Dr Carolyn Schultz - School of Agriculture, Food and Wine · Web viewDeveloping web-based toolkits...

School of Agriculture, Food & Wine

Summer Scholarship Projects 2017/2018

School of Agriculture, Food and Wine Summer Scholarship Projects 2017/2018

Biometry & Bioinformatics

Entomology & Plant Pathology

Farming Systems

Food & Nutrition

Plant_Biology & Biochemistry

Plant Genetics, Genomics & Breeding

Soil Science

Viticulture & Horticulture

Wine Science

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Biometry & Bioinformatics

Project Title: Developing web-based toolkits for typical data handling and analyses in plant science and plant breeding

Supervisor: Drs Andy Timmins, Olena Kravchuk, Mr Sam RogersE-mail: [email protected]: 0456137251Location: The Biometry Hub, 2nd floor, Main Bld, Waite Campus

Brief Project Outline: To develop cloud-based web portal capable of delivering a researcher-focussed and user-friendly access to advanced R-based statistical packages without requiring any knowledge of the R-programming by the user. This output will bring immediate benefits to research groups at Waite, engaged in plant and soil sciences.Expectations:

Essential: You are expected to be familiar with programing in R and be prepared to learn more in the first three weeks. You need to demonstrate a solid work ethics, your ability to work efficiently under supervision and to be a team player.

Desirable: It will help greatly if you are familiar with web-based technologies such as HTML, CSS, PHP and the Apache web-server; ideally you will have the knowledge of the Linux system administration.

Techniques/Skills Learnt:Depending on your skills at the application,

Intermediate/advanced R programming Intermediate/advanced skills in creating web-based toolkits Good understanding of cloud-based technologies

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Waite Undergraduate Summer Research Scholarship Project

Project Title: Ranked set sampling for defect assessment in vineyard

Supervisors: Dr Olena Kravchuk, Mr Peter KasprzakWith the assistance of Mr Warren Birchmore and Prof Eileen ScottE-mail: [email protected]: 0407790138Location: The Biometry Hub, 2nd floor, Main Bld, Waite Campus

Brief Project Outline: To develop an efficient sampling strategy that combines visual and instrumental assessment for defect quantification, in particular, for powdery mildew on grape bunches. The strategy will be implemented as a web-based application on the basis of R code. The data collected will be used as an example in a paper on the cost analysis of ranked set sampling in vineyard assessment. This output will bring immediate benefits to horticulture and agronomy research groups at Waite.Expectations:

Essential: You are expected to be familiar with the principles of disease assessment and sampling. You need to demonstrate a solid work ethics, your ability to work efficiently under supervision and to be a team player. You are expected to have excellent writing skills.

Desirable: It will help greatly if you are familiar with elements of R programming or prepared to put a solid effort into mastering the basics in the first three weeks of the program.

Techniques/Skills Learnt:Depending on your skills at the application,

Intermediate/advanced R programming Basic understanding of cloud-based technologies for online applications Solid understanding of the statistical principles of sampling

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Entomology & Plant Pathology

Project Title: Assessment of the Biosecurity risk associated with fruit shipping bins from Victoria

Supervisor: Dr Peter CrispE-mail: [email protected]: 0438879633Location: Waite and Riverland

Brief Project Outline: Fruit shipping bins move between orchards in South Australia’s Riverland and Orchard’s and Packing facilities in Victoria and New South Wales. It is possible that these bins carry fruit that may be infested with fruit fly larvae which can have a significant economic impact on SA’s horticultural industries.This project will be to inspect bins coming from interstate, assess the incidence of fruit in the bins and collection and dissection of any fruit to determine the presence or absence of fruit fly larvae or pupae. Inspections will be conducted at delivery points in orchards that will be organised in conjunction with industry representatives.

Techniques/Skills Learnt: Identification of fruit fly larvae and pupae using taxonomic and molecular methods. Develop an understanding of the economic losses that can be associated with

incursions of exotic pests Development of knowledge of Biosecurity risk pathways

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Project Title: The storage of beneficial and plant pathological fungi in honey bee hives and

its influence on bee health and longevity

Supervisor: Dr. Katja Hogendoorn E-mail: [email protected], [email protected] Phone: 8313 6555 / 0428 055 688Location: Waite Main Building, Waite Campus

Brief Project Outline:Honey bees, Apis mellifera L., can collect spores of plant pathogenic fungi that are associated with pollen or nectar and transfer them to the hive or to other flowers. This can contribute to the spread of plant diseases. The pollen stored in the hive is used to feed the larvae. It is unknown if spores of plant pathogenic fungi present on pollen can influence the health and longevity of the bees, or whether the spores are still viable after passing through the digestive tract of bees. Furthermore, it is important to investigate whether honey bees are vectors of plant pathogenic fungi in Australian crops. Therefore, this project will study (i) whether fungal spores mixed with an artificial diet can affect the health and longevity of larval honey bees; ii) whether fungal spores can survive through the digestive tract of bees and (iii) whether honey bees are vectors of plant pathogenic fungi in Almond orchards, weeds and native vegetation. The information obtained with this study will support agricultural and ecological plant management decisions to prevent and limit the spread of plant diseases among different crops and regions in Australia.

The student can contribute to all aspects of the project and preferences and skills (e.g. for lab or field work) will be taken into account. However, the student should not be allergic to honey bees.

Techniques/Skills Learnt: Laboratory techniques for isolation and cultivation of fungi Microscopy Molecular work – DNA extraction and PCR Field work – Management of honey bee hives and collection/sampling of bees Rearing of honey bee larvae in vitro Data collection, entry and analysis

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mailto:[email protected]



Project Title: Creating better food supplies for crop pollinating bees

Supervisors: Katja Hogendoorn, Scott GroomE-mail: [email protected]; [email protected]: 8313 6555 / 0409 728 869Location: Waite Main Building, Waite Campus

Brief Project Outline:The production of most fruit and nuts and of lucerne seed, relies on the presence of pollinators. For growers of these crops, high density and diversity of native pollinators can provide considerable free pollination services. We work in apple orchards in the Adelaide Hills and among lucerne crops around Keith to investigate what strategies growers can use to enhance the health and abundance of their crop pollinators. We specifically look at the management of native vegetation, and try to answer the following questions:- What species of native plants would be beneficial to plant around the crops? - What is the role of paddock trees in lucerne pollination?- What management strategies of the orchard floor can enhance apple pollination?

We would appreciate the assistance of two summer students with a wide range of tasks which will include: DNA extraction and PCR for molecular identification of bees, assessments of bee densities, seed set of lucerne, bee collection, data entry, identification of the pollen species on bee legs. Should you have preference for either lab-based or field-based components, we are happy to discuss the extent of your role in the project.

Techniques/Skills Learnt: Molecular work – DNA extraction, PCR, sequence alignment, phylogenetic analysis Field work – Experimental design, pollinator exclusion, manipulation Palynological methods – Pollen isolation, preparation and identification Bee collection – Standardised transects, dynamic (sweep netting) and passive (blue

vane traps) sampling Data recording and processing – Field data collection, data entry and analysis

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Project Title: Optimal moisture conditions for emergence of small numbers of Queensland Fruit fly pupae.

Supervisors: Peter Crisp and Cathy SmallridgeE-mail: [email protected]; [email protected]: 0438 879 633Location: Waite Main Building, Waite Campus

Brief Project Outline:Queensland fruit fly is an important pest of fruit in Australia. Research is ongoing into the production of masses of the fly in a factory setting for use in the Sterile Insect Technique to control populations in the wild. The lifecycle starts with the eggs, which are collected and placed on a larval diet until the larvae leave the diet (about 9 days) and pupate. At the end of a pupation period (about another 9 days), adult flies emerge. In the mass rearing situation, pupae are held together in their thousands, often several centimeters deep. However, in the laboratory, it is often required that small numbers of fruit fly pupae derived from different treatments are reared to adulthood. A large group of pupae has a smaller surface area: volume ratio overall from which to lose internal moisture relative to individually held pupae. It is possible that small numbers of pupae require additional moisture in their immediate environment to prevent desiccation prior to emergence as adults.

Techniques/Skills Learnt:The student would devise trials to optimise emergence of pupae held in small numbers. Some questions the student will answer include:

Is pupal emergence better when placed on a sponge moistened with a known amount of water?

Does additional water added during the pupation period improve emergence? Will adding too much water be detrimental to pupal development and have a negative

effect on adult fly emergence?

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Farming Systems

Project Title: The University of Adelaide’s Durum Wheat Breeding ProgramSupervisor: Associate Professor Jason Able & StaffE-mail: [email protected]: 83137075Location: Field & Lab, Waite Campus & Trial Sites

Brief Project Outline:Are you interested in plant breeding or plant genetics research? Do you have an interest in learning some aspects that contribute to a successful cereal breeding program? If so, then apply for this project and/or get in contact with Jason to discuss this opportunity further.

Techniques/Skills Learnt:You will have the chance to:

Learn how to harvest trial plots (start date dependent) Make F2 head selections at one of our trial sites (start date dependent) Analyse a selection of the 2017 yield data for 2018 selections with the breeder Possibility to learn and conduct some lab research (e.g. PCR, cloning)

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Project Title: Producing phosphorus efficient lines for wheat breeding

Supervisor: Dr. Xue GongE-mail: [email protected]: +61 (8) 8313 7398Location: Waite Main Building

Brief Project Outline:This project is supported by The Yitpi Foundation, which aims at developing phosphorus efficient lines for wheat breeding programs. Wheat is the most important crop worldwide, and phosphorus is the second most important but costly nutrient for wheat production. Although phosphate fertilizer has been used routinely in many of the Australian farms, plants rely on the phosphorus that has been built up in different soil pools rather than the phosphate fertilizer in the year of application. As a result, it is very important to increase crop’s ability to use phosphorus from the soil pools. Two wheat varieties, Yitpi and Carazinho, were used to produce a population of single seed descent lines that are potentially phosphorus efficient lines. The coming work is to characterize the population and shortlist the best lines for future work.

Techniques/Skills Learnt: Phenotyping wheat such as measuring harvest index, grain size and thousand grain

weight Working at different locations on campus glasshouse, growth chamber and

laboratories Writing scientific reports

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Project Title: Development of predictive models for pulse emergence

Supervisor: Lachlan Lake and Victor SadrasE-mail: [email protected]: 0400424942Location: Waite Campus

Brief Project Outline:This project aims to develop predictive models for time to emergence for different lines of the four main Australian pulse species, chickpea, lentil, fieldpea, faba bean and lupin. This will be achieved using replicated glasshouse experiments where five lines of each species are sown at five dates to generate a range of temperature and photoperiod. Temperature will be monitored and time to emergence recorded. Data will then be used to develop predictive emergence models. This research will be published in a peer reviewed journal and may be used in further research into phenology predictive models.

Techniques/Skills Learnt: Design, preparation and execution of replicated glasshouse experiments. Data collection, management, manipulation and analysis. Statistical methods and model design. Written communication skills with the goal of publication in peer reviewed journal.

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Food & Nutrition

Project Title: Micronutrient deficiencies and pregnancy outcomes

Supervisor: Dr Tina Bianco-Miotto, Prof Claire Roberts, Dr Tanja Jankovic-KarasoulosE-mail: [email protected]

Brief Project Outline:Pregnancy complications such as preeclampsia, intrauterine growth restriction, gestational diabetes and preterm birth affect about 20% of human pregnancies. These pregnancy complications predict lifelong health and sometimes mortality for the baby and/or the mother. Deficiencies in micronutrients in the mother’s diet including folate, vitamin D, selenium and zinc prior to and during pregnancy have been implicated in these adverse pregnancy outcomes. Exciting research in our laboratory has found clear associations between maternal micronutrient status and pregnancy outcomes. We have projects that investigate the associations of micronutrient status and pregnancy outcome as well as the role of the placenta in this association.

Techniques/Skills Learnt: Cell and tissue culture Immunohistochemistry Quantitative PCR Nucleic acid extractions and quantitation

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Project Title: Epigenetic regulation in the placenta

Supervisor: Dr Tina Bianco-Miotto, Prof Claire Roberts, Dr Tanja Jankovic-KarasoulosE-mail: [email protected]

Brief Project Outline:The best known function of the placenta is to mediate fetal-maternal exchange throughout pregnancy. It also plays a major role in directing maternal adaptation to pregnancy by secreting a variety of steroid and peptide hormones that modulate maternal physiology without which pregnancy could not be sustained. Although the placenta is a shared organ between mother and fetus, it is an extraembryonic tissue and is primarily regulated by the fetal genome. The placenta separates from mother and fetus after birth, making it a truly transient organ. For this reason, the epigenetic mechanisms involved in placenta development may not be under the same constraints as other tissues. Epigenetic mechanisms, like DNA methylation, regulate gene expression without altering the underlying DNA sequence and are critical during development. By determining how DNA methylation changes in the placenta throughout pregnancy and in response to adverse outcomes we can identify biomarkers indicative of future risk of pregnancy complications. This project will ideally suit an enthusiastic student who is interested in learning more about DNA methylation in the placenta.

Techniques/Skills Learnt: Nucleic acid extractions and quantitation Immunohistochemistry Quantitative PCR DNA methylation analyses

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Plant Biology & Biochemistry

Project Title: “CCC proteins in plants: important for salt and water transport, pathogen resistance and cell wall composition. How do they do it all?”

Supervisor: Stefanie WegeE-mail: [email protected]: +61 8 8313 6665Location: PRC, level 2, room 2.26a

Brief Project Outline:CCC proteins are ion transporters (potassium, sodium and chloride) and are potentially involved in active water transport, for example to establish root pressure. Root pressure is important to deliver water and nutrients to the shoot under conditions with low transpiration, for example during the night or during high humidity. Plants without functioning CCC proteins (knockout plants) have a severe phenotype: they are dwarfed, show extremely low fertility, complete loss of apical dominance, deformed leaves and alterations in seed coat composition. During the summer scholarship project, we will investigate the Arabidopsis thaliana (our model plant) ccc knockout mutant further, and compare new findings to the ccc knockout phenotype in rice (Oryza sativa). This will involve growing the plants in a large range of different growth conditions (light cycle, humidity, substrate, hydroponics, in vitro plates, etc) and documenting and quantifying observed phenotypic aspects. Documenting of phenotypes will be done by photography and by microscopy, including fluorescence based microscopy. Quantification will involve the use of programs like ImageJ and GraphPad Prism.

Techniques/Skills Learnt: A large variety of different Arabidopsis plant growth methods, including in vitro and

pot/soil based methods Scientific imaging, including photography and advanced microscopy Learn how to transform a complex observation into a measureable output (e.g. from

image to diagram)

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Project Title: Fungal penetration resistance in barley: development of a high-throughput screen.

Supervisors: Dr. Neil Shirley and Dr. Alan Little E-mail: [email protected]

Brief Project Outline:In plants, the cell walls are one of the first lines of defence protecting the cell from successful invasion and are a major factor in basal host resistance against fungal pathogens. As a defence response, plants reinforce the cell wall near the site of penetration by producing a dome-shaped apposition (papilla) between the epidermal wall and the plasma membrane. The polysaccharide composition of papillae that have been effective in preventing penetration by Blumeria graminis f. sp. hordei (Bgh) are traditionally believed to contain callose as the main polysaccharide component. However, recent evidence presented by our group demonstrated that effective papillae that are successful in preventing the penetration attempts of Bgh contain significantly higher concentrations of callose, arabinoxylan and cellulose (Chowdhury et al., 2014). The current methods utilised for screening a cultivar’s susceptibility to fungal infection involves standard disease resistance ratings by macroscopic and microscopic assays. This is time and labour intensive with long times required to generate symptoms on the leaves. The results can also be inaccurate due to the inherent variability of a subjective disease rating scale. This project aims to develop a quick and robust PCR method for quantitating the relative susceptibility of a barley cultivar to penetration by the powdery mildew causal agent, Blumeria graminis f.sp. hordei (Bgh). Once developed the assay will be utilised in a screen of barley germplasm and genetic analysis of potential resistance loci.

Techniques/Skills Learnt: Fungal infection assays RNA extraction Quantitative real time PCR

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Project Title: Design of biomimetic coatings to understand plant-pathogen relations

Supervisors: Dr. Bryan Coad and Dr. Alan Little E-mail: [email protected]

Brief Project Outline:Plant fungal pathogens have evolved highly sophisticated ways to infect crops and therefore are a threat to global food supply. On surfaces such as leaves, they first adhere to the surface and, interestingly, seem to know how to grow directionally towards ideal locations for infection before beginning surface penetration. If it were possible to better understand how the fungus senses and responds to the physical and chemical cues present on leaf surfaces, then we could develop strategies for interrupting infection, or develop plants which prevent adhesion or conceal inductive cues.We propose that artificial surfaces can be constructed to model natural leaf surfaces. By designing surfaces with well-defined chemical and physical properties to which the fungus can respond, we will be able to understand the essential triggers for infection. Additionally, studying the adhesion on surfaces will allow us to understand how secreted chemicals prepare the surface before infection. The overall aim is to replicate essential components of the leaf and assemble these into a biomimetic model. The goal of this research project is to make biomimetic surface coatings and investigate their biological response. This will involve using surface coating methods on materials such as glass slides, and to visualise the fungi using microscopy. This will provide an opportunity to learn about novel polymerisation techniques, characterisation of surfaces using surface analysis, and to visualise their biological effect.

Techniques/Skills Learnt: Surface coating techniques Surface analytical techniques Microscopy

Research Area: Biomaterials, interface science, bio-interfaces, plant-pathogen interactions.

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Project title: Natural variation in barley reproductive tissues

Supervisors: Ms Laura Wilkinson and A/Prof Matthew TuckerEmail: [email protected]: 0883139241Location: Wine Innovation Central Building, Waite Campus

Brief Project Outline: Grain production, size and quality in cereal crops are influenced by diverse developmental and environmental cues. During development, the grain is produced from the ovary, which resides in the base of flower. During early stages of floral development, the ovary must supply nutrients to the ovule to ensure the flower is fertile. During later stages, grain development depends upon transfer of nutrients from the ovary to the embryo and endosperm. Details of how the ovary influences ovule development as the barley flower reaches maturity are yet to be thoroughly described. In our lab we are studying female reproduction in plants and have identified barley cultivars that show reproducible differences in ovule morphology. Using microscopic techniques, the summer student will investigate the relationship between ovule, ovary and grain morphology in these cultivars. The student will also assess the expression of candidate genes controlling ovule morphology. Finally, using transgenic plants generated by the lab, the student will assess the impact of altered sugar metabolism upon ovary and grain morphology. This project will provide an introduction to cereal crop research in a young and dynamic lab that uses an array of techniques and materials compatible with diverse fields of research.

Techniques / Skills Learnt : Plant work including sample staging, tissue collection and dissection Fluorescent and light microscopy skills Quantitative PCR Genetic engineering

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Project Title: Quantitation of γ aminobutyric acid (GABA) in roots as a screening tool to select stress tolerant cereals.

Supervisor: Dr. Sunita Ramesh and prof. Stephen D TyermanE-mail: [email protected]; [email protected] (08) 83136665Location: Rm. 2.26a, Level 2 PRC, Gate 2B Hartley Grove, Waite Campus

Brief Project Outline:Abiotic stresses such as acidity (aluminium), alkalinity, salinity, drought and heat impact plant productivity and yield. Some plants tolerate these conditions better than others and identifying tolerant plants is a primary issue for scientists and breeders. Roots are the first to sense adverse conditions and root traits are one of the important indicators of how well the plant will cope with these conditions. γ aminobutyric acid (GABA) is a signalling molecule that is well known for its role in stress adaptation in mammals and recently our group showed that this molecule plays an important role in both acid and alkaline stress tolerance in cereals. Tolerant near isogenic line of wheat was found to have more GABA levels in the roots compared to the sensitive line under control conditions (Nature Communications, 2015). However the GABA concentrations reduced when the tolerant line encountered aluminium or alkaline stresses. We have some evidence to show that similar changes occur in barley under salt stress. Since GABA occurs in all living cells naturally, it is hypothesised that changes in GABA concentrations will occur under stresses and that these changes can be used as a screen to identify lines of wheat and barley that show tolerance to these stresses.

Student Project:Student will screen GABA concentrations in roots of 20 parental lines each of wheat and barley. In addition to GABA concentrations, other parameters such as root growth and length will also be measured. Seeds will be germinated on petridishes and 2-3 day old seedlings will be placed in treatment solutions in eppendorfs for 22h before quantifications of different parameters. Results from these experiments will form the basis to test long term growth under different stresses.

Techniques/Skills Learnt: Characterizing root traits Making nutrient solutions Designing experiments Enzyme assay Analysing experimental data Writing experimental reports Working in a multi-disciplinary laboratory

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Project title: Accelerating biological discovery through Artificial Intelligence

Supervisors: Matthew Gilliham, Rakesh David, Gustavo Carneiro

Project outline:The project aims to develop a computational platform combining Artificial Intelligence (AI) and Natural Language Processing techniques (NLP) to identify and extract relationships from published scientific literature. The project will first focus on integrating published information related to transport biology (based at the University of Adelaide node of ARC Centre of Excellence in Plant Energy Biology, CPEB - http://www.plantransig.com/) and builds on a previous study where novel cancer and malaria targets have been found by making links in the literature, demonstrating the technology can be applied to range of research questions (Nagarajan et al. 2015, doi: 10.1145/2783258.2788609). The platform will be used as a resource to reveal novel connections in the transport biology field and will assist in hypothesis generation and guide future experiments.The interdisciplinary project brings together biology labs across UA Faculties and Schools, expertise in AI from the School of Computer Science (CS) and an international industry partner with a proven track record in cognitive-based computing systems. The student undertaking the project will be based in The Australian Centre for Visual Technologies (ACVT) at the School of CS and the CPEB at the UA School of Agriculture, Food and Wine (AFW). Please contact A/Prof Gustavo Carneiro ([email protected]) (School of CS) or Dr Rakesh David ([email protected]) (CPEB, School of AFW) to discuss the opportunity further.

Skills learnt: Cloud-based analytical skills in AI and NLP techniques Interdisciplinary bioinformatics skills in literature retrieval and text mining Knowledge of transport biology and experimental techniques

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http://dl.acm.org/citation.cfm?doid=2783258.2788609

http://www.plantransig.com/


Plant Genetics, Genomics & Breeding

Project Title: Genomic analysis of fungal nucleotide sugar interconverting enzymes.

Supervisors: Dr. Julian Schwerdt and Dr. Alan LittleE-mail: [email protected]

Brief Project Outline:The fungal cell wall is perhaps the most ideal target for the treatment of fungal pathogens. The fungal cell wall represents a considerable metabolic investment as it accounts for 15–30% of the cellular biomass. It plays such a momentous role to survival and maintaining homeostasis that up to 20% of genes in the fungal genome are associated with cell wall biogenesis. The enzymes and signal transduction pathways that govern the synthesis of these cell wall components are prime targets for antifungal drugs. Knowledge of the cell wall composition and its biosynthesis will allow more targeted and tailored approaches towards disease control. To date, only a small percentage of fungal cell walls have been characterised. The ability of fungi to generate the necessary sugar nucleotide substrates for the synthesis of various cell wall components is determined by the presence of the nucleotide sugar interconverting enzymes. This project aims to characterise the distribution of each nucleotide sugar interconverting enzyme family across the available fungal genomes that have been fully sequenced. In doing so, we will generate a predictive map of what sugars each fungal species is capable of making and potentially incorporating into its cell wall.

Techniques/Skills Learnt: Bioinformatic analysis Cell wall biochemistry Fungal pathology

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Project Title: Studying grain weight in a wheat population

Supervisor: Melissa GarciaE-mail: [email protected]: 83139809Location: Plant Genomics Centre

Brief Project Outline:Grain weight is an important component of grain yield in cereals and understanding the genetics of grain weight can help breeders to select wheat plants with higher yields. This project is well suited to someone interested in genetics and plant breeding. The main objective of the project is to study the relationship between different regions of the genome and the grain weight in a wheat population.

Techniques/Skills Learnt:The student will have the opportunity to learn:

Post-harvest processing of wheat grains Perform basic statistical analysis Run laboratory experiments such as DNA extraction, PCR and genotyping Aspects of wheat genetics

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Project Title: How does the expression of ZIP transporter genes relate to plant zinc nutrition, and inoculation with arbusuclar mycorrhizal fungi?

Supervisor: Dr Stephanie Watts-WilliamsE-mail: [email protected]: 8313 6827 (out of office until August 28th – contactable by email)Location: Waite campus (Plant Research Centre)

Brief Project Outline:Zinc (Zn) deficiency, whether it occurs in soils, plants or humans, is a worldwide issue of high priority. Zinc deficiency is one of the most common and widespread micronutrient deficiencies in crop production, and is potentially the most limiting nutritional factor for cereal production. Arbuscular mycorrhizal fungi (AMF) colonise plant roots and proliferate external hyphae into the rhizosphere and beyond, maximising the volume of soil explored by the AM hyphae for inorganic nutrients such as phosphate (P) and Zn. This relationship with AMF can significantly improve the nutrition of the host plant; the benefits to plant nutrition from AMF are highest in soils depleted of these nutrients. Zinc is taken up into plants via ZIP (Zrt-Irt-like protein) membrane transporters. However, compared to other nutrients such as P, our knowledge of the basis of plant Zn uptake is limited – even more so when considering Zn uptake via AMF. In this project, we will study the expression of genes controlling for ZIP transporters, in different plants grown at various soil Zn concentrations, to understand how expression of ZIP genes plays a part in uptake of soil Zn via AMF.

Techniques/Skills Learnt: Preparation of samples for RNA extraction RNA extraction and DNase treatment cDNA synthesis PCR and gel electrophoresis Potentially qPCR (for gene expression analysis) Primer designing and optimisation Preparation of samples for nutrient analysis Data analysis

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Project Title: Using GM technologies to understand self-cannibalism in plants under stress

Supervisor: Dr Vanessa Melino, Alberto CasartelliE-mail: [email protected]; [email protected] Phone: 8313 1499Location: Plant Genomics Centre (PGC)

Brief Project Outline:Nitrogen fertilisers are the single most expensive input for cereal farmers in Australia. However, worldwide, cereals use less than 30% of the nitrogen fertiliser supplied to them, leading to the pollution of local waterways and the air. Plants can also use internal, organic sources of nitrogen during natural senescence and under stress conditions. In particular, we are interested in how plants use nitrogen derived from DNA and RNA. Plants that are effective at ‘self-cannibalism’ (breaking down their DNA and RNA) may have a growth advantage in stress environments.This project aims to evaluate the importance of DNA and RNA derived metabolites as a source of organic nitrogen when plants are grown in poor nitrogen soils. Additionally we will assess whether they provide protection for germinating seeds sown in dry soils. Australian bread wheat cultivars will be available to test this theory along with genetically modified (GM) Arabidopsis and rice lines which are unable to use internal organic nitrogen derived from DNA and RNA.

Techniques/Skills Learnt: Soil and hydroponic growth methods DNA extraction Genotyping by PCR techniques Phenotyping GM regulations

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Soil Science Project Title: How important are archaea for nitrification in Australian soils?

Supervisor: Gupta VadakattuE-mail: [email protected]: 08-83038579Location: Waite Campus

Brief Project Outline:Nitrification, the oxidation of ammonia (NH3) to nitrate (NO3), is mediated by microorganisms and is a key component of the nitrogen cycle in terms of soil N supply capacity to plants and environmental losses. Most research on soil microorganisms has concentrated on bacteria and fungi; only recently has the diversity and dynamics of soil archaeal communities been considered. Also, there is increasing evidence to show that they are playing a significant role in the cycling of carbon, nitrogen and plant-fungal interactions. Archaea have been found to abundant in Australian soils and they are influenced by land management. However, little is known about the importance of the recently discovered ammonia-oxidizing Thaumarchaeota (AOA) with potential for NH3 oxidation in N cycling in Australian agricultural soils.The aim of this project is to assess the relative contributions of AOA and ammonia-oxidizing bacteria (AOB) to nitrification using a newly developed assay and gene abundance assays in cereal crop and cotton soils.

Techniques/Skills Learnt:The project provides a unique opportunity to a student in gaining laboratory experience in soil biochemistry and molecular techniques:

Designing and setting-up of laboratory incubation experiments for testing specific hypothesis

Conduct chemical assays to measure nitrogen and carbon related properties in soil samples

Conduct DNA extraction and PCR assays to quantify AOA and AOB gene abundances

Data interpretation and statistical hypothesis skills.

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Project Title: Unlocking hidden value of carbon materials for mitigating pollution

Supervisor: Dr. Divina Navarro and Prof Mike MclaughlinE-mail: [email protected]: +618 8303 8587Location: Prescott building, Waite Campus

Brief Project Outline:Remediation is a process which aims to remove a contaminant or reduce the adverse effects of a contaminant to a level that is considered safe or acceptable. This can be done by: 1) removal and safe disposal of contaminated materials, 2) decontamination in place or without removal, and/or 3) encapsulation or stabilization. While removal and disposal (dig and dump) of contaminated material is conceptually “easy”, this remedial activity is expensive and not sustainable. Remediation in situ (without removal), hence, becomes an attractive alternative. Graphene is an example of a new carbon material with properties that make it an excellent candidate for use as an adsorbent to “fix” and immobilise contaminants in situ. Graphene is a single-atom thick layer of graphite that possesses high surface area to volume ratio, high adsorption/loading capability, and versatile surface chemistry. This makes graphene suitable for adsorbing large amounts of contaminants, with its surface chemistry providing specificity. No wonder it is touted as a “miracle material”! In this project, the student will work with us in evaluating the applicability of graphene in remediating of metal-contaminated water and soil. The student will help determine graphene’s ability to “fix” and immobilise contaminants in situ, as well as, determine how well it performs under relevant environmental scenarios (e.g. simulating rain, fertiliser addition, etc.). Results from this project can provide insights on the suitability of graphene as a remediation material. This is an excellent opportunity to gain some research experience, particularly in a field of great commercial significance.

Techniques/Skills Learnt: Characterisation of graphene materials Soil extraction methods Quantitative analysis of metals in water and soil Data handling and interpretation

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Project Title: Phosphorus speciation in phosphorus-efficient Australian native plants

Supervisor: Ashlea DooletteE-mail: [email protected]: 8313 8107Location: Davies Building 111, Waite Campus

Brief Project Outline:Recent advances in 31P NMR nuclear magnetic resonance (NMR) spectroscopy have made it possible to determine phosphorus (P) speciation of plant biomass in great detail. So far, application of this approach has been restricted to analysis of crop residues and grapevine biomass, where it has shown all plant biomass contains baseline concentrations of orthophosphate, phospholipids and nucleic acids (RNA, DNA), but some plant biomass contains additional P in the form of extra orthophosphate and inositol phosphate. This extra P occurs in specific plant organs (especially seeds, but also woody material of perennials such as grapevines) and more generally in plants with high P status (e.g. crops subjected to high rates of P fertilization). This provides a chemical demonstration of the outcomes of sophisticated plant P utilization strategies in the adequate to high P status range. Many Australian native plants thrive under low P conditions and although many of the strategies they employ (e.g. enhanced uptake through unique root architecture and tight internal recycling of P) have been identified, the impact of these strategies on plant P speciation has not been investigated. The aim of this project is to initiate a survey of P speciation in Australian native plant biomass, focussing on species known for their P efficiency.

Techniques/Skills Learnt: Plant sampling Chemical analyses, including NMR spectroscopy

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Project Title: Low-tech determination of soil water holding capacity

Supervisor: Ron SmernikE-mail: [email protected]: 8313 7436Location: Prescott Building 304, Waite Campus

Brief Project Outline:The ability of a soil to retain water that is accessible to plants is perhaps its most important attribute in an Australian agricultural context. From a soil physics perspective, plant available water is usually defined as the water held at matric suctions between 10 kPa (field capacity) and 1500 pKa (wilting point). Although these are routinely measured in soil physics labs, determination of wilting point water content in particular is time-consuming and requires expensive equipment. The aim of this project is to develop low-tech options for estimating plant available water that are cheap and quick, and can be used on-farm.

Techniques/Skills Learnt: Soil sampling Soil physical analyses, including particle separation and water content determination

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Viticulture & Horticulture

Project Title: “Talking grapevines”: Investigating volatile signalling in field-grown grapevines under water stress

Supervisors: Dr Vinay Pagay, Suzanne Balacey (PhD student) E-mail: [email protected], [email protected] Phone: 8313 0773Location: 1.93 Plant Research Centre, Waite Campus

Brief Project Outline: Plants emit and respond to an array of volatile organic signalling molecules under conditions of biotic and abiotic stresses. Although unknown in grapevines, preliminary evidence from our lab on potted grapevines shows that water-stressed vines communicate with their well-watered neighbours and elicit a physiological water stress response. This project will test the hypothesis that field-grown grapevines (‘source’ vines) under water stress emit volatile signals that induce ‘receiver’ plants to respond in kind. Growers may use a handful of source vines, or indeed other plants, in order to manipulate outcomes in nearby vines to improve their water use efficiency.

Techniques/Skills Learnt: Plant physiological measurements – growth, gas exchange, hydraulics Volatile chemical analysis – GC-MS Transcript analysis of key volatiles – RT-PCR Literature review Experimental design and statistical analysis of a replicated field trial

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Project Title: Comparison of Shiraz juice and wine composition resulting from berries of similar size and total soluble solids levels, but from two distinct harvest dates: Influence on organic acids, yeast assimilable nitrogen, concentration of phenolics and polysaccharidesSupervisors: Olaf Schelezki (PhD Student), Dr David JefferyE-mail: [email protected]; [email protected]

Brief Project Outline:Australian viticulture is characterised by a very warm and dry climate that leads to faster ripening dynamics of grapes compared to cool climate locations(Godden, 2010). Hence, the onset of berry ripening is advanced and the accumulation of total soluble solids (TSS) into the berry has been observed to decouple from the development of other grape components that are detrimental for the final wine quality, such as the composition of proanthocyanidins and volatiles (Sadras & Moran, 2012). To achieve the wine styles that are accepted by the market, winemakers are forced to stand by for the ripening of the entire berry composition, risking the shrivel of the berries and extreme total soluble solids levels that lead to excessive alcohol contents. One way to deal with this problem is the application of precision irrigation, a technique that has become a focus in viticultural research and in the industry. Once the TSS developement reaches a plateau (Figure 1) (stop of active sugar transport into the berry, start of softening of the berries), further sugar accumulation happens mainly by the decrease of berry fresh weight. This occurs naturally in a slow pace as well in cool climate regions, but is favoured in Australia through the frequent onset of berry shrivel. Irrigation is hence applied to remain a steady fresh weight of the berries to avoid a further increase of TSS, but favour the development and maturation of the remaining grape composition. Research conducted in CSU Wagga Wagga in fact could observe a predictable pattern of grape and wine flavour characteristics under these conditions (Figure 1), identifying a fresh and a mature fruit state of berry ripening that occur at the same time period after the plateau of TSS, independent of the vintage. The novelty of this experimental idea encourages further research to investigate the changes that occur in grape and wine composition. This project aims to qualify and quantify the differences of grapes (isometric in size and TSS) and the resulting wines of the fresh and mature fruit stages.Additionally to this main project, a smaller project has developed aiming to characterise the variability in the berry skin colour spectrum of Cabernet Sauvignon grapes and compare these differences to the methoxypyrazine concentrations in these grapes. High contents of methoxypyrazines such as IBMP are not desired for certain wine styles and the wine industry is searching for ways to optimise the currently used optical sorting machines to reduce the proportion of berries high in IBMP within a crop. The months of January and February before the harvest are crucial for observing the maturity of the grapes in the vineyard and manage the irrigation treatments to ensure a steady berry fresh weight during ripening. Grape samples will be taken from the McLaren vale vineyard and brought to the lab to analyse main quality parameters like berry weight, TSS, titratable acidity and pH. Based on these results, irrigation treatments will be executed by TWE and the fresh and mature fruit harvest dates will be identified. Further, the colour spectrum of a set of grape samples will be measured as well. The intern would be inducted and trained to properly sample grapes and analyse the samples in the lab. The intern will become familiar with the maturity and quality control of grapes and get experience with the impact of the harvest date choice on wine quality.

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Figure 1 The sugar accumulation dynamic under demand-adjusted hydration and the occurrence of distinct sensory perceptions.

Godden, P. a. M., Richard. (2010). Trends in the composition of Australian wine, 1984-2008. The Australian and New Zealand Grapegrower and Winemaker(558), 47-61.

Sadras, V. O., & Moran, M. A. (2012). Elevated temperature decouples anthocyanins and sugars in berries of Shiraz and Cabernet Franc. Australian Journal of Grape and Wine Research, 18(2), 115-122.

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