Science

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Now showing 1 - 10 of 13
  • (2008) Fei, W; Shui, G; Gaeta, Bruno; Du, Xi; Kuerschner, L; Brown, Andrew; Wenk, M; Parton, R; Yang, Hyuk-Seung; Li, Peng
    Journal Article
    Lipid droplets (LDs) are emerging cellular organelles that are of crucial importance in cell biology and human diseases. In this study, we present our screen of 4,700 Saccharomyces cerevisiae mutants for abnormalities in the number and morphology of LDs; we identify 17 fld (few LDs) and 116 mld (many LDs) mutants. One of the fld mutants (fld1) is caused by the deletion of YLR404W, a previously uncharacterized open reading frame. Cells lacking FLD1 contain strikingly enlarged (supersized) LDs, and LDs from fld1 Delta cells demonstrate significantly enhanced fusion activities both in vivo and in vitro. Interestingly, the expression of human seipin, whose mutant forms are associated with Berardinelli-Seip congenital lipodystrophy and motoneuron disorders, rescues LD-associated defects in fld1 Delta cells. Lipid profiling reveals alterations in acyl chain compositions of major phospholipids in fld1 Delta cells. These results suggest that an evolutionally conserved function of seipin in phospholipid metabolism and LD formation may be functionally important in human adipogenesis.

  • (2008) Mai-Prochnow, A; Lucas-Elio, P; Egan, S; Thomas, Torsten; Webb, JS; Sanchez-Amat, A; Kjelleberg, S
    Journal Article
    The marine bacterium Pseudoalteromonas tunicata produces an antibacterial and autolytic protein, AlpP, which causes death of a subpopulation of cells during biofilm formation and mediates differentiation, dispersal, and phenotypic variation among dispersal cells. The AlpP homologue (LodA) in the marine bacterium Marinomonas mediterranea was recently identified as a lysine oxidase which mediates cell death through the production of hydrogen peroxide. Here we show that AlpP in P. tunicata also acts as a lysine oxidase and that the hydrogen peroxide generated is responsible for cell death within microcolonies during biofilm development in both M. mediterranea and P. tunicata. LodA-mediated biofilm cell death is shown to be linked to the generation of phenotypic variation in growth and biofilm formation among M. mediterranea biofilm dispersal cells. Moreover, AlpP homologues also occur in several other gram-negative bacteria from diverse environments. Our results show that subpopulations of cells in microcolonies also die during biofilm formation in two of these organisms, Chromobacterium violaceum and Caulobacter crescentus. In all organisms, hydrogen peroxide was implicated in biofilm cell death, because it could be detected at the same time as the killing occurred, and the addition of catalase significantly reduced biofilm killing. In C. violaceum the AlpP-homologue was clearly linked to biofilm cell death events since an isogenic mutant (CVMUR1) does not undergo biofilm cell death. We propose that biofilm killing through hydrogen peroxide can be linked to AlpP homologue activity and plays an important role in dispersal and colonization across a range of gram-negative bacteria.

  • (2008) Egan, S; Thomas, Torsten; Kjelleberg, S
    Journal Article
    Marine sessile eukaryotic hosts provide a unique surface for microbial colonisation. Chemically mediated interactions between the host and colonising microorganisms, interactions between microorganisms in the biofilm community and surface-specific physical and chemical conditions impact differently on the diversity and function of surface-associated microbial assemblages compared with those in planktonic systems. Understanding the diversity and ecology of surface-associated microbial communities will greatly contribute to the discovery of next-generation, bioactive compounds. On the basis of recent conceptual and technological advances insights into the microbiology of marine living surfaces are improving and novel bioactives, including those previously ascribed as host derived, are now revealed to be produced by members of the surface-associated microbial community.

  • (2008) Thomas, Torsten; Evans, FF; Schleheck, D; Mai-Prochnow, A; Burke, C; Penesyan, A; Dalisay, DS; Stelzer-Braid, S; Saunders, N; Johnson, J; Ferriera, S; Kjelleberg, S; Egan, S
    Journal Article
    BACKGROUND: Colonisation of sessile eukaryotic host surfaces (e.g. invertebrates and seaweeds) by bacteria is common in the marine environment and is expected to create significant inter-species competition and other interactions. The bacterium Pseudoalteromonas tunicata is a successful competitor on marine surfaces owing primarily to its ability to produce a number of inhibitory molecules. As such P. tunicata has become a model organism for the studies into processes of surface colonisation and eukaryotic host-bacteria interactions. METHODOLOGY/PRINCIPAL FINDINGS: To gain a broader understanding into the adaptation to a surface-associated life-style, we have sequenced and analysed the genome of P. tunicata and compared it to the genomes of closely related strains. We found that the P. tunicata genome contains several genes and gene clusters that are involved in the production of inhibitory compounds against surface competitors and secondary colonisers. Features of P. tunicata's oxidative stress response, iron scavenging and nutrient acquisition show that the organism is well adapted to high-density communities on surfaces. Variation of the P. tunicata genome is suggested by several landmarks of genetic rearrangements and mobile genetic elements (e.g. transposons, CRISPRs, phage). Surface attachment is likely to be mediated by curli, novel pili, a number of extracellular polymers and potentially other unexpected cell surface proteins. The P. tunicata genome also shows a utilisation pattern of extracellular polymers that would avoid a degradation of its recognised hosts, while potentially causing detrimental effects on other host types. In addition, the prevalence of recognised virulence genes suggests that P. tunicata has the potential for pathogenic interactions. CONCLUSIONS/SIGNIFICANCE: The genome analysis has revealed several physiological features that would provide P. tunciata with competitive advantage against other members of the surface-associated community. We have also identified properties that could mediate interactions with surfaces other than its currently recognised hosts. This together with the detection of known virulence genes leads to the hypothesis that P. tunicata maintains a carefully regulated balance between beneficial and detrimental interactions with a range of host surfaces.

  • (2008) Tang, Chaka; Reyes, Josephine F; Luciani, Fabio; Francis, Andrew R.; Tanaka, Mark M
    Journal Article
    spolTools is a collection of online programs designed to manipulate and analyze spoligotype datasets of the Mycobacterium tuberculosis complex. These tools are integrated into a repository currently containing 1179 spoligotypes and 6278 isolates across 30 datasets. Users can search this database to export for external use or to pass on to the integrated tools. These tools include the computation of basic population genetic quantities, the visualization of clusters of spoligotype patterns based on an estimated evolutionary history and a procedure to predict emerging strains – genotypes associated with elevated transmission.

  • (2008) Reyes, Josephine F; Francis, Andrew R.; Tanaka, Mark M
    Journal Article
    Background: Molecular typing methods are commonly used to study genetic relationships among bacterial isolates. Many of these methods have become standardized and produce portable data. A popular approach for analyzing such data is to construct graphs, including phylogenies. Inferences from graph representations of data assist in understanding the patterns of transmission of bacterial pathogens, and basing these graph constructs on biological models of evolution of the molecular marker helps make these inferences. Spoligotyping is a widely used method for genotyping isolates of Mycobacterium tuberculosis that exploits polymorphism in the direct repeat region. Our goal was to examine a range of models describing the evolution of spoligotypes in order to develop a visualization method to represent likely relationships among M. tuberculosis isolates. Results: We found that inferred mutations of spoligotypes frequently involve the loss of a single or very few adjacent spacers. Using a second-order variant of Akaike's Information Criterion, we selected the Zipf model as the basis for resolving ambiguities in the ancestry of spoligotypes. We developed a method to construct graphs of spoligotypes (which we call spoligoforests). To demonstrate this method, we applied it to a tuberculosis data set from Cuba and compared the method to some existing methods. Conclusion: We propose a new approach in analyzing relationships of M. tuberculosis isolates using spoligotypes. The spoligoforest recovers a plausible history of transmission and mutation events based on the selected deletion model. The method may be suitable to study markers based on loci of similar structure from other bacteria. The groupings and relationships in the spoligoforest can be analyzed along with the clinical features of strains to provide an understanding of the evolution of spoligotypes.

  • (2008) Luciani, Fabio; Francis, Andrew; Tanaka, Mark
    Journal Article
    Molecular techniques such as IS6110-RFLP typing and spacer oligonucleotide typing (spoligotyping) have aided in understanding the transmission patterns of Mycobacterium tuberculosis. The degree of clustering of isolates on the basis of genotypes is informative of the extent of transmission in a given geographic area. We analyzed 130 published data sets of M. tuberculosis isolates, each representing a sample of bacterial isolates from a specific geographic region, typed with either or both of the IS6110-RFLP and spoligotyping methods. We explored common features and differences among these samples. Using population models, we found that the presence of large clusters (typically associated with recent transmission) as well as a large number of singletons (genotypes found exactly once in the data set) is consistent with an expanding infectious population. We also estimated the mutation rate of spoligotype patterns relative to IS6110 patterns and found the former rate to be about 10-26% of the latter. This study illustrates the utility of examining the full distribution of genotype cluster sizes from a given region, in the light of population genetic models. (C) 2007 Elsevier B.V. All rights reserved.

  • (2008) Venturi, Vanessa; Kedzierska, K; Tanaka, Mark; Turner, Stephen; Doherty, P; Davenport, Miles
    Journal Article
    The CD8(+) T cell response is important in the control of many viral and other infections. There have been many studies aimed at better understanding the influence of T cell receptor diversity on immune responses and the evolution of the T cell receptor repertoire over time and through the various stages of immune responses to infection. In recent years, there has been an increase in both the number of studies using T cell receptor data and the volume of T cell receptor data generated per study. Appropriate analytical tools are required to analyse this data. We present a robust approach to assessing the similarity between samples of the T cell receptor repertoire, which we demonstrate on published data of subsets of the influenza A virus (DNP366)-N-b- and D(b)PA(224)- specific CD8+ T cell responses in mice sorted on the expression of CD62L, which is a marker distinguishing central and effector memory cells. (C) 2007 Elsevier B.V. All rights reserved.

  • (2008) Gerressu, M; Elam, Gillian; Shain, R; Dimmitt Champion, J; Brook, G; Elford, J; Bonell, C; French, R; Stephenson, Jodie; Imrie, John
    Report

  • (2008) LeBard, Rebecca; Quinnell, Rosanne
    Conference Paper
    Undergraduate science students are given opportunities to link the descriptions of scientific phenomena presented in lectures to their own observations of similar scientific phenomena in practical classes so as to reinforce key concepts. Being able to conceptually move between the scientific phenomena and the abstracted figures or equations that represent those phenomena is a key skill. Developing this skill, and confidence with applying this skill, is the implicit objective of many undergraduate practical classes. However, students seem unable to adequately explain their observations, despite the implementation of many “how to” guides, and this is of concern, which is why we seek to identify some of the factors that seem to impede students from being able to correctly translate and explain scientific data. We audited 118 laboratory reports in from second year molecular biology students to assess students’ abilities to correctly record and calculate data, appropriately present data, and clearly explain the representation of their data. Each of these abilities were linked to criteria in the report marking scheme students had been provided and for the purpose of our audit, graded as to whether the students completed the task poorly or not at all (1), adequately with some errors (2), or correctly and clearly (3). The data showed that a high proportion of students could not complete these tasks correctly and confirms that students have difficulty moving between the phenomena they observe and its abstract presentation. Having identified and quantified where students are having difficulties, we will use this information to inform the design of an online learning module to improve the conceptual linkages between a) an observed scientific phenomenon, b) the experimental data c) how these data are presented and d) interpreted. We expect to be able to determine the efficacy of this approach by re-auditing laboratory reports, after the online module is in place.