School of Botany - Theses

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A systematic revision of the Harpetidae (Trilobita) and a critique of cladistic biogeographic methodology

Ebach, Malte C. (University of Melbourne, 2002)

The ten genera of Harpetidae (Bohemoharpes, Brachyhipposiderus, Dolichoharpes, Dubhglasina, Eoharpes, Harpes, Kielania, Lioharpes, Scotoharpes and gen. nov.) are reviewed. The monophyly of the Harpetidae is corroborated, and all ingroup genera can be defended as monophyletic groups except for the non-monophyletic Scotoharpes group. Emended diagnoses are provided for all the genera within the family. The three subfamilies Dolichoharpinae, Eoharpetinae and Harpetinae are placed in synonymy within the Harpetidae. The genera Australoharpes and Sinoharpes are placed in synonymy with Dubhglasina. Thorslundops and Wegelinia are placed in synonymy with Hibbertia, and the subgenus Lioharpes (Fritchaspis) placed in synonymy with Lioharpes. Four new species of Kielania (Kielania spp. 1-4) and a new genus (gen. nov.) and two new species (gen. nov. spp. 1-2) are described for the first time. Using these eight harpetid genera (Bohemoharpes, Dubhglasina, Eoharpes, Harpes, Hibbertia, Kielania, Lioharpes and Scotoharpes), the cladistic methods of standard parsimony and three-item analysis are compared. The methodological integrity of these methods is thoroughly examined and their inner workings exposed. Many cladists today use these programs without investigating how the black box of algorithms functions or the implications of the process they apply to the input data. Three-item analysis emerges as the more rigorous method, satisfying the discovery paradigm. Several cladograms based on three-item analysis that specify monophyletic taxa from the Siluro- Ordovician are transformed to taxon-area cladograms and combined to uncover geographic congruence. Cladistic biogeography uncovers geographic congruence using cladistic-based methodologies. The agreement of several taxon-area cladograms rarely yields a fully resolved result. Areas may overlap, taxa may not be evenly distributed and thus, ambiguity may be prevalent in the data. Ambiguity is incongruence and may be resolved by reducing paralogy and resolving potential information. During the last 20 years, several new approaches in cladistic biogeography (i.e. Brooks Parsimony Analysis, Assumption 0) have interpreted ambiguity as congruence. These methods are problematic because they are generational. Methods constructed under the generation paradigm are qualifiers for flawed concepts and immunize such concepts from falsifying evidence. A critique of modified Brooks Parsimony Analysis (BPA) reveals that taking an a priori evolutionary stance in biogeography leads to flaws in implementation. Area cladistics adopts paralogy-free sub-tree analysis, using Assumption 2, to discover the relative positions of continents through time. Geographic congruence is best explained by allopatry (geographic isolation). Vicariance, dispersal and combinations of both are recognized causes for allopatric speciation. Area cladistics highlights the concept that all these events occur in response to geological changes (e.g. continental drift) either directly, by geographic boundaries, or indirectly, at the level of ocean currents. Examples from the literature and from the harpetid genus Hibbertia all agree with the geological process. The examples include Ordovician-Silurian and Lower Devonian trilobites to yield a general areagram, which is a representational branching diagram that depicts the relationships of areas. Finding one common biogeographic pattern from several unrelated groups is a qualitative approach to interpret the positions of continental margins through time. Area cladistics is not a substitute for palaeomaps that are derived from palaeomagnetic data, but general areagrams add to the body of knowledge and yield more precise interpretations of the Earth's past.
Microprobe-localisation and ecophysiological studies of manganese-hyperaccumulating plants

Fernando, Denise Rita Marie. (University of Melbourne, 2008)
Fungal diversity in remnant vegetation patches along an urban to rural gradient

Newbound, Mark Gavin. (University of Melbourne, 2008)

Remnant vegetation patches in urban areas are valuable for biodiversity conservation, as well as recreation and community education. Fungi are a functionally important, and often overlooked, aspect of the diversity of remnants. Fungi are highly diverse, accounting for around 8% of the world�s species. They are critical in food webs and for nutrient cycling. Symbiotic mycorrhizal relationships between plants and fungi are important for plant nutrition, seedling establishment, and can affect the composition of plant communities. This thesis presents an investigation into how the distribution and occurrence of fungi in remnants are influenced by the level of surrounding urbanisation. The research was set in the city of Melbourne, Victoria. Surveys were made of both above and below ground fungal structures in remnant vegetation patches along an urban to rural gradient. Above ground, species of macrofungi were surveyed over two years by the collection and identification of fruiting bodies. Two below ground surveys were made. In the first, mycorrhizal root tips of two eucalypt species were sampled along a gradient. The second used a molecular method, terminal restriction length polymorphism (TRFLP), to assess diversity in bulk soil samples taken from sites. The fruiting body surveys produced the most informative results. Distinctions were made between properties affecting saprotrophic species, which derive carbohydrates from decaying organic matter, and ectomycorrhizal (ECM) fungi, which obtain carbohydrates from symbiotic plant hosts. A total of 199 species were found, with close to four times more saprotrophic than ECM species. Urbanisation appeared to have little effect on diversity, which was influenced more by particular site properties. Saprotrophic species richness decreased with increasing canopy openness; ECM richness decreased with higher soil pH and available phosphorus; and the ratio of saprotrophs to ECM increased with greater soil nitrate. Some management practices based on the findings are suggested to promote fungal diversity within urban remnants. A second topic in the thesis is an investigation of methods used to survey fungi. Assessments of fungal diversity are problematic because fungi are cryptic, highly diverse and patchily distributed. To help improve the efficiency of fruiting body surveys, Bayesian models were made to identify the environmental factors that influence fruiting. These suggested that to increase the probability of detecting species, frequent fruiting body surveys should be made in late autumn to early winter when the average value for rainfall minus evaporation for the previous 28 days is above -1 mm per day. Analyses were also made to compare the efficiency of the fruiting body and TRFLP survey methods. These found that species present were four times more likely to be found using TRFLP. However the TRFLP results did not correlate with environmental properties, probably because different fungal functional groups could not be differentiated. Thus, although less efficient for finding the total number of species present, fruiting body surveys provided a more representative sample of the fungal community. In conclusion, remnant vegetation in urban settings appears to be a valuable repository of macrofungal diversity, although doubts remain because of the limits of the surveying methods used.
The regulation of sirodesmin PL biosynthesis in the plant pathogenic fungus, leptosphaeria maculans

Fox, Ellen M. (University of Melbourne, 2008)

Sirodesmin PL is an epipolythiodioxopiperazine (ETP) toxin produced by the ascomycete Leptosphaeria maculans, which causes blackleg disease of canola (Brassica napus). This toxin is required for full virulence of L. maculans on stems of B. napus. Previous studies have shown that sirodesmin PL biosynthesis involves a cluster of 18 co-regulated genes and that disruption of the non-ribosomal peptide synthetase gene (sirP) in this cluster prevents the production of sirodesmin PL. The aim of my project was to determine how the production of sirodesmin PL is regulated. Two approaches were used to determine this. The first approach involved RNAi-mediated silencing of a candidate regulator, sirZ, encoded within the sirodesmin PL biosynthetic gene cluster. This gene encodes a putative Zn(II)2Cys6 DNA-binding protein, SirZ. The RNAi-mediated silencing of sirZ transcription revealed that SirZ is responsible for the regulation of sirodesmin PL production, via regulating the transcription of cluster genes. The second approach was to screen a library of L. maculans T-DNA insertional mutants for sirodesmin-deficient isolates and then determine the identity of the mutated gene(s). Four sirodesmin-deficient isolates were identified in a screen of over 200 L. maculans insertional mutants. Further characterization of these four mutants revealed that each contained a single T-DNA insertion in non-coding regions of the genome. The genes closest to each of the T-DNA insertion sites were a putative secreted protein, a conserved hypothetical protein, a putative transcription factor and a gene showing sequence similarity to fungal regulators of the cross-pathway control system. The role of the latter gene (named LmcpcA) in the regulation of sirodesmin PL production was analysed further using RNAi-mediated silencing. Under nutrient-rich conditions, the RNAi-mediated silencing of LmcpcA did not affect the regulation of sirodesmin PL production or transcription of sirodesmin PL biosynthetic genes, sirZ and sirP. However, upon amino acid starvation, silencing of LmcpcA transcription resulted in enhanced transcription of sirZ and sirP, compared to the wild type strain. These findings suggest that LmcpcA plays a role in the regulation of sirodesmin PL production in L. maculans in response to amino acid availability. Another ascomycete, Aspergillus fumigatus produces the well-characterized ETP, gliotoxin. To determine if the regulation of ETP production is conserved across fungi, an A. fumigatus mutant carrying a deletion in the pathway-specific regulator of gliotoxin production, gliZ (created by Dr. Jin-Woo Bok from Prof. Nancy Keller�s laboratory), was transformed with an entire copy of L. maculans sirZ or PlgliZ, the putative pathway-specific regulator of gliotoxin production in Pencillium lilacinoechinulatum. Complementation was not observed. Bioinformatic analysis of upstream regions of ETP biosynthetic genes in A. fumigatus, L. maculans and P. lilacinoechinulatum led to the prediction of a conserved binding element for GliZ, SirZ and PIGliZ, respectively. The step in the biosynthetic pathway whereby sulphur molecules are introduced into the core ETP structure has not been described, but has been proposed to involve cysteine as the sulphur donor. This step is thought to be catalysed by gene products of ETP cluster genes gliI or sirI, in A. fumigatus and L. maculans, respectively. Analysis of an A. fumigatus mutant carrying a deletion of gliI revealed that this gene is essential for gliotoxin production. The potential role of this gene in gliotoxin (or sirodesmin PL) production remains unknown.
Dissecting antibiotic targeting in the malaria parasite Plasmodium falciparum

Johnson, Russell Andrew. (University of Melbourne, 2008)
Purification and characterisation of the cyanogenic ?-glucosidase from Eucalyptus cladocalyx

Fox, Jennifer L. (University of Melbourne, 2007)

Many plant species contain cyanogenic glycosides, a group of nitrogen containing defense compounds. These compounds are hydrolysed by cyanogenic ?-glucosidases to release glucose, an aglycone and HCN, in a process known as cyanogenesis. Cyanogenic glycosides are spatially separated from their degrading enzymes (Poulton 1990). However, when a herbivore macerates cyanogenic tissue the cell compartments and tissues are mixed, allowing the cyanogenic P-glucosidases access to their substrate. Eucalyptus cladocalyx is endemic to Kangaroo Island and the Flinders Ranges, Australia. This species contains the cyanogenic glycoside prunasin, in high concentrations, in its leaves, stems and reproductive tissues (Gleadow 1999). The distribution of the prunasin within E. cladocalyx and its response to different environmental conditions has been well characterised (Gleadow 1999). However, there is little known about the enzyme that hydrolyses prunasin in this species. The project aims were to develop a purification protocol for the E. cladocalyx cyanogenic ?-glucosidase, to study the kinetics of the enzyme, and to obtain amino acid sequence information through proteomic techniques. A purification protocol was developed to extract and partially purify the cyanogenic P- glucosidase from E. cladocalyx leaves (Chapter 2). Leaves from Eucalyptus species are recalcitrant to protein extraction (Gaspar et al. 1997), and therefore a number of strategies were employed during purification to maximise protein extraction. For example, after grinding the E. cladocalyx leaves were washed with acetone. This removed chlorophyll and other pigments and lipids from the leaf material that interfere with protein extraction. In addition, PVPP and a non-ionic detergent were included in the extraction buffer. The purification protocol contained different types of chromatographic media including affinity (Con A chromatography), hydrophobic interaction (phenyl sepharose), Ceramic Hydroxyapatite and size exclusion (HW-50F) chromatography. A lectin column, Concanavalin A (Con A) sepharose was used early in the purification protocol. Binding of the cyanogenic P-glucosidase to the Con A sepharose suggests that the E. cladocalyx enzyme is glycosylated. In the next step of the purification protocol the cyanogenic ?-glucosidase activity was retained on a phenyl sepharose column, and eluted in a relatively broad peak. Ceramic hydroxyapatite chromatography proved to be a good technique for purifying the cyanogenic p-glucosidase as the enzyme bound to this column strongly and eluted in a single, sharp peak. A size exclusion column estimated the molecular weight of the E. cladocalyx ?-glucosidase to be 60.4 kDa. Catalytically active aggregates were observed during purification. It is not known whether these aggregates are formed in vivo, or were experimentally induced. SDS-PAGE analysis of the most pure fraction of the cyanogenic (3-glucosidase indicated that the enzyme was not homogenous. This fraction contained proteins of 84, 64, 56, 30 and 28 kDa. A kinetic study of the E. cladocalyx (?-glucosidse identified some key characteristics of the enzyme (Chapter 3). The pH optimum of the enzyme was estimated to be 5.72, which is similar to many other plant (3-glucosidases. This optimum is consistent with a defensive role, since the pH of leaf tissue macerates is often acidic (Gross et al. 1982). The temperature optimum of the E. cladocalyx was 40 �C. The Km value of the E. cladocalyx cyanogenic (3-glucosidase towards its natural substrate, prunasin, was determined to be 5.7 mM. This value is consistent with the high concentration of prunasin present in the young leaves of seedling (50 mg g"1 dry weight; Gleadow et al. 1999), and is also similar to many other cyanogenic P-glucosidases. The kinetic analysis indicates that substrate inhibition occurs at high prunasin concentrations (greater than 10 mM). The substrate specificity of the enzyme shows a degree of strictness towards the sugar moiety. The E. cladocalyx cyanogenic p-glucosidase hydrolysed chromogenic ortho-nitrophenyl substrates with glucose and fucose sugar residues comparatively well compared to the hydrolysis of prunasin. ortho-Nitrophenyl substrates with galactose and xylose sugar residues were not hydrolysed well. Amygdalin, the 6-0-?-D- glucopyranoside of prunasin, was hydrolysed at 3.1% of the rate of prunasin. Amygdalin has not been detected in E. cladocalyx tissue. Attempts were made to determine amino acid sequence from pure fractions of the cyanogenic P-glucosidase. Tryptic digests of partially pure E. cladoclayx ?-glucosidase fractions were made, and sequence was obtained from one peptide. The amino acid sequence from this peptide was sequenced de novo from the MS/MS spectra following ESI-MS. Two interpretations of the sequence could be made, SQYSGATVTVYK and SQYSGTDRVYK. Both of these sequences were used to search sequence databases. The most proteins with best matches these peptides were a protein from Danio rerio with RNA binding homology and a protein from Gallus gallus with similarity to calsyntenin-3, (calcium binding protein), respectively. Other bioinformatic analysis of plant ?-glucosidases was performed. Phylogenetic analysis revealed grouping together of plant ?-glucosidases often by families (eg. myrosinases in the Cruciferaceae) or with other enzymes hydrolysing similar substrates (eg. mannosidases, disaccharidases). From this study it can be concluded that the cyanogenic p-glucosidase from E. cladocalyx leaves shares many characteristics with other plant P-glucosidases. Further work should involve further proteomic analyses to obtain conclusive amino acid sequence from the cyanogenic P-glucosidase.
Phylogeny and biogeography of eucalyptus subgenus Eudesmia

Gibbs, Adele Katherine. (University of Melbourne, 2007)

Eucalyptus L�H�r. (Myrtaceae) is a dominant feature of the Australian landscape and an ecologically and economically important genus for the timber industry, for the distillation of essential oils and as native vegetation. Within Eucalyptus, three main clades are recognized as subgenera: Eudesmia, Symphyomyrtus and Eucalyptus. Subgenus Eudesmia currently includes 26 species and subspecies that are distributed across the tropical � temperate regions of Western Australia, Northern Territory, Queensland and the central arid deserts of Western Australia and South Australia, and the focus of this thesis. The classification and phylogeny of subg. Eudesmia to date are poorly resolved, and require further investigation. The aims of this project were to determine the phylogenetic relationships of the eudesmid eucalypts using molecular and morphological data, and to investigate the historical biogeography of the eudesmid group. The phylogeny is used as the basis of a revised classification and to identify key diagnostic morphological characters. A phylogeny including all taxa in subg. Eudesmia was constructed using DNA sequences of the internal transcribed spacer (ITS) and the external transcribed spacer (ETS) regions from nuclear ribosomal DNA, the psbA-trnH intergenic spacer region from chloroplast DNA, and morphology, including a glasshouse trial to raise seedlings from seed. Parsimony analyses were conducted using PAUP* and Bayesian inference using MrBayes computer programs. Pseudogenes were identified for the ITS-1 region, and thus the ITS-1 region was excluded from this study. Three indels were scored as informative from the molecular regions. Morphological characters were defined from adult leaves, buds, flowers, fruit, seedling leaf shape and arrangement. Scanning electron microscopy and light microscopy were used to study the seeds, trichomes, and floral characters. The characters were coded as binary or multistate, with quantitative characters gap-coded. Thirty two informative characters were identified, and included fruit shape, seed shape, cotyledon size and shape, trichome type, ovule row number and the leaf stage of trichome loss. Paralogy-free subtree analysis was used to understand the historical relationships of the biogeographic areas where eudesmids occur. The minimum area tree (with 100% consistency) had a basal trichotomy of: MacPherson/Macleay area, a clade of �Western� areas, including the Northern Desert, Pilbara, Western Desert, Geraldton Sandplains and Interzone, and northern and eastern areas, from the Kimberley to Cape York and Queensland. The eudesmids appear to reflect two biogeographic tracks found in previous studies, (1) Northern-Eastern Australia, and (2) South West WA and desert areas. Vicariance barriers can be correlated with ecological and historical events, and have various ages ranging from the Eocene to the Pleistocene. A summary tree with the greatest resolution was constructed from the congruent clades from all the molecular and morphological phylogenies. Five taxonomic series are recommended in a revised classification. The largest series is Eudesmieae, which includes fourteen species, and is further divided into five subseries and two superspecies. Most of these species have stamens in four bundles, and this series is congruent with Pryor and Johnson�s series Tetragonae. The other series are Similes (E. lirata and E. similis), Baileyanae (E. baileyana), Tetrodontae (E. tetrodonta), and Miniatae with five species.
Cell expansion in the elongation mutants of barley (Hordeum vulgare), a model grass

Warrener, Dyani. (University of Melbourne, 2006)

Cell expansion is fundamental to plant growth and morphogenesis, and how individual cells expand influences the morphology of the plant tissues and organs they comprise. This thesis describes a class of barley mutants, the elongation (elo) mutants, in which point mutations in unknown genes affect normal cell expansion. The elo mutants were isolated in a screen for dwarf mutants of barley and a description of five elo lines are presented here. Three elo mutants were recessive (elo1-elo3) and two were semi-dominant (elo4 and elo5). In the semi-dominant lines, the homozygous individuals generally displayed a more severe phenotype than heterozygotes. In order to investigate the functions of the ELO genes, a series of approaches was adopted. Chapter 2 contains a morphological description of each line, including examination of internal morphology of leaves, roots and seeds, and external morphology of leaves and roots. The five elo lines are dwarfed in stature compared to wild-type (WT), with above-ground organs shorter than WT in all lines and roots shorter in all but one of the lines (elo1). A phenotype common to all elo mutants is the presence of radially swollen cells on the leaf epidermis. Leaf epidermal cells were also found to be reduced in length compared to their WT counterparts, indicating that the elo phenotypes result from defects in processes essential to cell expansion in barley. Although all lines had radially swollen leaf epidermal cells, the extent of the aberrant cell expansion phenotype varied between the elo lines, with radial swelling restricted to leaf epidermal cells in some lines and more widespread in others. For example, radial swelling in elo1 was limited to intercostal leaf epidermal cells, while homozygous elo5 seedlings had radially swollen leaf epidermal cells, as well as swelling in all cell types of roots. Developing leaves and roots of two elo mutants (elo3 and elo5) were examined to gain a better understanding of when aberrant cell expansion first occurred. In both lines, radial swelling coincided with the zone of cell elongation. In addition to cell expansion defects, two of the mutations, elo2 and elo5, affected cell division. Additional periclinal cell division planes in leaf epidermal cells resulted in increased cell layers in the leaf epidermis of elo2 and elo5 homozygotes and the aleurone layer of elo2 seeds. Incorrect anticlinal divisions that were oblique rather than perpendicular to the growth axis also occurred in epidermal cell files of homozygous and heterozygous elo 5 leaves. Radial swelling has previously been seen in plants where cellulose biosynthesis is inhibited. To determine whether the radial swelling phenotype of the elo mutants was the result of decreased cell wall cellulose content, differences in the wall polysaccharide composition between WT and the elo mutants were investigated (Chapter 3). A number of techniques were used to determine cell wall composition in WT and elo tissue, including chemical derivitisation of cell wall carbohydrates, FTIR microspectroscopy and immuno-localisation of cell wall epitopes using monoclonal antibodies. Analysis of the cell wall composition of WT and elo leaf blades revealed a reduction in cellulose content in elo leaf cell walls, with a concomitant increase in levels of GAX and pectin. Although little or no difference to cell wall composition was detected in root cell walls, the phenotype and the wall analysis data from leaves indicate that the elo mutations affect cellulose biosynthesis in primary cell walls. To date, no mutants have been described that affect primary wall synthesis in a plant with type II cell walls. Thus, studying the elo mutants provides valuable insights into primary wall synthesis in this group of plants, and allows comparisons to be made with similar processes in plants with a type I cell wall. Transcript analysis of members of the cellulose synthase (CESA) superfamily were also performed in two lines, elo3 and elo5, to determine whether reduced cellulose content could be attributed to a reduction in transcript levels of these genes. Although reduced cellulose content can cause radial swelling, the architecture of the cell wall is also thought to play a part: cellulose microfibrils in elongating cells are inserted into the wall matrix transverse to the growth axis to prevent lateral cell expansion and favour expansion along the growth axis. Decreased cellulose content is also often accompanied by the disordered deposition of cellulose microfibrils into the cell wall. Microfibrils in elongating root cells of two elo lines, elo3 and elo5, were examined to determine whether the radial swelling phenotype was accompanied by altered microfibril deposition in these cells (Chapter 4). Cell walls of elo3 and heterozygous elo5 showed no difference in microfibril organisation compared to WT; however, homozygous elo5 cell walls had a greater proportion of cells with randomly-oriented cellulose microfibrils, indicating that the elo5 mutation affects the correct organisation of cellulose microfibrils in elongating cells. Radial swelling can also result from disruptions to cortical microtubule arrays in elongating cells. For this reason, cortical microtubule arrays were examined in elongating cells of eloS and elo5 roots (Chapter 4). This revealed that cortical microtubule arrays form left-handed helices in elongating cells of these lines, and hence a mutation affecting the orientation of cortical microtubules could be the cause of radial swelling phenotypes in both elo3 and elo5. The precise functions of the ELO proteins in plant growth and development will require identification of the genes that encode them. Progress towards this goal was made by mapping four of the elo genes to regions within the barley genome (Chapter 5). Three of the elo genes, elo1, elo2 and elo5 mapped to the long arm of chromosome 1H and the fourth gene, elo3, mapped to the long arm of chromosome 3H. This represents the first step towards map-based cloning of the elo genes, which is essential to understanding their roles in cell expansion in barley. The final Chapter of this thesis (Chapter 6) summarises the research findings from this study and proposes potential roles for the ELO genes based on their phenotypes. Future research directions are also considered.
The recovery of trout cod through the restoration of large wood habitats

Nicol, Simon James. (University of Melbourne, 2005)

Large wood (LW) forms an integral part of the habitat structure of freshwater systems. This thesis investigates the hypothesis that LW is important structural habitat for native fish in the lowland rivers of the Murray-Darling Basin in eastern Australia and whether its restoration can result in the recovery of the threatened trout cod (Maccullochella macquariensis). Trout cod has undergone a major decline in distribution and abundance and its natural distribution is now limited to a 150 km length of the Murray River. The decline in the species has coincided with the degradation of the Murray-Darling river ecosystems. Degrading processes have occurred over the entire current and historical range of the species, except for removal of LW habitat, which has not occurred in the area where it currently remains. A focus of trout cod recovery is the restoration of this LW habitat, on the assumption that the lack of this physical habitat, is a reason for the failure of the species to re-establish population in parts of its former range. The first problem encountered was that the absence of quantitative evidence describing the association between trout and its physical habitat use. A small radio-telemetry data set that included measurements of the habitat used by known individuals and habitat available was analysed to describe this association. A conditional case-control model was used. The selected model supported the notion that the occurrence of trout cod was closely associated with LW habitats. The odds ratio from this analysis indicated that trout cod were 131 times more likely to occupy a site if LW was present. The radio-telemetry data provided a description of trout cod habitat use at a micro-habitat scale, however LW habitats can occur at much larger scales as LW also occurs in large and complex log jams in this section of the Murray River. To examine whether this larger scale habitat influenced the number of trout cod and other native fish a sampling program was implemented. This examined whether the quantity of LW habitat, its location in the river channel and the presence of potential competitors influenced the density of native fish using this habitat. The observations indicated that river morphology could influence the density of LW in area where it accumulates. Secondly, the density of LW influenced the number of native fish using this habitat. The a priori expectation of spatial partitioning of this habitat by potential competitors was not detected at this scale. To test the validity of the associations observed, a manipulative experiment was conducted where LW was added to 14 sites. The response on these treatment sites was unequivocal for trout cod, with a biologically important increase in the number of trout cod observed. The results were equivocal for the other species, indicating that for these species other habitat variables may be required to increase the number of occupants. This result demonstrated the importance of testing these associations before, or as part of restoration activities. The information collected on trout cod habitat was used to build a stochastic meta-population model to explore the likely outcomes of LW habitat restoration and to examine how parameter uncertainty influenced possible outcomes. The selection of sites that minimised environmental correlation between meta-populations, but retained dispersal connectivity, provided the greatest reduction in estimated extinction risk for trout cod. The thesis concludes with an evaluation of the criteria for down-listing the species assuming that successful restoration had been implemented. The use of IUCN rules for down-listing purposes was sensitive to the likely uncertainty in the specific information required when using these rules. A complementary set of criteria was developed that allow the status of recovery to be evaluated.
Biology of the mitochondrion of the malaria causing parasite Plasmodium falciparum

Van Dooren, Giel (University of Melbourne, 2005)

In this thesis, I examine the biology of the mitochondrial organelle of the malaria-causing parasite Plasmodium falciparum. Mitochondria are eukaryotic organelles derived through endosymbiosis from proteobacteria, a process that probably occurred early in eukaryotic evolution. Mitochondria are typically associated with energy generating functions, but are known to perform a wide range of other functions. Although a known drug target, the functions of the P. falciparum mitochondrion are largely unknown. In this thesis, I provide bioinformatic evidence that this organelle is capable of electron transport and catabolism of organic compounds through an unusual tricarboxylic acid cycle. I also identify proteins that probably function in several biosynthetic processes, including haem biosynthesis, coenzyme Q biosynthesis and iron-sulfur cluster biosynthesis. I provide evidence that proteins from several of these pathways and processes localise to the mitochondrion. I also examine the morphology, division and segregation of mitochondria in asexual stages of P. falciparum parasites. I show that the mitochondrion associates with the apicoplast (plastid) organelle during segregation, and identify proteins that may be involved in organellar division in P. falciparum.

School of Botany - Theses

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