Optimisation of Banana streak virus (BSV) diagnostic assays

Bananas are one of the world�fs most important crops, serving as a staple food and an important source of income for millions of people in the subtropics. Pests and diseases are a major constraint to banana production. To prevent the spread of pests and disease, farmers are encouraged to use disease�] and insect�]free planting material obtained by micropropagation. This option, however, does not always exclude viruses and concern remains on the quality of planting material. Therefore, there is a demand for effective and reliable virus indexing procedures for tissue culture (TC) material. Reliable diagnostic tests are currently available for all of the economically important viruses of bananas with the exception of Banana streak viruses (BSV, Caulimoviridae, Badnavirus). Development of a reliable diagnostic test for BSV is complicated by the significant serological and genetic variation reported for BSV isolates, and the presence of endogenous BSV (eBSV). Current PCR�] and serological�]based diagnostic methods for BSV may not detect all species of BSV, and PCR�]based methods may give false positives because of the presence of eBSV. Rolling circle amplification (RCA) has been reported as a technique to detect BSV which can also discriminate between episomal and endogenous BSV sequences. However, the method is too expensive for large scale screening of samples in developing countries, and little information is available regarding its sensitivity. Therefore the development of reliable PCR�]based assays is still considered the most appropriate option for large scale screening of banana plants for BSV. This MSc project aimed to refine and optimise the protocols for BSV detection, with a particular focus on developing reliable PCR�]based diagnostics Initially, the appropriateness and reliability of PCR and RCA as diagnostic tests for BSV detection were assessed by testing 45 field samples of banana collected from nine districts in the Eastern region of Uganda in February 2010. This research was also aimed at investigating the diversity of BSV in eastern Uganda, identifying the BSV species present and characterising any new BSV species. Out of the 45 samples tested, 38 and 40 samples were considered positive by PCR and RCA, respectively. Six different species of BSV, namely Banana streak IM virus (BSIMV), Banana streak MY virus (BSMYV), Banana streak OL virus (BSOLV), Banana streak UA virus (BSUAV), Banana streak UL virus (BSULV), Banana streak UM virus (BSUMV), were detected by PCR and confirmed by RCA and sequencing. No new species were detected, but this was the first report of BSMYV in Uganda. Although RCA was demonstrated to be suitable for broad�]range detection of BSV, it proved time�]consuming and laborious for identification in field samples. Due to the disadvantages associated with RCA, attempts were made to develop a reliable PCR�]based assay for the specific detection of episomal BSOLV, Banana streak GF virus (BSGFV), BSMYV and BSIMV. For BSOLV and BSGFV, the integrated sequences exist in rearranged, repeated and partially inverted portions at their site of integration. Therefore, for these two viruses, primers sets were designed by mapping previously published sequences of their endogenous counterparts onto published sequences of the episomal genomes. For BSOLV, two primer sets were designed while, for BSGFV, a single primer set was designed. The episomalspecificity of these primer sets was assessed by testing 106 plant samples collected during surveys in Kenya and Uganda, and 33 leaf samples from a wide range of banana cultivars maintained in TC at the Maroochy Research Station of the Department of Employment, Economic Development and Innovation (DEEDI), Queensland. All of these samples had previously been tested for episomal BSV by RCA and for both BSOLV and BSGFV by PCR using published primer sets. The outcome from these analyses was that the newly designed primer sets for BSOLV and BSGFV were able to distinguish between episomal BSV and eBSV in most cultivars with some B�]genome component. In some samples, however, amplification was observed using the putative episomal�]specific primer sets where episomal BSV was not identified using RCA. This may reflect a difference in the sensitivity of PCR compared to RCA, or possibly the presence of an eBSV sequence of different conformation. Since the sequences of the respective eBSV for BSMYV and BSIMV in the M. balbisiana genome are not available, a series of random primer combinations were tested in an attempt to find potential episomal�]specific primer sets for BSMYV and BSIMV. Of an initial 20 primer combinations screened for BSMYV detection on a small number of control samples, 11 primers sets appeared to be episomal�]specific. However, subsequent testing of two of these primer combinations on a larger number of control samples resulted in some inconsistent results which will require further investigation. Testing of the 25 primer combinations for episomal�]specific detection of BSIMV on a number of control samples showed that none were able to discriminate between episomal and endogenous BSIMV. The final component of this research project was the development of an infectious clone of a BSV endemic in Australia, namely BSMYV. This was considered important to enable the generation of large amounts of diseased plant material needed for further research. A terminally redundant fragment (.1.3 �~ BSMYV genome) was cloned and transformed into Agrobacterium tumefaciens strain AGL1, and used to inoculate 12 healthy banana plants of the cultivars Cavendish (Williams) by three different methods. At 12 weeks post�]inoculation, (i) four of the five banana plants inoculated by corm injection showed characteristic BSV symptoms while the remaining plant was wilting/dying, (ii) three of the five banana plants inoculated by needle�]pricking of the stem showed BSV symptoms, one plant was symptomless while the remaining had died and (iii) both banana plants inoculated by leaf infiltration were symptomless. When banana leaf samples were tested for BSMYV by PCR and RCA, BSMYV was confirmed in all banana plants showing symptoms including those were wilting and/or dying. The results from this research have provided several avenues for further research. By completely sequencing all variants of eBSOLV and eBSGFV and fully sequencing the eBSIMV and eBSMYV regions, episomal BSV�]specific primer sets for all eBSVs could potentially be designed that could avoid all integrants of that particular BSV species. Furthermore, the development of an infectious BSV clone will enable large numbers of BSVinfected plants to be generated for the further testing of the sensitivity of RCA compared to other more established assays such as PCR. The development of infectious clones also opens the possibility for virus induced gene silencing studies in banana.

Passenger transmission and productiveness of transit lines with high loads

Deterministic transit capacity analysis applies to planning, design and operational management of urban transit systems. The Transit Capacity and Quality of Service Manual (1) and Vuchic (2, 3) enable transit performance to be quantified and assessed using transit capacity and productive capacity. This paper further defines important productive performance measures of an individual transit service and transit line. Transit work (p-km) captures the transit task performed over distance. Passenger transmission (p-km/h) captures the passenger task delivered by service at speed. Transit productiveness (p-km/h) captures transit work performed over time. These measures are useful to operators in understanding their services’ or systems’ capabilities and passenger quality of service. This paper accounts for variability in utilized demand by passengers along a line and high passenger load conditions where passenger pass-up delay occurs. A hypothetical case study of an individual bus service’s operation demonstrates the usefulness of passenger transmission in comparing existing and growth scenarios. A hypothetical case study of a bus line’s operation during a peak hour window demonstrates the theory’s usefulness in examining the contribution of individual services to line productive performance. Scenarios may be assessed using this theory to benchmark or compare lines and segments, conditions, or consider improvements.

The promise of Iceland

Memoir, 288 pages. An account of journeys made by the author from Australia to Iceland as a way of interrogating notions of cultural belonging, family, and homecoming. "In 1990, Kári Gíslason travelled to Iceland to meet his father for the first time. What he finds is not what he expected. Born from a secret liaison between a British mother and an Icelandic father, Kári Gíslason was the subject of a promise – a promise elicited from his father to not reveal his identity. The Icelandic city of Reykjavík, where Kári was born, was also home to his father and his father’s wife and five children – none of whom knew of Kári’s existence. Moving regularly between Iceland and Australia, he grew up aware of his father’s identity, but understanding that it was the subject of a secret pact between his parents. At the age of 27, he makes a decision to break the pact and contacts his father’s other family. What follows, and what leads him there, makes for a riveting journey over landscapes, time and memory. Kári travels from the freezing cold winters of Iceland to the shark net at Sydney’s Balmoral, an unsettled life in the English countryside and the harsh yellow summer of Brisbane, and back again. He traces the steps of his mother who answered an ad in The Times for an English-speaking secretary in 1970 and found herself in Iceland among the ‘Army of Foreign Secretaries’, and in the arms of a secret lover. Iceland becomes the substitute for the father Kári never really knew as he discovers the meaning of ‘home’ and closes the circle of his own fatherless life."-- publisher website

Next-generation sequencing of cervical DNA detects human papillomavirus types not detected by commercial kits

Background Human papillomavirus (HPV) is the aetiological agent for cervical cancer and genital warts. Concurrent HPV and HIV infection in the South African population is high. HIV positive (+) women are often infected with multiple, rare and undetermined HPV types. Data on HPV incidence and genotype distribution are based on commercial HPV detection kits, but these kits may not detect all HPV types in HIV + women. The objectives of this study were to (i) identify the HPV types not detected by commercial genotyping kits present in a cervical specimen from an HIV positive South African woman using next generation sequencing, and (ii) determine if these types were prevalent in a cohort of HIV-infected South African women. Methods Total DNA was isolated from 109 cervical specimens from South African HIV + women. A specimen within this cohort representing a complex multiple HPV infection, with 12 HPV genotypes detected by the Roche Linear Array HPV genotyping (LA) kit, was selected for next generation sequencing analysis. All HPV types present in this cervical specimen were identified by Illumina sequencing of the extracted DNA following rolling circle amplification. The prevalence of the HPV types identified by sequencing, but not included in the Roche LA, was then determined in the 109 HIV positive South African women by type-specific PCR. Results Illumina sequencing identified a total of 16 HPV genotypes in the selected specimen, with four genotypes (HPV-30, 74, 86 and 90) not included in the commercial kit. The prevalence's of HPV-30, 74, 86 and 90 in 109 HIV positive South African women were found to be 14.6 %, 12.8 %, 4.6 % and 8.3 % respectively. Conclusions Our results indicate that there are HPV types, with substantial prevalence, in HIV positive women not being detected in molecular epidemiology studies using commercial kits. The significance of these types in relation to cervical disease remains to be investigated.

A protocol for the rapid isolation of full geminivirus genomes from dried plant tissue

A high-throughput method of isolating and cloning geminivirus genomes from dried plant material, by combining an Extract-n-Amp™-based DNA isolation technique with rolling circle amplification (RCA) of viral DNA, is presented. Using this method an attempt was made to isolate and clone full geminivirus genomes/genome components from 102 plant samples, including dried leaves stored at room temperature for between 6 months and 10 years, with an average hands-on-time to RCA-ready DNA of 15 min per 20 samples. While storage of dried leaves for up to 6 months did not appreciably decrease cloning success rates relative to those achieved with fresh samples, efficiency of the method decreased with increasing storage time. However, it was still possible to clone virus genomes from 47% of 10-year-old samples. To illustrate the utility of this simple method for high-throughput geminivirus diversity studies, six Maize streak virus genomes, an Abutilon mosaic virus DNA-B component and the DNA-A component of a previously unidentified New Word begomovirus species were fully sequenced. Genomic clones of the 69 other viruses were verified as such by end sequencing. This method should be extremely useful for the study of any circular DNA plant viruses with genome component lengths smaller than the maximum size amplifiable by RCA. © 2008 Elsevier B.V. All rights reserved.

Rapid host adaptation by extensive recombination

Experimental investigations into virus recombination can provide valuable insights into the biochemical mechanisms and the evolutionary value of this fundamental biological process. Here, we describe an experimental scheme for studying recombination that should be applicable to any recombinogenic viruses amenable to the production of synthetic infectious genomes. Our approach is based on differences in fitness that generally exist between synthetic chimaeric genomes and the wild-type viruses from which they are constructed. In mixed infections of defective reciprocal chimaeras, selection strongly favours recombinant progeny genomes that recover a portion of wild-type fitness. Characterizing these evolved progeny viruses can highlight both important genetic fitness determinants and the contribution that recombination makes to the evolution of their natural relatives. Moreover, these experiments supply precise information about the frequency and distribution of recombination breakpoints, which can shed light on the mechanistic processes underlying recombination. We demonstrate the value of this approach using the small single-stranded DNA geminivirus, maize streak virus (MSV). Our results show that adaptive recombination in this virus is extremely efficient and can yield complex progeny genomes comprising up to 18 recombination breakpoints. The patterns of recombination that we observe strongly imply that the mechanistic processes underlying rolling circle replication are the prime determinants of recombination breakpoint distributions found in MSV genomes sampled from nature. © 2009 SGM.

Replicative intermediates of maize streak virus found during leaf development

Geminiviruses of the genera Begomovirus and Curtovirus utilize three replication modes: complementary-strand replication (CSR), rolling-circle replication (RCR) and recombinationdependent replication (RDR). Using two-dimensional gel electrophoresis, we now show for the first time that maize streak virus (MSV), the type member of the most divergent geminivirus genus, Mastrevirus, does the same. Although mastreviruses have fewer regulatory genes than other geminiviruses and uniquely express their replication-associated protein (Rep) from a spliced transcript, the replicative intermediates of CSR, RCR and RDR could be detected unequivocally within infected maize tissues. All replicative intermediates accumulated early and, to varying degrees, were already present in the shoot apex and leaves at different maturation stages. Relative to other replicative intermediates, those associated with RCR increased in prevalence during leaf maturation. Interestingly, in addition to RCR-associated DNA forms seen in other geminiviruses, MSV also apparently uses dimeric open circular DNA as a template for RCR. © 2010 SGM.

Improvising a future in the performing arts : a new strategy to help performance studies students successfully shift between academic culture, professional culture, industry and career?

If there is one thing performance studies graduates should be good at, it is improvising – play and improvisation are central to the contemporary and cultural performance practices we teach and the methods by which we teach them. Objective, offer, acceptance, advancing, reversing, character, status, manipulation, impression management, relationship management – whether we know them from Keith Johnson’s theatre theories or Erving Goffman’s theatre theories, the processes by which we play out a story, scenario or social situation to our own benefit are familiar. We understand that identity, action, interaction and its personal, aesthetic, professional or political outcomes are unpredictable, and that we need to adapt to changeable and uncertain circumstances to achieve our aims. Intriguingly, though, in a Higher Education environment that increasingly emphasises employability, skills in play, improvisation and self-performance are never cited as critical graduate attributes. Is the ability to play, improve and produce spontaneous new self-performances learned in the academy worth articulating into an ability to play, improvise and product spontaneous new self-performances after graduates leave the academy and move into the role of a performing arts professional in industry? A study of the career paths of our performance studies graduates over the past decade suggests that addressing the challenges they face in moving between academic culture, professional culture, industry and career in terms of improvisation and play principles may be very productive. In articles on performing arts careers, graduates are typically advised to find a market for their work, and develop career self-management, management and marketing skills, together with an ability to find, make and maintain relationships and opportunities for themselves. Transitioning to career is cast as a challenging process, requiring these skills, because performing arts careers do not offer the security, status and stability of other careers. Our data confirms this. In our study, though, we found that strategies commonly used to build the resilience, self-reliance and persistence graduates require – talking about portfolio careers, parallel careers, and portable, transferable or translatable skills, for example – can engender panic as easily as they engender confidence. In this paper, I consider what happens when we re-articulate some of the skills scholars and industry stakeholders argue are critical in allowing graduates to shift successfully from academy to industry in terms of skills like improvisation, play and self-performance that are already familiar, meaningful and much-practiced amongst performance studies graduates.

Economic growth and inequality patterns in the presence of costly technology adoption and uncertainty

We develop a stochastic endogenous growth model to explain the diversity in growth and inequality patterns and the non-convergence of incomes in transitional economies where an underdeveloped financial sector imposes an implicit, fixed cost on the diversification of idiosyncratic risk. In the model endogenous growth occurs through physical and human capital deepening, with the latter being the more dominant element. We interpret the fixed cost as a ‘learning by doing’ cost for entrepreneurs who undertake risk in the absence of well developed financial markets and institutions that help diversify such risk. As such, this cost may be interpreted as the implicit returns foregone due to the lack of diversification opportunities that would otherwise have been available, had such institutions been present. The analytical and numerical results of the model suggest three growth outcomes depending on the productivity differences between the projects and the fixed cost associated with the more productive project. We label these outcomes as poverty trap, dual economy and balanced growth. Further analysis of these three outcomes highlights the existence of a diversity within diversity. Specifically, within the ‘poverty trap’ and ‘dual economy’ scenarios growth and inequality patterns differ, depending on the initial conditions. This additional diversity allows the model to capture a richer range of outcomes that are consistent with the empirical experience of several transitional economies.

Digital futures for cultural and media studies

An ambitious rendering of the digital future from a pioneer of media and cultural studies, a wise and witty take on a changing field, and our orientation to it Investigates the uses of multimedia by creative and productive citizen-consumers to provide new theories of communication that accommodate social media, participatory action, and user-creativity Leads the way for new interdisciplinary engagement with systems thinking, complexity and evolutionary sciences, and the convergence of cultural and economic values Analyzes the historical uses of multimedia from print, through broadcasting to the internet Combines conceptual innovation with historical erudition to present a high-level synthesis of ideas and detailed analysis of emergent forms and practices Features an international focus and global reach to provide a basis for students and researchers seeking broader perspectives

"Are there any right or wrong answers in teaching philosophy": ethics, epistemology, and philosophy in the classroom

This article assesses undergraduate teaching students’ assertion that there are no right and wrong answers in teaching philosophy. When asked questions about their experiences of philosophy in the classroom for primary children, their unanimous declaration that teaching philosophy has ‘no right and wrong answers’ is critically examined across the three sub-disciplinary areas to which they were generally referring, namely, pedagogy, ethics, and epistemology. From a pedagogical point of view, it is argued that some teaching approaches may indeed be more effective than others, and some pupils’ opinions less defensible, but pedagogically, in terms of managing the power relations in the classroom, it is counter-productive to continually insist on notions of truth and falsity at every point. From an ethical point of view, it is contended that anti-realist approaches to meta-ethics may represent a viable intellectual position, but from the point of view of normative ethics, notions of right and wrong still retain significant currency. From an epistemological point of view, it is argued using Karl Poppers’ work that while it may be difficult to determine what constitutes a right answer, determining a wrong one is far more straightforward. In conclusion, it is clear that prospective teachers engaging in philosophy in the classroom, and also future teachers in general, require a far more nuanced philosophical understanding of the notions of right and wrong and truth and falsity. In view of this situation, it we wish to promote the effective teaching of philosophical thinking to children, or produce educators who can understand the conceptual limits of the claims they make and their very real and often serious practical and social consequences, it is recommended that philosophy be reinstated to a fundamental, foundational place within the pre-service teaching curriculum.

Confronting the shortage of skilled and professional workers : A large scale industry-school partnership initiative

In most of the advanced economies, students are losing interest in careers especially in engineering and related industries. Hence, western economies are confronting a critical skilled labour shortage in areas of technology, science and engineering. The aim of this paper is to document how the organisational and institutional elements of one industry-school partnerships initiative – The Gateway Schools Program - contribute to productive knowledge sharing and networking. In particular this paper focuses on an initiative of an Australian State government in response to a perceived crisis around the skills shortage in an economy transitioning from a localised to a global knowledge production economy. The Gateway Schools initiative signals the first sustained attempt in Australia to incorporate schools into production networks through strategic partnerships linking them to partner organisations at the industry level. We provide case examples of how four schools operationalise the partnerships with the mining and energy industries and how these partnerships as knowledge assets impact the delivery of curriculum and capacity building among teachers. A program theory approach to analysis, informed by theoretical perspectives of Bailey (1994), Bagnall (2007) and Walsh (2004) was adopted. Each of these theorists provides a related but different perspective on the establishment, purpose, and effectiveness respectively of partnerships. Our ultimate goal is to define those characteristics of successful partnerships that do contribute to enhanced interest and engagement by students in those careers that are currently experiencing critical shortages.

Between formal and informal : the shakeout in China’s online video industry

While a rich body of literature in television and film studies and media policy studies has tended to focus on the media activities in the formal sector, we know much less about informal media activities, its influence on state policies, as well as the dynamics between the formal and the informal sectors. This article examines these issues with reference to a particularly revealing period following a large-scale government crackdown on peer-to-peer video sharing sites in China in 2008. By analyzing the aim and consequences of the state action, I point to the counter-productive effect in terms of cultural loss and the resurgence of offline piracy; and show the positive impact on forcing the informal into the formal sector, and pressuring the formal to innovate. Meanwhile, an increasing rapprochement between professional and user-created content leads to a new relationship between formal and informal sectors. This case demonstrates the importance of considering the dynamics between the two sectors. It also offers compelling evidence of the role of the informal sector in engendering state action, which in turn impacted on the co-evolution of the formal and the informal sectors.

Policy, citizenship and governance : the case of disability and employment policy in Australia

Current discussions regarding the relationship between welfare governance systems and employment promotion in disability policy appeal to a rejuvenated neo-liberal and paternalistic understanding of welfare governance. At the core of this rationality is the argument that people with disabilities not only have rights, but also duties, in relation to the State. In the Australia welfare system, policy tools are deployed to produce a form of self-discipline, whereby the State emphasises personal responsibility via assessment tools, ‘mutual obligation’ policy, and motivational strategies. Drawing on a two-year semi-longitudinal study with 80 people with a disability accessing welfare benefits, we examine how welfare governance subject recipients to strategies to produce productive citizens who are able to contribute to the national goal of maintaining competitiveness in the global economy. Participants’ interviews reveal the intended and unintended effects of this activation policy, including some acceptance of the logic of welfare-to-work and counter-hegemonic resistance to de-valued social identities.

High load transit line passenger transmission and productiveness efficiencies

Performance of urban transit systems may be quantified and assessed using transit capacity and productive capacity in planning, design and operational management activities. Bunker (4) defines important productive performance measures of an individual transit service and transit line, which are extended in this paper to quantify efficiency and operating fashion of transit services and lines. Comparison of a hypothetical bus line’s operation during a morning peak hour and daytime hour demonstrates the usefulness of productiveness efficiency and passenger transmission efficiency, passenger churn and average proportion line length traveled to the operator in understanding their services’ and lines’ productive performance, operating characteristics, and quality of service. Productiveness efficiency can flag potential pass-up activity under high load conditions, as well as ineffective resource deployment. Proportion line length traveled can directly measure operating fashion. These measures can be used to compare between lines/routes and, within a given line, various operating scenarios and time horizons to target improvements. The next research stage is investigating within-line variation using smart card passenger data and field observation of pass-ups. Insights will be used to further develop practical guidance to operators.