266 results for Conference poster

  • CellML: Cellml.org, Tools and Community

    Lawson J.; Lloyd C.; Noble P.; Hunter P.; Nielsen P. (2007)

    Conference poster
    The University of Auckland Library

    Poster presented at ICSB2007 The purpose of CellML is to store and exchange computer-based mathematical models of as wide a range of scale and subject as posssible. For example, biochemical signalling and metabolic systems can be embedded in electrophysiological models of excitable cells in CellML. The CellML language is an open standard based on the XML markup language and is being developed by the Bioengineering Institute at the University of Auckland and affiliated research groups [1]. The majority of computational biology publications aim to discuss their model but often fail to provide a comprehensive set of instructions for recreating the model, or include errors preventing reproduction of published model outputs. Publishing a paper with a link to a CellML model facilitates the wide distribution and recreation of that model, and additionally forces the modeller to carefully consider matters such as unit consistency. The CellML specification and application programming interfaces (API) are driven by a core team, but a growing international community is involved in work related to CellML. A community website (www.cellml.org) has been set up as a focal point for the community and also functions as a model repository. A number of groups are developing software tools for CellML and using the language for research in computational biology. A repository of almost 300 unique CellML models is available at www.cellml.org/models: these are computational models from peer-reviewed publications that have been coded into CellML. These models are undergoing an active curation process based on the MIRIAM standard, proposed by the international biological modelling community [2]. This process includes provision of comprehensive documentation, annotation with citation and model author metadata, maintenance of file modification histories, and correspondence with model authors to ensure that models define all required initial conditions and parameters. The CellML community strongly supports collaboration with other groups to continue to set standards for curation and distribution of biological models. A number of free / open source software tools for developing and simulating CellML models are available, including Physiome CellML Environment (PCEnv) and Cellular Open Resource (COR). Other modelling environments such as JSim and Virtual Cell also support the CellML format. Information on further tools such as validators, debuggers and simulation specific packages can be found at www.cellml.org/tools. In the near future, models in the cellml.org model repository will be completely annotated with ontologies such as BioPaX and references to databases such as UniProt. Models will be broken down into the components from which they are comprised, and these components will themselves be curated, providing a toolbox of standardised computational parts from which new models can be created, in an in silico analogy to the MIT Registry of Standard Biological parts (http://parts.mit.edu/registry/index.php/Main_Page). An API has recently been developed for software tools to allow interaction between CellML and SVG diagrams of models, such as biochemical pathway schematics, and work is also underway to standardise graphical representations of CellML models. For more information, please join the CellML community mailing list at http://www.cellml.org/mailman/listinfo/cellml-discussion. 1.) Cuellar, A.A., Lloyd, C. M., Nielsen, P. F., Bullivant, D. P., Nickerson, D. P., Hunter, P. J. "An Overview of CellML 1.1, a Biological Model Description Language" Simulation, 2003, 79, No. 12, 740-747 2.) Le Novere, N., Finney, A., Hucka, M., Bhalla, U.S., Campagne, F., Collado-Vides, J., Crampin, E.J., Halstead, M., Klipp, E., Mendes, P., Nielsen, P., Sauro, H., Shapiro, B., Snoep, J.L., Spence, H.D., Wanner, B.L. "Minium information requested in the annotation of biochemical models (MIRIAM)" Nature Biotechnology, 2005, 23 1509-1515

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  • Mechanisms Of Differences In Ventilation Distribution In The Upright, Supine, And Prone Postures

    Tawhai, Merryn; Hedges, Kerry (2011-05-13)

    Conference poster
    The University of Auckland Library

    Rationale: Measurements of ventilation distribution using various imaging modalities have suggested that the distribution of ventilation in the supine and prone postures is less evidently gravitational than when the lung is upright, and with some studies showing little difference between ventilation distributions in the prone and supine lung. This is despite the concurrent observations of a significant gradient in tissue density when supine, and a typically smaller - or absent - tissue density gradient prone. In this study we use a computational model of lung tissue elasticity coupled to air-flow to study the relationship between posture, density distribution, and ventilation. Methods: An imaging-based geometric model of the lung and airway tree that was developed in a separate study was used here. Flow in the airways was simulated using a one-dimensional fluid dynamics model that includes flow-dependent airway resistance and coupling to tissue elasticity at the airway walls and at the acini. A finite deformation elasticity model was used to predict the effect of gravity on tissue deformation, and the non-linear elasticity of each acinar tissue unit during simulated breathing. The upright lung volume was defined from pulmonary function testing; the supine and prone volumes were assumed to be the same, and equal to the supine air volume as calculated from the subject's computed tomography imaging acquired at FRC. Tissue density and ventilation at each of the ~32,000 distributed acini in the model were averaged within iso-gravitational slices of 10 mm thickness. Results: The gradient of tissue density predicted by the model was markedly larger in supine than in upright or prone. Ratios of the maximum to minimum slice density were 1.95, 1.51, and 1.39 for supine, prone, and upright, respectively. Ventilation in the upright model increased on average towards the dependent tissue, whereas ventilation in supine and prone was decreased in the most dependent and non-dependent regions. The ratios of maximum to minimum slice ventilation were 1.09, 1.03, and 1.31 for supine, prone, and upright, respectively. Conclusions: A lack of gravitational distribution of ventilation in the supine and prone postures compared with upright is predicted on the basis of the smaller size of the horizontal lung and a shift of the dependent tissue to a less-compliant region of the sigmoidal pressure-volume curve at its lower asymptote. This is the same mechanism that results in early filling of the non-dependent tissue when inhaling from residual volume.

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  • The use of whole community bacterial indicators to monitor ecological health, function and variability within stream biofilms

    Lear, Gavin; Boothroyd, IK; Lewis, Gillian (2009-08-30)

    Conference poster
    The University of Auckland Library

    This study describes the extent of variability in biofilm bacterial community structure across a broad range of spatial and temporal scales and assesses whether this may be used as an indicator of stream ecological health and function. A community DNA fingerprinting technique (Automated Ribosomal Intergenic Spacer Analysis - ARISA) was used to examine the structure of bacterial communities within freshwater stream biofilms. When compared with macrobenthic invertebrate community assemblages using multi-dimensional scaling techniques, similar broad-scale trends in population structure were revealed between organisms at these different trophic levels. For both communities, spatial variability in community structure was greater between streams than within each site, or compared to temporal variability measured over 1 year. Distance-based redundancy analysis of both bacterial ARISA and macroinvertebrate data estimated that the largest cause of variation in community structure was due to differences in catchment land-use, rather than any single water quality parameter (e.g. ph or ammoniacal nitrogen). Multidimensional scaling of ARISA data also revealed significant differences in community structure between urban, and less impacted stream sites, providing evidence that whole-bacterial communities could be used as an indicator of freshwater ecological health, analogous to the way that macroinvertebrate communities have been used for many years. In conclusion, we propose the analysis of whole bacterial communities as a cost-effective, high throughput alternative indicator of freshwater ecological health.

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  • Human Adenovirus ecology in environmental waters in New Zealand

    Dong, Yimin; Lewis, Gillian (2008-08-17)

    Conference poster
    The University of Auckland Library

    A major New Zealand study of pathogen occurrence in surface freshwaters identified occurrence of human adenovirus in 30% of sites and samples by qualitative PCR based methods. The source or nature of these viruses was not clear from the study and raises important questions in both viral ecology and human health protection. The aim of this study was to begin to unravel these questions by (i) development of specific quantitative analysis methods for adenoviruses in water and (ii) to target identifiable groups of adenovirus associated with human respiratory or gastrointestinal infections. These quantitative group specific real time PCR methods were tested in drinking water, recreational water, river water and wastewater. Adenovirus was detected in all primary wastewater samples tested (n=10) at high genome copy number (1.87 x104 to 4.6 x106 per litre) and in 33% (n=15) of the river water and 11% (n=27) of the treated drinking water samples. In addition, adenovirus was detected in 5 of the 6 estuarine recreational water samples (17 to 1190 virus genome copies per litre). DNA sequence analysis suggested that human adenovirus group C (respiratory infection associated) were most commonly associated with river, recreational and drinking water. Group F adenovirus (gastroenteritis associated viruses) were found to dominate in most wastewater (5 - 100 % total adenovirus) but were not detected in surface waters. This study suggests that the ecology of specific groups or types of adenovirus is sufficiently different, external to the host, to have important implications for human health risk assessment.

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  • Delayed Cerebral Post-arteriole Dilation is Consistent with Observations at Multiple Spatial and Temporal Scales: Evidence from Mathematical Modelling

    Barrett, MJP; Tawhai, MH; Suresh, Vinod (2011-05-25)

    Conference poster
    The University of Auckland Library

    Background and aims: Observations from different neurovascular imaging modalities provide conflicting evidence about the presence and/or extent of volume changes in post-arteriole blood vessels. At the level of individual vessels, two-photon imaging during functional activation shows a rapid increase in arteriolar diameter, but little or no increase in capillaries or venules 1 . In contrast, 'bulk' measurements of flow-volume relationships show large increases in arterial volume 2 , and smaller - but still significant - increases in venous volume 3 . Here, we reconcile these competing observations using a dynamic, biophysically based mathematical model of the hemodynamic response. Methods: We use the widely known Windkessel model that represents blood flow as analogous to electrical current, and networks of blood vessels as analogous to electrical resistances and capacitances. The model also includes a novel description of vascular compliance, viscoelastic effects, and stimulus-driven vasodilation. Experimental observations at progressively more detailed scales are used to constrain and validate the model, following a 'top down' approach. In addition, we test the assumption that post-arteriole vessels do not dilate, and use the model to predict observations at progressively more aggregated scales, following a 'bottom up' approach. Results: Model predictions of the total, arterial, and venous steady state flow-volume relationships agree well with experimental observations, as do predictions of transient changes in flow and volume during functional activation. The model also predicts rapid arteriole dilation during activation. Interestingly, this is accompanied by slow increases in capillary and venule diameter that - for brief stimulation - are near indistinguishable from baseline noise. When assuming no dilation of capillaries or venules, there are only minor differences between the model predictions at the single vessel scale. However, predictions at more aggregated scales are qualitatively and quantitatively different from experimental observations. Conclusions: The model presented here is able to reproduce the main features of experimental observations over a range of spatial and temporal scales. These results suggest that arterial dilation represents the majority of regional cerebral blood volume increases during functional activation, especially during brief stimulation. However, passive dilation in capillaries and venules may be increasingly significant during extended stimulation. This is an important consideration when interpreting or comparing results from neurovascular imaging modalities, such as optical methods and magnetic resonance imaging.

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  • Effect of light regimes on the utilisation of an exogenous carbon source by freshwater biofilm communities

    Lear, Gavin; Lewis, Gillian (2007-06-23)

    Conference poster
    The University of Auckland Library

    Biofilms are a major source of ‘in stream’ primary production, exhibiting high population density, and being an important source of carbon for microbial heterotrophs. Changing patterns of land-use within freshwater catchment areas may greatly impact on stream biofilm microbial community structure, which in turn may influence the speed and extent with which full ecosystem recovery may occur. This study reports how freshwater biofilm communities respond to additions of acetate, used as a proxy for organic matter, the primary source of carbon within shaded forests and headwater streams. The use of [ 13C] acetate and subsequent isolation of 13C-labelled nucleic acids from the metabolically active fraction of the bacterial community enabled substrate assimilating organisms to be identified. In addition, biofilms were exposed to varied levels of incident light to assess the relative contribution of phototrophic and heterotrophic nutrition.

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  • Ecosystem responses to multiple-stressor gradients: Nutrient and sediment addition to experimental stream channels

    Wagenhoff, A; Matthaei, CD; Lear, Gavin; Lewis, Gillian; Townsend, CR (2009-05-16)

    Conference poster
    The University of Auckland Library

    Agricultural land use can strongly affect stream ecosystems by increasing levels of nutrients and fine sediment cover on the streambed. Knowledge of patterns in ecological responses along gradients of these two stressors will help define thresholds of harm. Leaf breakdown rates, algal and bacterial communities are directly and/or indirectly influenced by nutrient supply and fine sediment cover. To investigate the effects of stressor gradients and their interactions on these biological response parameters, we designed a full-factorial experiment in circular stream-side channels with eight levels each of nutrients (36 to 6900 μg·l-1 DIN, 1.4 to 450 μg·l-1 DRP) and fine sediment (0 to 100 % cover). Algal biomass, bacterial diversity and leaf pack decomposition were determined after three weeks of exposure to both stressors. Algal biomass was significantly higher in channels with lower levels of fine sediment. Bacterial diversity generally increased with increasing nutrient concentrations up to an intermediate nutrient level but then decreased again with the exception of reaching the highest diversity overall at the top nutrient level. Thus, increased levels of nutrients and fine sediment caused major changes to the algal and bacterial communities. In turn, these changes affect other food-web components as well as ecosystem functioning, including decomposition.

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  • Three-Dimensional Structural Characterization of Tissue Engineered and Native Ovine Pulmonary Valves

    Eckert, Chad; Gerneke, Dane; Le Grice, Ian; Gottlieb, David; Mayer, JE; Sacks, MS (2009-04)

    Conference poster
    The University of Auckland Library

    OBJECTIVES: Efforts in tissue-engineered heart valves (TEHV) have shown increasingly equivalent mechanical/structural properties compared to native valves, though a literature gap exists regarding detailed structural information. This work was performed to provide such data of implanted TEHV, the native pulmonary valve (PV), and pre-implant scaffold to better understand developing TEHV. METHODS: Dynamically-cultured in vivo samples (“pre-implant”) and ovine TEHV PV in vitro samples (“explant”) were produced based on previous techniques; ovine PVs were excised. Samples were stained with picrosirius red and resinmounted. Using extended-volume scanning laser confocal microscopy (EV-SLCM), 1.5 x 1.5 x 0.4 mm full-thickness samples were imaged at 1 pixel/μm in 1 μm Z-direction steps. Custom software was used to process and visualize samples. Collagen, cell nuclei, and scaffold volume fractions were quantified; scaffold fiber trajectory and length were tracked using custom software. RESULTS: In a scaffold representative volume (90 μm thick), 104 fibers were tracked with a mean fiber length of 137.94 μm 55.4 μm (Fig.1). A comparison between pre-implant and explant samples showed collagen volume fraction increasing from 76.6% to 85.9%, with nuclei and scaffold decreasing from 2.8% to 0.5% and from 5.9% to 0.8%, respectively. With the native collagen volume fraction measured at 70%, pre-implant and explant samples showed an increase in collagen. CONCLUSIONS: This work captured important differences between in vivo/in vitro TEHV constituents; it is the first known work to utilize EV-SLCM on TEHV. A comparison to the native valve showed structural differences that could impact longterm functionality and improve design.

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  • Doped Diamond-Like Carbon (DLC) coated surfaces to reduce fouling from milk

    Patel, Jaiminkumar; Bansal, B; Jones, MI; Hyland, M (2010-11-09)

    Conference poster
    The University of Auckland Library

    In the dairy industry, fouling of processing surfaces is a common and unresolved problem. Surface modification, for example through the application of a surface coating, can alter the surface properties of a material, and may be a potential way to reduce fouling. Typical dairy plant stainless steel surfaces were modified by the deposition of doped Diamond-Like Carbon (DLC) films with varying concentration of doped elements. These modified surfaces were studied for their fouling behavior with milk at both laboratory and pilot scale. None of the doped DLC modified surfaces investigated in the study presented benefits in fouling reduction as compared to unmodified surface.

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  • The development of online learning environments (OLEs) at The University of Auckland Library: collaboration, integration and usability testing

    Zdravkovic, Neda (2013-04-09)

    Conference poster
    The University of Auckland Library

    In order to meet the learning needs of a large number of in-house, flexible learning and distance-learning students from a variety of disciplines, The University of Auckland Library has enhanced the provision of information and academic literacy instruction through the design of online learning environments. Learning Services Librarians, learning designers and subject librarians from The University of Auckland Library have collaborated with faculty, Centre for Academic Development staff, graphic design professionals and web developers to design online courses and tutorials, such as: • Academic Integrity - stand-alone online academic integrity course, compulsory for all new students at the University of Auckland from Semester I 2013; • COMLAW 101: New Zealand’s Legal Framework - curriculum- integrated information literacy online tutorial designed for COMLAW 101: Law in a Business Environment academic course with 2000 students each year; • POPLHLTH 701: Research Methods in Health - curriculum- integrated online information literacy learning environment for postgraduate students completing the POPLHLTH 701: Research Methods in Health course and compulsory assessment activity bearing 15% course mark; • FTVMS 100: Assignment Research Path – curriculum-integrated information literacy online tutorial and compulsory assessment activity (10% course mark) designed for FTVMS 100: Media studies first year undergraduate course with 1000 students each year; • Understanding Your Reading List - generic information literacy online tutorial designed for all first year undergraduate students. The focus of the paper will be on the development framework of online courses, curriculum-integrated and generic tutorials and the analysis of different stages of each project, their collaborative nature and usability testing practices applied (user observation, focus group interviews, surveys) and outcomes. It will introduce CourseBuilder as a web-based tool for the design of online learning environments and activities, its features, functionalities and published outputs. CourseBuilder, developed by the University of Auckland’s Centre for Academic Development, is an authoring tool that provides customisable templates to develop online interactive activities (eg, case studies, reflections and quizzes), import text, insert media, monitor student responses and more. Finally the paper will describe issues and challenges during each development stage, as well as benefits and limitations of using an online learning environment development system.

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  • Talking Allowed!

    Davies, Maree; Sinclair, A (2011)

    Conference poster
    The University of Auckland Library

    Research on the Paideia Method (a method for discussing a topic) was conducted in 20 classrooms across five schools, of varying socioeconomic environments (ages 11-13) in Auckland, New Zealand, in 2010. The researchers sought to further examine the results from their pilot study of the Paideia Seminar, entitled 'Talking Allowed: I like it when the teacher lets us talk without telling us what to say', trialed in 2008 (Sinclair & Davies, 2011). In addition, in order to provide the optimum conditions to prepare the students for the face-to-face seminars, an online component (open source software) was added as an alternative medium to assist students in their preparation. The research questions were: What happens to the Nature of Interaction, and the Complexity of the Discussion when students participate in a Paideia Seminar, and an on-line discussion in preparation for the face-to-face seminar? What is the optimal role of the teacher when participating in a Paideia Seminar and an on-line discussion to increase complexity of discussion?

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  • Using network science to explore innovation

    O'Neale, DR; Hendy, SH (2013-06-06)

    Conference poster
    The University of Auckland Library

    We live in a world were scientific and technical advances require increasingly specialised knowledge while drawing expertise from ever more diverse technical areas. In an effort to better understand the relationships between different areas of innovation, and the role of specialisation, diversity and ubiquity in national and regional economies, we have mined several million patent records from the European Patent Office, along with their classification codes, and used them to construct a network of “patent-space”. Patents provide a rich data set when studying innovation. Networks of scientific publications, such as that in [1], formed from inter-journal citations, illustrate the links between different disciplines as new knowledge is created, while networks of countries and the goods they export, such as the “product-space” network in [2], give insight into the economic complexity (or otherwise) and the likely areas of growth for national economies. Using patents allows us to take an intermediate view and investigate the role of science and innovation in economic growth. We take an approach similar to [2], identifying when individual countries or geographic regions have a “revealed comparative advantage” with respect to particular technical areas. We have constructed a proximity network as a base-map for the space of patentable innovation. We find that patent-space is heterogeneous and highly structured, and that the structure depends on the size or “granularity” of the regions that data is aggregated into. By overlaying data for particular regions on the patent-space base map we are able to explore temporal and regional trends – in particular how the innovation systems of different countries has produced quite different areas of specialisation. Figure 1: Patent-space for New Zealand (left) and South Korea (right) - two countries with very different innovation systems. Nodes represent patent classification classes. Nodes are dark when the country has a comparative advantage in that area and faded out otherwise. Nodes are connected if a comparative advantage with respect to one classification tends to occur in conjunction with a connected classification. [1] L. Leydesdorff & I. Rafols, Journal of the American Society for Information Science and Technology (2008). [2] C. Hidalgo & R. Hausmann, Proceedings of the National Academy of Sciences (2009).

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  • What influences the association between previous and future crashes among cyclists.

    Tin Tin, Sandar; Woodward, Alistair; Ameratunga, Shanthi (2014-10-09)

    Conference poster
    The University of Auckland Library

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  • Retrospective host specificity testing of Cotesia urabae to assess the risk posed to the New Zealand nolid moth Celama parvitis

    Avila Olesen, Gonzalo; Withers, TM; Holwell, GI (2014-08-11)

    Conference poster
    The University of Auckland Library

    Additional retrospective testing of the gum leaf skeletoniser (Uraba lugens) biological control agent Cotesia urabae was conducted against the endemic moth Celama parvitis. Although this native was included in host specificity testing before EPA approved the parasitoid's release, this work aimed to increase the sample size to better assess the potential risk posed. The effect that different periods of host deprivation and prior oviposition experience had on the parasitoid's readiness to attack, was examined in a sequence of no-choice tests. No parasitoids emerged from the 52% of larvae that survived to pupation, thus, confirming C. parvitis as a non-host. Dissections of larvae that died during laboratory rearing revealed that 63% had contained a parasitoid, but no C. urabae parasitoid larvae developed beyond the second instar. Significant differences were found in the attack times according to the parasitoid's deprivation levels (age), and it was also observed that the duration until first attack significantly decreased after each non-target presentation.

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  • The Regional Structure of Technical Innovation

    O'Neale, DR; Hendy, SC (2014-06-04)

    Conference poster
    The University of Auckland Library

    There is strong evidence that the productivity per capita of cities and regions increases with population. One likely factor behind this phenomenon is agglomeration; densely populated regions are able to bring together otherwise unlikely combinations of individuals and organisations with diverse, specialised capabilities. But clearly not all possible combinations of capability are equally valuable, nor are they equally likely. In order to investigate patterns in the typical combinations of capabilities, we have used the REGPAT patent database to construct a bipartite network of geographic regions and the patent classes for which those regions display a revealed comparative advantage. By identifying the pairs of patent classes that are most likely to co-occur within regions, we can infer relationships between the classes, giving a new network that maps out the structure of technical innovation. The resulting network has a core-periphery structure with a central group of highly connected technologies surrounded by branches of more specialised combinations. We investigate measures such as the diversity of regional patent portfolios and the ubiquity of patent classes across regions. We find that diversity is positively correlated with regional population, while the average ubiquity of patents in a region’s patent portfolio is negatively correlated. This suggests that more populous regions are able to expand into more specialised and higher value parts of the patent network.

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  • Sequence Coverage Abnormalities and Sex-Specific Autosomal Regions in Cattle

    Lopdell, Thomas; Harland, C; Johnson, T; Keehan, M (2012-08-21)

    Conference poster
    The University of Auckland Library

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  • Detection of tissue- and sex-specific gene expression in Bos taurus using high depth RNA sequencing

    Lopdell, Thomas; Littlejohn, M (2013-08-13)

    Conference poster
    The University of Auckland Library

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  • Bacterially mediated manganese deposition in novel "anelli" within the biofilms of an impacted urban stream

    Smith, JP; Lewis, Gillian (2007-12-02)

    Conference poster
    The University of Auckland Library

    The purpose of this work is to identify bacteria responsible for the formation of manganese containing anelli within stream biofilms, and study their distribution. Manganese oxidising bacteria are part of a diverse group of organisms found commonly within many disparate environments, which deposit manganese and iron biominerals within biofilms and flocs [1]. The purpose of microbial manganese oxidation is poorly understood, but may be associated with energy production, mobilisation of nutrients, protection and/or detoxification [1, 2]. Manganese has a high sorptive capacity for heavy metals, metalloids, and other ions, as well as a strong oxidizing potential, and therefore frequently induces co-precipitation of cations present within the surrounding environment [1]. Within urban streams contaminants such as heavy metals may therefore potentially be concentrated within steam biofilms in the presence of manganese oxidising bacteria.

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  • Effects of Storm water metal contaminats on microbial communities in stream biofilm revealed by Automated Ribosomal Intergenic Spacer Analysis (ARISA)

    Ancion, Pierre; Lear, Gavin; Lewis, Gillian (2008-08-17)

    Conference poster
    The University of Auckland Library

    Stormwater metal contaminants are known to be a threat to our freshwater environments but little is known about their effects on stream micro-organisms. This project investigates accumulation and release of the most common stormwater metal contaminants (zinc, copper and lead) in stream biofilms and their effects on bacterial populations.

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  • Molecular investigation of protozoan diversity in stream biofilms

    Dopheide, AJ; Lear, Gavin; Lewis, Gillian (2006-11-21)

    Conference poster
    The University of Auckland Library

    This research aims to test the following hypothesis: that molecular biological methods will allow description of protozoan diversity and ecology in streams.

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