Day/Time: Thursday 11am (unless otherwise specified)
Venue after 23rd August: CSIRO, Australian Tropical Science & Innovation Precinct, James Cook University, Douglas Campus
Venue up to 20th August: CSIRO Davies Laboratory
Seminar Room.
Seminar details
will be updated as they are finalised
NB Venue is new building at the James Cook University
Wednesday 25th August
Adapting to Drought in the San Joaquin Valley of California
Dr Jim Ayars, USDA
Abstract
This is an overview of the strategies being taken by farmers in the San Joaquin Valley of California to cope with the current limited water supplies. It gives a brief case study of the response of one irrigation district.
About the speaker
Dr. Jim Ayars is a research agricultural engineer with the U.S. Department of Agricultural – Agricultural Research Service in Parlier, CA. He has 30 years of experience in research related to the integrated management of irrigation and drainage systems in arid irrigated agriculture. He has investigated the management of irrigation systems in the presence of shallow saline ground water and in-situ use of ground water by crops. He is currently studying the water requirements of horticultural crops grown in the saline soils of the San Joaquin Valley.
17th August
Title TBA
Dr Willem A. Schreüder, President, Principia Mathematica Inc.
Abstract
TBA
About the speaker
Dr. Schreüder (BSc Hons, MSc, MS, PhD) specializes in numerical analysis, mathematical modelling, computational fluid dynamics and parallel systems. He has extensive experience in applying complex numerical models to practical problems and the development of scientific software to solve these problems. He has developed and applied software for mathematical models, scientific visualization and geographic information systems. His modeling expertise include general computational fluid dynamics, ground and surface water hydrology and contaminant transport, heat and mass transport, turbulence modeling, dynamic systems and operations research. Dr. Schreüder also has extensive experience in networked computer systems and system administration, and is a contributor to the GNU and Qt projects.
4th June
Measuring and modelling nitrogen and phosphorus leaching losses from cropping systems
Michael van der Laan,
University of Pretoria/South African Sugarcane Research Institute, South Africa
Abstract
The leaching of nitrogen (N) and phosphorus (P) from the rootzone of cropping systems is a major contributor of non-point source pollution that can result in deterioration of fresh water quality. Such leaching losses are, however, extremely challenging to measure and quantify due to uncertainties associated with the estimation of deep drainage and the concentrations of N and P in the drainage water. Modelling is therefore often used to improve our ability to quantify these leaching losses. In this presentation I discuss (i) measurements carried out using wetting front detectors and suction cups in large drainage lysimeters to improve understanding of N and P movement through the soil profile, (ii) the power of using a combined measurement and modeling approach to estimate N and P leaching losses, and (iii) the use of long term modeling to analyse and compare N and P leaching losses from a dryland versus an irrigated cropping system. The long term modelling results showed that N and P losses from an irrigated system were 4-fold higher than for a dry land system under the same soil and climatic conditions. It also showed that introduction of a crop rotation and a ‘room for rain’ irrigation strategy could lead to substantial decreases in leaching losses in the irrigated system.
About the speaker
Michael van der Laan received his BSc(Agric) Agronomy in 2003 and his MSc(Agric) Agronomy in 2006 from the University of Pretoria. He recently completed his PhD thesis titled ‘Development, testing and application of a crop nitrogen and phosphorus model to investigate leaching losses at the local scale’. His research focussed on leaching of nitrogen and phosphorus from the root zone of agronomic cropping systems and developing predictive capability to further address and mitigate such losses. Since 2006, Michael has worked on several Water Research Commission projects involving the technology transfer of an irrigation scheduling computer model, non-point source pollution from agriculture, the use of wetting front detectors to improve irrigation and fertilization management practices, and sustainable biosolid land application and co-disposal strategies. Michael is currently working at the South African Sugarcane Research Institute.
3rd June
SNP's and chips (without the tomato sauce)
Stephen Goodswen, Postgraduate Student, CSIRO Livestock Industries
Abstract
The presentation will be in 3 parts:
- Part 1: An introduction to Stephen Goodswen
As one of 8 refugees to move to Townville as a result of the Rendel laboratory closure in Rockhampton, I’m sure many of the Davies laboratory residents have thought who is that old bloke with the funny accent? Well, this part of the presentation is a brief history of where I’ve come from and the meandering path I’ve taken to get to this point in time.
- Part 2: “Things you need to know” to understand part 3
So as not to throw newcomers to genomics into the deep end, this part of the presentation will entail an explanation of terminology used in part 3. Terms to cover are: genotypes, Single Nucleotide Polymorphisms (SNPs), SNP genotyping arrays, linkage disequilibrium, whole genome association studies, and marker-assisted selection for genetic improvement of livestock.
- Part 3: Linking whole genome SNP association studies to functional knowledge
Whole genome association studies (WGAS) using highly dense single nucleotide polymorphisms (SNPs) are a set of methods to identify DNA markers associated with variation in a particular complex trait of interest. One of the main outcomes from these studies is a subset of statistically significant SNPs. Finding the potential biological functions of such SNPs can be an important step towards further use in human and agricultural populations (e.g., for identifying genes related to susceptibility to complex diseases or genes playing key roles in development or performance). This part of the presentation introduces some software programs, that I have developed as part of my postgraduate research degree, to link SNPs to functional knowledge.
4th May
21st Century Cotton: a low water& pesticide rotation crop for the Burdekin - progress with a feasibility study
Mr Stephen Yeates, Senior Research Scientist, CSIRO Plant Industry
Abstract
Cotton production is not new to the Burdekin having been attempted twice previously in the 1940’s and 1960’s. Unfortunately these previous attempts were not proceeded by R&D tailored to the unique environment for growing cotton that is the Burdekin. Moreover since the 1960’s Australia has become a world leader in cotton production and breeding with a local skills base to match. This greater knowledge base combined with new GM technologies may overcome many biotic and management constraints to cotton production in the region. In addition a desire from local farmers to consider cotton as a rotation crop in their sugar farming systems combined with investment from new farmers from southern Australia seeking more reliable irrigation supplies has driven test faming of cotton in recent years. This presentation will address firstly some ‘MYTHS’ regarding cotton water and pesticide usage in Australia, then secondly will overview the current cotton R&D and test farming in the Burdekin.
About the speaker
Stephen Yeates has 28 years experience as a crop physiologist and agronomist researching cotton, tropical grain legumes, sorghum and corn. For the past 15 years he has been a senior research scientist with the Commonwealth Scientific and Industrial Research Organisation (CSIRO). With respect to GM cotton research his early research focused on the efficacy, adaption and farming systems development of Bt cotton in tropical Australia. Between 2004 and 2009 he has studied the impact that the high insect protection of 2 gene Bt cotton varieties (Bollgard II®) has had on crop morphology, plant water relations and hence irrigation management in temperate Australia. The changed irrigation practices that were an outcome of this research have had a significant impact in improving the yield and water use efficiency of these varieties in Australia. He is currently researching the integration of GM cotton (Bt and gyphosate resistant) as a rotation crop in sugar cane farming systems in north eastern Australia.
POSTPONED
Socio-economic Profiling of Tropical Rivers
Silva Larson, CSIRO Sustainable Ecosystems
Abstract
This seminar presents some of the findings of the Tropical Rivers and Coastal Knowledge (TRaCK) Project 3.1. People and Economy.
Tropical rivers of Australia are defined as catchments stretching from Broome in Western Australia to Cape York in Queensland, draining into either the Timor Sea or Gulf of Carpentaria. This seminar will provide an overview of the socio-economic characteristics of this unique Australian region. Integrated conceptual framework for the socio-economic profiling will be presented first, followed by examples of the individual catchment profiles developed for the project. In addition, tropical rivers catchments were compared and contrasted as to identify catchments which are socio-economically ‘similar’ or ‘dissimilar’. Emerging catchment clusters will be presented and discussed.
In summary, the socio-economic profiling identified considerable differences both between and within the catchments in the north. Biophysical and cultural differences, as well as differences in human, social and institutional capital and available infrastructure, will play a large role in determining both the opportunities for development (mining, agriculture, tourism) as well as capacities of the communities in those catchments to identify opportunities and take the advantage of the opportunities as they present themselves.
For further information please visit: www.track.gov.au/project-portals/socio-economic-profiling-tropical-rivers
22nd April
Genetic improvement of resistance to infectious diseases in livestock
Ali Abdirahman, PhD student, CSIRO Livestock Industries
Abstract
Breeding for enhanced resistance to infectious disease is an effective means of improving the health, fitness, livestock production as well as the prevention of human diseases. There is substantial evidence of genetic variation in resistance or susceptibility to infectious diseases within and between breeds. With the availability of genetic markers, gene expression technologies and statistical methods, one could establish markers-disease association. Such markers could be used to identify breeding animals with superior or inferior genes for disease resistance which can then be used as part of a marker assisted selection (MAS) program. This could provide an additional means of controlling the spread of contagious disease such as bovine tuberculosis and infectious bovine keratoconjunctivitis (IBK).
18th March
Co-expression Networks: What they are, and why you should care
Dr Nathan S. Watson-Haigh, OCE Postdoctoral Fellow, CSIRO Livestock Industries
Abstract
The traditional scientific approach of reductionism aims to understand complex systems by breaking them down into their constituents and understanding how these work and interact. In systems biology we try to understand how a higher-level processes interact to affect the whole rather than understanding, in detail, those individual processes. The system biology approach has gained momentum over recent years following the general acceptance that knowing the DNA sequence (genome) of an organism does not provide all the answers we had hoped for in understanding an individuals observable characteristic, or phenotype. Instead, we need to better understand each level of the complex system, of which the genome is the lowest, and how these interact to explain the variability in a phenotype. In the post-genomics era there is an abundance of data coming from established and emerging high-throughput technologies in transcriptomics, metabolomics and proteomics. Each of these attempts to quantify a different level in a complex system involving DNA, RNA, protein and metabolites, all interacting to provide control of cellular behaviour and responses and finally the observable phenotype.
A co-expression network is a representation of which genes are co-expressed under certain conditions. It is assumed that co-expressed genes are under some common control mechanism and the analysis of such a network will identify clusters, or modules, of highly interconnected, co-expressed genes involved in the experimental perturbation. I will talk about what co-expression networks are, how they can be analysed and how their use can provide insights into the molecular mechanism of action of a drug on Merino wool traits even when standard differential gene expression analyses fail. Many of the co-expression network analysis methodologies are not restricted to gene expression data alone but can be more generally applicable to any network-type of data.
About the speaker
I am an Office of the Chief Executive (OCE) postdoctoral fellow in the systems genetics team in CSIRO Livestock Industries. I have a biological background where I studied pharmacology at undergraduate level at the University of Bath, England. My PhD was done at the University of York, England where I developed tools and methodologies for molecular phylogenetics in order to pin-point the root, or the oldest part of the eukaryotic tree. Following my PhD, I worked as a postdoc at the University of Sheffield, England on a large collaborative project looking at the molecular adaptation of Arabidopsis lyrata spp. petraea, a sub-arctic alpine plant closely related to A. thaliana. My role there was as a bioinformatician to support and develop tools for a more systems biology approach to the analysis of ecological, transcriptomic, metabolomic and proteimic data. My current focus remains within a systems biology context, but with an application to the prediction and improvement of complex livestock production traits.
4th March
Livestock Improvement in Omics Era – Overview and Directions of Systems Genetics Research Group at CSIRO Davies Laboratory
Dr Haja Kadarmideen, Principal Research Scientist, CSIRO Livestock Industries
Abstract
Livestock improvement is going through paradigm shift in harnessing the power of recent technological advances in high throughput genetics / genomics as well as in automated livestock management and monitoring systems. In this context, this talk will give an overview of the past, current and future methods for genetic improvement of livestock. Brief introduction to the “new” systems genetics team in Davies Lab, its current activities and future research directions will be made.
About the speaker
Dr Haja Kadarmideen is currently a principal research scientist and leader of systems genetics team in CSIRO Livestock Industries and Adjunct Professor at the University of New England. Haja has veterinary medicine background with further 17 years of research and teaching experience in quantitative genetics & genomics, animal breeding, bioinformatics and computational biology in 6 countries. He was a tenure-track professor and head of statistical & quantitative genetics group at ETH Zurich, Switzerland for 6 years, prior to joining CSIRO in 2006.
Haja currently focuses on systems genetics approaches to accurately predict animal performance and in studying genotype-environmental-managemental interactions in production, reproduction, grazing and tropical adaptation of cattle in North Australia. Haja is a member of advisory committee for CSIRO-wide transformational biology capability platform.
18th February
Hydrological Science & Policy for Water Management
10.00am Professor Shahbaz Khan will present on the topic Integrated Water Resource Management implications for irrigation
11.00am Tea break
11.15am Dr Ken Knox will present on the topic Surface Water/Groundwater Interactions
Abstract
Our international experts will cover the following issues within their presentations:
- To what degree current water problems are a result of a failure to recognise existing hydrological information (& why does this occur?)
- To what degree current water problems are a result of a lack of hydrological information
- How scientific data have been used to influence/change water management policy
- How scientific data have been used to influence/change water (or environmental) legislation
- Examples of what has happened after the instigation of 3 or 4 (or both)
- Lessons for how we can do better in future
About the speakers
Professor Shahbaz Khan is the Senior Programme Specialist and Chief of Section on Sustainable Water Resources Development and Management with UNESCO. Professor Khan actively contributed to the development and management of the Hydrology for the Environment, Life and Policy (HELP) Programme as the Chair of the international steering committee and the regional coordinator for Australasia.
Professor Khan has an outstanding multidisciplinary background in water law and policy, management, civil engineering, information technology, graphical information systems & remote sensing, economics and integrating societal water demands with the environment. He received his Master and PhD degrees in water resources technology and management from the University of Birmingham, UK in 1992 and 1995 respectively. His other major qualifications include Master of International Environmental Law from the Macquarie University, Australia and Master of Applied Environmental Economics from the Imperial College, University of London, UK.
Prior to his role with UNESCO, Professor Khan was Professor and Director at the Charles Sturt University, Research Leader at CSIRO, and Programme Leader, System Harmonisation at the Cooperative Research Centre for Irrigation Futures, Australia.
Dr Ken Knox is a consultant with URS Corporation, and formerly the Chief Deputy State Engineer for the State of Colorado, USA and adjunct professor with the University of Denver. Dr Knox has extensive experience in water resources research, engineering, management and policy. This includes responsibility for negotiating, on behalf of the State of Colorado, interstate and international water sharing agreements (compacts).
Recent negotiations have successfully integrated groundwater-surface water interactions into what were previously surface water only compacts. This includes integrating groundwater as a reliable source of water into water resources planning and management activities to provide confidence to all water users seeking a reliable and high quality source of water supply to meet existing and future demands.
Dr Knox received his BSc in Chemical Engineering from the Colorado State University in 1982 and his Master and PhD degrees in Civil Engineering from the Colorado State University in 1991 and 2004, respectively.
7th January
The Florida Climate Institute: A platform for developing effective responses to climate variability and change
Dr Wendy-Lin Bartels, Research Associate, University of Florida, USA
Abstract
Climate variability and climate change pose substantial economic and environmental risks to all sectors in the State of Florida. Droughts, tropical storms with heavy rainfall, high winds, coastal flooding, and freeze events cause loss of life and property and damage to the natural resources of Florida. Regional climate change scenarios are needed to analyze vulnerabilities, to engage public agencies and industrial partners, and to assess options that will increase resilience and adaptive capacity. The Florida Climate Institute provides a platform for research that quantifies Florida’s climate patterns and creates seasonal, decadal, and longer-term climate forecasts and scenarios for Florida based on best scientific methods. This presentation offers an overview of the multi-disciplinary partnerships that constitute the Florida Climate Institute and describes the decision support tools and research projects that are currently being implemented to link scientists with local stakeholders in research, extension and education programs.
About the speaker
Wendy-Lin Bartels is a Research Associate with the South East Climate Consortium and the Florida Climate Institute at the University of Florida. Her work involves engaging stakeholder groups and decision makers in Florida’s coastal and agricultural sectors as they prepare for and adapt to a changing and variable climate. Specifically, she conducts and coordinates anthropological research to identify the needs, interests, perceptions, and vulnerabilities within these groups. She also evaluates the tools and systems developed by researchers to determine how climate information can best serve farmers, water managers, and others in their decision making and planning. Wendy-Lin has a PhD in interdisciplinary ecology with a concentration in tropical conservation and development, a Master’s in science communication, and Bachelor of Science in botany and molecular genetics. She conducted her dissertation research in the Brazilian Amazon, where she explored a multi-stakeholder land-use planning process that encourages small-scale producers to implement sustainable practices that provide environmental services. Wendy-Lin continues to collaborate with partners in Brazil and has worked internationally as a professional facilitator. Her broad career goal is to better understand the factors that facilitate dialog among diverse stakeholders as they negotiate the impacts of climate change. |
