A functional screen identifies lateral transfer of beta-glucuronidase (gus) from bacteria to fungi

Lateral gene transfer (LGT) from prokaryotes to microbial eukaryotes is usually detected by chance through genome-sequencing projects. Here, we explore a different, hypothesis-driven approach. We show that the fitness advantage associated with the transferred gene, typically invoked only in retrospect, can be used to design a functional screen capable of identifying postulated LGT cases. We hypothesized that beta-glucuronidase (gus) genes may be prone to LGT from bacteria to fungi (thought to lack gus) because this would enable fungi to utilize glucuronides in vertebrate urine as a carbon source. Using an enrichment procedure based on a glucose-releasing glucuronide analog (cellobiouronic acid), we isolated two gus(+) ascomycete fungi from soils (Penicillium canescens and Scopulariopsis sp.). A phylogenetic analysis suggested that their gus genes, as well as the gus genes identified in genomic sequences of the ascomycetes Aspergillus nidulans and Gibberella zeae, had been introgressed laterally from high-GC gram(+) bacteria. Two such bacteria (Arthrobacter spp.), isolated together with the gus(+) fungi, appeared to be the descendants of a bacterial donor organism from which gus had been transferred to fungi. This scenario was independently supported by similar substrate affinities of the encoded beta-glucuronidases, the absence of introns from fungal gus genes, and the similarity between the signal peptide-encoding 5' extensions of some fungal gus genes and the Arthrobacter sequences upstream of gus. Differences in the sequences of the fungal 5' extensions suggested at least two separate introgression events after the divergence of the two main Euascomycete classes. We suggest that deposition of glucuronides on soils as a result of the colonization of land by vertebrates may have favored LGT of gus from bacteria to fungi in soils.

Soil Carbon Turnover Measurement by Physical Fractionation at a Forest-to-Pasture Chronosequence in the Brazilian Amazon

The effect of conversion from forest-to-pasture upon soil carbon stocks has been intensively discussed, but few studies focus on how this land-use change affects carbon (C) distribution across soil fractions in the Amazon basin. We investigated this in the 20 cm depth along a chronosequence of sites from native forest to three successively older pastures. We performed a physicochemical fractionation of bulk soil samples to better understand the mechanisms by which soil C is stabilized and evaluate the contribution of each C fraction to total soil C. Additionally, we used a two-pool model to estimate the mean residence time (MRT) for the slow and active pool C in each fraction. Soil C increased with conversion from forest-to-pasture in the particulate organic matter (> 250 mu m), microaggregate (53-250 mu m), and d-clay (< 2 mu m) fractions. The microaggregate comprised the highest soil C content after the conversion from forest-to-pasture. The C content of the d-silt fraction decreased with time since conversion to pasture. Forest-derived C remained in all fractions with the highest concentration in the finest fractions, with the largest proportion of forest-derived soil C associated with clay minerals. Results from this work indicate that microaggregate formation is sensitive to changes in management and might serve as an indicator for management-induced soil carbon changes, and the soil C changes in the fractions are dependent on soil texture.

Land use effects on soil carbon fractions in the southeastern United States. II. changes in soil carbon fractions along a forest to pasture chronosequence

Since land use change can have significant impacts on regional biogeochemistry, we investigated how conversion of forest and cultivation to pasture impact soil C and N cycling. In addition to examining total soil C, we isolated soil physiochemical C fractions in order to understand the mechanisms by which soil C is sequestered or lost. Total soil C did not change significantly over time following conversion from forest, though coarse (250-2,000 mum) particulate organic matter C increased by a factor of 6 immediately after conversion. Aggregate mean weight diameter was reduced by about 50% after conversion, but values were like those under forest after 8 years under pasture. Samples collected from a long-term pasture that was converted from annual cultivation more than 50 years ago revealed that some soil physical properties negatively impacted by cultivation were very slow to recover. Finally, our results indicate that soil macroaggregates turn over more rapidly under pasture than under forest and are less efficient at stabilizing soil C, whereas microaggregates from pasture soils stabilize a larger concentration of C than forest microaggregates. Since conversion from forest to pasture has a minimal impact on total soil C content in the Piedmont region of Virginia, United States, a simple C stock accounting system could use the same base soil C stock value for either type of land use. However, since the effects of forest to pasture conversion are a function of grassland management following conversion, assessments of C sequestration rates require activity data on the extent of various grassland management practices.

Green transport infrastructure: from motorways to bikeways

In an age when escalating fuel prices, global warming and world resource depletion are of great concern, sustainable transport practices promise to define a new way of mobility into the future. With its comparatively minimal negative environmental impacts, non reliance on fuels and positive health effects, the simple bicycle ofers significant benefits to humankind. These benefits are evident worldwide where bicycles are successfully endorsed through improved infrastructure, supporting policies, public education and management. In Australia, the national, state and locall governments are introducing measures to improve and support green transport. This is necessary as current bicycle infrastructure is not always sufficient and the longstanding conflict with motorized transport still exists. The aim for the future is to implement sustainable hard and soft bicycle infrastructure globally; the challenges of such a task can be illustrated by the city of Brisbane, Australia.

From Jindabyne to 'Jindabyne' : immigrant and indigenous specters

This paper reads Ray Lawrence's film Jindabyne (2006) in order to consider how "Australian" connotes as "immigrant" or "Indigenous" in contemporary Australia. Although the film is an adaptation of an American short story, it exploits an existing grammar of place in Australian cultural production in order to interrogate this very culture. If questions of race, gender, and class have haunted post-settlement Australia, Lawrence's film simultaneously stages these spectres and gestures towards the necessary failure of any attempt to exorcise them in a place where indigeneity is invisible. Thus, the location of Jindabyne, the town drowned in the name of progress, offers an exemplary visual metaphor for the failed project of identity formation in a place where forgetting is a survival tool.

From reader to writer : citizen journalism as news produsage

Today, participatory or citizen journalism – journalism which enables readers to become writers – exists online and offline in a variety of forms and formats, operates under a number of editorial schemes, and focusses on a wide range of topics from the specialist to the generic, and the micro-local to the global. Key models in this phenomenon include veteran sites Slashdot and Indymedia, as well as news-related Weblogs; more recent additions into the mix have been the South Korean OhmyNews, which in 2003 was “the most influential online news site in that country, attracting an estimated 2 million readers a day” (Gillmor, 2003a, p. 7), with its new Japanese and international offshoots, as well as the Wikipedia with its highly up-to-date news and current events section and its more recent offshoot Wikinews, and even citizen-produced video news as it is found in sites such as YouTube and Current.tv.

The probability archive : from essence to uncertainty in the growth of knowledge

From a ‘cultural science’ perspective, this paper traces one aspect of a more general shift, from the realist representational regime of modernity to the productive DIY systems of the internet era. It argues that collecting and archiving is transformed by this change. Modern museums – and also broadcast television – were based on determinist or ‘essence’ theory; while internet archives like YouTube (and the internet as an archive) are based on ‘probability’ theory. The paper goes through the differences between modernist ‘essence’ and postmodern ‘probability’; starting from the obvious difference that in a museum each object is selected by experts for its intrinsic properties, while on the internet you don’t know what you will find. The status of individual objects is uncertain, although the productivity of the overall archive is unlimited. The paper links these differences with changes in contemporary culture – from a Newtonian to a quantum universe, progress to risk, institutional structure to evolutionary change, objectivity to uncertainty, identity to performance. Borrowing some of its methodology from science fiction, the paper uses examples from museums and online archives, ranging from the oldest stone tool in the world to the latest tribute vid on the net.

From bricks to clicks : hybrid commercial spaces in the landscape of early literacy and learning

In their quest for resources to support children’s early literacy learning and development, parents encounter and traverse different spaces in which discourses and artifacts are produced and circulated. This paper uses conceptual tools from the field of geosemiotics to examine some commercial spaces designed for parents and children which foreground preschool learning and development. Drawing on data generated in a wider study I discuss some of the ways in which the material and virtual commercial spaces of a transnational shopping mall company and an educational toy company operate as sites of encounter between discourses and artifacts about children’s early learning and parents of preschoolers. I consider how companies connect with and ‘situate’ people as parents and customers, and then offer pathways designed for parents to follow as they attempt to meet their very young children’s learning and development needs. I argue that these pathways are both material and ideological, and that are increasingly tending to lead parents to the online commercial spaces of the world wide web. I show how companies are using the online environment and hybrid offline and online spaces and flows to reinforce an image of themselves as authoritative brokers of childhood resources for parents that is highly valuable in a policy climate which foregrounds lifelong learning and school readiness.

Moving tele-monitoring and tele-treatment from promise to practice : a business model approach for a chronic lower back pain application

The availability of new information and communication technologies creates opportunities for new, mobile tele-health services. While many promising tele-health projects deliver working R&D prototypes, they often do not result in actual deployment. We aim to identify critical issues than can increase our understanding and enhance the viability of the mobile tele-health services beyond the R&D phase by developing a business model. The present study describes the systematic development and evaluation of a service-oriented business model for tele-monitoring and -treatment of chronic lower back pain patients based on a mobile technology prototype. We address challenges of multi-sector collaboration and disruptive innovation.

A Bayesian approach to assess interaction between known risk factors: The risk of lung cancer from exposure to asbestos and smoking

We review the literature on the combined effect of asbestos exposure and smoking on lung cancer, and explore a Bayesian approach to assess evidence of interaction. Previous approaches have focussed on separate tests for an additive or multiplicative relation. We extend these approaches by exploring the strength of evidence for either relation using approaches which allow the data to choose between both models. We then compare the different approaches.

Grounded theory : a methodological spiral from positivism to postmodernism

Aim. Our aim in this paper is to explain a methodological/methods package devised to incorporate situational and social world mapping with frame analysis, based on a grounded theory study of Australian rural nurses' experiences of mentoring. Background. Situational analysis, as conceived by Adele Clarke, shifts the research methodology of grounded theory from being located within a postpositivist paradigm to a postmodern paradigm. Clarke uses three types of maps during this process: situational, social world and positional, in combination with discourse analysis. Method. During our grounded theory study, the process of concurrent interview data generation and analysis incorporated situational and social world mapping techniques. An outcome of this was our increased awareness of how outside actors influenced participants in their constructions of mentoring. In our attempts to use Clarke's methodological package, however, it became apparent that our constructivist beliefs about human agency could not be reconciled with the postmodern project of discourse analysis. We then turned to the literature on symbolic interactionism and adopted frame analysis as a method to examine the literature on rural nursing and mentoring as secondary form of data. Findings. While we found situational and social world mapping very useful, we were less successful in using positional maps. In retrospect, we would argue that collective action framing provides an alternative to analysing such positions in the literature. This is particularly so for researchers who locate themselves within a constructivist paradigm, and who are therefore unwilling to reject the notion of human agency and the ability of individuals to shape their world in some way. Conclusion. Our example of using this package of situational and social worlds mapping with frame analysis is intended to assist other researchers to locate participants more transparently in the social worlds that they negotiate in their everyday practice. © 2007 Blackwell Publishing Ltd.

From allure to ethics : design as a ‘creative industry'

In this chapter I look at the question of design and ethics in a situation where design as a set of related economic practices has been re-positioned as a key identifier for a new kind of ideas-driven industry - the creative industries. Previously marginal to cultural policy in the form of applied arts, in the creative industries agenda design became a privileged meeting place, or indeed broker, for art and industry, economy and commerce. I explore the new kinds of ethical challenges this brings.

Transition from n- to p-type of spray pyrolysis deposited Cu doped ZnO thin films for NO2 sensing

The structural, optical, and gas-sensing properties of spray pyrolysis deposited Cu doped ZnO thin films were investigated. Gas response of the undoped and doped films to N02 (oxidizing) gas shows an increase and decrease in resistance, respectively, indicating p-type conduction in doped samples. The UV-Vis spectra of the films show decrease in the bandgap with increasing Cu concentration in ZnO. The observed p-type conductivity is attributed to the holes generated by incorporated Cu atoms on Zn sites in ZnO thin films. The X-ray diffraction spectra showed that samples are polycrystalline with the hexagonal wurtzite structure and increasing the concentration of Cu caused a decrease in the intensity of the dominant (002) peak. The surface morphology of films was studied by scanning electron microscopy and the presence of Cu was also confirmed by X-ray photoelectron spectroscopy. Seebeck effect measurements were utilized to confirm the p-type conduction of Cu doped ZnO thin films. Copyright © 2009 American Scientific Publishers All rights reserved.