School of Agriculture, Food and Ecosystem Sciences - Theses
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ItemA genetic evaluation of dystocia in Australian Holstein-friesian cattle(University of Melbourne, 2004)This thesis presents the first large-scale study of the genetic and non-genetic influences on dystocia (calving difficulty) for dairy cows in Australia, and their costs, focusing especially on the Holstein-Friesian breed, but also with some analyses of frequently occurring crossbreeds. Analyses used data collected since 1986, collected by the Holstein-Friesian Association of Australian and the Australian Dairy Herd Improvement Scheme. The calving traits examined were gestation length, calf size, dystocia (measured as any or none, severe or none, and none, slight and severe). I investigated the influence on calving ease of non-genetic variables such as month of calving, cow age or parity, calf sex, and breed of cow and bull. The genetic parameters were estimated: the heritabilities and genetic correlations between traits calculated, separately for primiparous and multiparous, and for sires, maternal grandsires and the maternal effects. Costs associated with dystocia (such as labour costs, loss or fertility, veterinary costs and deaths of cow and or calf) are estimated, and a cost model for dystocia under Australian conditions is proposed. The influence of crossbreeding on calving was investigated, especially with respect to dystocia and calf mortality. Recommendations are made for improving the recording system and the evaluation of bulls, as the sire of calf and as the sire of cow.
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ItemNo Preview AvailableProcesses and implications of scald formation on the Eastern Dundas tableland : a case study(University of Melbourne, 2004)This thesis develops an understanding of the processes driving the formation of iron and saline rich scalds in groundwater discharge zones on the Eastern Dundas Tableland. The thesis tests the hypothesis that: The development of land degradation patterns around groundwater discharge zones on the Eastern Dundas Tablelands is not driven by salt concentrations, a consequence of water tables that have risen since European settlement and land clearing, but is the result of the disturbance to the soil environment of discharge zones since land clearing. The research proved the hypothesis correct and identified the transmission of hydrogen sulfide within the groundwater as a key factor in the severity of the degradation. The research also found land clearing may have altered the seasonal flow systems operating within the regolith, which are responsible for the spread of salinity and erosion within primary groundwater discharge zones. The Eastern Dundas Tablelands consist of a fractured rock aquifer, where the unweathered ignimbrites and lavas are hydrologically connected to the overlying regolith. Analyses of groundwater levels, pressures and chemistry indicate the groundwater flow paths to discharge zones increase in length with depth, such that discharge water is sourced from groundwater varying in depth of circulation (up to 150 metres) and flow path length (tens of metres to kilometres). A portion of discharge water flows through the unweathered volcanic aquifer and equilibrates with the rock, becoming reduced. The groundwater flow therefore contains hydrogen sulfide and has reducing capacity. This water then flows preferentially along large scale structures towards discharge zones. The location of groundwater discharge zones is controlled by the intersection between horizontal and sub vertical subsurface structures. Iron and saline rich scalding only occurs where groundwater flow with reducing capacity and containing hydrogen sulphide discharges. Iron and saline scalding is absent where only seasonal groundwater discharge not containing hydrogen sulfide occurs. Measurements of the discharge zones' soil and water EC, Ph and redox potential and the soil chemistry indicate degradation is the result of a combination of processes and is not solely the result of soil salting. Discharge water in wet months is covered by bacteria growth that reduces and oxidises iron and sulfur. During dry periods distinct iron precipitates form crusts on soil surfaces and clog soil pores. Salt efflorescence forms on soil surface and the oxidation of ferrous sulfide creates severe acidity. Evaporation accumulates salts in the discharge zones that are then spread downslope by seasonal break-of-slope discharge. Break of slope discharges erode highly sodic A horizon soils, radially expanding the area of degradation. Relatively constant groundwater levels, historical information and the carbon age of discharge water (2540 years) suggest discharge at the soil surface of the Eastern Dundas Tablelands occurred at least as early as the first records of European settlement. Little to no evidence exists suggest rising groundwater levels, caused by increased recharge since land clearing, have initiated the degradation of discharge zones. The pH, redox potential and measured quantities of ferrous material and sulfur in groundwater suggest iron and saline scalding is initiated by the interaction of the reduced groundwater of the regional groundwater flow and reducible material (iron) in the discharge zone. Prior to the clearing of native vegetation, reduced groundwater flow was able to discharge at the soil surface without coming into contact with reducible material (iron). Any hydrogen sulfide in discharge water was able to dissipate into the atmosphere, removing the reducing capacity of the water. Since clearing, iron has been redistributed into groundwater flow paths. Iron is reduced by the groundwater flow before the hydrogen sulfide is able to dissipate with ferrous and iron sulfide rich minerals forming within discharge zones. Upon oxidation, iron rich precipitates (ferrihydrite and schwertmannite) form in soil pores and along the soil surface with the oxidation of ferrous sulfide creating severe acidity (pH <4). The degree of degradation is directly related to the rate and volume of groundwater discharge. The least degraded areas coincide with point-flowing springs, the wettest areas of iron and saline scalds. Within point flowing springs, permanent saturation prevents the oxidation of ferrous sulfide material, the formation of iron crust and the accumulation of salts via evaporation. The most severe degradation coincides with areas of diffuse discharge, where the drying of the soil surface leads to iron precipitate formation, salt accumulation and severe acidity as ferrous sulfide material oxidises. The process of iron and saline rich scalding can be halted, and the area remediated if: � reducible material is removed from the groundwater discharge zone, preventing the reduced groundwater from mobilising iron and forming iron-sulfide material; and � the discharge zone is fully submersed in water, such as a dam. In this case, groundwater hydrogen sulfide will dissipate into the atmosphere, removing the reducing capacity of groundwater discharge.
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ItemNo Preview AvailableUsing selective DNA pooling to map QTL affecting milk production traits in Australian dairy cattle(University of Melbourne, 2004)
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ItemMolecular and immunological characterization of major Bermuda grass pollen allergen Cyn d 1( 2004)This thesis describes the molecular and immunological characterization of the major group 1 pollen allergen Cyn d 1 from Bermuda grass. A Bermuda grass (Cynodon dactylon) pollen cDNA library was constructed and a full length cDNA encoding Cyn d 1 gene was selected for further molecular and immunological characterization. Earlier studies had shown that bacterially expressed recombinant Cyn d 1 protein was non-IgE reactive due to lack of post-translational glycosylation in prokaryotic expression system. But in the present study, the expression of biologically active recombinant Cyn d 1 in E. coli was found to be reactive with serum IgE from Bermuda grass pollen sensitive patients. Further studies were undertaken to determine the IgE-binding regions of Cyn d 1 by generating a series of overlapping fragments of varying lengths covering the entire allergen molecule. These fragments were individually expressed in E. coli and the purified proteins were analysed to compare their IgE reactivity using sera pool from grass pollen allergic patients. This study led to the identification of two major IgE-binding regions and, deletion of either or both regions resulted in a significant reduction in the IgE reactivity. This information gathered from epitope mapping along with modern computational tools provided important clues to select residues to target for site directed mutagenesis for producing low IgE binding variants of Cyn d 1. To characterize the amino acid residues from Cyn d 1 which interact with IgE, the sequence was scanned by site-directed mutagenesis taking into account the sequence of homologous non allergenic 0-expansin gene, EXPB1, from Arabidopsis. Cyn d 1 hypoallergenic mutant forms with reduced IgE binding have been engineered based on the structural homology of non allergenic Arabidopsis beta expansin protein EXPB1 as a model. Nine potential IgE-interacting residues were identified and characterized, and based on these residues eight mutant Cyn d 1 variants with different combinations of mutated residues were designed and produced. Three out of the eight mutants showed reduced IgE-binding capacity as studied in vitro by immunodot blot and direct ELISA analysis. Hypoallergenic forms of the Cyn d 1 allergen can aid in the development of immunotherapeutic reagents for treatment of grass pollen allergy. Due to IgE-cross-reactivity, allergic patients exhibit broad sensitization to pollens of most grass species. Allergens from different sources can show immunological cross reactivity, often resulting from conservation of IgE epitopes. Therefore, immunoblot inhibition assays were performed using recombinant proteins to test the specific pattern of cross reactivity between allergens from Bermuda grass pollen (Chloridoedeae sub family) and Rye grass pollen (Pooideae sub family). The allergen profile of Rye grass pollen comprises Lol p 1 (group 1) and Lol p 5 (group 5), the two major allergen groups, Bermuda grass pollen on the other hand contains only Cyn d 1 (group 1) allergen. The group 1 allergens show very high amino acid sequence identity (80 %) and share common epitopes. The inhibition studies revealed a high degree of cross reactivity between the group 1 allergens from both grasses but none was observed between group 1 allergen from Bermuda grass and group 5 allergen from rye grass pollen. Rye grass pollen extract completely inhibited Bermuda grass pollen extract but not vice versa. These results suggest that basis of overall low level of cross reactivity between the Pooids and Chloridooids as observed by RAST can be attributed to absence of group 5 allergen from Chloridoids. Sequence comparison has identified a homologue ((3-expansin clone At2g20750 or EXPB1) in Arabidopsis of the Cyn d 1 gene. The EXPB1 protein is 42% similar to the Cyn d 1 protein. The function of some pollen allergen genes has been suggested based on their homologies with genes of known sequence. Expansins are a family of proteins that are known to induce extension of plant cell walls. A study was undertaken to determine the expression pattern of EXPB1 in Arabidopsis. RT-PCR analysis, in situ hybridization and GFP-promoter construct were used to study the pattern of gene expression of EXPB1 in Arabidopsis. RT-PCR analysis revealed EXPB1 transcripts only in floral tissue and the EXPB1 transcripts were localized in pollens by in situ hybridization. The absence of EXPB1 transcripts in any other tissues like leaf, stem and root indicates that the EXPB1 gene has pollen specific expression. GFP-promoter fusions showed high level of expression in tri-cellular pollen.
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ItemPhysiological and phylogenetic patterns in eucalyptus spp. responses to salinity and drought( 2004)Increasing aridity is regarded as a major driving force behind the evolution of the genus Eucalyptus. Previous investigations have identified both morphological and physiological characteristics whose properties, both in distribution and function, correlate strongly with adaptation to saline and arid environments. One such response is the regulation of osmotic potential via both acclimating and constitutive mechanisms. The identity of solutes contributing to these responses has hitherto remained unknown. Substantial evidence for the role(s) of cyclitols (cyclic polyols) during stressful conditions has been gleaned from previous investigations in both tree and herbaceous species. Here I uncover contrasting biochemical mechanisms for the regulation of osmotic potential among eucalypt species, with broad implications for taxonomy and evolution. For the first time, targeted biochemical profiling has uncovered a quantitative yet discrete link between eucalypt taxonomy and adaptation to arid environments. The distribution of cyclitols among eucalypt species correlates strongly with other demonstrated adaptations to arid conditions. Analysis of Eucalyptus leptophylla leaf tissues from trees growing along a topographic gradient encompassing hyper-saline lakes, suggests that cyclitols contribute significantly to osmotic adjustment induced by drought. The presence of substantial quantities of cyclitols in xylem sap of E. leptophylla suggests additional roles in the signalling of plant stress reponses. Determination of the contribution of low molecular weight carbohydrates, polyols and inorganic ions towards the regulation of osmotic potential in glasshouse grown E. spathulata (Hook.) show that salt and drought stress elicit contrasting mechanisms of solute concentration. Under salt stress, seedlings reduce osmotic potential by accumulating large quantities of inorganic ions in leaf tissues, presumably sequestrating them into the vacuole. Under drought stress, seedlings reduce osmotic potential through the concentration of constitutively present solutes - particularly that of the cyclitol quercitol. Targeted biochemical profiling of 13 species of Eucalyptus originating from contrasting rainfall environments revealed equally contrasting biochemical responses to drought stress. In species originating from low rainfall environments, the constitutive concentration of quercitol is the major mechanism of osmotic regulation whilst species originating from high rainfall environments osmotically adjust through the active accumulation of sucrose. These results suggest that the solutes governing both acclimating and constitutive regulation of osmotic potential in Eucalyptus species have finally been identified. The implications of these findings are discussed in the context of plant adaptation to saline and arid environments.
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