Prediction of transcriptional regulatory interactions in bacteria : a comparative genomics approach

Exponential growth of genomic data in the last two decades has made manual analyses impractical for all but trial studies. As genomic analyses have become more sophisticated, and move toward comparisons across large datasets, computational approaches have become essential. One of the most important biological questions is to understand the mechanisms underlying gene regulation. Genetic regulation is commonly investigated and modelled through the use of transcriptional regulatory network (TRN) structures. These model the regulatory interactions between two key components: transcription factors (TFs) and the target genes (TGs) they regulate. Transcriptional regulatory networks have proven to be invaluable scientific tools in Bioinformatics. When used in conjunction with comparative genomics, they have provided substantial insights into the evolution of regulatory interactions. Current approaches to regulatory network inference, however, omit two additional key entities: promoters and transcription factor binding sites (TFBSs). In this study, we attempted to explore the relationships among these regulatory components in bacteria. Our primary goal was to identify relationships that can assist in reducing the high false positive rates associated with transcription factor binding site predictions and thereupon enhance the reliability of the inferred transcription regulatory networks. In our preliminary exploration of relationships between the key regulatory components in Escherichia coli transcription, we discovered a number of potentially useful features. The combination of location score and sequence dissimilarity scores increased de novo binding site prediction accuracy by 13.6%. Another important observation made was with regards to the relationship between transcription factors grouped by their regulatory role and corresponding promoter strength. Our study of E.coli ��70 promoters, found support at the 0.1 significance level for our hypothesis | that weak promoters are preferentially associated with activator binding sites to enhance gene expression, whilst strong promoters have more repressor binding sites to repress or inhibit gene transcription. Although the observations were specific to �70, they nevertheless strongly encourage additional investigations when more experimentally confirmed data are available. In our preliminary exploration of relationships between the key regulatory components in E.coli transcription, we discovered a number of potentially useful features { some of which proved successful in reducing the number of false positives when applied to re-evaluate binding site predictions. Of chief interest was the relationship observed between promoter strength and TFs with respect to their regulatory role. Based on the common assumption, where promoter homology positively correlates with transcription rate, we hypothesised that weak promoters would have more transcription factors that enhance gene expression, whilst strong promoters would have more repressor binding sites. The t-tests assessed for E.coli �70 promoters returned a p-value of 0.072, which at 0.1 significance level suggested support for our (alternative) hypothesis; albeit this trend may only be present for promoters where corresponding TFBSs are either all repressors or all activators. Nevertheless, such suggestive results strongly encourage additional investigations when more experimentally confirmed data will become available. Much of the remainder of the thesis concerns a machine learning study of binding site prediction, using the SVM and kernel methods, principally the spectrum kernel. Spectrum kernels have been successfully applied in previous studies of protein classification [91, 92], as well as the related problem of promoter predictions [59], and we have here successfully applied the technique to refining TFBS predictions. The advantages provided by the SVM classifier were best seen in `moderately'-conserved transcription factor binding sites as represented by our E.coli CRP case study. Inclusion of additional position feature attributes further increased accuracy by 9.1% but more notable was the considerable decrease in false positive rate from 0.8 to 0.5 while retaining 0.9 sensitivity. Improved prediction of transcription factor binding sites is in turn extremely valuable in improving inference of regulatory relationships, a problem notoriously prone to false positive predictions. Here, the number of false regulatory interactions inferred using the conventional two-component model was substantially reduced when we integrated de novo transcription factor binding site predictions as an additional criterion for acceptance in a case study of inference in the Fur regulon. This initial work was extended to a comparative study of the iron regulatory system across 20 Yersinia strains. This work revealed interesting, strain-specific difierences, especially between pathogenic and non-pathogenic strains. Such difierences were made clear through interactive visualisations using the TRNDifi software developed as part of this work, and would have remained undetected using conventional methods. This approach led to the nomination of the Yfe iron-uptake system as a candidate for further wet-lab experimentation due to its potential active functionality in non-pathogens and its known participation in full virulence of the bubonic plague strain. Building on this work, we introduced novel structures we have labelled as `regulatory trees', inspired by the phylogenetic tree concept. Instead of using gene or protein sequence similarity, the regulatory trees were constructed based on the number of similar regulatory interactions. While the common phylogentic trees convey information regarding changes in gene repertoire, which we might regard being analogous to `hardware', the regulatory tree informs us of the changes in regulatory circuitry, in some respects analogous to `software'. In this context, we explored the `pan-regulatory network' for the Fur system, the entire set of regulatory interactions found for the Fur transcription factor across a group of genomes. In the pan-regulatory network, emphasis is placed on how the regulatory network for each target genome is inferred from multiple sources instead of a single source, as is the common approach. The benefit of using multiple reference networks, is a more comprehensive survey of the relationships, and increased confidence in the regulatory interactions predicted. In the present study, we distinguish between relationships found across the full set of genomes as the `core-regulatory-set', and interactions found only in a subset of genomes explored as the `sub-regulatory-set'. We found nine Fur target gene clusters present across the four genomes studied, this core set potentially identifying basic regulatory processes essential for survival. Species level difierences are seen at the sub-regulatory-set level; for example the known virulence factors, YbtA and PchR were found in Y.pestis and P.aerguinosa respectively, but were not present in both E.coli and B.subtilis. Such factors and the iron-uptake systems they regulate, are ideal candidates for wet-lab investigation to determine whether or not they are pathogenic specific. In this study, we employed a broad range of approaches to address our goals and assessed these methods using the Fur regulon as our initial case study. We identified a set of promising feature attributes; demonstrated their success in increasing transcription factor binding site prediction specificity while retaining sensitivity, and showed the importance of binding site predictions in enhancing the reliability of regulatory interaction inferences. Most importantly, these outcomes led to the introduction of a range of visualisations and techniques, which are applicable across the entire bacterial spectrum and can be utilised in studies beyond the understanding of transcriptional regulatory networks.

Michel Foucault : the unconscious of history and culture

Michel Foucault: The unconscious of history and culture The French thinker, Michel Foucault (1926–84), is noted for his extensive and controversial forays into the historical disciplines. When his work first began to circulate in the 1950s and 1960s, historians did not quite know what to make of it and philosophers resented the appearance of what they saw as the importation of the tedium of concrete events into the pure untainted realm of ideas. If these responses to his work remain alive and well decades after Foucault's death, the uptake of his work has become far more complex. To restrict ourselves to the discipline of history here: if one very visible and vocal camp of historians remains deeply ambivalent about his work, this merely disguises the fact that a far larger contingent of historians of all kinds – not just those located in history departments – use his ideas quite unremarkably ...

Diversity and Differentiation

New ways of working are being embraced by early childhood educators as they cope with demands from national reforms and changing communities. While reformers are pressing for social equity and improved outcomes for families and children, communities are diverging in terms of ethnicity, culture, language and socioeconomic status. As a consequence, early childhood educators are being challenged to expand their existing repertoire of practices in order to more effectively provide quality learning experiences for every child in their care. Practice enhancement and differentiated pedagogy are needed to address the additional needs of an increasing number of diverse learners. Community expectations are particularly focused on better educational supports for children in five cluster areas: • Culturally diverse and Indigenous backgrounds • ‘at risk’ because of socio-economic and abuse conditions • Communicative, emotional and behavioural disorders • Disabilities and learning difficulties and • Recognised gifts and talents This chapter focuses on some everyday ractices that can be used strategically to better support all children, including those with additional educational needs. All practices are well supported in the literature and are substantiated by either research findings or strong, socially determined values. They also very ‘doable’ and sustainable in today’s dynamic and multifaceted early childhood settings. Seven keys practices will be introduced, together with examples of how they can be applied to both enhance the learning of individual children and to strengthen a sense of group belonging. The practices are: • Having positive beliefs about all children • Learning about each child • Building meaningful relationships around the child • Creating supportive learning environments for the child • Providing engaging learning experiences for the child • Differentiating instruction for the child • Using child progress data to improve learning and teaching

The Tashi project 2004-2010 : developing methods for creating theatre works that fully engage children aged between 3 and 10

Over a seven-year period, Mark Radvan directed a suite of children’s theatre productions adapted from the original Tashi stories by Australian writers Anna and Barbara Fienberg. The Tashi Project’s repertoire of plays performed to over 40,000 children aged between 3 and 10 years old, and their carers, in seasons at the Out of the Box Festival, at Brisbane Powerhouse and in venues across Australia in two interstate tours in 2009 and 2010. The project investigated how best to combine an exploration of theatrical forms and conventions, with a performance style evolved in a specially developed training program and a deliberate positioning of young children as audiences capable of sophisticated readings of action, symbol, theme and character. The results of this project show that when brought into appropriate relationship with the theatre artists, young children aged 3-5 can engage with sophisticated narrative forms, and with the right contextual framing they enjoy heightened dramatic and emotional tension, bringing to the event sustained and highly engaged concentration. Older children aged 6-10 also bring sustained and heightened engagement to the same stories, providing that other more sophisticated dramatic elements are woven into the construction of the performances, such as character, theme and style.

Strategies for mentoring pedagogical knowledge

Fundamental for mentoring a preservice teacher is the mentor’s articulation of pedagogical knowledge, which in this research draws upon specific practices, viz: planning, timetabling lessons, preparation, teaching strategies, content knowledge, problem solving, questioning, classroom management, implementation, assessment, and viewpoints for teaching. Mentoring is haphazard; consequently mentors need a pedagogical knowledge framework and a repertoire of pedagogical knowledge strategies to guide a preservice teacher’s development. Yet, what are strategies for mentoring pedagogical knowledge practices? This qualitative research investigates mentoring strategies assigned to pedagogical knowledge from 27 experienced mentor teachers. Findings showed that there were multiple strategies that can be linked to specific pedagogical knowledge practices. For example, mentoring strategies associated with planning for teaching can include co-planning, verbally reflecting on planning with the mentee, and showing examples of the mentor teacher’s planning (e.g., teacher’s plans, school plans, district and state plans). This paper provides a bank of practical strategies for mentoring pedagogical knowledge practices to assist a preservice teacher’s development.

Characterising one-to-one conservatoire teaching : Some implications of a quantitative analysis

Despite the significant recent growth in research relating to instrumental, vocal and composition tuition in higher education, little is known about the diversity of approaches that characterise one-to-one teaching in the Conservatoire, and what counts as optimal practice for educating 21st-century musicians. Through analysis of video-recorded one-to-one lessons that draws on a ‘bottom up’ methodology for characterising pedagogical practices (Taylor, 2012; Taylor et al, 2012), this paper provides empirical evidence about the nature of one-to-one pedagogy in one Australian institution. The research aims (1) to enable a better understanding of current one-to-one conservatoire teaching; and (2) to build and improve upon existing teaching practice using authentic insights gained through systematic investigation. The authors hope the research will lead to a better understanding of the diversity and efficacy of the pedagogical practice within the specific context in which the study was conducted, and beyond, to Conservatoire pedagogy generally.

Sampling environmental acoustic recordings to determine bird species richness

Acoustic sensors can be used to estimate species richness for vocal species such as birds. They can continuously and passively record large volumes of data over extended periods. These data must subsequently be analyzed to detect the presence of vocal species. Automated analysis of acoustic data for large numbers of species is complex and can be subject to high levels of false positive and false negative results. Manual analysis by experienced surveyors can produce accurate results; however the time and effort required to process even small volumes of data can make manual analysis prohibitive. This study examined the use of sampling methods to reduce the cost of analyzing large volumes of acoustic sensor data, while retaining high levels of species detection accuracy. Utilizing five days of manually analyzed acoustic sensor data from four sites, we examined a range of sampling frequencies and methods including random, stratified, and biologically informed. We found that randomly selecting 120 one-minute samples from the three hours immediately following dawn over five days of recordings, detected the highest number of species. On average, this method detected 62% of total species from 120 one-minute samples, compared to 34% of total species detected from traditional area search methods. Our results demonstrate that targeted sampling methods can provide an effective means for analyzing large volumes of acoustic sensor data efficiently and accurately. Development of automated and semi-automated techniques is required to assist in analyzing large volumes of acoustic sensor data. Read More: http://www.esajournals.org/doi/abs/10.1890/12-2088.1

Generate : Youth Culture and Migration Heritage in Western Sydney

Executive Summary This report is the first in-depth exploration of identity and popular culture among Middle Eastern and Asian youth. It documents preliminary research findings on the contribution of Middle Eastern and Asian youth to Sydney’s cultural life and migration heritage. While young people from these communities, the largest migrant communities in NSW, are often negatively portrayed, this research has focused on their social practices of cultural invention, opening up new and creative means of mobilising cultural difference. These young people’s cultural negotiations between migrant family background and the wider society require real engagement with difference and provide rich resources for invigorating the multicultural fabric of the nation. Their repertoire of cultural skills and their involvement in different cultural worlds are often viewed as evidence of not ‘belonging’ to the mainstream or dominant culture. However, the results of our research reveal that the ‘in-betweenness’ of these young people often enables them to move easily between different social and cultural groupings, embracing cultural diversity as inherent and integral to their everyday experience, that is, ‘normal’ to urban life. In this report, we document the changing nature of friendship networks and family relations, the particular meanings and uses of different languages and expressions, and the patterns of consumption of Middle Eastern and Asian youth. In these everyday activities these young people contribute to a changing migration heritage and are redefining what it means to be Australian.

Exploring new and emerging models for nonlinear performative works

This dissertation seeks to define and classify potential forms of Nonlinear structure and explore the possibilities they afford for the creation of new musical works. It provides the first comprehensive framework for the discussion of Nonlinear structure in musical works and provides a detailed overview of the rise of nonlinearity in music during the 20th century. Nonlinear events are shown to emerge through significant parametrical discontinuity at the boundaries between regions of relatively strong internal cohesion. The dissertation situates Nonlinear structures in relation to linear structures and unstructured sonic phenomena and provides a means of evaluating Nonlinearity in a musical structure through the consideration of the degree to which the structure is integrated, contingent, compressible and determinate as a whole. It is proposed that Nonlinearity can be classified as a three dimensional space described by three continuums: the temporal continuum, encompassing sequential and multilinear forms of organization, the narrative continuum encompassing processual, game structure and developmental narrative forms and the referential continuum encompassing stylistic allusion, adaptation and quotation. The use of spectrograms of recorded musical works is proposed as a means of evaluating Nonlinearity in a musical work through the visual representation of parametrical divergence in pitch, duration, timbre and dynamic over time. Spectral and structural analysis of repertoire works is undertaken as part of an exploration of musical nonlinearity and the compositional and performative features that characterize it. The contribution of cultural, ideological, scientific and technological shifts to the emergence of Nonlinearity in music is discussed and a range of compositional factors that contributed to the emergence of musical Nonlinearity is examined. The evolution of notational innovations from the mobile score to the screen score is plotted and a novel framework for the discussion of these forms of musical transmission is proposed. A computer coordinated performative model is discussed, in which a computer synchronises screening of notational information, provides temporal coordination of the performers through click-tracks or similar methods and synchronises the audio processing and synthesized elements of the work. It is proposed that such a model constitutes a highly effective means of realizing complex Nonlinear structures. A creative folio comprising 29 original works that explore nonlinearity is presented, discussed and categorised utilising the proposed classifications. Spectrograms of these works are employed where appropriate to illustrate the instantiation of parametrically divergent substructures and examples of structural openness through multiple versioning.

Middle schooling and scientific literacy : bringing the students to science

This study is about young adolescents' engagement in learning science. The middle years of schooling are critical in the development of students' interest and engagement with learning. Successful school experiences enhance dispositions towards a career related to those experiences. Poor experiences lead to negative attitudes and rejection of certain career pathways. At a time when students are becoming more aware, more independent and focused on peer relationships and social status, the high school environment in some circumstances offers more a content-centred curriculum that is less personally relevant to their lives than the social melee surrounding them. Science education can further exacerbate the situation by presenting abstract concepts that have limited contextual relevance and a seemingly difficult vocabulary that further alienates adolescents from the curriculum. In an attempt to reverse a perceived growing disinterest by students to science (Goodrum, Druhan & Abbs, 2011), a study was initiated based on a student-centred unit designed to enhance and sustain adolescent engagement in science. The premise of the study was that adolescent students are more responsive toward learning if they are given an appropriate learning environment that helps connect their learning with life beyond the school. The purpose of this study was to examine the experiences of young adolescents with the aim of transforming school learning in science into meaningful experiences that connected with their lives. Two areas were specifically canvassed and subsumed within the study to strengthen the design base. One area that of the middle schooling ideology, offered specific pedagogical approaches and a philosophical framework that could provide opportunities for reform. The other area, the construct of scientific literacy (OECD, 2007) as defined by Holbrook and Rannikmae, (2009) appeared to provide a sense of purpose for students to aim toward and value for becoming active citizens. The study reported here is a self-reflection of a teacher/researcher exploring practice and challenging existing approaches to the teaching of science in the middle years of schooling. The case study approach (Yin, 2003) was adopted to guide the design of the study. Over a 6-month period, the researcher, an experienced secondary-science teacher, designed, implemented and documented a range of student-centred pedagogical practices with a Year-7 secondary science class. Data for this case study included video recordings, journals, interviews and surveys of students. Both quantitative and qualitative data sources were employed in a partially mixed methods research approach (Leech & Onwuegbuzie, 2009) dominated by qualitative data with the concurrent collection of quantitative data to corroborate interpretations as a means of analysing and developing a model of the dynamic learning environment. The findings from the case study identified five propositions that became the basis for a model of a student-centred learning environment that was able to sustain student participation and thus engagement in science. The study suggested that adolescent student engagement can be promoted and sustained by providing a classroom climate that encourages and strengthens social interaction. Engagement in science can be enhanced by presenting developmentally appropriate challenges that require rigorous exploration of contextually relevant learning environments; supporting students to develop connections with a curriculum that aligns with their own experiences. By setting an environment empathetic to adolescent needs and understandings, students were able to actively explore phenomena collaboratively through developmentally appropriate experiences. A significant outcome of this study was the transformative experiences of an insider, the teacher as researcher, whose reflections provide an authentic model for reforming pedagogy. The model and theory presented became an adjunct to my repertoire for science teaching in the middle years of schooling. The study was rewarding in that it helped address a void in my understanding of middle years of schooling by prompting me to re-think the notion of adolescence in the context of the science classroom. This study is timely given the report "The Status and Quality of Year 11 and 12 Science in Australian Schools" (Goodrum, Druhan & Abbs, 2011) and national curricular changes that are being proposed for science (ACARA, 2009).

Desirable attributes and practices for mentees : mentor teachers' expectations

Research indicates attributes and practices for mentor teachers that can be used for effective mentoring. Universities provide guidelines for preservice teacher (mentee) engagement in schools generally from anecdotal evidence, however, what are desirable attributes and practices for mentees? This qualitative study gathers data from 25 mentor teachers through extended response questionnaire and audio-recorded focus group discussions about attributes and practices for mentees. Findings showed that desirable attributes for mentees included: enthusiasm, being personable, commitment to children, lifelong learning/love of learning, open/reflective to feedback, develop resilience, and taking responsibility for their learning, while desirable practices included: planned and preparation for teaching, reflective practices, understanding school and university policies, knowing students for differentiated learning, and building a teaching repertoire (e.g. teaching strategies, behaviour management, content knowledge, and questioning skills). Preservice teachers need to consider teachers’ suggestions on desirable attributes and practices that can help them achieve positive teaching experiences.

Giving voice to service providers who work with survivors of torture and trauma

Clinicians who support people from refugee and asylum seeking backgrounds are routinely exposed to stories of trauma as part of their work. Hearing these stories can be highly distressing for clinicians, but simultaneously provide opportunities for positive personal growth. Adopting a longitudinal qualitative design, we interviewed twelve service providers at two time points a year apart. We used a semistructured interview protocol and analyzed the data according to interpretative phenomenological analysis. Five superordinate and 19 constituent themes emerged from the analysis at Time 1 and Time 2. We found that participants were both positively and negatively affected by their work, and their experiences remained relatively stable across time. The participants highlighted the use of organizational and personal coping strategies to help minimize distress and maximize wellbeing. Adopting a broad repertoire of such strategies is not only advantageous for the service providers, but ultimately for those people they seek to assist.

A new plasmid display technology for the in vitro selection of functional phenotype–genotype linked proteins

Background: Display technologies which allow peptides or proteins to be physically associated with the encoding DNA are central to procedures which involve screening of protein libraries in vitro for new or altered function. Here we describe a new system designed specifically for the display of libraries of diverse, functional proteins which utilises the DNA binding protein nuclear factor κB (NF-κB) p50 to establish a phenotype–genotype link between the displayed protein and the encoding gene. Results: A range of model fusion proteins to either the amino- or carboxy-terminus of NF-κB p50 have been constructed and shown to retain the picomolar affinity and DNA specificity of wild-type NF-κB p50. Through use of an optimal combination of binding buffer and DNA target sequence, the half-life of p50–DNA complexes could be increased to over 47 h, enabling the competitive selection of a variety of protein–plasmid complexes with enrichment factors of up to 6000-fold per round. The p50-based plasmid display system was used to enrich a maltose binding protein complex to homogeneity in only three rounds from a binary mixture with a starting ratio of 1:108 and to enrich to near homogeneity a single functional protein from a phenotype–genotype linked Escherichia coli genomic library using in vitro functional selections. Conclusions: A new display technology is described which addresses the challenge of functional protein display. The results demonstrate that plasmid display is sufficiently sensitive to select a functional protein from large libraries and that it therefore represents a useful addition to the repertoire of display technologies.

A new plasmid display technology for the in vitro selection of functional phenotype-genotype linked proteins

Background Display technologies which allow peptides or proteins to be physically associated with the encoding DNA are central to procedures which involve screening of protein libraries in vitro for new or altered function. Here we describe a new system designed specifically for the display of libraries of diverse, functional proteins which utilises the DNA binding protein nuclear factor κB (NF-κB) p50 to establish a phenotype-genotype link between the displayed protein and the encoding gene. Results A range of model fusion proteins to either the amino- or carboxy-terminus of NF-κB p50 have been constructed and shown to retain the picomolar affinity and DNA specificity of wild-type NF-κB p50. Through use of an optimal combination of binding buffer and DNA target sequence, the half-life of p50-DNA complexes could be increased to over 47 h, enabling the competitive selection of a variety of protein-plasmid complexes with enrichment factors of up to 6000-fold per round. The p50-based plasmid display system was used to enrich a maltose binding protein complex to homogeneity in only three rounds from a binary mixture with a starting ratio of 1:108 and to enrich to near homogeneity a single functional protein from a phenotype-genotype linked Escherichia coli genomic library using in vitro functional selections. Conclusions A new display technology is described which addresses the challenge of functional protein display. The results demonstrate that plasmid display is sufficiently sensitive to select a functional protein from large libraries and that it therefore represents a useful addition to the repertoire of display technologies.

Art of sleeping - "Like a Thief"

Research background Art of Sleeping’s “Like a Thief” is an EP of popular music produced at Airlock studios and released in 2012 by the record label Dew Process. “Like a Thief” contributes to studies in the field of music production, as well as furthering research into the role of of national radio play in the development of emerging musicians and artists. Using Australian bands such as Boy and Bear as a reference point, the EP showcases the vocal range of Caleb Hodges and investigates possibilities in extending the modes of musicality possible within the recording studio through use of multiple layering of processed keyboards and electric guitar. Scholars such as Ben Eltham and journalists such as Everett True have written about the importance of the support of Australia’s national youth broadcaster Triple J in the early stages of a band’s development. The approach of the production of the EP was conceived with this agenda in mind, and asked, what can we learn about the relationships between popular music production, distribution and consumption, and the role that national public radio has come to play in the Australian context? Research contribution This project has identified that certain avenues of the music industry continue to aligned with Triple J airplay, that these avenues play an important role in the level of success that artists are likely to achieve, and that targeted understanding of music production techniques and aesthetics may contribute to success in this regard. Research significance The EP’s two singles were both in the top 100 most frequently played tracks on Triple J in 2012, and the band were able to leverage this exposure in securing a record deal with Dew Process, along with being selected as part of the competitive peer review process for festival performances such as Splendour in the Grass. The work received positive peer reviews, with indieshuffle writing: “Brisbane's Art of Sleeping are a truly talented band. … the five-piece gained plenty of local attention earlier this year with their stunning single "Empty Hands.” This was the first single off their new EP, Like a Thief, which was produced by the renowned Yanto Browning (The Medics, The Jungle Giants) … The EP includes five tracks of incredible power and sentiment … Title track "Like a Thief” is … [a] standout, again a vast and expansive song which showcases the band's completeness”