Stochastic models for regulatory networks of the genetic toggle switch

Bistability arises within a wide range of biological systems from the λ phage switch in bacteria to cellular signal transduction pathways in mammalian cells. Changes in regulatory mechanisms may result in genetic switching in a bistable system. Recently, more and more experimental evidence in the form of bimodal population distributions indicates that noise plays a very important role in the switching of bistable systems. Although deterministic models have been used for studying the existence of bistability properties under various system conditions, these models cannot realize cell-to-cell fluctuations in genetic switching. However, there is a lag in the development of stochastic models for studying the impact of noise in bistable systems because of the lack of detailed knowledge of biochemical reactions, kinetic rates, and molecular numbers. In this work, we develop a previously undescribed general technique for developing quantitative stochastic models for large-scale genetic regulatory networks by introducing Poisson random variables into deterministic models described by ordinary differential equations. Two stochastic models have been proposed for the genetic toggle switch interfaced with either the SOS signaling pathway or a quorum-sensing signaling pathway, and we have successfully realized experimental results showing bimodal population distributions. Because the introduced stochastic models are based on widely used ordinary differential equation models, the success of this work suggests that this approach is a very promising one for studying noise in large-scale genetic regulatory networks.

Surveying the state of higher education in energy efficiency, in Australian engineering curriculum

This paper presents the method and results of a survey of 27 of the 33 Australian universities teaching engineering education in late 2007, undertaken by The Natural Edge Project (hosted by Griffith University and the Australian National University) and supported by the National Framework for Energy Efficiency. This survey aimed to ascertain the extent of energy efficiency (EE) education, and to identify preferred methods to assist in increasing the extent to which EE education is embedded in engineering curriculum. In this paper the context for the survey is supported by a summary of the key results from a variety of surveys undertaken over the last decade internationally. The paper concludes that EE education across universities and engineering disciplines in Australia is currently highly variable and ad hoc. Based on the results of the survey, this paper highlights a number of preferred options to support educators to embed sustainability within engineering programs, and future opportunities for monitoring EE, within the context of engineering education for sustainable development (EESD).

The impact of nonlinear exposure risk relationships on seasonal time series data: modelling danish neonatal birth anthropometric data

Background Birth weight and length have seasonal fluctuations. Previous analyses of birth weight by latitude effects identified seemingly contradictory results, showing both 6 and 12 monthly periodicities in weight. The aims of this paper are twofold: (a) to explore seasonal patterns in a large, Danish Medical Birth Register, and (b) to explore models based on seasonal exposures and a non-linear exposure-risk relationship. Methods Birth weight and birth lengths on over 1.5 million Danish singleton, live births were examined for seasonality. We modelled seasonal patterns based on linear, U- and J-shaped exposure-risk relationships. We then added an extra layer of complexity by modelling weighted population-based exposure patterns. Results The Danish data showed clear seasonal fluctuations for both birth weight and birth length. A bimodal model best fits the data, however the amplitude of the 6 and 12 month peaks changed over time. In the modelling exercises, U- and J-shaped exposure-risk relationships generate time series with both 6 and 12 month periodicities. Changing the weightings of the population exposure risks result in unexpected properties. A J-shaped exposure-risk relationship with a diminishing population exposure over time fitted the observed seasonal pattern in the Danish birth weight data. Conclusion In keeping with many other studies, Danish birth anthropometric data show complex and shifting seasonal patterns. We speculate that annual periodicities with non-linear exposure-risk models may underlie these findings. Understanding the nature of seasonal fluctuations can help generate candidate exposures.

Engineering sustainable solutions program : critical literacies for engineers portfolio

Purpose While a number of universities in Australia have embraced concepts such as project/problem‐based learning and design of innovative learning environments for engineering education, there has been a lack of national guidance on including sustainability as a “critical literacy” into all engineering streams. This paper was presented at the 2004 International Conference on Engineering Education in Sustainable Development (EESD) in Barcelona, Spain, outlining a current initiative that is seeking to address the “critical literacy” dilemma. Design/methodology/approach The paper presents the positive steps taken by Australia's peak engineering body, the Institution of Engineers Australia (EA), in considering accreditation requirements for university engineering courses and its responsibility to ensure the inclusion of sustainability education material. It then describes a current initiative called the “Engineering Sustainable Solutions Program – Critical Literacies for Engineers Portfolio” (ESSP‐CL), which is being developed by The Natural Edge Project (TNEP) in partnership with EA and Unesco. Findings Content for the module was gathered from around the world, drawing on research from the publication The Natural Advantage of Nations: Business Opportunities, Innovation, and Governance in the Twenty‐first Century. Parts of the first draft of the ESSP‐CL have been trialled at Griffith University, Queensland, Australia with first year environmental engineering students, in May 2004. Further trials are now proceeding with a number of other universities and organisations nationally and internationally. Practical implications It is intended that ESSP‐CL will be a valuable resource to universities, professional development activities or other education facilities nationally and internationally. Originality/value This paper fulfils an identified information/resources need.

Improving the provision of learning assistance services in higher education

This study is motivated by the need to look continually for ways to improve Griffith University's learning assistance services so that they meet the changed needs of stakeholders and are at the same time cost-effective and efficient. This study uses the conceptual tools of cultural-historical activity theory and expansive visibilisation to investigaate the developmenet and transformation of learning assistance services at Griffith University, one of Australia's largest mult-campus universities.

The design and development of an undergraduate signal processing laboratory

The School of Electrical and Electronic Systems Engineering of Queensland University of Technology (like many other universities around the world) has recognised the importance of complementing the teaching of signal processing with computer based experiments. A laboratory has been developed to provide a "hands-on" approach to the teaching of signal processing techniques. The motivation for the development of this laboratory was the cliche "What I hear I remember but what I do I understand." The laboratory has been named as the "Signal Computing and Real-time DSP Laboratory" and provides practical training to approximately 150 final year undergraduate students each year. The paper describes the novel features of the laboratory, techniques used in the laboratory based teaching, interesting aspects of the experiments that have been developed and student evaluation of the teaching techniques

Fiduciary Duty and the Atmospheric Trust

This book explores the application of concepts of fiduciary duty or public trust in responding to the policy and governance challenges posed by policy problems that extend over multiple terms of government or even, as in the case of climate change, human generations. The volume brings together a range of perspectives including leading international thinkers on questions of fiduciary duty and public trust, Australia's most prominent judicial advocate for the application of fiduciary duty, top law scholars from several major universities, expert commentary from an influential climate policy think-tank and the views of long-serving highly respected past and present parliamentarians. The book presents a detailed examination of the nature and extent of fiduciary duty, looking at the example of Australia and having regard to developments in comparable jurisdictions. It identifies principles that could improve the accountability of political actors for their responses to major problems that may extend over multiple electoral cycles.

Stochastic modelling of T cell homeostasis for two competing clonotypes via the master equation

Stochastic models for competing clonotypes of T cells by multivariate, continuous-time, discrete state, Markov processes have been proposed in the literature by Stirk, Molina-París and van den Berg (2008). A stochastic modelling framework is important because of rare events associated with small populations of some critical cell types. Usually, computational methods for these problems employ a trajectory-based approach, based on Monte Carlo simulation. This is partly because the complementary, probability density function (PDF) approaches can be expensive but here we describe some efficient PDF approaches by directly solving the governing equations, known as the Master Equation. These computations are made very efficient through an approximation of the state space by the Finite State Projection and through the use of Krylov subspace methods when evolving the matrix exponential. These computational methods allow us to explore the evolution of the PDFs associated with these stochastic models, and bimodal distributions arise in some parameter regimes. Time-dependent propensities naturally arise in immunological processes due to, for example, age-dependent effects. Incorporating time-dependent propensities into the framework of the Master Equation significantly complicates the corresponding computational methods but here we describe an efficient approach via Magnus formulas. Although this contribution focuses on the example of competing clonotypes, the general principles are relevant to multivariate Markov processes and provide fundamental techniques for computational immunology.

Analysing mentoring dialogues for developing a preservice teacher’s classroom management practices

Mentors (cooperating classroom teachers) have a shared responsibility with universities for developing preservice teachers’ pedagogical practices, particularly towards becoming reflective practitioners. Preservice teachers need to participate actively in their own learning, by reflecting and acting on the mentor’s constructive feedback provided during planning and feedback dialogue sessions. This case study uses feedback practices outlined within a five-factor mentoring model to analyse dialogue between a mentor and her respective mentee during different stages in their school-based programs (first practicum). This investigation uses multiple data sources such as video and audio-recorded interviews, archival documents from participants such as lesson plans, reflections and reports to examine preservice teacher’s reflections and implementations of practice as a result of her mentor’s feedback (e.g., establish expectations, review lesson plans, observe teaching then provide oral and written feedback, and evaluate progress). Findings indicated that reflective thinking was more apparent when the mentor did not dominate conversations but instead asked astute pedagogical knowledge questions to facilitate the mentee’s reflections on practice.