Flux balance analysis of biological systems: applications and challenges

Systems level modelling and simulations of biological processes are proving to be invaluable in obtaining a quantitative and dynamic perspective of various aspects of cellular function. In particular, constraint-based analyses of metabolic networks have gained considerable popularity for simulating cellular metabolism, of which flux balance analysis (FBA), is most widely used. Unlike mechanistic simulations that depend on accurate kinetic data, which are scarcely available, FBA is based on the principle of conservation of mass in a network, which utilizes the stoichiometric matrix and a biologically relevant objective function to identify optimal reaction flux distributions. FBA has been used to analyse genome-scale reconstructions of several organisms; it has also been used to analyse the effect of perturbations, such as gene deletions or drug inhibitions in silico. This article reviews the usefulness of FBA as a tool for gaining biological insights, advances in methodology enabling integration of regulatory information and thermodynamic constraints, and finally addresses the challenges that lie ahead. Various use scenarios and biological insights obtained from FBA, and applications in fields such metabolic engineering and drug target identification, are also discussed. Genome-scale constraint-based models have an immense potential for building and testing hypotheses, as well as to guide experimentation.

Laboratory information management software for genotyping workflows: Applications in high throughput crop genotyping

Background: With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow Results: A laboratory information management system (LIMS) has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat) genotyping data from the legume (chickpea, groundnut and pigeonpea) and cereal (sorghum and millets) crops of importance in the semi-arid tropics. Conclusions: A laboratory information management system is available that has been found useful in the management of microsatellite genotype data in a moderately high throughput genotyping laboratory. The application with source code is freely available for academic users and can be downloaded from http://www.icrisat.org/bt-software-d-lims.htm

Preservice early childhood teachers and designers partnering for change at The Lone Pine Koala Sanctuary: An interdisciplinary education and design for sustainability project

This presentation discusses and critiques a current case study of a project in which Early Childhood preservice teachers are working in partnership with Design students to develop principles and concepts for the design and construction of an early childhood centre. This centre, to be built on the grounds of the iconic Lone Pine Koala Sanctuary in Brisbane , focuses on Education for Sustainability (EfS), sustainable design and sustainable business. Interdisciplinary initiatives between QUT staff and students from two Faculties (Education and Creative Industries) have been situated in the real –world context of this project. This practical, authentic project has seen stakeholders take an interdisciplinary approach to sustainability, opening up new ways of thinking about early childhood centre design, particularly with respect to operation and function. Interdisciplinarity and a commitment to genuine partnerships have created intellectual spaces to re-think the potential of the disciplines to be interwoven so that future professionals from different fields might come together to learn from each other and to address the sustainability imperative. The case study documents and explores the possibilities that the Lone Pine project offers for academics and students from Early Childhood and Design to collaboratively inform the Sanctuary’s vision for the Centre. The research examines how students benefit from practical, real world, community-integrated learning; how academic staff across two disciplines are able to work collaboratively within a real-world context; and how external stakeholders experience and benefit from the partnership with university staff and students. Data were collected via a series of focus group and individual interviews designed to explore how the various stakeholders (staff, students, business partners) experienced their involvement in the interdisciplinary project. Inductive and deductive thematic analysis of these data suggest many benefits for participants as well as a number of challenges. Findings suggest that the project has provided students with ‘real world’ partnerships that reposition early childhood students’ identities from ‘novice’ to ‘professional’, where their knowledge, expertise and perspectives are simultaneously validated and challenged in their work with designers. These partnerships are enabling preservice teachers to practice a new model of early childhood leadership in sustainability, one that is vital for leading for change in an increasingly complex world. This presentation celebrates, critiques and problematises this project, exploring wider implications for other contexts in which university staff and students may seek to work across traditional boundaries, thus building partnerships for change.

Applications of CLIMEX modelling leading to improved biological control

Wilmot Senaratne, Bill Palmer and Bob Sutherst recently published their paper 'Applications of CLIMEX modelling leading to improved biological control' in Proceedings of the 16th Australian Weeds Conference. They looked at three examples where modern climate matching techniques using computer software produces decisions and results than might happen using previous techniques such as climadiagrams. Assessment of climatic suitability is important at various stages of a biological control project; from initial foreign exploration, to risk assessment in preparation for the release of a particular agent, through to selection of release sites that maximise the agent´s chances of initial establishment. It is now also necessary to predict potential future distributions of both target weeds and agents under climate change.

Responses of two species of mesquite to initial and follow-up applications of selected herbicides in a potted trial

Quilpie mesquite (Prosopis velutina) is an invasive woody weed that is believed to have been introduced into south-west Queensland in the 1930s. Following the withdrawal of 2,4,5-T, research on P. pallida resulted in revised recommendations for control of all Prosopis spp. in Queensland. Adoption of many of these recommendations for Quilpie mesquite control produced substandard results. Following a pilot trial, a shade-house experiment was conducted to determine the differences in susceptibility of two species of mesquite, P. velutina and P. pallida, to commonly available herbicides. It was hypothesized that P. velutina was less susceptible than P. pallida, based upon claims that the registered chemical recommendations for Prosopis spp. were not sufficiently effective on P. velutina. Nine foliar herbicide treatments were applied to potted shade-house plants. Treatment effects indicated differing susceptibility between the two species. P. velutina consistently showed less response to metsulfuron, fluroxypyr, 2,4-D/picloram and triclopyr/picloram, compared to the glyphosate formulations, where negligible differences occurred between the two species. The response to glyphosate was poor at all rates in this experiment. Re-application of herbicides to surviving plants indicated that susceptibility can decrease when follow-up application is in autumn and the time since initial application is short. The relationship between leaf structure and the volume of spray adhering to a plant was assessed across species. The herbicide captured by similar-sized plants of each species differed, with P. pallida retaining a greater volume of herbicide.

Constellations: A participatory, online application for research collaboration in higher education interdisciplinary courses

The research establishes a model for online learning centering on the needs of integrative knowledge practices. Through the metaphor of Constellations, the practice-based research explores the complexities of working within interdisciplinary learning contexts and the potential of tools such as the Folksonomy learning platform for providing necessary conceptual support.

Remote sensing applications for cotton.

This paper compares classified normalized difference vegetation index images of cotton crops derived from both low and high resolution satellite imagery to determine the most accurate and feasible option for Australian cotton growers. It also demonstrates a rapid automated processing and internet delivery system for distributing satellite SPOT-2 imagery. Also provided is the profile of two case studies conducted in the Darling Towns demonstrating the potential benefit of adopting this technology for improving in-season agronomic crop assessments and therefore enable improved management decisions to be made.

Future switching technology: bacterial protein-based programmable all-optical switch for integrated optics applications?

We report on the bacterial protein-based all-optical switches which operate at low laser power, high speed and fulfil most of the requirements to be an ideal all-optical switch without any moving parts involved. This consists of conventional optical waveguides coated with bacteriorhodopsin films at switching locations. The principle of operation of the switch is based on the light-induced refractive index change of bacteriorhodopsin. This approach opens the possibility of realizing proteinbased all-optical switches for communication network, integrated optics and optical computers.

Heat pipes-concepts, materials and applications

The heat pipe is an innovative engineering structure characterized by its capacity to transfer large quantities of heat through relatively small cross-sectional areas with very small temperature differences; it also possesses high thermal conductance and low thermal impedance. In recent times, heat pipes in various forms and designs have found a wide variety of applications. This paper briefly presents the basic concepts of heat pipes, recent innovations in design and their applications.

Adventures in plant anatomy – not just a pigment of my imagination

An overview of teaching and research activities in the area of plant anatomy at QUT is provided. The current status of teaching of technical skills in plant anatomy is discussed briefly. Examples of applications of plant anatomy to a diverse range of fields are provided, including the crossover between art and science.

Scoping genetic tools, their limitations and applications for wild fisheries management

FRDC has commissioned a review of the role that existing and future genetic technologies may play in addressing critical challenges facing the exploitation of wild fisheries. Wild fisheries management has been assisted by genetic research for over 50 years and in Australia, this research has been largely funded by FRDC. Both fisheries management and the methods of genetic analysis have changed significantly during this time. Given these dynamics, as well as perceptions that communication between fisheries managers and geneticists has been poor in some cases, there is a strong need to reassess the ways in which genetic research can contribute to fisheries and for all stakeholders to critically examine each other's needs and capabilities.

Pre-service early childhood teachers and designers partnering for change at The Lone Pine Koala Sanctuary: An interdisciplinary education and design for sustainability project

This presentation discusses and critiques a current case study of a project in which Early Childhood preservice teachers are working in partnership with Design students to develop principles and concepts for the design and construction of an early childhood centre. This centre, to be built on the grounds of the iconic Lone Pine Koala Sanctuary in Brisbane , focuses on Education for Sustainability (EfS), sustainable design and sustainable business. Interdisciplinary initiatives between QUT staff and students from two Faculties (Education and Creative Industries) have been situated in the real –world context of this project. This practical, authentic project has seen stakeholders take an interdisciplinary approach to sustainability, opening up new ways of thinking about early childhood centre design, particularly with respect to operation and function. Interdisciplinarity and a commitment to genuine partnerships have created intellectual spaces to re-think the potential of the disciplines to be interwoven so that future professionals from different fields might come together to learn from each other and to address the sustainability imperative. The case study documents and explores the possibilities that the Lone Pine project offers for academics and students from Early Childhood and Design to collaboratively inform the Sanctuary’s vision for the Centre. The research examines how students benefit from practical, real world, community-integrated learning; how academic staff across two disciplines are able to work collaboratively within a real-world context; and how external stakeholders experience and benefit from the partnership with university staff and students. Data were collected via a series of focus group and individual interviews designed to explore how the various stakeholders (staff, students, business partners) experienced their involvement in the interdisciplinary project. Inductive and deductive thematic analysis of these data suggest many benefits for participants as well as a number of challenges. Findings suggest that the project has provided students with ‘real world’ partnerships that reposition early childhood students’ identities from ‘novice’ to ‘professional’, where their knowledge, expertise and perspectives are simultaneously validated and challenged in their work with designers. These partnerships are enabling preservice teachers to practice a new model of early childhood leadership in sustainability, one that is vital for leading for change in an increasingly complex world. This presentation celebrates, critiques and problematises this project, exploring wider implications for other contexts in which university staff and students may seek to work across traditional boundaries, thus building partnerships for change.

Genotyping for genetic association studies: Methods and applications

In this thesis, two separate single nucleotide polymorphism (SNP) genotyping techniques were set up at the Finnish Genome Center, pooled genotyping was evaluated as a screening method for large-scale association studies, and finally, the former approaches were used to identify genetic factors predisposing to two distinct complex diseases by utilizing large epidemiological cohorts and also taking environmental factors into account. The first genotyping platform was based on traditional but improved restriction-fragment-length-polymorphism (RFLP) utilizing 384-microtiter well plates, multiplexing, small reaction volumes (5 µl), and automated genotype calling. We participated in the development of the second genotyping method, based on single nucleotide primer extension (SNuPeTM by Amersham Biosciences), by carrying out the alpha- and beta tests for the chemistry and the allele-calling software. Both techniques proved to be accurate, reliable, and suitable for projects with thousands of samples and tens of markers. Pooled genotyping (genotyping of pooled instead of individual DNA samples) was evaluated with Sequenom s MassArray MALDI-TOF, in addition to SNuPeTM and PCR-RFLP techniques. We used MassArray mainly as a point of comparison, because it is known to be well suited for pooled genotyping. All three methods were shown to be accurate, the standard deviations between measurements being 0.017 for the MassArray, 0.022 for the PCR-RFLP, and 0.026 for the SNuPeTM. The largest source of error in the process of pooled genotyping was shown to be the volumetric error, i.e., the preparation of pools. We also demonstrated that it would have been possible to narrow down the genetic locus underlying congenital chloride diarrhea (CLD), an autosomal recessive disorder, by using the pooling technique instead of genotyping individual samples. Although the approach seems to be well suited for traditional case-control studies, it is difficult to apply if any kind of stratification based on environmental factors is needed. Therefore we chose to continue with individual genotyping in the following association studies. Samples in the two separate large epidemiological cohorts were genotyped with the PCR-RFLP and SNuPeTM techniques. The first of these association studies concerned various pregnancy complications among 100,000 consecutive pregnancies in Finland, of which we genotyped 2292 patients and controls, in addition to a population sample of 644 blood donors, with 7 polymorphisms in the potentially thrombotic genes. In this thesis, the analysis of a sub-study of pregnancy-related venous thromboses was included. We showed that the impact of factor V Leiden polymorphism on pregnancy-related venous thrombosis, but not the other tested polymorphisms, was fairly large (odds ratio 11.6; 95% CI 3.6-33.6), and increased multiplicatively when combined with other risk factors such as obesity or advanced age. Owing to our study design, we were also able to estimate the risks at the population level. The second epidemiological cohort was the Helsinki Birth Cohort of men and women who were born during 1924-1933 in Helsinki. The aim was to identify genetic factors that might modify the well known link between small birth size and adult metabolic diseases, such as type 2 diabetes and impaired glucose tolerance. Among ~500 individuals with detailed birth measurements and current metabolic profile, we found that an insertion/deletion polymorphism of the angiotensin converting enzyme (ACE) gene was associated with the duration of gestation, and weight and length at birth. Interestingly, the ACE insertion allele was also associated with higher indices of insulin secretion (p=0.0004) in adult life, but only among individuals who were born small (those among the lowest third of birth weight). Likewise, low birth weight was associated with higher indices of insulin secretion (p=0.003), but only among carriers of the ACE insertion allele. The association with birth measurements was also found with a common haplotype of the glucocorticoid receptor (GR) gene. Furthermore, the association between short length at birth and adult impaired glucose tolerance was confined to carriers of this haplotype (p=0.007). These associations exemplify the interaction between environmental factors and genotype, which, possibly due to altered gene expression, predisposes to complex metabolic diseases. Indeed, we showed that the common GR gene haplotype associated with reduced mRNA expression in thymus of three individuals (p=0.0002).

Real-time locating systems applications in construction

Real-time locating systems (RTLSs) are considered an effective way to identify and track the location of an object in both indoor and outdoor environments. Various RTLSs have been developed and made commercially available in recent years. Research into RTLSs in the construction sector is ubiquitous and results have been published in many construction-related academic journals over the past decade. A succinct and systematic review of current applications would help academics, researchers and industry practitioners in identifying existing research deficiencies and therefore future research directions. However, such a review is lacking to date. This paper provides a framework for understanding RTLS research and development in the construction literature over the last decade. The research opportunities and directions of construction RTLS are highlighted. Background information relating to construction RTLS trends, accuracy, deployment, cost, purposes, advantages and limitations is provided. Four major research gaps are identified and research opportunities and directions are highlighted.

Plasma polymerised thin films for flexible electronic applications

The significant advancement and growth of organic and flexible electronic applications demand materials with enhanced properties. This paper reports the fabrication of a nonsynthetic polymer thin film using radio frequency plasma polymerisation of 3,7-dimethyl-1,6-octadien-3-ol. The fabricated optically transparent thin film exhibited refractive index of approximately 1.55 at 500 nm and rate of deposition was estimated to be 40 nm/min. The surface morphology and chemical properties of the thin films were also reported in this paper. The optical band gap of the material is around 2.8 eV. The force of adhesion and Young's modulus of the linalool polymer thin films were measured using force-displacement curves obtained from a scanning probe microscope. The friction coefficient of linalool polymer thin films was measured using the nanoscratch test. The calculated Young's modulus increased linearly with increase in input power while the friction coefficient decreased.