School of BioSciences - Research Publications
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ItemProteomics and Deep Sequencing Comparison of Seasonally Active Venom Glands in the Platypus Reveals Novel Venom Peptides and Distinct Expression Profiles(AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC, 2012-11)The platypus is a venomous monotreme. Male platypuses possess a spur on their hind legs that is connected to glands in the pelvic region. They produce venom only during the breeding season, presumably to fight off conspecifics. We have taken advantage of this unique seasonal production of venom to compare the transcriptomes of in- and out-of-season venom glands, in conjunction with proteomic analysis, to identify previously undiscovered venom genes. Comparison of the venom glands revealed distinct gene expression profiles that are consistent with changes in venom gland morphology and venom volumes in and out of the breeding season. Venom proteins were identified through shot-gun sequenced venom proteomes of three animals using RNA-seq-derived transcripts for peptide-spectral matching. 5,157 genes were expressed in the venom glands, 1,821 genes were up-regulated in the in-season gland, and 10 proteins were identified in the venom. New classes of platypus-venom proteins identified included antimicrobials, amide oxidase, serpin protease inhibitor, proteins associated with the mammalian stress response pathway, cytokines, and other immune molecules. Five putative toxins have only been identified in platypus venom: growth differentiation factor 15, nucleobindin-2, CD55, a CXC-chemokine, and corticotropin-releasing factor-binding protein. These novel venom proteins have potential biomedical and therapeutic applications and provide insights into venom evolution.
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ItemN-Glycosylation Determines Ionic Permeability and Desensitization of the TRPV1 Capsaicin Receptor(AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC, 2012-06-22)The balance of glycosylation and deglycosylation of ion channels can markedly influence their function and regulation. However, the functional importance of glycosylation of the TRPV1 receptor, a key sensor of pain-sensing nerves, is not well understood, and whether TRPV1 is glycosylated in neurons is unclear. We report that TRPV1 is N-glycosylated and that N-glycosylation is a major determinant of capsaicin-evoked desensitization and ionic permeability. Both N-glycosylated and unglycosylated TRPV1 was detected in extracts of peripheral sensory nerves by Western blotting. TRPV1 expressed in HEK-293 cells exhibited various degrees of glycosylation. A mutant of asparagine 604 (N604T) was not glycosylated but did not alter plasma membrane expression of TRPV1. Capsaicin-evoked increases in intracellular calcium ([Ca(2+)](i)) were sustained in wild-type TRPV1 HEK-293 cells but were rapidly desensitized in N604T TRPV1 cells. There was marked cell-to-cell variability in capsaicin responses and desensitization between individual cells expressing wild-type TRPV1 but highly uniform responses in cells expressing N604T TRPV1, consistent with variable levels of glycosylation of the wild-type channel. These differences were also apparent when wild-type or N604T TRPV1-GFP fusion proteins were expressed in neurons from trpv1(-/-) mice. Capsaicin evoked a marked, concentration-dependent increase in uptake of the large cationic dye YO-PRO-1 in cells expressing wild-type TRPV1, indicative of loss of ion selectivity, that was completely absent in cells expressing N604T TRPV1. Thus, TRPV1 is variably N-glycosylated and glycosylation is a key determinant of capsaicin regulation of TRPV1 desensitization and permeability. Our findings suggest that physiological or pathological alterations in TRPV1 glycosylation would affect TRPV1 function and pain transmission.
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ItemUsing decision support tools in emergency animal disease planning and response: Foot and mouth disease (CEBRA Project 1404D), Technical Report prepared for the Department of Agriculture and Water Resources(University of Melbourne, 2016)Modelling studies both in Australia and overseas have shown that vaccination can be very effective in reducing the size and duration of an FMD outbreak. Vaccination is most effective in reducing the duration and size of an outbreak when used early and is less effective the longer you delay. However, a decision to vaccinate early in the outbreak may result in using vaccination in situations where it is not actually required, with consequent implications for post-outbreak surveillance, the management of vaccinated animals and the ability to regain FMD-free status and access to markets. Overall, the choice of control measure to adopt in an FMD outbreak will thus depend on the variable and potentially conflicting objectives of the control program. As an important component of disease planning and preparedness for the department, the project will report on key information that could be used in an FMD outbreak to infer the potential scale of an outbreak and information to support disease management decision-making.
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ItemIncorporating economic components in Australia's FMD modelling capability and evaluating post-outbreak management to support return to trade (CEBRA project 1608D), Technical Report for the Department of Agriculture, Water and Environment(University of Melbourne, 2017)Following an outbreak of FMD, surveillance will be required to demonstrate that infection has been eradicated from the population and enable any remaining movement restrictions to be lifted within the country. Proof of freedom will also be needed to satisfy trading partners and regain access to international markets. Although vaccination is increasingly being recognised as an important tool to assist in containing and eradicating FMD outbreaks, it will make achieving recognition of free status more difficult—keeping vaccinated animals in the population will delay the period until FMD-free status is regained under the World Organisation for Animal Health (OIE) guidelines and add additional complications to the postoutbreak surveillance program. There is no agreed approach to post-outbreak management of vaccinated animals in AUSVETPLAN with the options being to: (1) allow vaccinated animals to remain in the population to live out their normal commercial lives (vaccinate-to-live); (2) remove all vaccinated animals from the population (vaccinateand- remove). Under option 2, vaccinated animals could be subject to (a) slaughter to waste i.e. remove and dispose of vaccinated animals; or (b) slaughter and salvage i.e. attempt to sell either raw or processed product from vaccinated animals. For (b) there may be some residual value of products that could offset some of the costs. The project will bring together epidemiological and economic expertise from the Department, the Australian National University, and CEBRA to formally explore and establish a science-based and cost effective approach to regaining free-status after an FMD outbreak as expeditiously as possible. The project will expand the Department’s modelling capability as well as providing insights into postoutbreak FMD management and contribute to Australia’s FMD preparedness.
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ItemNational-level farm demographic data for preparedness of highly-infectious livestock disease epidemics. Review of data sources in New Zealand, approach to modelling populations and the effect of population uncertainty on disease modelling.(University of Melbourne, 2016)Isolation and strict biosecurity measures implemented by Australia and New Zealand have prevented the incursion of many organisms of biosecurity concern. The agricultural industry is a key part of the economy for both countries, and preventing the arrival of diseases of concern, including foot-and-mouth (FMD) disease, is crucial to maintaining access to international markets, reputation, and protecting the economy and industry. Early detection of, and a rapid, effective response to such diseases have a large impact on limiting the economic damage caused by epidemics. An acknowledged weakness of biosecurity preparedness and response to agricultural diseases in both countries is the lack of a single source of accurate, up-to-date farm livestock demographics information. This report reviews the use of animal counts for investigation of, preparedness for and response to exotic animal disease outbreaks, and analyses the available New Zealand datasets in depth. Gaps and weaknesses in the current data landscape are documented. The project objectives then focus on developing methodologies to estimate national-level farm demographic data and assess the use of modelled and inaccurate data in disease simulation models. There are nine key deliverables outlined in the report which were carried out over the two year duration of the project.
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ItemInsect Antennal Morphology: The Evolution of Diverse Solutions to Odorant Perception(Yale University, 2018-12-01)Chemical communication involves the production, transmission, and perception of odors. Most adult insects rely on chemical signals and cues to locate food resources, oviposition sites or reproductive partners and, consequently, numerous odors provide a vital source of information. Insects detect these odors with receptors mostly located on the antennae, and the diverse shapes and sizes of these antennae (and sensilla) are both astonishing and puzzling: what selective pressures are responsible for these different solutions to the same problem - to perceive signals and cues? This review describes the selection pressures derived from chemical communication that are responsible for shaping the diversity of insect antennal morphology. In particular, we highlight new technologies and techniques that offer exciting opportunities for addressing this surprisingly neglected and yet crucial component of chemical communication.
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ItemWider sampling reveals a non-sister relationship for geographically contiguous lineages of a marine mussel(WILEY, 2014-06)The accuracy of phylogenetic inference can be significantly improved by the addition of more taxa and by increasing the spatial coverage of sampling. In previous studies, the brown mussel Perna perna showed a sister-lineage relationship between eastern and western individuals contiguously distributed along the South African coastline. We used mitochondrial (COI) and nuclear (ITS) sequence data to further analyze phylogeographic patterns within P. perna. Significant expansion of the geographical coverage revealed an unexpected pattern. The western South African lineage shared the most recent common ancestor (MRCA) with specimens from Angola, Venezuela, and Namibia, whereas eastern South African specimens and Mozambique grouped together, indicating a non-sister relationship for the two South African lineages. Two plausible biogeographic scenarios to explain their origin were both supported by the hypotheses-testing analysis. One includes an Indo-Pacific origin for P. perna, dispersal into the Mediterranean and Atlantic through the Tethys seaway, followed by recent secondary contact after southward expansion of the western and eastern South African lineages. The other scenario (Out of South Africa) suggests an ancient vicariant divergence of the two lineages followed by their northward expansion. Nevertheless, the "Out of South Africa" hypothesis would require a more ancient divergence between the two lineages. Instead, our estimates indicated that they diverged very recently (310 kyr), providing a better support for an Indo-Pacific origin of the two South African lineages. The arrival of the MRCA of P. perna in Brazil was estimated at 10 [0-40] kyr. Thus, the hypothesis of a recent introduction in Brazil through hull fouling in wooden vessels involved in the transatlantic itineraries of the slave trade did not receive strong support, but given the range for this estimate, it could not be discarded. Wider geographic sampling of marine organisms shows that lineages with contiguous distributions need not share a common ancestry.
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ItemIntraspecific genetic lineages of a marine mussel show behavioural divergence and spatial segregation over a tropical/subtropical biogeographic transition(BMC, 2015-05-31)BACKGROUND: Intraspecific variability is seen as a central component of biodiversity. We investigated genetic differentiation, contemporary patterns of demographic connectivity and intraspecific variation of adaptive behavioural traits in two lineages of an intertidal mussel (Perna perna) across a tropical/subtropical biogeographic transition. RESULTS: Microsatellite analyses revealed clear genetic differentiation between western (temperate) and eastern (subtropical/tropical) populations, confirming divergence previously detected with mitochondrial (COI) and nuclear (ITS) markers. Gene flow between regions was predominantly east-to-west and was only moderate, with higher heterozygote deficiency where the two lineages co-occur. This can be explained by differential selection and/or oceanographic dynamics acting as a barrier to larval dispersal. Common garden experiments showed that gaping (periodic closure and opening of the shell) and attachment to the substratum differed significantly between the two lineages. Western individuals gaped more and attached less strongly to the substratum than eastern ones. CONCLUSIONS: These behavioural differences are consistent with the geographic and intertidal distributions of each lineage along sharp environmental clines, indicating their strong adaptive significance. We highlight the functional role of diversity below the species level in evolutionary trends and the need to understand this when predicting biodiversity responses to environmental change.
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ItemAdaptive Traits Are Maintained on Steep Selective Gradients despite Gene Flow and Hybridization in the Intertidal Zone(PUBLIC LIBRARY SCIENCE, 2011-06-14)Gene flow among hybridizing species with incomplete reproductive barriers blurs species boundaries, while selection under heterogeneous local ecological conditions or along strong gradients may counteract this tendency. Congeneric, externally-fertilizing fucoid brown algae occur as distinct morphotypes along intertidal exposure gradients despite gene flow. Combining analyses of genetic and phenotypic traits, we investigate the potential for physiological resilience to emersion stressors to act as an isolating mechanism in the face of gene flow. Along vertical exposure gradients in the intertidal zone of Northern Portugal and Northwest France, the mid-low shore species Fucus vesiculosus, the upper shore species Fucus spiralis, and an intermediate distinctive morphotype of F. spiralis var. platycarpus were morphologically characterized. Two diagnostic microsatellite loci recovered 3 genetic clusters consistent with prior morphological assignment. Phylogenetic analysis based on single nucleotide polymorphisms in 14 protein coding regions unambiguously resolved 3 clades; sympatric F. vesiculosus, F. spiralis, and the allopatric (in southern Iberia) population of F. spiralis var. platycarpus. In contrast, the sympatric F. spiralis var. platycarpus (from Northern Portugal) was distributed across the 3 clades, strongly suggesting hybridization/introgression with both other entities. Common garden experiments showed that physiological resilience following exposure to desiccation/heat stress differed significantly between the 3 sympatric genetic taxa; consistent with their respective vertical distribution on steep environmental clines in exposure time. Phylogenetic analyses indicate that F. spiralis var. platycarpus is a distinct entity in allopatry, but that extensive gene flow occurs with both higher and lower shore species in sympatry. Experimental results suggest that strong selection on physiological traits across steep intertidal exposure gradients acts to maintain the 3 distinct genetic and morphological taxa within their preferred vertical distribution ranges. On the strength of distributional, genetic, physiological and morphological differences, we propose elevation of F. spiralis var. platycarpus from variety to species level, as F. guiryi.
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ItemMarine forests of the Mediterranean-Atlantic Cystoseira tamariscifolia complex show a southern Iberian genetic hotspot and no reproductive isolation in parapatry(NATURE RESEARCH, 2018-07-11)Climate-driven range-shifts create evolutionary opportunities for allopatric divergence and subsequent contact, leading to genetic structuration and hybrid zones. We investigate how these processes influenced the evolution of a complex of three closely related Cystoseira spp., which are a key component of the Mediterranean-Atlantic seaweed forests that are undergoing population declines. The C. tamariscifolia complex, composed of C. tamariscifolia s.s., C. amentacea and C. mediterranea, have indistinct boundaries and natural hybridization is suspected. Our aims are to (1) infer the genetic structure and diversity of these species throughout their distribution ranges using microsatellite markers to identify ancient versus recent geographical populations, contact zones and reproductive barriers, and (2) hindcast past distributions using niche models to investigate the influence of past range shifts on genetic divergence at multiple spatial scales. Results supported a single, morphologically plastic species the genetic structure of which was incongruent with a priori species assignments. The low diversity and low singularity in northern European populations suggest recent colonization after the LGM. The southern Iberian genetic hotspot most likely results from the role of this area as a climatic refugium or a secondary contact zone between differentiated populations or both. We hypothesize that life-history traits (selfing, low dispersal) and prior colonization effects, rather than reproductive barriers, might explain the observed genetic discontinuities.