School of BioSciences - Research Publications

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    Proteomics and Deep Sequencing Comparison of Seasonally Active Venom Glands in the Platypus Reveals Novel Venom Peptides and Distinct Expression Profiles
    Wong, ESW ; Morgenstern, D ; Mofiz, E ; Gombert, S ; Morris, KM ; Temple-Smith, P ; Renfree, MB ; Whittington, CM ; King, GF ; Warren, WC ; Papenfuss, AT ; Belov, K (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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    N-Glycosylation Determines Ionic Permeability and Desensitization of the TRPV1 Capsaicin Receptor
    Veldhuis, NA ; Lew, MJ ; Abogadie, FC ; Poole, DP ; Jennings, EA ; Ivanusic, JJ ; Eilers, H ; Bunnett, NW ; McIntyre, P (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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    Global Diversity of Brittle Stars (Echinodermata: Ophiuroidea)
    Stohr, S ; O'Hara, TD ; Ben, T ; Laudet, V (PUBLIC LIBRARY SCIENCE, 2012-03-02)
    This review presents a comprehensive overview of the current status regarding the global diversity of the echinoderm class Ophiuroidea, focussing on taxonomy and distribution patterns, with brief introduction to their anatomy, biology, phylogeny, and palaeontological history. A glossary of terms is provided. Species names and taxonomic decisions have been extracted from the literature and compiled in The World Ophiuroidea Database, part of the World Register of Marine Species (WoRMS). Ophiuroidea, with 2064 known species, are the largest class of Echinodermata. A table presents 16 families with numbers of genera and species. The largest are Amphiuridae (467), Ophiuridae (344 species) and Ophiacanthidae (319 species). A biogeographic analysis for all world oceans and all accepted species was performed, based on published distribution records. Approximately similar numbers of species were recorded from the shelf (n = 1313) and bathyal depth strata (1297). The Indo-Pacific region had the highest species richness overall (825 species) and at all depths. Adjacent regions were also relatively species rich, including the North Pacific (398), South Pacific (355) and Indian (316) due to the presence of many Indo-Pacific species that partially extended into these regions. A secondary region of enhanced species richness was found in the West Atlantic (335). Regions of relatively low species richness include the Arctic (73 species), East Atlantic (118), South America (124) and Antarctic (126).
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    Finding the undiscovered roles of genes: an approach using mutual ranking of coexpressed genes and promoter architecture-case study: dual roles of thaumatin like proteins in biotic and abiotic stresses
    Deihimi, T ; Niazi, A ; Ebrahimi, M ; Kajbaf, K ; Fanaee, S ; Bakhtiarizadeh, MR ; Ebrahimie, E (SPRINGER INTERNATIONAL PUBLISHING AG, 2012)
    Regarding the possible multiple functions of a specific gene, finding the alternative roles of genes is a major challenge. Huge amount of available expression data and the central role of the promoter and its regulatory elements provide unique opportunely to address this issue. The question is that how the expression data and promoter analysis can be applied to uncover the different functions of a gene. A computational approach has been presented here by analysis of promoter regulatory elements, coexpressed gene as well as protein domain and prosite analysis. We applied our approach on Thaumatin like protein (TLP) as example. TLP is of group 5 of pathogenesis related proteins which their antifungal role has been proved previously. In contrast, Osmotin like proteins (OLPs) are basic form of TLPs with proved role only in abiotic stresses. We demonstrated the possible outstanding homolouges involving in both biotic and abiotic stresses by analyzing 300 coexpressed genes for each Arabidopsis TLP and OLP in biotic, abiotic, hormone, and light microarray experiments based on mutual ranking. In addition, promoter analysis was employed to detect transcription factor binding sites (TFBs) and their differences between OLPs and TLPs. A specific combination of five TFBs was found in all TLPs presenting the key structure in functional response of TLP to fungal stress. Interestingly, we found the fungal response TFBs in some of salt responsive OLPs, indicating the possible role of OLPs in biotic stresses. Thirteen TFBS were unique for all OLPs and some found in TLPs, proposing the possible role of these TLPs in abiotic stresses. Multivariate analysis showed the possibility of estimating models for distinguishing biotic and abiotic functions of TIPs based on promoter regulatory elements. This is the first report in identifying multiple roles of TLPs and OLPs in biotic and abiotic stresses. This study provides valuable clues for screening and discovering new genes with possible roles in tolerance against both biotic and abiotic stresses. Interestingly, principle component analysis showed that promoter regulatory elements of TLPs and OLPs are more variable than protein properties reinforcing the prominent role of promoter architecture in determining gene function alteration.
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    Protein Interaction Network of Arabidopsis thaliana Female Gametophyte Development Identifies Novel Proteins and Relations
    Hosseinpour, B ; HajiHoseini, V ; Kashfi, R ; Ebrahimie, E ; Hemmatzadeh, F ; Esteban, FJ (PUBLIC LIBRARY SCIENCE, 2012-12-11)
    Although the female gametophyte in angiosperms consists of just seven cells, it has a complex biological network. In this study, female gametophyte microarray data from Arabidopsis thaliana were integrated into the Arabidopsis interactome database to generate a putative interaction map of the female gametophyte development including proteome map based on biological processes and molecular functions of proteins. Biological and functional groups as well as topological characteristics of the network were investigated by analyzing phytohormones, plant defense, cell death, transporters, regulatory factors, and hydrolases. This approach led to the prediction of critical members and bottlenecks of the network. Seventy-four and 24 upregulated genes as well as 171 and 3 downregulated genes were identified in subtracted networks based on biological processes and molecular function respectively, including novel genes such as the pathogenesis-related protein 4, ER type Ca(2+) ATPase 3, dihydroflavonol reductase, and ATP disulfate isomerase. Biologically important relationships between genes, critical nodes, and new essential proteins such as AT1G26830, AT5G20850, CYP74A, AT1G42396, PR4 and MEA were found in the interactome's network. The positions of novel genes, both upregulated and downregulated, and their relationships with biological pathways, in particular phytohormones, were highlighted in this study.
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    A female preference for experienced males in the almond moth, Cadra cautella
    McNamara, KB ; McKenzie, JL ; Elgar, MA ; Jones, TM (SPRINGER, 2012-08)
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    Effects of pulse versus steady recruitment on sessile marine communities
    Sams, MA ; Keough, MJ (SPRINGER, 2012-09)
    Variation in patterns of propagule establishment (recruitment) has important effects on population dynamics and the structure of some communities. Most experimental studies have varied recruitment by changing the nature of a single event early in community development, but recruitment can also vary from steady rates of arrival to highly episodic 'pulse' events, causing differences in the temporal spacing of individuals recruiting into patches. We examined whether two different temporal patterns of recruitment of sessile invertebrates affected temperate marine communities in southeastern Australia in two experiments that were run at different times at the same site and that manipulated several different species. Target species entered communities as either a single pulse of recruits within a 2-week period or steady input of the same total number of recruits over a longer time period (5-6 weeks). The pattern of recruitment had variable effects on community structure. The colonial ascidian Botryllus schlosseri did not have a strong influence on community structure whether it recruited in a single pulse or steadily. The cover of B. schlosseri was higher when recruitment occurred as a single pulse. In a second experiment, botryllid ascidians caused changes in the composition of communities when they recruited steadily compared to when they did not recruit or didemnids recruited, but caused no differences in communities when they recruited in a shorter pulse. In contrast, recruitment frequency of didemnid ascidians had little effect, though their presence/absence caused community differences. Though we found that different temporal recruitment patterns can alter community composition, the life history and ecology of particular taxa as well as differences in environmental background processes are likely to influence the strength of these effects.
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    Human-induced versus historical habitat shifts: identifying the processes that shaped the genetic structure of the threatened grassland legless lizard, Delma impar
    Maldonado, SP ; Melville, J ; Peterson, GNL ; Sumner, J (SPRINGER, 2012-10)
    Historical and contemporary events are known to affect the genetic structure and diversity of species. Thus, in order to design effective conservation management strategies for threatened species, it is important to identify the processes that shaped their genetic patterns. The Striped Legless Lizard, Delma impar, is currently listed as a threatened species, and is restricted to the temperate grasslands of south eastern Australia. This habitat has undergone both historical climatic and recent anthropogenic distributional changes. We used mitochondrial DNA (mtDNA) and microsatellite markers to examine the phylogeography and population genetic structure of D. impar. Analysis of mtDNA revealed four distinct historically isolated lineages with high levels of genetic divergence that have been isolated for more than 1 million years. These lineages should be considered separate Evolutionarily Significant Units (ESU) for management purposes. Analysis of microsatellite genotypes did not reveal evidence of strong population sub-structuring despite recent anthropogenic fragmentation within the south west Victorian ESU. However, three populations were identified by the program Structure, which coincide with the transition of two regions with distinct soil and vegetation characteristics. Spatial autocorrelation analyses indicate that D. impar do not disperse long distances as they are genetically structured at distances less than 400 m.
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    Plant homeostasis of foliar manganese sinks: specific variation in hyperaccumulators
    Fernando, DR ; Woodrow, IE ; Baker, AJM ; Marshall, AT (SPRINGER, 2012-11)
    Plant manganese (Mn) hyperaccumulation provides unusual insight into homeostasis of this essential micronutrient, in particular its excessive storage in shoot tissues. The compartmentation of hyperaccumulated foliar Mn appears exceptional among metal hyperaccumulators, since it occurs via specific microdistribution patterns. Here, three associated Mn hyperaccumulators, Virotia neurophylla, Maytenus fournieri, and Garcinia amplexicaulis exhibiting distinctly different Mn detoxification strategies were examined. Non-invasive sample preparation in conjunction with cryo scanning electron microscopy (SEM) was used to obtain in vivo quantitative microprobe X-ray and anatomical data from fully hydrated cells. Highly vacuolated large palisade mesophyll cells in V. neurophylla leaves were found to contain around 650 mM Mn. The large non-photosynthetic hypodermal cells of M. fournieri leaves, also with high vacuolar content, and the main site for Mn disposal, had an estimated mean vacuolar Mn concentration of around 600 mM. Previous qualitative X-ray mapping had shown Mn to be almost evenly sequestered across the entire leaf cross section of G. amplexicaulis. However, quantitative data obtained here showed a marked variation in localised concentrations that ranged between ~15 and >800 mM. Notable among these were mean values of >600 mM in spongy mesophyll cells, and ~800 mM within cells of a narrow sub epidermal layer preceding the palisade mesophyll. This study demonstrated the extraordinary Mn carrying capacities of different types of leaf cell vacuoles.