Viruses of banana in East Africa

Bananas are one of the world's most important food crops, providing sustenance and income for millions of people in developing countries and supporting large export industries. Viruses are considered major constraints to banana production, germplasm multiplication and exchange, and to genetic improvement of banana through traditional breeding. In Africa, the two most important virus diseases are bunchy top, caused by Banana bunchy top virus (BBTV), and banana streak disease, caused by Banana streak virus (BSV). BBTV is a serious production constraint in a number of countries within/bordering East Africa, such as Burundi, Democratic Republic of Congo, Malawi, Mozambique, Rwanda and Zambia, but is not present in Kenya, Tanzania and Uganda. Additionally, epidemics of banana streak disease are occurring in Kenya and Uganda. The rapidly growing tissue culture (TC) industry within East Africa, aiming to provide planting material to banana farmers, has stimulated discussion about the need for virus indexing to certify planting material as virus-free. Diagnostic methods for BBTV and BSV have been reported and, for BBTV, PCR-based assays are reliable and relatively straightforward. However for BSV, high levels of serological and genetic variability and the presence of endogenous virus sequences within the banana genome complicate diagnosis. Uganda has been shown to contain the greatest diversity in BSV isolates found anywhere in the world. A broad-spectrum diagnostic test for BSV detection, which can discriminate between endogenous and episomal BSV sequences, is a priority. This PhD project aimed to establish diagnostic methods for banana viruses, with a particular focus on the development of novel methods for BSV detection, and to use these diagnostic methods for the detection and characterisation of banana viruses in East Africa. A novel rolling-circle amplification (RCA) method was developed for the detection of BSV. Using samples of Banana streak MY virus (BSMYV) and Banana streak OL virus (BSOLV) from Australia, this method was shown to distinguish between endogenous and episomal BSV sequences in banana plants. The RCA assay was used to screen a collection of 56 banana samples from south-west Uganda for BSV. RCA detected at least five distinct BSV isolates in these samples, including BSOLV and Banana streak GF virus (BSGFV) as well as three BSV isolates (Banana streak Uganda-I, -L and -M virus) for which only partial sequences had been previously reported. These latter three BSV had only been detected using immuno-capture (IC)-PCR and thus were possible endogenous sequences. In addition to its ability to detect BSV, the RCA protocol was also demonstrated to detect other viruses within the family Caulimoviridae, including Sugar cane bacilliform virus, and Cauliflower mosaic virus. Using the novel RCA method, three distinct BSV isolates from both Kenya and Uganda were identified and characterised. The complete genome of these isolates was sequenced and annotated. All six isolates were shown to have a characteristic badnavirus genome organisation with three open reading frames (ORFs) and the large polyprotein encoded by ORF 3 was shown to contain conserved amino acid motifs for movement, aspartic protease, reverse transcriptase and ribonuclease H activities. As well, several sequences important for expression and replication of the virus genome were identified including the conserved tRNAmet primer binding site present in the intergenic region of all badnaviruses. Based on the International Committee on Taxonomy of Viruses (ICTV) guidelines for species demarcation in the genus Badnavirus, these six isolates were proposed as distinct species, and named Banana streak UA virus (BSUAV), Banana streak UI virus (BSUIV), Banana streak UL virus (BSULV), Banana streak UM virus (BSUMV), Banana streak CA virus (BSCAV) and Banana streak IM virus (BSIMV). Using PCR with species-specific primers designed to each isolate, a genotypically diverse collection of 12 virus-free banana cultivars were tested for the presence of endogenous sequences. For five of the BSV no amplification was observed in any cultivar tested, while for BSIMV, four positive samples were identified in cultivars with a B-genome component. During field visits to Kenya, Tanzania and Uganda, 143 samples were collected and assayed for BSV. PCR using nine sets of species-specific primers, and RCA, were compared for BSV detection. For five BSV species with no known endogenous counterpart (namely BSCAV, BSUAV, BSUIV, BSULV and BSUMV), PCR was used to detect 30 infections from the 143 samples. Using RCA, 96.4% of these samples were considered positive, with one additional sample detected using RCA which was not positive using PCR. For these five BSV, PCR and RCA were both useful for identifying infected samples, irrespective of the host cultivar genotype (Musa A- or B-genome components). For four additional BSV with known endogenous counterparts in the M. balbisiana genome (BSOLV, BSGFV, BSMYV and BSIMV), PCR was shown to detect 75 infections from the 143 samples. In 30 samples from cultivars with an A-only genome component there was 96.3% agreement between PCR positive samples and detection using RCA, again demonstrating either PCR or RCA are suitable methods for detection. However, in 45 samples from cultivars with some B-genome component, the level of agreement between PCR positive samples and RCA positive samples was 70.5%. This suggests that, in cultivars with some B-genome component, many infections were detected using PCR which were the result of amplification of endogenous sequences. In these latter cases, RCA or another method which discriminates between endogenous and episomal sequences, such as immuno-capture PCR, is needed to diagnose episomal BSV infection. Field visits were made to Malawi and Rwanda to collect local isolates of BBTV for validation of a PCR-based diagnostic assay. The presence of BBTV in samples of bananas with bunchy top disease was confirmed in 28 out of 39 samples from Malawi and all nine samples collected in Rwanda, using PCR and RCA. For three isolates, one from Malawi and two from Rwanda, the complete nucleotide sequences were determined and shown to have a similar genome organisation to previously published BBTV isolates. The two isolates from Rwanda had at least 98.1% nucleotide sequence identity between each of the six DNA components, while the similarity between isolates from Rwanda and Malawi was between 96.2% and 99.4% depending on the DNA component. At the amino acid level, similarities in the putative proteins encoded by DNA-R, -S, -M, - C and -N were found to range between 98.8% to 100%. In a phylogenetic analysis, the three East African isolates clustered together within the South Pacific subgroup of BBTV isolates. Nucleotide sequence comparison to isolates of BBTV from outside Africa identified India as the possible origin of East African isolates of BBTV.

Molecular phylogeny supports the paraphyletic nature of the genus Trogoderma (Coleoptera: Dermestidae) collected in the Australasian ecozone

To date, a molecular phylogenetic approach has not been used to investigate the evolutionary structure of Trogoderma and closely related genera. Using two mitochondrial genes, Cytochrome Oxidase I and Cytochrome B, and the nuclear gene, 18S, the reported polyphyletic positioning of Trogoderma was examined. Paraphyly in Trogoderma was observed, with one Australian Trogoderma species reconciled as sister to all Dermestidae and the Anthrenocerus genus deeply nested within the Australian Trogoderma clade. In addition, time to most recent common ancestor for a number of Dermestidae was calculated. Based on these estimations, the Dermestidae origin exceeded 175 million years, placing the origins of this family in Pangaea.

Influence of medium range transport of particles from nucleation burst on particle number concentration within the urban airshed

An elevated particle number concentration (PNC) observed during nucleation events could play a significant contribution to the total particle load and therefore to the air pollution in the urban environments. Therefore, a field measurement study of PNC was commenced to investigate the temporal and spatial variations of PNC within the urban airshed of Brisbane, Australia. PNC was monitored at urban (QUT), roadside (WOO) and semi-urban (ROC) areas around the Brisbane region during 2009. During the morning traffic peak period, the highest relative fraction of PNC reached about 5% at QUT and WOO on weekdays. PNC peaks were observed around noon, which correlated with the highest solar radiation levels at all three stations, thus suggesting that high PNC levels were likely to be associated with new particle formation caused by photochemical reactions. Wind rose plots showed relatively higher PNC for the NE direction, which was associated with industrial pollution, accounting for 12%, 9% and 14% of overall PNC at QUT, WOO and ROC, respectively. Although there was no significant correlation between PNC at each station, the variation of PNC was well correlated among three stations during regional nucleation events. In addition, PNC at ROC was significantly influenced by upwind urban pollution during the nucleation burst events, with the average enrichment factor of 15.4. This study provides an insight into the influence of regional nucleation events on PNC in the Brisbane region and it the first study to quantify the effect of urban pollution on semi-urban PNC through the nucleation events. © 2012 Author(s).

Effects of cultivar on rodent damage in Australian macadamia orchards

The Black rat (Rattus rattus), a serious pest of Australian macadamia orchards has been estimated to cause up to 30% crop damage in Australian orchards. In recent years an increase in the number of commercially available cultivars has seen a change in orchard characteristics in Australia, primarily effecting fruiting and flowering patterns. This has been suggested to affect the feeding behaviour of rodents and in turn altered the damage process. In this study we compare the extent of damage in orchards containing one of three prevalent cultivars (A4/A16, A268 and HAES 344/741) and investigate the influence of these cultivars, particularly their distinctive fruiting traits, on rodent damage within the orchard. We demonstrate that the temporal pattern and extent of damage differs between cultivar types. Newer Australian macadamia cultivars tested in this study were found to be far more susceptible to rodent damage than the older Hawaiian developed cultivars, most likely due to an extended fruiting period and thinner shells. This has resulted in a more sustained period of crop damage than the patterns of crop damage observed in previous Australian studies. Crop damage caused by R. rattus is significantly higher in orchards that maintain high levels of canopy resources through the fruiting season and we postulate that this is due to the extended fruiting periods of the new cultivars used. The maintenance of canopy resource load in turn corresponds to high crop damage, in this study resulting in crop losses of up to 25%.

Prandtl number scaling of the unsteady natural convection boundary layer adjacent to a vertical flat plate for Pr > 1 subject to ramp surface heat flux

It is found in the literature that the existing scaling results for the boundary layer thickness, velocity and steady state time for the natural convection flow over an evenly heated plate provide a very poor prediction of the Prandtl number dependency of the flow. However, those scalings provide a good prediction of two other governing parameters’ dependency, the Rayleigh number and the aspect ratio. Therefore, an improved scaling analysis using a triple-layer integral approach and direct numerical simulations have been performed for the natural convection boundary layer along a semi-infinite flat plate with uniform surface heat flux. This heat flux is a ramp function of time, where the temperature gradient on the surface increases with time up to some specific time and then remains constant. The growth of the boundary layer strongly depends on the ramp time. If the ramp time is sufficiently long, the boundary layer reaches a quasi steady mode before the growth of the temperature gradient is completed. In this mode, the thermal boundary layer at first grows in thickness and then contracts with increasing time. However, if the ramp time is sufficiently short, the boundary layer develops differently, but after the wall temperature gradient growth is completed, the boundary layer develops as though the startup had been instantaneous.

Practical client puzzles in the standard model

Client puzzles are cryptographic problems that are neither easy nor hard to solve. Most puzzles are based on either number theoretic or hash inversions problems. Hash-based puzzles are very efficient but so far have been shown secure only in the random oracle model; number theoretic puzzles, while secure in the standard model, tend to be inefficient. In this paper, we solve the problem of constucting cryptographic puzzles that are secure int he standard model and are very efficient. We present an efficient number theoretic puzzle that satisfies the puzzle security definition of Chen et al. (ASIACRYPT 2009). To prove the security of our puzzle, we introduce a new variant of the interval discrete logarithm assumption which may be of independent interest, and show this new problem to be hard under reasonable assumptions. Our experimental results show that, for 512-bit modulus, the solution verification time of our proposed puzzle can be up to 50x and 89x faster than the Karame-Capkum puzzle and the Rivest et al.'s time-lock puzzle respectively. In particular, the solution verification tiem of our puzzle is only 1.4x slower than that of Chen et al.'s efficient hash based puzzle.

Australian Learning and Teaching Council, Learning and Teaching Academic Standards Statement for Architecture

The development of the Learning and Teaching Academic Standards Statement for Architecture (the Statement) centred on requirements for the Master of Architecture and proceeded alongside similar developments in the building and construction discipline under the guidance and support of the Australian Deans of Built Environment and Design (ADBED). Through their representation of Australian architecture programs, ADBED have provided high-level leadership for the Learning and Teaching Academic Standards Project in Architecture (LTAS Architecture). The threshold learning outcomes (TLOs), the description of the nature and extent of the discipline, and accompanying notes were developed through wide consultation with the discipline and profession nationally. They have been considered and debated by ADBED on a number of occasions and have, in their fi nal form, been strongly endorsed by the Deans. ADBED formed the core of the Architecture Reference Group (chaired by an ADBED member) that drew together representatives of every peak organisation for the profession and discipline in Australia. The views of the architectural education community and profession have been provided both through individual submissions and the voices of a number of peak bodies. Over two hundred individuals from the practising profession, the academic workforce and the student cohort have worked together to build consensus about the capabilities expected of a graduate of an Australian Master of Architecture degree. It was critical from the outset that the Statement should embrace the wisdom of the greater ‘tribe’, should ensure that graduates of the Australian Master of Architecture were eligible for professional registration and, at the same time, should allow for scope and diversity in the shape of Australian architectural education. A consultation strategy adopted by the Discipline Scholar involved meetings and workshops in Perth, Melbourne, Sydney, Canberra and Brisbane. Stakeholders from all jurisdictions and most universities participated in the early phases of consultation through a series of workshops that concluded late in October 2010. The Draft Architecture Standards Statement was formed from these early meetings and consultation in respect of that document continued through early 2011. This publication represents the outcomes of work to establish an agreed standards statement for the Master of Architecture. Significant further work remains to ensure the alignment of professional accreditation and recognition procedures with emerging regulatory frameworks cascading from the establishment of the Tertiary Education Quality and Standards Agency (TEQSA). The Australian architecture community hopes that mechanisms can be found to integrate TEQSA’s quality assurance purpose with well-established and understood systems of professional accreditation to ensure the good standing of Australian architectural education into the future. The work to build renewed and integrated quality assurance processes and to foster the interests of this project will continue, for at least the next eighteen months, under the auspices of Australian Learning and Teaching Council (ALTC)-funded Architecture Discipline Network (ADN), led by ADBED and Queensland University of Technology. The Discipline Scholar gratefully acknowledges the generous contributions given by those in stakeholder communities to the formulation of the Statement. Professional and academic colleagues have travelled and gathered to shape the Standards Statement. Debate has been vigorous and spirited and the Statement is rich with the purpose, critical thinking and good judgement of the Australian architectural education community. The commitments made to the processes that have produced this Statement reflect a deep and abiding interest by the constituency in architectural education. This commitment bodes well for the vibrancy and productivity of the emergent Architecture Discipline Network (ADN). Endorsement, in writing, was received from the Australian Institute of Architects National Education Committee (AIA NEC): The National Education Committee (NEC) of the Australian Institute of Architects thank you for your work thus far in developing the Learning and Teaching Academic Standards for Architecture In particular, we acknowledge your close consultation with the NEC on the project along with a comprehensive cross-section of the professional and academic communities in architecture. The TLOs with the nuanced levels of capacities – to identify, develop, explain, demonstrate etc – are described at an appropriate level to be understood as minimum expectations for a Master of Architecture graduate. The Architects Accreditation Council of Australia (AACA) has noted: There is a clear correlation between the current processes for accreditation and what may be the procedures in the future following the current review. The requirement of the outcomes as outlined in the draft paper to demonstrate capability is an appropriate way of expressing the measure of whether the learning outcomes have been achieved. The measure of capability as described in the outcome statements is enhanced with explanatory descriptions in the accompanying notes.

Disobedient Citizens : Press Depictions of Striking School Teachers in NSW and Anti-Vietnam War Demonstrators in NSW and Victoria in 1968

Across Australia in 1968, students demonstrating against the Vietnam War engaged in confrontational behaviour. The metropolitan daily newspapers,the most important source of news for most people, enthusiastically reported the scenes. The demonstrations were exciting. Sensational headlines and photographs captured the interest of readers and influenced their opinions. But radical opposition to government policies at the time was not limited to university students opposing the Vietnam War. Teachers had become increasingly critical of conditions in schools, with Victorian secondary school teachers having stopped work on a number of occasions since 1965. In October 1968, both primary and secondary school teachers in New South Wales participated in eastern Australia’s first state-wide teachers’ strike. As Sydney’s Sun commented on 1 October 1968, “The teachers’ strike threw the ... education system into chaos ... A huge proportion of the State’s 2764 schools were silent and empty.” Similarities with the anti-war demonstrations were obvious. Although not as confrontational, the New South Wales teachers’ strike was a publicity-seeking action. This examination of the teachers’ more restrained, but more effective, approach to challenging government policies provides a new voice and vision to our understandings of the diverse nature of radicalism in Australia in the 1960s.

Ozone-initiated particle formation, particle aging, and precursors in a laser printer

An increasing number of researchers have hypothesized that ozone may be involved in the particle formation processes that occur during printing, however no studies have investigated this further. In the current study, this hypothesis was tested in a chamber study by adding supplemental ozone to the chamber after a print job without measurable ozone emissions. Subsequent particle number concentration and size distribution measurements showed that new particles were formed minutes after the addition of ozone. The results demonstrated that ozone did react with printer-generated volatile organic compounds (VOCs) to form secondary organic aerosols (SOAs). The hypothesis was further confirmed by the observation of correlations among VOCs, ozone, and particles concentrations during a print job with measurable ozone emissions. The potential particle precursors were identified by a number of furnace tests, which suggested that squalene and styrene were the most likely SOA precursors with respect to ozone. Overall, this study significantly improved scientific understanding of the formation mechanisms of printer-generated particles, and highlighted the possible SOA formation potential of unsaturated nonterpene organic compounds by ozone-initiated reactions in the indoor environment. © 2011 American Chemical Society.

A case study examination of the influence of cultural diversity in the multicultural nursing workforce on the quality of care and patient safety in a Saudi Arabian hospital

The purpose of the study: The purpose of this study is to investigate the influence of cultural diversity, in a multicultural nursing workforce, on the quality and safety of patient care and the work environment at King Abdul-Aziz Medical City, Riyadh region. Study background: Due to global migration and workforce mobility, to varying degrees, cultural diversity exists in most health services around the world, particularly occurring where the health care workforce is multicultural or where the domestic population comprises minority groups from different cultures speaking different languages. Further complexities occur when countries have a multicultural workforce which is different from the population for whom they care, in addition to the workers being from culturally diverse countries and with different languages. In Saudi Arabia the health system is mainly staffed by expatriate nurses who comprise 67.7% of the total number of nurses. Study design: This research utilised a case study design which incorporated multiple methods including survey, qualitative interviews and document review. Methods: The participant nurses were selected for the survey via a population sampling strategy; 319 nurses returned their completed Safety Climate Survey questionnaires. Descriptive and inferential statistics (Kruskal–Wallis test) were used to analyse survey data. For the qualitative component of the study, a purposive sampling strategy was used; 24 nurses were interviewed using a semi-structured interview technique. The documentary review included KAMC-R policy documents that met the inclusion criteria using a predetermined data abstraction instrument. Content analysis was used to analyse the policy documents data. Results: The data revealed the nurses‘ perceptions of the clinical climate in this multicultural environment is that it was unsafe, with a mean score of 3.9 out of 5. No significant difference was detected between the age groups or years of experience of the nurses and the perception of safety climate in this context; the study did reveal a statistically significant difference between the cultural background categories and the perception of safety climate. The qualitative phase indicated that the nurses within this environment were struggling to achieve cultural competence; consequently, they were having difficulties in meeting the patients‘ cultural and spiritual needs as well as maintaining a high standard of care. The results also indicated that nurses were disempowered in this context. Importantly, there was inadequate support by the organisation to manage the cultural diversity issue and to protect patients from any associated risks, as demonstrated by the policy documents and supported by the nurses‘ experiences. The study also illustrated the limitations of the conceptual framework of cultural competence when tested in this multicultural workforce context. Therefore, this study generated amendments to the model that is suitable to be used in the context of a multicultural nursing workforce. Conclusion: The multicultural nature of this nursing work environment is inherently risky due to the conflicts that arise from the different cultural norms, beliefs, behaviours and languages. Further, there was uncertainty within the multicultural nursing workforce about the clinical and cultural safety of the patient care environment and about the cultural safety of the nursing workforce. The findings of the study contribute important new knowledge to the area of patient and nurse safety in a multicultural environment and contribute theoretical development to the field of cultural competence. Specifically, the findings will inform policy and practice related to patient care in the context of cultural diversity.