Living systems

2013 opportunities: research projects

Academic staff

Academic name


Professor Steve Simpson

Charles Perkins Centre

School of Biological Sciences, Faculty of Science

Professor Max Bennet

Brain and Mind Research Institute (BMRI)

Professor John Crawford

Charles Perkins Centre

Professor Madeleine Beekman

School of Biological Sciences, Faculty of Science

A/Professor Mike Charleston

Engineering and Information Technologies

A/Professor Mary Myerscough

School of Mathematics and Statistics, Faculty of Science

Professor Liaquat Hossain

Engineering and Information Technologies

Professor Louise Baur

Sydney Medical School

Professor Ian Caterson

Charles Perkins Centre

A/Professor Tim  Gill

Sydney Medical School

Research projects

Modelling biological interactions: from individuals to ecosystems

Continued production of healthy food depends on the maintenance of ecosystems and associated services. It has long been considered a Holy Grail among ecologists to discover general principles of population interactions, although such principles remain elusive.

Ecologists have recently argued that an understanding of ecological interactions must be founded on models that take into account how animals actually behave and work. Developing such models will provide a new quantitative ecology and a paradigm shift in the biological sciences.

Using a modelling framework the project will explore the links between the traits of individual organisms, populations and communities. This will involve integrating recent advances in three disciplines:

(a) agent-based modelling, whereby interacting individuals following biologically defined local rules generate complex patterns at larger scales

(b) state-space geometric models of nutrition that enable salient resources, organismal traits and their interactions to be identified and quantified

(c) models for representing environments across multiple scales, with which agents can interact in silico.

Models will be tested and developed in laboratory and field experiments on locusts, social insects, large mammal herbivores and soil organisms.

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Nutrition and the origin of phenotype

Phenotype is an emergent consequence of the interaction between processes at the level of gene expression and the nutritional and physical environment at the whole-organism and community level.

This interaction is poorly understood at the mechanistic level and this project will aim to further develop ongoing work on theoretical models for this interaction that can be used to understand how organisms adapt to different nutritional environments.

Plants and fungi offer convenient model systems because of their importance for soil and primary food production, and also because of their contrasting growth forms. Many plants undergo determinate growth meaning that they pass through prescribed developmental phases leading up to reproduction and senescence.

The fungi by contrast undergo indeterminate growth and can persist indefinitely in time and spatial extent. This has significant implications for the way that the environmental variability interacts with developmental progression and partitioning of nutritional resources.

This in turn affects the phenotype dynamics in these organisms, and therefore for the structure and functioning of communities.

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Securing the future of water and soil

Agricultural soil degradation threatens to reduce global food production by 30% in the next 20 years unless trends are reversed. Furthermore, even moderately degraded soil stores fifty per cent less water making irrigation and storage of rain water extremely inefficient. Finally, soil is the source of almost all of the nutrition required to sustain human health.

This project aims to develop a dynamical systems model of the interactions in the soil-plant-microbe system that will form the theoretical foundation of approaches to reverse these trends. It will focus on the role of carbon in fuelling a novel homeostatic mechanism in soil.

This mechanism results from the interaction between microbial activity and the packing of soil particles and gives rise to the spontaneous organisation of soil at scales that govern microbial activity and hydraulic properties. It acts to recover structure and natural fertility and, together with coordinated management of the plant community, yield beneficial hydrological and nutritional properties of soil.

In helping to secure soil and water using carbon, the approach has the potential to also contribute significantly to the sequestration of carbon in soil and so mitigate the effects of climate change.

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Do genes have memory?

Every cell in an organism has the same DNA, however, as cells proliferate in early development, or during growth, some cells begin to behave differently as a result of exposure to different environments or stimuli.

These changes can become irreversible even after the environment changes or the stimulus is removed. There is growing evidence that although these behavioural changes cannot be explained in terms of changes in the DNA sequence of the cells, they can be inherited as cells divide, and in some cases can be inherited when the organism reproduces.

Thus, offspring can inherit behaviours from their parents that arose as a consequence of environments that they themselves have never experienced. The consequences of such epigenetic regulation of behaviour are profound as it opens up the possibility that cells such as cancer cells, or organisms such as crop plants, can be pre-conditioned to behave in desirable ways by exposing them or their parents to prescribed stimuli.

The role of transgenerational epigenetic inheritance in important environmentally-related diseases such as obesity and cardio-vascular disease has relatively recently come to light and has fundamentally important implications for our understanding of predisposition to disease and the crucial role of both paternal and maternal nutrition in pre- and post-conception periods.

It also changes the way we think about evolution and natural selection. This project will aim to elucidate the mechanisms underlying epigenetic processes by studying the phenomenon in different but complementary systems and building computational models for the related interaction networks.

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The evolutionary ecology of complex microbial communities

Soil and the resident microbial community support all terrestrial life and provide ecosystem services of such value to render them irreplaceable. These services include climate regulation, flood prevention, the provision of fresh water and perhaps most importantly, agriculture.

Similarly, the microbial community in the gut perform a multitude of critical processes that maintain human health, including nutrition, immunology and signalling through the gut-brain axis.

These systems share common underlying challenges in their complexity, difficulty of measurement and the lack of useful laboratory models. Nevertheless, progress has been made and both areas will benefit from a mutual sharing of technologies, concepts and approaches.

This project will aim to draw together the conceptual developments in both gut and soil biology to develop a holistic theory of the link between microbial community structure, nutritional complexity and the function and resilience of the system.

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Complex brain networks and nutrition

There have been major advances in the quantitative description of complex brain network organisations. These networks possess modularity, connected hubs and small-world topology. This occurs at both the level of single neurons as well as at the level of complete brain neuroimaging.

Techniques such as human electroencephalography as well as structural and functional magnetic resonance imaging and animal positron emission tomography are available at the Brain and Mind Research Institute to collect data and test hypotheses concerning these networks.

We are particularly interested in the analysis of networks involving modules in the prefrontal cortex and their interaction with modules in the limbic cortex which play the central role in stress, anxiety and depression, and where nutrition and lifestyle play a very significant role.

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New approaches to early detection of chronic disease

The program will provide a systematic review of empirical studies of health literacy to indicate the limitations of current literature and to highlight the importance of the proposed research agenda on social networks on preventive healthcare.

In particular, it is noted that the individualistic premise of current literature in which individuals are treated as isolated and passive actors. Thus, low health literacy is considered simply as an individual trait independent of support and resources in an individual's social environment.

To remedy this, this research will take into account social support network that people can draw on when problems arise due to their health literacy limitations. Examination of the proposed agenda will make two main contributions:  

– First, we will gain a better understanding of the causal effects of health literacy and identify missing links in the delivery of care for patients with low health literacy.

– Second, if social support network buffers the adverse effects of low health literacy, more effective interventions can be designed to address differences in individuals' social support network system in addition to individual differences in reading and comprehension. More targeted and more cost-efficient efforts could also be taken to identify and reach those who not only have low health literacy but also lack the resources and support to bridge the unmet literacy demands of their health conditions.

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Social network effects on delivery of quality health care

The novelty of this research lies in how it draws on structural properties of individuals in a social and health care network to explain health outcomes.

With the pervasive growth of information and communication technologies (ICT), social network studies now encompass computer supported cooperative networks, online communities and virtual teams in its realm of explaining the link between the various social and healthcare networks that support individual recovery and or treatments for chronic disease and mental health.

Aligning with the social network perspective of perceiving individual outcomes as the consequence of network structure, this research constructs a theoretical framework for understanding individual performance in the domain of integrated care and general practice.

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Physical, mental and psychological health through personal networks

Family network and social network are strongly associated with health assessment for elderly people. Based on the findings from this study, family network and social network should be considered as important factors in developing health promotion programs for elderly people.

We explore the underlying relationships between the personal social networks and its impact on physical, mental and psychological health of aging population. In particular, we aim to examine the impact of family network and social network on individual physical, mental, and psychological health for each surveyed country as well at macro level exploring aggregate level dataset.

Focusing on the micro level, we cluster the data samples on individual demographic characteristics of age, sex, and locality of birth place. We then test the impact of family network and social network on physical, mental and psychological health of elderly people using approaches similar to a macro level for each cluster.

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