All future 2013 events

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Stable Isotopes in Biosphere Systems Workshop (SIBS)   View Summary
3 February 2013 to 10 February 2013

WHEN: 3-10 February 2013


The use of the behaviour of stable isotopes to decipher and monitor biosphere processes continues to expand. Greater accessibility, portability, speed and sensitivity of analytical instruments is allowing for wider uses and for explorations of previously difficult to study systems.

This course is directed to post-graduate students and post-docs with biological/ecological backgrounds who are interested in applying stable isotope tools for their research.

We will focus on stable isotopes of C, N and O and their behaviour in plant, plant-soil, plant-atmosphere, soil-microbe, soil-atmosphere and plant-microbe processes.

Learning will be structured around lectures by specialists and student-led projects with direct support by course instructors (see SCHEDULE).

Please click below to see:


Instruments that will be available for demonstrations as well as for individual/group projects include:

  • Tunable Diode Laser Absorption Spectrometer (TGA100A, Cambell Scientific) for CO2 online in real-time.
  • Picarro CO2 cavity ring-down spectrometer (G1101-i) for CO2 in air.
  • Picarro H2O cavity ring-down spectrometer (L1102i) for oxygen (δ18 O) and hydrogen (δ2 H).
  • Los Gatos Isotopic water Analyser (IWA-45EP) for oxygen and hydrogen.
  • Ratio Mass Spectrometer (IRMS; Delta V Advantage, Thermo Finnigan) for C and N in solids and CO2.


The course will take place at the Cobbitty Campus of the University of Sydney. Accommodations are available in conveniently located University Lodge. A tuition cost of $1000 will cover course cost, accommodation and meals. Competitive scholarships are available.

More information about Cobbitty Campus is available here and on Google here.


  • University of Sydney: Margaret Barbour (MB), Yolima Carrillo (YC), Feike Dijkstra (FD),Peter Franks (PF), Jia Hu (JH), Claudia Keitel (CK), Andrew Merchant (AM), Kevin Simonin (KS)
  • Australian National University: Susanne von Caemmerer (SVC), Lucas Cernusak (LC), John Evans (JE), Graham Farquhar (GF)
  • Institute for Landscape Biogeochemistry (Germany): Arthur Gessler (AG)
  • Max-Planck-Institute for Biogeochemistry (Germany): Gerd Gleixner (GG)


Please email the course organizers by 23 November 2012 (DEADLINE):

Kevin Simonin
Jia Hu
Yolima Carrillo
Claudia Keitel

ARE Seminar by Professor Robert D Cairns (McGill University)   View Summary
19 February 2013

Faustmann's Formulae for Forest Capital

The relationship of the economics of a simple, stylized forestry to capital theory is studied. Investment and two r-percent rules are discussed. A forest's two resources, the stand and the land, act in conjunction as a single capital asset. If capital is comprehensively defined, there is no role for the concept of an internal rate of return. A forest provides real options in optimal and sub-optimal rotation patterns. Old growth has superficial similarities to a exhaustible resource, but the forest still consists of two resources that, in conjunction, behave comparably to a plantation forest.

Professor Robert D. Cairns is from the Department of Economics and Cireq at McGill University.

All welcome to attend.

DES Seminar by Dr Denis Angers    View Summary
5 March 2013

Soil Carbon Sequestration in Agroecosystems.

Abstract TBA

Dr Denis Angers is a Principal Research Scientist for Agriculture Canada in Quebec and Adjunct Professor, McGill University, Montreal.

All welcome to attend.

Combined DES/PFS Seminar by Professor Salah Sukkarieh (USyd)   View Summary
8 March 2013

The Autonomous Farm


Over the last 5 years there has been a growing interest in the use of automated machinery and software processes amongst various agricultural and environment groups. Interestingly its been more of a technology pull then a push driven by international competitiveness, high labour costs (especially during harvesting), and a shrinking workforce. This talk will present some of our R&D on the use of robotic air and ground vehicles for environment monitoring and more recently in specific horticulture applications. The talk will also present what elements are being seen as important to piece together in defining a futuristic farm that is fully automated.

Professor Sukkarieh is Professor of Robotics and Intelligent Systems at Sydney University andDirector of Research and Innovation - Australian Centre for Field Robotics.

All welcome to attend.

ARE Seminar by A/Prof Greg Hertzler   View Summary
15 March 2013
Climate change and transformation of Australian wheat dominant agriculture. Abstract: The long term sustainability of Australian crop and livestock farms faces a substantial threat in the form of the uncertainty associated with climate change and climate variability. Uncertainties associated with the nature and magnitude of climate impacts presents a challenge for decision-making. Adaptation decisions can be made at the level of (1) adjustments to practices and technologies, (2) changes to production systems, or (3) transformation of industries, for example, by relocation to new geographical areas. Adjustments to existing practices are easy to make relative to changes to production systems or transformations at the industry level. Switching between production regimes requires new investments and infrastructure and can leave assets stranded. These changes can be partially or wholly irreversible but hysteresis effects can make switching difficult and mistakes costly to reverse. Real Options offers a framework to structure thinking and analysis of these difficult choices. Previous work has demonstrated how this decision framework applied to adaptation, referred to as 'Real Options for Adaptive Decisions' (ROADs), extends traditional economic analyses of agricultural investment decisions based on net present values to better represent incomplete knowledge and uncertainty. This project uses transects across space as proxies for future climate scenarios. We draw upon climate data, and data for representative farms, to calibrate real options models. In this report, we present the results of this analysis of the transformation of wheat dominant cropping systems in South Australia, New South Wales, and Western Australia. We find that farmers' decisions, as much as a changing climate, determine how agriculture will be transformed. All welcome to attend
ARE Seminar by Dr Emily Gray (ABARES)   View Summary
22 March 2013

ABARES productivity research - analysis and policies for growth.


Productivity growth, reflecting improvements in the efficiency with which farmers combine market inputs to produce outputs, has been the dominant means by which Australia's agriculture sector has increased output. Ongoing improvements in productivity have also enabled farmers to maintain profitability and the competitiveness of the agriculture sector more broadly. However, there is evidence that agricultural productivity growth has slowed in recent decades. In this presentation Emily Gray discusses ABARES research on measuring and analysing trends in agricultural productivity growth and considers opportunities for governments and industry to promote productivity.

Emily Gray is a research economist in ABARES Productivity, Water and Social Sciences Branch. Since joining ABARES is 2009, Emily has worked on agricultural productivity.

ARE Seminar by PhD candidate Darian Naidoo   View Summary
12 April 2013

Dangerous Information: How Should Youth be Informed About the Returns to Education?


This paper investigates the policy opportunities implied by the potential inaccuracy of youths' expectations regarding the returns to education. Using data from the Cape Area Panel Study in South Africa on actual and expected returns, we investigate a sequential decision making model of educational investment to identify inaccuracy in expectations of the return to grade 12. We also find that about 27% of the return to grade 12 in this context is attributable to the value of accessing higher education options, though this varies by race and gender. We consider different types of information provision to youth about the returns to education. We find that information provision about the average returns that does not include option values may lead to some youth making sub-optimal investment decisions. We conclude that information provision should be targeted (specific to individual characteristics) and that it should be provided in a sequential decision making framework.

DES Seminar by Dr John Turner (Forsci Pty Ltd)   View Summary
19 April 2013

Analysis of long term changes in a radiate pine plantation

Planting of radiata pine at Lidsdale State Forest (near Lithgow, NSW) commenced in 1920 on poor quality farmland. Research related to the relatively poor performance of the plantation commenced in 1961 and covered soils, nutrition, hydrology and nutrition cycling. The plantation is now moving into its third rotation (a rotation is approx. 30 years) and issues on inter-rotational productivity and changes in soils, nutrient distribution and turnover, and hydrology are being addressed. A main issue relates to methodologies, particularly the relationships of short term to long term studies, and the applicability of plot data to the forest, catchment or landscape level.

Dr Turner worked for State Forests of New South Wales for more than 30 years, initially as a Forester, then Senior Research Scientist and for the last 10 years as Director of Research. He completed his Doctorate at the University of Washington and worked with the International Biological Program. Johns' research has been wide ranging and productive. He has published more than 150 scientific publications, on forest nutrition, nutrient cycling, management of forest soils, development of site specific management systems, impacts of harvesting and management of sites, and maintenance and increase of productivity of forest stands. He has undertaken various consultancies with a major focus on analysing potential plantation areas and defining species and management regimes to provide a desired commercial and or environmental outcome for the client. He collaborated in establishing Forsci Pty Ltd. in 1996.

Forsci Pty Ltd specialises in providing high quality scientific information and research to forest managers and planners to improve management and management systems in forests. Major areas of emphasis are soils, tree nutrition, productivity, research review, research design and implementation, salinity, and carbon accumulation in native forests and intensively managed forests including exotic and native plantations, and reclamation areas. Forsci focuses on forest research mainly in collaboration with private companies.

Digital soil mapping under the integral lens   View Summary
24 May 2013
Department seminar series: Digital soil mapping under the integral lens: A post disciplinary approach conceptualising a meta soil model of the future. Sabine Grunwald
DES Seminar by Professor Sabine Grunwald (University of Florida)   View Summary
24 May 2013

Digital Soil Mapping Under the Integral Lens - A Post-disciplinary Approach Conceptualizing a Meta Soil Model of the Future


Population growth, global climate and land use changes, and disturbances have profoundly accelerated soil evolution in the Anthropocene jeopardizing the sustainability of the soil resource at local, regional, and global scales. Digital soil mapping (DSM) and modelling have emerged over the past decades to assess soil properties and processes across various space and time dimensions and have created a multi-disciplinary interface between soil and environmental sciences, geosciences, statistics, geostatistics, computer sciences, and others. I will present few DSM applications from the southeastern U.S. and highlight data fusion strategies, methodologies, and findings. One pertinent question is what role DSM can play in a changing and complexifying world converging to inter-, trans-, and post-disciplinary worldviews. The grand challenges entail to preserve healthy and functioning soils as part of the physio- and biospheres for future generations. In this talk I will adopt the lens of Integral Theory to situate DSM in a post-disciplinary future drawing on integral methodological, ontological, and epistemological pluralism. The dichotomy between interior and exterior perspectives and approaches will be given special attention because it limits further expansion of quantitative soil science. Barriers and opportunities will be outlined to create a meta-paradigmatic soil model of the future.

About Professor Grunwald

Sabine is Professor in the Soil and Water Science Department, University of Florida, U.S. She is Visiting Professor on sabbatical at the Faculty of Agriculture and Environment, University of Sydney (January - July 2013). Her research interests are in soil-landscape modeling, pedometrics, digital soil mapping, and soil and remote sensing applications. Her specific research interest are to: (i) assess the impact of land use and climate change on carbon sequestration and soil & water quality, (ii) elucidate on the impact of environmental stressors on soil and terrestrial carbon, (iii) develop multi-scale predictive models of soil and environmental properties across various spatial and temporal scales, (iv) investigate biophysical feedbacks (soil-vegetation-water-atmosphere interactions) and carbon/nutrient dynamics. She serves on the Editorial Board of Geoderma and is Associate Editor of Soil Sci. Soc. Am. Journal. She has served as member of the Pedometrics Advisory Group since 2011 and was Vice Chair of the Commission of Pedometrics, IUSS (2004-2006). She held several positions in divisions/communities/workgroups in the Soil Science Society of America (SSSA) and American Society of Agronomy (ASA), and is currently Chair of the ASA Community Global Digital Soil Map and was Chair (2008-2012) of the Digital Soil Mapping Workgroup, Div. S-5 Pedology. She teaches several graduate level courses including Soil-Landscape Modeling and GIS in Land Resource Management.

All welcome.

Those that cannot make it to the ATP can join the seminar live by following the link below and registering as a guest.

PFS Seminar by Peri Thomas   View Summary
31 May 2013

Myrtle rust infection: defence gene targets in Eucalyptus grandis


Eucalyptus grandis is an Australian Myrtaceae tree grown for timber in many parts of the world and for which the draft annotated genome sequence was recently released (2011). Known to be susceptible to Puccinia psidii sensu lato (myrtle rust), E. grandis is a useful study organism for investigating host response to this exotic fungal pathogen, first identified in Australia in 2010. Chitinases are present in plants and cleave glycosidic bonds of chitin, the major structural component of fungal cell walls. They are encoded by an important class of genes known to be up-regulated in plants in response to pathogens. Up-regulation of chitinases is also an indicator for systemic acquired resistance (SAR). The current study identified forty chitinase gene models within the E. grandis sequence data. Sequences were aligned and analysed as conforming to the currently recognised chitinase classes (I-IV). Primers were designed for six of these genes and two house-keeping genes that successfully amplified their targets in inoculated and control plants. Inoculated plants had varying responses with 40% resistant to the pathogen. On subsequent inoculation, using the same pathogen, none of the plants were susceptible indicating systemic acquired resistance (SAR). Determining the different classes of chitinases, and development of specific primers, provides the basis for a quantitative expression assay to be conducted on infected E. grandis.

DES Seminar by Mana Gharun (PhD Candidate)   View Summary
31 May 2013

Forests and water in the high country of south-east Australia.

High country eucalypt forests are invaluable sources of freshwater in south-east Australia. Studies of the hydrology of eucalypt forests have focused on ash-type eucalypt species that are highly restricted in their distribution to areas with moderate climates and deep soils. On the other hand, mixed species foothill forests, that comprise the largest proportion of the forest estate in the State of Victoria, are poorly known hydrologically. This presentation comprises four main studies:

  • Study 1: A baseline survey of tree water use in mixed-species forests was conducted within the Cotter catchment and in foothill forests of Victoria. The impact of bushfires on mixed-species forests that was hypothesised to vary from ash-type forests was investigated
  • Study 2: Variations in water use within the catchment were traced down to differences in physiological and anatomical regulations by different eucalypt species
  • Study 3: A soil-plant-atmosphere model was validated for simulating tree water use, and in a different approach a model was proposed and tree water use was mapped across the study catchment.
  • Study 4: Recommendations are given for improving stream flow prediction from forested catchments by theoretical integration of our observations, within a conceptual framework.
ARE Seminar by Professor Chris O'Donnell (University of Queensland)   View Summary
31 May 2013

Econometric Estimates of Productivity and Efficiency Change in the Australian Northern Prawn Fishery


Bayesian methods are used to compute and decompose Fare-Primont indexes of total factor productivity (TFP) change in the Australian Northern Prawn Fishery (NPF). Fare-Primont indexes are used because i) they satisfy all basic axioms from index number theory, ii) they can be exhaustively decomposed into measures of environmental change and efficiency change (i.e., there are no residual `effects'), and iii) they can be computed using only quantity data (i.e., no prices are needed). Bayesian estimation methodology is used because i) it can solve an endogeneity problem that arises in the econometric estimation of multiple-input multiple-output distance functions, ii) it can be used to draw valid finite-sample inferences concerning nonlinear functions of the model parameters (e.g., measures of technical efficiency), and iii) non-sample information (e.g., information provided by economic theory) can be easily incorporated into the estimation process. Results for the NPF for the period 1974--2010 are summarised in terms of characteristics of estimated posterior pdfs for measures of TFP change, environmental change, technical efficiency change, and scale efficiency change.

DES Seminar by Senani Karunaratn (PhD Candidate)   View Summary
7 June 2013

Modelling soil organic carbon in space and time


In recent times there is an increasing interest in the quantification of the variation of soil organic carbon (SOC) in space and time. Quantification of this variation is important since SOC contributes positively to soil functions. In addition, SOC also helps to reduce the impacts of climatic change by storing carbon in soil which is termed "soil carbon sequestration". In order to capture this variation we tested both statistical as well as processes models of SOC namely RothC model. Therefore, this research has examined in detail;

  • assessment of changes in SOC using legacy soil data as the baseline survey
  • mapping the measurable pools of the RothC model at the catchment scale
  • simulation of the SOC across catchment scale with aid of RothC model using readily available spatial data
  • calibration of the rate constants of the RothC model at the catchment scale using Bayesian inverse modelling approach
DES Seminar by Jessica Heath (PhD Candidate)   View Summary
14 June 2013

Wildfire impact on Sydney water supply catchments: vulnerability of the hydrological cycle.


Wildfires can lead to considerable hydrological changes within a sub-catchment which ultimately affects flow at its outlet due to the denudation of vegetation cover and changing of soil properties. Studies in relation to water yield response post-wildfire have been conducted in Victoria, but these studies cannot truly represent vegetative species around Sydney due to their different environmental adaptations. Therefore, the purpose of this research project is to explore the impact of wildfire on the Sydney water supply catchments, examining different components of the hydrological cycle. This research has focused on:

  • Changes in water yield post-wildfire;
  • Soil total carbon and water repellency response;
  • Vegetation recovery using Landsat imagery; and
  • Vegetation recovery using Modis imagery.

All welcome.

Camden Open Day for Schools   View Summary
14 June 2013

Camden Open Day is a full day program especially designed for high school students in years 9-10 interested in the environment, agriculture and veterinary science. Students have the opportunity to explore a research and teaching campus and experience agriculture, environment and veterinary science at the University of Sydney.

Invitation only

DES Seminar by Yunying Fang (PhD Candidate)   View Summary
21 June 2013



Agriculture HSC Seminar   View Summary
27 June 2013

Program and speakers:

9.15am Arrive/Registrations

9.30am Pain relief - addressing animal ethics and welfare in beef cattle

Dr Peter White, Lecturer in Veterinary Physiology, Faculty of Veterinary Science, University of Sydney.

10.00 am Surviving the challenging business of farming

Dr Russell Bush, Senior Lecturer in Livestock Production, Faculty of VeterinaryScience, University of Sydney.

10.30am Break

10.45am Managing grassland ecosystems - an environment of complex


Dr Lachlan Ingram, Senior Research Fellow, Plant Breeding Institute, Faculty of Agriculture and Environment, University of Sydney.

11.15am Adapting to Australia's variable and changing climate

Dr Peter Ampt, Lecturer in Natural Resource Management, Faculty of Agriculture and Environment, University of Sydney.

11.45 am Lunch

12.30pm Seeking statistical success - optimising experimental design

Dr Peter Thomson, Associate Professor in Biometry, Faculty of Veterinary Science, University of Sydney.

1.00pm Entry requirements for degrees in the Faculty's of Veterinary Science;Science; and Agriculture & Environment

Ms Vanda Northwood, Manager, Undergraduate Recruitment and Schools Outreach Science Marketing & Communication Unit, Division of Natural Sciences

2.00pm Finish

Cost: FREE

RSVP: Friday 21st June

Marion Saddington:, ph 9351 1787, fax 9351 1618 or

Russell Bush:, ph 9351 1785, mob 0429 986 022, fax 9351 1693

This includes a sensational sausage sandwich (vegeburgers for vegetarians), drink and notes on the


It is essential that we have an accurate number for catering purposes by this date.

Please inform us of those requiring a vegetarian meal.

DES Seminar by Lucy Lui (PhD Candidate)   View Summary
28 June 2013

Indeterminate Fungal Growth and Nutritional Heterogeneity


Fungi play an important role in ecology. They can be found in nutritionally complex environments. Roots of around 80% of land plant species have an association with fungi and these fungi can utilize up to 20% of net plant photosynthates. We know little about how fungal growth responds to nutritional heterogeneity in the environment. In the last three years, I have used both laboratory experiments and mathematic models as approaches to try and understand this question. In this talk, I will present the results from this study.

All welcome to attend.

DES Seminar by Michael LeBlanc (PhD Candidate, Laval University, Quebec)   View Summary
12 July 2013

Michael LeBlanc, a PhD student in soil and environment at the Department of Soil and Agrifood Engineering, Laval University, Quebec City, Canada, has been working under the supervision of Alex McBratney and Budiman Minasny for the past 3 months. His talk will be about:

Conceptualization of soil classes using numerical classification in Matane and Matapedia regions, Canada

Soil survey is usually conducted with the aim to generate information on the distribution of soil (class) over an area. Conventionally, the process of making soil classes is based on intuitive expert's opinions or a defined set of rules. To improve on this subjective classification approach, we need to quantitatively analyse the information collected from soil survey. The soil profile, described by a sequence of horizons with different morphological characteristics, is usually the unit observation of the soil diversity in an area. Pedometrical techniques allow us to turn this information into more objective soil classes based on the degree of similarity between the soil profiles. The aim of my work is to propose a numerical classification of soils for an agricultural area in the province of Québec, Canada. We used a new fuzzy clustering approach which is partially supervised with modal soil profiles (end members). This technique offers the ability to capture soil classes characterised by extreme properties and low abundance, which is typical in a soil dataset at a regional scale. Numerical classification will give us the quantitative basis to relate the soil class with the conservation and fertilization trials realized in the east part of Canada.

All welcome to attend.

Seminar by Dr Paul Wilson (University of Nottingham, School of Biosciences)   View Summary
15 July 2013

Dr Wilson will speak about his research in the area ofenergy feedstock supply. Bioenergy is one of three main research areas in which Dr Wilson is currently active. He is also active in the areas of Rural Business Research andEconomics, Efficiency and Environment: Farm to Fork.

Further information:

All welcome to attend.

DES Seminar by William Ke Zhao (PhD Candidate)   View Summary
19 July 2013

Complexity and the Macroeconomics of Sustainability: Australian Water Security and Asian Food Security.


Towards the end of the twenty-first century, the impact of climate change on the Murray-Darling Basin could significantly increase. The Murray-Darling Basin is known as Australia's "food bowl" - nearly 40% of the total value of agricultural production in Australia is grown there. Many of the discussions concerning the macroeconomic causes and effects of water security have revolved around optimal economic growth. We develop an alternative economy simulation model based on effective demand - a concept that connects the economic and ecological systems. From this new definition we link income distribution and useful work, and therefore connect Keynesian economics with ecological economics. We apply this technique to the Murray-Darling Basin through three aspects: micro land/water user, micro food consumer and macro economy in order to reflect the feedbacks in the dynamical system and the heterogeneity of agents within it.

In the coming decades, global water shortages and food insecurity pose the real risk of regional food crises leading to conflicts and mass refugee movements. The developing economies of Asia are experiencing serious environmental and social problems that threaten to undermine future development, food security, and regional stability. Previous work has suggested some approaches to deal with the prediction of regional food riots but has not harnessed all of the benefits of system theory based on quantified catastrophic shifts. We develop an index system involving a basal characteristics index, a dynamic factors index, a trigger potency index, a policy effectiveness index and a threat severity index. We fuse the index system and Lorenz-style differential equations in order to predict the threat in the coming decades, given the current situation.

DES Seminar by Derek Yates (PhD Candidate)   View Summary
26 July 2013

Using local and historic data to enhance rainfall forecasts.



DES Seminar Richard Muita (by PhD Candidate )   View Summary
2 August 2013

Dry spells forecasting in Kenya and Australia: Adapting agriculture to climate change.


Kenya and the Murray Darling Basin (MDB) of Australia are mostly arid or semi-arid and key agriculture regions. However, persistent dry periods and the timing of dry spells directly impact the availability of soil moisture and hence crop production. Research on drought in these regions has not yielded desirable results in addressing this problem and the predictive skill of current seasonal forecasts remain relatively low. This thesis therefore investigate the characteristics of dry spells, develops intra and inter-seasonal to annual dry spells forecasts in these regions as well as analyse farmers decisions related to forecasts in Kenya.

All welcome to attend.

ARE Seminar by Professor Francesc Hernandez-Sancho (University of Valencia)   View Summary
15 August 2013

A Management and Global Optimization Model for Water Supply Planning

The integrated water resources management approach has proven to be a suitable option for efficient, equitable and sustainable water management. In water-poor regions experiencing acute and/or chronic shortages, optimization techniques are a useful tool for supporting the decision process of water allocation. In order to maximize the value of water use, a global optimization model was developed which involves multiple supply sources (conventional and non-conventional) and multiple users. Penalties, representing monetary losses in the event of an unfulfilled water demand, have been incorporated into the objective function. This model represents a novel approach which considers water distribution efficiency and the physical connections between water supply and demand points. Subsequent empirical testing using data from a Spanish Mediterranean river basin demonstrated the usefulness of the global optimization model to solve existing water imbalances at the river basin level.

All welcome to attend. Please note change in day from Friday to Thursday.

ARE Seminar by Dr Cong Si Pham (Deakin University)   View Summary
30 August 2013

Is China a Threat to Other Exporters?An Empirical Investigation of Trade in Electronics.


Using data of product-level exports of Asian and South American exporters this paper empirically looks into the effects of Chinese exports in electronics on the intensive and extensive margins of exports of its competitors for the period 1992-2011. Applying the IV approach we found that China's exports increase exports by East Asian and South American exporters while they reduce exports by India especially for the period after the 2007-08 global financial crisis. As for the extensive margin of trade in electronics the results of the IV probit regression show that China adversely influences the probability of having positive exports by its competitors to foreign markets by forcing them to leave these markets or by preventing them from entering these markets. This negative impact on the extensive margin of exports by Chinese competitors is however largest for the period following the 2007 financial crisis.

Cong S. Pham is a Lecturer in Economics at the School of Accounting, Economics and Finance, Deakin University. Before joining Deakin University, from 2005 to 2008, he was working as a Consultant in the Development Research Group of the World Bank in Washington D.C. His research areas are international trade, applied econometrics and economic development. Specifically, he is currently working on topics such as the gravity equation in international trade, the determinants of product specialization in world trade, the relationship between trade liberalization and poverty of Vietnam and the impact of China in world trade…etc. Dr. Cong S. Pham has published in economics journals like JIE and REStat. He holds a Ph.D. in Economics from Syracuse University.

DES Seminar by Marco Harbusch (PhD Candidate)   View Summary
30 August 2013

Xylem conduit structure and adaptation mechanisms of Eucalyptus to environmental conditions


Species in the genus Eucalyptus are the most important constituents of the overstorey in a large number of Australian ecosystems. Tree height is largely limited by hydrological constraints. Xylem vessel structure is responsible for the efficiency of water transport up the tree towards the leaves. Different structural mechanisms within xylem vessels contribute to maximum tree height. The so called 'tapering' of vessels, describing the decreasing diameter of the vessels towards the apex, is one such mechanism.

Wood density is related to xylem architecture such as size and distribution of vessels. A change in wood density will affect hydraulic architecture and consequentially, the height of individual trees. As there is a positive relationship between wood density and temperature and water availability, trees can respond to changes in environmental conditions. The climate in Australia is predicted to become warmer, and in many cases drier. It is therefore reasonable to speculate that changes in wood anatomy caused by climatic changes may lead to a reduction in height and consequently, a reduction in carbon sequestration capacity of an ecosystem on a large scale.

This project contributes to our understanding of plant-water relations of Eucalyptus, and of possible structural adaptations of trees to increasing temperature and/or reduced water availability as a result of climate change. Xylem vessel features that could explain variation in maximum tree height were investigated using a number of species of Eucalyptus growing naturally under a broad range of climatic conditions.

ARE Seminar by Dr Paul Burke (ANU)   View Summary
6 September 2013

Reducing Biomass Dependence in the Home: Evidence from National-Level Data

Indoor air pollution from biomass combustion is an important cause of mortality and poor health outcomes in developing countries. This study employs national-level data for a large sample of countries to investigate the factors that facilitate reductions in residential biomass use. Our results identify female labor force participation and urbanization as more important than income in driving these transitions. The paper also presents a macro-level quantification of the effect of biomass use on mortality rates. The combined results indicate that reduced biomass dependence is a key avenue via which female empowerment leads to improved health outcomes.

All welcome to attend.

DES Seminar by Dr Damien Field   View Summary
6 September 2013

The dimensions of Soil Security


Soil security, an overarching concept of soil motivated by sustainable development, is concerned with the maintenance and improvement of the global soil resource to produce food, fibre and fresh water, contribute to energy and climate sustainability, and to maintain the biodiversity and the overall protection of the ecosystem. Security is used here for soil in the same sense that it is used widely for food and water. It is argued that soil has an integral part to play in the global environmental sustainability challenges of food security, water security, energy sustainability, climate stability, biodiversity, and ecosystem service delivery. Indeed, soil has the same existential status as these issues and should be recognized and highlighted similarly. The concept of soil security is multi-dimensional. It acknowledges the five dimensions of (1) capability, (2) condition, (3) capital, (4) connectivity and (5) codification, of soil entities which encompass the social, economic and biophysical sciences and recognize policy and legal frameworks. The soil security concept is compared with the cognate, but more limited, notions of soil quality, health and protection.

All welcome to attend

DES Seminar by Mike McLaughlin (CSIRO)   View Summary
13 September 2013

Perspectives on new fertilizer formulations to increase nutrient use efficiency


With the increasing cost of plant nutrients and the requirement to increase food production to feed the world's expanding population, there is a need to develop better ways to diagnose nutrient deficiencies in soils and to develop more effective fertilisers to alleviate these deficiencies. Much research is currently on-going to improve the efficiency of fertiliser formulations, and it is important that the fundamental reactions and mechanisms of nutrient dissolution, diffusion and plant uptake are understood if we are to improve fertiliser efficiency. It is also important to evaluate in detail new products that claim to increase nutrient use efficiency to ensure that mechanisms of action claimed are evident. This presentation will examine some of the new phosphorus, sulfur and micronutrient fertilisers developed in the last 5 years as well as enhancers of nutrient use efficiency, with a focus on examining the underlying mechanisms of action and quantification of efficiency under field conditions.

Mike McLaughlin is a Professor in the School of Agriculture Food and Wine and Director of the University of Adelaide Fertiliser Technology Research Centre. He is also a Fellow of CSIRO and works in CSIRO's Sustainable Agriculture Flagship Program. Mike is a graduate of the University of Ulster in N. Ireland, from the University of Reading (UK) and from the University of Adelaide. Mike's research interests are the behaviour of nutrients and contaminants in soils and the improvement of fertiliser efficiency in agriculture

ARE Seminar by Christoph Neumann (Energy Research Center of Lower Saxony)   View Summary
20 September 2013

Price formation of exhaustible resources


Although Germany has an ambitious energy strategy with the aim of a low carbon economy, around 87% of the primary energy consumption was based on the fossil energies oil, coal, gas and uranium in 2012, which all belong to the category of exhaustible resources (BMWi 2012). Harold Hotelling already described in 1931 the economic theory of non-renewable resources (Hotelling 1931). The Hotelling rule states that the prices, more specifically the scarcity rent, of these resources will rise at the rate of interest and consumption will decline over time. The equilibrium implies social optimality. However, the market prices of exhaustible resources are usually not following the theoretical price paths and most of the empirical studies reject the theory. Nevertheless the rule "continues to be a central feature of models of non-renewable resource markets in the literature" (Livernois 2008).

We believe that there are difficulties in the (traditional) empirical verification but this should not lead to the invalidity of the theory in general. Our research, by using the experimental method, shows that the Hotelling rule has its justification. Furthermore, we think that the logic according to the Hotelling rule is one influencing factor among others in the price formation of exhaustible resources, therefore deviations are possible in real markets

DES Seminar by Dr John Knight (FAE Research Fellow)   View Summary
20 September 2013

Heat and mass transfer in soils and other natural porous media


I will give brief overviews of work I did on several projects at Queensland University of Technology and at CSIRO, without getting into too many technical or mathematical details. They are all about heat, water or gas flow in soils or other porous media.

Bagasse is the cellulose residue from crushed sugar cane. It is produced by sugar mills and then stored in large heaps to dry and provide fuel for the next crushing season. When exposed to air it oxidises and this produces heat, which can in extreme cases lead to spontaneous combustion. At QUT we modelled the effects of compaction and size of the bagasse piles, and made predictions which were generally in line with experience in the sugar industry.

When there are centre pivot irrigation systems drawing water from a river and causing recharge to the groundwater, a groundwater mound builds up under the circular recharge area. It will reach an equilibrium in which the vertical recharge is balanced by the lateral flow of groundwater to the river. I show how to calculate the shape and maximum height of the steady groundwater mound.

When there is an underground leakage of liquid hydrocarbons they spread out in a thin layer on top of the groundwater. Hydrocarbon vapour then diffuses upwards until it reacts with oxygen diffusing downwards. A building obstructs the flow of oxygen and so hydrocarbon vapour may diffuse into the building, leading to an explosion.Greg Davis at CSIRO Land and Water in Perth and I have derived a simple relation between the building width and the occurrence of vapour underneath it.

John Knight has been recently appointed as a Research Fellow within our Department. John is an applied Mathematician and throughout his research career he has been modelling heat and mass transfer in the natural environment.

All welcome to attend.

2013 Spatially Enabled Livestock Management Symposium   View Summary
26 September 2013 to 27 September 2013

Relevant topics include:

precision livestock management

remote autonomous monitoring of animals, vegetation and environment

wireless sensor networks

precision rangeland management

GNSS/GPS livestock tracking

virtual fencing

national scale livestock movement analysis

behavioural modelling in livestock

remote sensing of pastures

spatial pasture modelling

For more information:

Lachlan Ingram +61 4 5876 7677

Mark Trotter +61 2 6773 2465

The 2013 SELM is being held in conjunction with the 2013 International Grasslands Congress (ICG) which will run in the week preceding SELM. For more information on the ICG see:

Post ICG and Pre-SELM SMARTfarm / Precision Grazing Management tour:

This tour will run from the 22nd to the 24th September and comprises a tour based around Armidale in Northern NSW. The tour will include visits to the UNE campus, UNE SMARTfarm, CSIRO Chiswick Research Station and Sundown Pastorals "Sundown Valley" property. The tour highlights include a hands-on technology demonstration by the University of New England Precision Agriculture Research Group including the use of EM38 sensors, Crop Circle and Greenseeker Active Optical Sensors, Raptor airborne multispectral and thermal system and various data management systems used in a grazing systems context. Participants will also get a practical tutorial session on the use of the Pastures From Space program. See GPS livestock tracking, Taggle ear tag tracking, Pedigree Matchmaker, walk-overweigh systems, auto-drafting, soil moisture and climate sensor networks, satellite pasture biomass monitoring, active optical sensing for pasture biomass and growth, farm based video conferencing and precision fertiliser management strategies.

For more information see: or contact tour organiser Mark Trotter -


Is available at the following locations:

• Camden Valley Inn and Country Club ($135-165/night)

290 Remembrance Drive (Old Hume Highway), Camden Park NSW 2570

• Crown Hotel ($120/night)

187 Argyle Street, Camden, NSW 2570

• Narellan Motor Inn ($150-175/night)

2/5 The Old Northern Road, Narellan, NSW, 2567

For slightly cheaper accommodation (self-contained cabins) you could also try

• The Poplar Tourist Park ($95-125/night)

21 Macarthur Road, Elderslie (Camden) NSW 2570


On Thursday, morning tea, lunch and afternoon tea will be provided and also as part of your symposium fees a formal dinner will held on Wednesday night (25th September). Breakfasts and dinner on Thursday night (should people stay) is entirely up to attendees.


Unfortunately public transport is not great around the Camden area. Should people be flying into Sydney Airport, we would recommend catching the train from there to Campbelltown railway station (on the Airport & Eastern Hills line). Once at Campbelltown, it is possible to either catch the 890 bus (Narellan Motor Inn, Crown Hotel, Poplar Tourist Park) or the 895 bus (Camden Valley Inn, Narellan Motor Inn, Crown Hotel or Poplar Tourist Park). Catching a taxi from the station to one of those accommodation locations will cost you in the order of $25-42

There will be some limited ability for the organisers to pick up and return people to hotels but in the main we would recommend either organising a ride with some one who has a vehicle or using taxi's. ($30-35 one-way).

Should you wish to hire vehicle while here, Thrifty Rentals are about a 10 min walk from Campbelltown Station (


There is plenty of parking available at Centre for Carbon, Water and Food or on the opposite side of the road in the Vet precinct.

For more information:

Lachlan Ingram +61 4 5876 7677

Mark Trotter +61 2 6773 2465

To submit and abstract please contact one of the organisers

for the template. Please note that this is an abstract only


Abstracts are due 30 June 2013.

Please submit your abstract to:

DES Seminar by Dr Nathan Odgers (Research Fellow)   View Summary
27 September 2013

A digital soil mapping workflow incorporating spatial disaggregation of soil map units and prediction of soil properties with uncertainty


Soil polygon maps are a rich source of information on the spatial distribution of soil. The polygons in these maps delineate areas of land that belong to map units, or commonly-occurring assemblages of soil classes. Spatial disaggregation of soil polygon maps attempts to map the spatial distribution of the individual soil classes, which is often obscured by their aggregation into map units. Our DSMART algorithm performs the spatial disaggregation and produces maps of the estimated probabilities of occurrence of the soil classes that comprise a soil polygon map. The probability maps can then be used to generate maps of soil properties and their associated uncertainties.

Nathan is currently working in the Federal Government's Terrestrial Ecology Research Network (TERN) Soil and Landscape Grid of Australia Facility, where he investigates the spatial disaggregation of legacy soil polygon maps and how to use the disaggregated maps in new techniques for digital soil property mapping.

All welcome to attend.

PBI Narrabri Field Day 2013   View Summary
2 October 2013

The annual field day of the University of Sydney's IA Watson Grains Research Centre will be held at Narrabri on Wednesday October 2nd. The centre at Narrabri is part of the Plant Breeding Institute and research and training conducted at the site addresses issues of importance to northern grain growers. Come and hear about new developments including advances in crown rot resistance of wheat, pulse breeding and research and the national effort to enhance the water-use-efficiency of wheat. The centre has an extensive post-graduate training program and student work will be on display.

The centre at Narrabri has changed considerably in recent years with the establishment of new infrastructure, new staff appointments and a greatly expanded research program. Director, Prof. Richard Trethowan said, "I would encourage everyone to attend the field day if they are able (particularly those who haven't visited recently). Our research is now much more than just planting breeding and the opportunities for collaboration are many."

The program begins at 9:30am at the IA Watson Grains Research Centre located 7km north of town on the Newell Highway and concludes at 1pm with a complimentary barbeque lunch.

All are welcome.

RSVP: Essential by 25 September

DES Seminar by Dr Sharon O'Rourke (Visiting Marie Curie Fellow)   View Summary
11 October 2013

Assessment of soil carbon security using emerging techniques in hyperspectral imaging, X-ray florescence and pedometrics


The objective of this research is to understand the role of small-scale spatial organisation of soil organic carbon (C) within topsoil with respect to the long-term security of the abiotic carbon store. Carbon security is important because much analysis of land use, land use change and forestry assumes that there is a degree of permanently sequestered C as part of the system of reporting. The issue of soil C security needs to be addressed before C sequestration programmes can be advanced and deployed with confidence to ensure an increase in national soil C stocks is secure. In this presentation I would like to introduce the Csecure project and outline how I hope to map C at the micro scale.

Sharon is a visiting Marie Curie fellow hosted by our Department of Environmental Sciences. Sharon is funded under the European FP7 Marie Curie Fellowship programme for a period of three years, and is currently working under the mentorship of Alex McBratney.

All welcome to attend.

ARE Seminar by Dr Thilak Mallawaarachchi (University of Queensland)   View Summary
11 October 2013

Agricultural adaptation: challenges and opportunities


Agriculture is traditionally considered a 'risky business' and production under uncertainty is the accepted norm. The sector is characterised by many comparatively small and heterogeneous producers. They interact directly with prevailing climatic and biological conditions and continually grapple with risk associated with climate and biology, and market volatility. Individual farmers' ability to deal with these risks and take advantage of change will determine their future success where they face choices involving enduring, innovating, or exiting agriculture altogether. In this seminar, how the Australian farming industry has adapted to a range of climatic, institutional and market factors over time will be explored. It suggests that those adaptations have made the industry more responsive to an external operating environment that the industry has little or no control. Having successfully adapted to past conditions, the question is whether the productivist agenda that helped agriculture in expanding food and fibre output would continue to be relevant in guiding the sector forward. The 'heat is building up in the system' from a number of fronts: radiative forcing of the atmosphere, rapidly evolving preferences and values, and increasing inability of markets to account for externalities. While these coordination complexities grow, leading to increasing uncertainty in the production environment, farms are also seen as sources of multiple outputs, with only partial recompense available in heavily contested markets. The key challenge now is to increase agricultural productivity without increasing pressure on natural environments or consuming more fossil fuels, and to do that in ways that offer greater choices for consumers. This will require strategies that allow efficient coordination in providing marketed and unpaid goods and services from land. Elements of a research agenda that explores the merits of 'intelligent organisations' that seek to optimise learning and knowledge management will be outlined as a possible advance in facilitating efficient coordination under increasing uncertainty.

Professional Biography

For the past 24 years, Thilak has been exploring resource management issues in agriculture from a public policy perspective focusing on farm, region, national and international levels. From irrigation management in the Murray-Darling Basin, land use planning in the Great Barrier Reef catchments to smallholder farming in East Africa, the central issue confronting policy is to understand trade-offs in enhancing resource productivity in ways that maximise net economic benefits. Thilak's core effort has been to understand the decision-making complexity in these settings to aid public policy. Thilak was awarded the Australian Agricultural and Resource Economics Society (AARES) PhD price in 2002. Thilak has held various positions in the Australian Government Department of Agriculture, including ABARES. Thilak has also worked in CSIRO and James Cook University and enjoys a longstanding association with UQ School of Economics Risk and Sustainable Management Group (RSMG) led by John Quiggin where Thilak works as Principal Research Fellow.


All welcome to attend.

ARE Seminar by Professor Jeffrey T. LaFrance (Monash University)   View Summary
18 October 2013

Drink No Wine Before Its Time


The tendency for an excise tax to increase the average quality of a good is often referred to as the Alchian-Allen effect (Alchian and Allen 1964). This result has been credited to the UCLA oral tradition prior to the publication of Alchian and Allen's textbook (Borcherding and Silberberg 1978). Barzel (1976) explained this effect in terms of product attributes; an ad valorem tax is based on all product attributes, while an excise tax affects only certain product attributes. Many authors have refined and expanded these initial analyses (Gould and Segall 1969; Borcherding and Silberberg 1978; Umbeck 1980; Leffler 1982; Kaempfer and Brastow 1985; Cowen and Tabarrok 1995; James and Alston 2002; Razzonlini, Shughart and Tollison 2003). Many products, such as wine, aged cheese, cultured pearls, timber, and livestock production are characterized by multi-period production processes. We analyze the effects of taxes on the quantity and quality of a good - cellarable red wine - in a dynamic perfectly competitive market economy. Quantity is chosen at the initial point in time of each cycle for the production, storage and aging, sales, and consumption of the good. Quality is determined by the length of time the good is aged prior to sale, and storage time affects the market value of the product, a share of which is captured by the tax authority. We evaluate four taxes commonly observed throughout the world in the wine market: an ad valorem retail sales tax assessed as a percentage of price and collected on the date of sale; a volumetric retail sales tax assessed at a fixed rate per unit and collected on the date of sale; an ad valorem storage tax assessed as a percentage of the current market value and collected in each period prior to sale; and a volumetric storage tax assessed at a fixed rate per unit and collected in each period prior to sale. We derive the effects of tax instruments on quantity and quality and show equivalence results for tax systems that span the space of possible quantity and quality outcomes. We identify the conditions for the competitive private no-tax equilibrium to be optimal. We also find conditions for the typical wine tax system in developed economies to be optimal. These results are linked to a longstanding debate in nonmarket valuation.

Jeffrey T. LaFrance grew up on a veterinary farm and ranch operation on the banks of the Clark Fork of the Yellowstone River, east of the town of Bridger, Montana in the United States. He earned a Bachelor of Science (1977) and Master of Science (1979) degrees in economics at Montana State University and a Ph.D. (1983) in agricultural and resource economics at the University of California, Berkeley. He was a Senior Fulbright Scholar at LaTrobe University in 1989. He is a Fellow of the Agricultural and Applied Economics Association (AAEA, whose former name is the American Agricultural Economics Association), a Distinguished Scholar of the Western Agricultural Economics Association (WAEA), and has received numerous awards from these and other organizations. He has served on the editorial boards of the American Journal of Agricultural Economics (AJAE), Western Journal of Agricultural Economics, Journal of Environmental Economics and Management, Journal of Agricultural and Resource Economics (JARE), and the Australian Journal of Agricultural and Resource Economics, has been associate editor of the AJAE, editor of the JARE, referee for many scholarly journals, and on numerous committees of the AAEA and WAEA. He has been on the faculty at Montana State University, the University of Washington, the University of Arizona, the University of California-Berkeley, and Washington State University.

All welcome to attend.

DES Seminar by Vicky Aerts (PhD Candidate)   View Summary
18 October 2013

In the line of fire: Physiological responses of plants to smoke


In the first decade of the 21st century Australia endured a sustained drought period, resulting in an increase in bushfires and smoke. The increase in smoke has emerged as a major risk for some agricultural industries, especially viticulture. In recent years, wine producers have experienced substantial financial losses and decline in product quality due to smoke taint. The chemistry involved in smoke taint in wine is currently widely studied in Western Australia, South Australia, New South Wales and Victoria, but the physiological effects of smoke on grapevines and other agricultural and native species is relatively unknown. As Australia's future climate is predicted to become drier and warmer, the trend for an increase in annual bushfire events and its impacts is inevitable.

This project investigates the effect of smoke from bushfires and prescribed burns on native and exotic plant physiology. Leaf gas exchange measurements were made in the field on a range of plant species before and after exposure to different types of smoke. Anatomical parameters of the leaves used in the experiments were investigated to provide information about traits related to the different responses to smoke exposure. In the glasshouse and laboratory, gas exchange measures were made under more controlled conditions and some of the bigger fractions of smoke (CO2 and CO) were monitored during plant exposure. These data are being used to assess whether current models of photosynthesis can capture the impact smoke has on this process for two agricultural species.

4th Year Undergraduate Honours Student Conference - Stepping Out with Fresh Ideas (SOwFI)   View Summary
7 November 2013 to 8 November 2013

The Faculty of Agriculture and Environment will once again be hosting its annual 4th Year Honours Conference - Stepping Out with Fresh Ideas (SOwFI) on 7 & 8 November 2013. The venue for this unique student event will be The Carriage Works in Australian Technology Park. The Conference, which is part of the students' 4th year honours program, facilitates an opportunity for our students to present their research in a public forum. The students will be presenting their research in both a poster and oral presentation form, taking their academic experiences to a new level.

The program will feature the research of students completing the Faculty's Agricultural Economics, Resource Economics, Science in Agriculture, Horticultural Science and Environmental Systems degrees. As part of the Faculty's applied degree programs, students are partnered with a Faculty researcher for their individual research projects which reflect not only their learning journey throughout their candidature, but the research and analytical skills developed throughout their degrees.

As the applied scientists, environmental specialists and agricultural economist and resource economist of the future, the students are guided in focusing their research on the economic, resource management, environmental and scientific issues of the Australian Landscape and economy, as well as internationally, and their research projects are aimed at producing research of a publishable journal standard.

PFS Postgraduate Seminar Day    View Summary
12 November 2013

09:00 - 09:05 Welcome

09:05 - 09:25 Brian Abbott:Tomato flavour and nutrition - improvement with salt treatment.

09:25 - 10:15 Sahar Al-Dhaher: Properties of starch from soft waxy wheat varieties.

10:15 - 10:35 Muhammad Al Samir: Genetic and physiological studies to improve heat stress tolerance in tomato.

10:35 - 10:50 Morning tea (please bring cake)

10:50 - 11:40 Molook Al Fadly: Genotype and environmental influence on quality characteristics of Australian wheat varieties.

11:40 - 12:00 Mary Otieno: Desiccation tolerance of Rhizobia for improved survival on seed application.

12:00 - 12:50 Dominic Cross: Sarah Mansfield Better management of cotton refuges.

12:50 - 13:10 Janet Basani: Brian Jones Understanding the mechanisms of wood formation through the modification of Auxin Response Factor (ARF) gene expression.

13:10 - 14:00 Lunch (provided)

14:00 - 14:20 Duygu Karabork:Exploration of the inheritance of heat tolerance in wheat.

14:20 - 15:10 Kai Lin Ek: More than meets the eye - Nutritional qualities of potatoes.

15:10 - 15:30 Timothy Paath: The potential of wild rice (Oryza meridionalis and Oryza australiensis) to improve the phosphorus and water-use-efficiency of upland rice.

15:30 - 15:45 Afternoon tea (please bring cake)

15:45 - 16:05 Yihan Qu: Understanding the molecular basis for effectiveness of soybean-

Bradyrhizobium symbioses.

16:05 - 16:55 Kazi Rashid: Is there any variety-based response to plant growth promoting (PGP) micro-organisms in wheat?

16:55 - 17:15 Paul Adu-Gyamfi: The physiological basis of drought tolerance identified from genetic association analysis.

PFS Seminar by Dr Claudia Vickers (University of Queensland)   View Summary
13 November 2013

Isoprenoids: from biological function in plants to metabolic engineering in microbes

Isoprenoids are an extremely large and diverse group of compounds with many different biological activities. Many higher order isoprenoids (e.g. carotenoids, tocopherols, ABA) are involved in plant stress responses. Lower order volatile isoprenoids (VIP) are known to be involved in biotic stress responses; however, these VIP also play a less well-known role in abiotic stress responses. These roles will be discussed in the context of generic oxidative stress responses and the behavior of VIP using isoprene (2-methyl-1,3-butadiene, C5H8) as a model example. In addition to their interesting biological roles, isoprenoids have many industrial uses. These range from specialized applications (e.g. anti-cancer and anti-malarial pharmaceuticals) through to bulk chemical feedstocks (e.g., isoprene, which is polymerized to make synthetic rubbers and elastomers) and end products (e.g. isoprenoid jet fuel components). However, yields of these compounds from their natural sources are generally very low, and extraction and purification can be problematic. In order to achieve industrial-scale production, carbon flux must be re-directed into isoprenoid pathways. We are using metabolic engineering with systems and synthetic biology tools to re-design microbes for industrial isoprenoid production from cheap, renewable feedstocks such as sucrose. These systems and synthetic biology tools are also being applied to understand carbon flux through isoprenoid pathways. Understanding flux regulation will help us understand metabolic control over production of important isoprenoids such as isoprene. In addition to its roles in stress responses, isoprene is emitted in such large amounts from the biosphere that it has a significant effect on atmospheric chemistry: it has a climate-forcing effect, so understanding its biosynthesis is of particular importance.

Claudia Vickers completed her PhD at The University of Queensland on gene expression in the barley endosperm in 2004. She worked at the University of Essex in England for 3 years on biological functions of isoprene before returning to the University of Queensland. She is now a Senior Research Fellow in microbial metabolic engineering at the Australian Institute for Bioengineering and Nanotechnology. She re-designs yeast and E. coli for production of industrially useful biochemicals (primarily isoprenoids) using systems and synthetic biology tools.

Relevent Publications

  1. Vickers, C.E.; Possell, M.; Cojocariu, C.; Velikova, V.; Laothawornkitkul, J.; Ryan, A.; Mullineaux, P.M.; Hewitt, C.N. (2009) Isoprene synthesis protects transgenic tobacco plants from oxidative stress. Plant, Cell & Environment 32 (5):520 - 531
  2. Vickers, C. E., Gershenzon, J., Lerdau, M. T., & Loreto, F. (2009) A unified mechanism of action for volatile isoprenoids in plant abiotic stress. Nature Chemical Biology 5:283-291
  3. Vickers, C.E.; Blank, L.M.; Kroemer, J.O. (2010) Chassis cells for industrial biochemical production. Nature Chemical Biology 6(12):875-877
  4. Williams, T.C.; Nielsen, L.K.; Vickers, C.E. (2013) Engineered quorum-sensing using pheromone-mediated cell-to-cell communication in Saccharomyces cerevisiae. ACS Synthetic Biology 2(3):136-149
  5. Sabri, S.; Steen, J.A.; Bongers, M.; Nielsen, L.K.; Vickers, C.E. (2013) Knock-in/Knock-out (KIKO) vectors for rapid integration of large DNA sequences, including whole metabolic pathways, onto the Escherichia coli chromosome at well-characterised loci. Microbial Cell Factories, 12:60
DES Seminar by Waqar Ahmad (PhD Candidate)   View Summary
15 November 2013



Liming represents a common management practice for agricultural production on acidic soils, which include the low-rainfall zones of south-eastern Australia, the high rainfall zone of north-eastern Australia and the mediterranean climatic zone of Western Australia. In Australia about 2.5 Mt of lime is applied annually to the agricultural fields. Moreover, the rate of lime application is being considerably increased on such soils for better crop production. Liming promotes CO2-C fluxes through the dissolution of carbonates and, by its secondary effect on the microbial population and activities as a result of increased soil pH. Besides liming, mulching is another common practice in some cropping systems. However, there is limited knowledge about the priming effects of lime and mulching on the native soil carbon. Additionally contribution of lime to total carbon fluxes is not properly quantified in acidic soils. Further, under the changed scenario of climate the non-biological dissolution of lime and its temperature dependence is important to accurately account for the lime contribution to greenhouse gases from liming of acidic soils. This aspect of liming is largely unknown.

This project contributes to our understanding with regard to the dynamics of organic and inorganic carbon in acidic soils and in lime and/ or mulch amended acidic soils. Glass-house and laboratory experiments were conducted to examine the interactive effects of liming, plant root activity (wheat) and temperature on carbon dynamics. The differences in the natural abundance in δ13C between C3-organic C dominant acidic soil (≈ -27‰) and agricultural lime (≈ -8‰) were utilised to quantitatively measure the source of CO2-C produced in lime amended acidic soil. Further, in growth chamber experiments, 15N isotope labelling technique was included to better understand soil carbon and nitrogen dynamics.

The investigation of the temperature sensitivity of the lime derived C in the absence and presence of growing plants is one of the salient features of this research.


  • Temperature sensitivity and C release in acidic soil are lime and mulch mediated.
  • Native soil C is more sensitive to temperature than the lime-C and mulch-C.
  • Q10 value of the C released from lime in the absence of mulch was 2.41.
  • Lime and temperature interaction in the absence and presence of plants contributed largely to the total soil C fluxes suggesting that inorganic and organic carbon dynamics in limed acidic soil are mediated by plants.

The mobility of DOC was also increased in the presence of lime. Hence, the translocation of DOC could lead to the loss of C (secondary effect of liming).

All welcome to attend.

DES Seminar by Sanaa Issa (PhD Candidate)   View Summary
22 November 2013

Hydrologic and geologic integrated study for understanding the salinity problems of the Mount Annan area, Western Sydney, Australia.


Salinity in South Western Sydney, NSW is a major emerging urban problem. The occurrence of salinity is affected by climate variability as well as human management. Any change in the hydrological balance, either natural or induced by land management, is likely to affect the extent and severity of salinity occurrence. The primary objective of this study is to understand the dynamics of salinity in the Mount-Annan area of South Western Sydney, which is suggested to be primarily related to rising groundwater. Waterlevel data collected from the loggers installed in the monitoring network drilled in this area have been analysed and interpreted. A two-dimensional (2-D) hydrogeologic conceptual model for the area under study has been developed. This model is based on soil chemical and physical data analyses, namely the electrical conductivity (EC), Cation exchange capacity (CEC), pH, particle size distribution (PSD), and the available geologic and drilling information. Recharge is a key component in the modelling of groundwater flow, and has important implications for groundwater quality in a groundwater system. Two new methods for recharge estimation have been developed. These methods have been applied to the groundwater level data measured from 6 sites in the Mount Annan area. The new methods are presented in a time series framework of precipitation and groundwater level data. The hydrological conceptual model derived, and the recharge estimated are being used an input for three-dimensional (3-D) groundwater flow modelling. The observed groundwater data are being used for the calibration of the numerical model so that the predicted and observed groundwater data are fitted well.

All welcome to attend.

Pedal power in action at Reel Food Night   View Summary
28 November 2013

Join the Youth Food Movement for an evening of conversation and film at a pedal-powered pop-up cinema in the warehouse surrounds of Pier 2/3 in Walsh Bay. To be held on 28 November, the fourth installment of the Reel Food Nights series, sponsored by the Faculty of Agriculture and Environment, will feature lively discussion from experts across the food system as they explore solutions to some of the planet's most pressing food issues.

Grab a delicious meal from food trucks like The Veggie Patch Van and settle in for a screening of our own Youth Food Movement original short film - exploring our role in the future of small-scale agriculture and localised Sydney food systems by tracing the story behind our food from paddock to plate. We'll also introduce you to some of the passionate young farmers who feed us.

Your ticket includes a welcome drink - choose from The Apple Thief cider, Rocks Brewing Co. beer, or iced tea from Kettle Town - plus entry to the film screening and an interactive panel discussion afterwards. We'll be hosting a number of experts from across the food system to engage in a lively dialogue that explores solutions to the most pressing food issues.