By serology PAV-like isolates were identified in Ethiopia, Lebanon. Morocco. Syria. and Tunisia. and MA V-like isolates were identified from Morocco and Tunisia. The PAV-like type was the most common in all countries surveyed. Screening for BYDV resistance by natural infection has been carried out in a number of countries of the region during the last few years. Screening for resistance by aphid inoculation was initiated in Syria in 1986 at the International Center for Agricultural Research in the Dry Areas (ICARDA). Such screening is expected to follow in other countries of the region soon.

Survey of Spring Oats for Barley Yellow Dwarf Viruses in Illinois

During the spring of 1987, 1,215 samples of spring oats (Avena sativa L.) were collected in Madison, Champaign, Woodford, Warren, and DeKalb counties, Illinois. At each site on each of three sampling dates, 45 samples were collected (regardless of symptoms) in a W pattern in I ha and tested for the PAY, MAV, RPV, and RMV serotypes of barley yellow dwarf virus (BYDV) by direct doubleantibody sandwich enzyme-linked immunosorbent assay (ELISA). RMV was not detected at any location. PAY and RPV were detected at all locations, as early as 17 April in Champaign County. The incidences of P A V and RPV from all plants sampled ranged from 2 to 64% and from 2 to 88%, respectively. Highest incidences of both strains were in May samples [rom Woodford County. MAV was detected in lower incidences (2-16%) only in samples from the central region of the state (Champaign, Woodford, and Warren counties). The presence of MA V serotypes was confirmed in triple-antibody sandwich ELISA with the MA V -specific MAFF2 monoclonal antibody from L. Torrance. In the last previous survey for BYDV in Illinois during 1967-1968 (1), about 75% of the isolates were PAY and about 20% were RPV; single isolates of RMV and MAV were found. Twenty years later, 55% were PAY, 39% were RPV, and 6% were MAV.

Concomitant or sequential administration of live attenuated Japanese encephalitis chimeric virus vaccine and yellow fever 17D vaccine : randomized double-blind phase II evaluation of safety and immunogenicity

A randomized, double-blind, study was conducted to evaluate the safety, tolerability and immunogenicity of a live attenuated Japanese encephalitis chimeric virus vaccine (JE-CV) co-administered with live attenuated yellow fever (YF) vaccine (YF-17D strain; Stamaril(®), Sanofi Pasteur) or administered successively. Participants (n = 108) were randomized to receive: YF followed by JE-CV 30 days later, JE followed by YF 30 days later, or the co-administration of JE and YF followed or preceded by placebo 30 days later or earlier. Placebo was used in a double-dummy fashion to ensure masking. Neutralizing antibody titers against JE-CV, YF-17D and selected wild-type JE virus strains was determined using a 50% serum-dilution plaque reduction neutralization test. Seroconversion was defined as the appearance of a neutralizing antibody titer above the assay cut-off post-immunization when not present pre-injection at day 0, or a least a four-fold rise in neutralizing antibody titer measured before the pre-injection day 0 and later post vaccination samples. There were no serious adverse events. Most adverse events (AEs) after JE vaccination were mild to moderate in intensity, and similar to those reported following YF vaccination. Seroconversion to JE-CV was 100% and 91% in the JE/YF and YF/JE sequential vaccination groups, respectively, compared with 96% in the co-administration group. All participants seroconverted to YF vaccine and retained neutralizing titers above the assay cut-off at month six. Neutralizing antibodies against JE vaccine were detected in 82-100% of participants at month six. These results suggest that both vaccines may be successfully co-administered simultaneously or 30 days apart.

Application of higher order statistics/spectra in biomedical signals : a review

For many decades correlation and power spectrum have been primary tools for digital signal processing applications in the biomedical area. The information contained in the power spectrum is essentially that of the autocorrelation sequence; which is sufficient for complete statistical descriptions of Gaussian signals of known means. However, there are practical situations where one needs to look beyond autocorrelation of a signal to extract information regarding deviation from Gaussianity and the presence of phase relations. Higher order spectra, also known as polyspectra, are spectral representations of higher order statistics, i.e. moments and cumulants of third order and beyond. HOS (higher order statistics or higher order spectra) can detect deviations from linearity, stationarity or Gaussianity in the signal. Most of the biomedical signals are non-linear, non-stationary and non-Gaussian in nature and therefore it can be more advantageous to analyze them with HOS compared to the use of second order correlations and power spectra. In this paper we have discussed the application of HOS for different bio-signals. HOS methods of analysis are explained using a typical heart rate variability (HRV) signal and applications to other signals are reviewed.

The Certainty of Yellow

Interview and short story published in Avid Reader Magazine.

Statistics of tricoherence

Statistics of the estimates of tricoherence are obtained analytically for nonlinear harmonic random processes with known true tricoherence. Expressions are presented for the bias, variance, and probability distributions of estimates of tricoherence as functions of the true tricoherence and the number of realizations averaged in the estimates. The expressions are applicable to arbitrary higher order coherence and arbitrary degree of interaction between modes. Theoretical results are compared with those obtained from numerical simulations of nonlinear harmonic random processes. Estimation of true values of tricoherence given observed values is also discussed

Implementation of ICD-11... perspectives from the Australian Bureau of Statistics

As the development of ICD-11 progresses, the Australian Bureau of Statistics is beginning to consider what will be required to successfully implement the new version of the classification. This paper will present early thoughts on the following: building understanding amongst the user community of upcoming changes and the implications of those changes; the need for training of coders and data users; development of analytical methods and conduct of comparability studies; processes to test, accept and implement new or updated coding software; assessment of coding quality; changes to data analyses and reporting processes; updates to regular publications; and assessing the resources required for successful implementation.

Understanding evaluation of learning support in mathematics and statistics

With rapid and continuing growth of learning support initiatives in mathematics and statistics found in many parts of the world, and with the likelihood that this trend will continue, there is a need to ensure that robust and coherent measures are in place to evaluate the effectiveness of these initiatives. The nature of learning support brings challenges for measurement and analysis of its effects. After briefly reviewing the purpose, rationale for, and extent of current provision, this article provides a framework for those working in learning support to think about how their efforts can be evaluated. It provides references and specific examples of how workers in this field are collecting, analysing and reporting their findings. The framework is used to structure evaluation in terms of usage of facilities, resources and services provided, and also in terms of improvements in performance of the students and staff who engage with them. Very recent developments have started to address the effects of learning support on the development of deeper approaches to learning, the affective domain and the development of communities of practice of both learners and teachers. This article intends to be a stimulus to those who work in mathematics and statistics support to gather even richer, more valuable, forms of data. It provides a 'toolkit' for those interested in evaluation of learning support and closes by referring to an on-line resource being developed to archive the growing body of evidence. © 2011 Taylor & Francis.

Phenomenography : “Follow the yellow brick road!”

Imagine that is you holding the glass, and the separate larger picture of the glass to the left, is how much wine is inside the glass you are holding. Now, first of all, no tricks, truthfully answer the following question...

Ingroup and role identity influences on the initiation and maintenance of students' voluntary attendance at peer study sessions for statistics

Background: Although class attendance is linked to academic performance, questions remain about what determines students’ decisions to attend or miss class. Aims: In addition to the constructs of a common decision-making model, the theory of planned behaviour, the present study examined the influence of student role identity and university student (in-group) identification for predicting both the initiation and maintenance of students’ attendance at voluntary peer-assisted study sessions in a statistics subject. Sample: University students enrolled in a statistics subject were invited to complete a questionnaire at two time points across the academic semester. A total of 79 university students completed questionnaires at the first data collection point, with 46 students completing the questionnaire at the second data collection point. Method: Twice during the semester, students’ attitudes, subjective norm, perceived behavioural control, student role identity, in-group identification, and intention to attend study sessions were assessed via on-line questionnaires. Objective measures of class attendance records for each half-semester (or ‘term’) were obtained. Results: Across both terms, students’ attitudes predicted their attendance intentions, with intentions predicting class attendance. Earlier in the semester, in addition to perceived behavioural control, both student role identity and in-group identification predicted students’ attendance intentions, with only role identity influencing intentions later in the semester. Conclusions: These findings highlight the possible chronology that different identity influences have in determining students’ initial and maintained attendance at voluntary sessions designed to facilitate their learning.

Implementing an enhanced repository statistics system for QUT ePrints

Queensland University of Technology (QUT) was one of the first universities in Australia to establish an institutional repository. Launched in November 2003, the repository (QUT ePrints) uses the EPrints open source repository software (from Southampton) and has enjoyed the benefit of an institutional deposit mandate since January 2004. Currently (April 2012), the repository holds over 36,000 records, including 17,909 open access publications with another 2,434 publications embargoed but with mediated access enabled via the ‘Request a copy’ button which is a feature of the EPrints software. At QUT, the repository is managed by the library.QUT ePrints (http://eprints.qut.edu.au) The repository is embedded into a number of other systems at QUT including the staff profile system and the University’s research information system. It has also been integrated into a number of critical processes related to Government reporting and research assessment. Internally, senior research administrators often look to the repository for information to assist with decision-making and planning. While some statistics could be drawn from the advanced search feature and the existing download statistics feature, they were rarely at the level of granularity or aggregation required. Getting the information from the ‘back end’ of the repository was very time-consuming for the Library staff. In 2011, the Library funded a project to enhance the range of statistics which would be available from the public interface of QUT ePrints. The repository team conducted a series of focus groups and individual interviews to identify and prioritise functionality requirements for a new statistics ‘dashboard’. The participants included a mix research administrators, early career researchers and senior researchers. The repository team identified a number of business criteria (eg extensible, support available, skills required etc) and then gave each a weighting. After considering all the known options available, five software packages (IRStats, ePrintsStats, AWStats, BIRT and Google Urchin/Analytics) were thoroughly evaluated against a list of 69 criteria to determine which would be most suitable. The evaluation revealed that IRStats was the best fit for our requirements. It was deemed capable of meeting 21 out of the 31 high priority criteria. Consequently, IRStats was implemented as the basis for QUT ePrints’ new statistics dashboards which were launched in Open Access Week, October 2011. Statistics dashboards are now available at four levels; whole-of-repository level, organisational unit level, individual author level and individual item level. The data available includes, cumulative total deposits, time series deposits, deposits by item type, % fulltexts, % open access, cumulative downloads, time series downloads, downloads by item type, author ranking, paper ranking (by downloads), downloader geographic location, domains, internal v external downloads, citation data (from Scopus and Web of Science), most popular search terms, non-search referring websites. The data is displayed in charts, maps and table format. The new statistics dashboards are a great success. Feedback received from staff and students has been very positive. Individual researchers have said that they have found the information to be very useful when compiling a track record. It is now very easy for senior administrators (including the Deputy Vice Chancellor-Research) to compare the full-text deposit rates (i.e. mandate compliance rates) across organisational units. This has led to increased ‘encouragement’ from Heads of School and Deans in relation to the provision of full-text versions.

Fusing loop detector and probe vehicle data to estimate travel time statistics on signalized urban networks

This article presents a methodology that integrates cumulative plots with probe vehicle data for estimation of travel time statistics (average, quartile) on urban networks. The integration reduces relative deviation among the cumulative plots so that the classical analytical procedure of defining the area between the plots as the total travel time can be applied. For quartile estimation, a slicing technique is proposed. The methodology is validated with real data from Lucerne, Switzerland and it is concluded that the travel time estimates from the proposed methodology are statistically equivalent to the observed values.