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  • Journal article
    Lee WH, Salek-Ardakani S, Pandolfi PP, Brady HJ, Boer JD, Williams Oet al., 2012,

    NPM-MLF1 synergizes with Npm haploinsufficiency to enhance myeloid progenitor activity.

    , Leukemia, Vol: 26(5), Pages: 1110-1112
  • Journal article
    Nie R-E, Xue H-J, Hua Y, Yang X-K, Vogler APet al., 2012,

    Distinct species or colour polymorphism? Life history, morphology and sequence data separate two <i>Pyrrhalta</i> elm beetles (Coleoptera: Chrysomelidae)

    , SYSTEMATICS AND BIODIVERSITY, Vol: 10, Pages: 133-146, ISSN: 1477-2000
    • Cite
    • Citations: 14
  • Journal article
    Banks-Leite C, Ewers RM, Metzger JP, 2012,

    Unravelling the drivers of community dissimilarity and species extinction in fragmented landscapes

    , ECOLOGY, Vol: 93, Pages: 2560-2569
  • Journal article
    Barrett O, Sottocornola R, Lo Celso C, 2012,

    In vivo imaging of hematopoietic stem cells in the bone marrow niche.

    , Methods Mol Biol, Vol: 916, Pages: 231-242

    Even though hematopoietic stem cells (HSC) are amongst the first somatic stem cells exploited for therapeutic purposes, their application is still limited by the inability to expand them ex vivo without impairing their function. Moreover, it has recently emerged that several types of leukemia develop and relapse through complex interactions with bone marrow (BM) components and may directly affect the HSC and their niche. Increasing attention has therefore been dedicated to the BM microenvironment the HSC reside in, with the view that a better understanding of the molecular regulators of HSC-niche interaction in vivo will allow improving HSC mobilization, collection and transplantation and provide clues for the development of innovative leukemia treatments. This chapter focuses on a recently established technique for the visualization of transplanted hematopoietic stem and progenitor cells (HSPC) within the calvarium bone marrow of live mice (Lo Celso et al. Nature 457:92-96, 2007). Intravital microscopy is a rapidly developing field, driven by constant improvement in both detection technologies (i.e., spatial resolution, depth of penetration, spectral definition) and probe availability (i.e., increasingly sophisticated genetic and chemical reporter systems). We therefore discuss the current limitations and challenges related to intravital microscopy of the HSC niche and introduce a number of potential imaging approaches, which could be promising candidates for future development of this technique.
  • Journal article
    Staples C, Ahmed S, Ewers RM, 2012,

    Sensitivity of GIS patterns to data resolution: a case study of forest fragmentation in New Zealand

    , NEW ZEALAND JOURNAL OF ECOLOGY, Vol: 36, Pages: 203-209, ISSN: 0110-6465
  • Journal article
    Wiesler SC, Burrows PC, Buck M, 2012,

    A dual switch controls bacterial enhancer-dependent transcription

    , Nucleic Acids Res, Vol: 40, Pages: 10878-10892, ISSN: 1362-4962

    Bacterial RNA polymerases (RNAPs) are targets for antibiotics. Myxopyronin binds to the RNAP switch regions to block structural rearrangements needed for formation of open promoter complexes. Bacterial RNAPs containing the major variant sigma(54) factor are activated by enhancer-binding proteins (bEBPs) and transcribe genes whose products are needed in pathogenicity and stress responses. We show that (i) enhancer-dependent RNAPs help Escherichia coli to survive in the presence of myxopyronin, (ii) enhancer-dependent RNAPs partially resist inhibition by myxopyronin and (iii) ATP hydrolysis catalysed by bEBPs is obligatory for functional interaction of the RNAP switch regions with the transcription start site. We demonstrate that enhancer-dependent promoters contain two barriers to full DNA opening, allowing tight regulation of transcription initiation. bEBPs engage in a dual switch to (i) allow propagation of nucleated DNA melting from an upstream DNA fork junction and (ii) complete the formation of the transcription bubble and downstream DNA fork junction at the RNA synthesis start site, resulting in switch region-dependent RNAP clamp closure and open promoter complex formation.
  • Journal article
    Wiesler SC, Weinzierl RO, 2012,

    High-throughput purification of affinity-tagged recombinant proteins

    , J Vis Exp, ISSN: 1940-087X

    X-ray crystallography is the method of choice for obtaining a detailed view of the structure of proteins. Such studies need to be complemented by further biochemical analyses to obtain detailed insights into structure/function relationships. Advances in oligonucleotide- and gene synthesis technology make large-scale mutagenesis strategies increasingly feasible, including the substitution of target residues by all 19 other amino acids. Gain- or loss-of-function phenotypes then allow systematic conclusions to be drawn, such as the contribution of particular residues to catalytic activity, protein stability and/or protein-protein interaction specificity. In order to attribute the different phenotypes to the nature of the mutation--rather than to fluctuating experimental conditions--it is vital to purify and analyse the proteins in a controlled and reproducible manner. High-throughput strategies and the automation of manual protocols on robotic liquid-handling platforms have created opportunities to perform such complex molecular biological procedures with little human intervention and minimal error rates. Here, we present a general method for the purification of His-tagged recombinant proteins in a high-throughput manner. In a recent study, we applied this method to a detailed structure-function investigation of TFIIB, a component of the basal transcription machinery. TFIIB is indispensable for promoter-directed transcription in vitro and is essential for the recruitment of RNA polymerase into a preinitiation complex. TFIIB contains a flexible linker domain that penetrates the active site cleft of RNA polymerase. This linker domain confers two biochemically quantifiable activities on TFIIB, namely (i) the stimulation of the catalytic activity during the 'abortive' stage of transcript initiation, and (ii) an additional contribution to the specific recruitment of RNA polymerase into the preinitiation complex. We exploited the high-throughput purification method to genera
  • Journal article
    Lincoln CN, Fitzpatrick AE, van Thor JJ, 2012,

    Photoisomerisation Quantum Yield and Non-linear Cross-Sections with Femtosecond Excitation of the Photoactive Yellow Protein

    , Phys Chem Chem Phys, Pages: 15752-15764
  • Journal article
    Spanu PD, 2012,

    The Genomics of Obligate (and Nonobligate) Biotrophs

    , ANNUAL REVIEW OF PHYTOPATHOLOGY, VOL 50, Vol: 50, Pages: 91-109, ISSN: 0066-4286
  • Journal article
    Clements A, Young JC, Constantinou N, Frankel Get al., 2012,

    Infection strategies of enteric pathogenic <i>Escherichia coli</i>

    , GUT MICROBES, Vol: 3, Pages: 71-87, ISSN: 1949-0976
  • Journal article
    Rosindell J, Jansen PA, Etienne RS, 2012,

    Age structure in neutral theory resolves inconsistencies related to reproductive-size threshold

    , Journal of Plant Ecology, Vol: 5, Pages: 64-71

    AimsNeutral theory consists of a suite of models that assume ecological equivalence among individual organisms. They have been most commonly applied to tropical forest tree communities either as null models or as approximations. Neutral models typically only include reproductive adults; therefore, fitting to empirical tree community data requires defining a reproductive-size threshold, which for trees is usually set arbitrarily to a diameter at breast height (DBH) of 100 mm. The inevitable exclusion of some reproductive adults and inclusion of some saplings cause a non-random sampling bias in neutral model fits. Here, we investigate this problem and resolve it by introducing simple age structure into a neutral model.MethodsWe compared the performance and sensitivity of DBH threshold of three variants of a spatially explicit neutral model: the traditional model, a model incorporating random sampling and a model with two distinct age classes—reproductive adults and saplings. In the age-structured model, saplings are offspring from adults that disperse according to a Gaussian dispersal kernel around the adults. The only extra parameter is the ratio of adults to saplings, which is not a free parameter but directly measurable. We used species–area relation- ships (SARs) to explore the predicted effect of saplings on the species richness at different scales in our model. We then evaluated the three model variations to find the parameters required to maintain the ob- served level of species richness in the 50-ha plot on Barro Colorado Island (BCI). We repeated our analysis filtering the data at differentINTRODUCTIONNeutral theory refers to a collection of neutral models each as- suming ecological equivalence between individuals (Bellminimum tree-size thresholds in order to find the effect this threshold has on our results. Lastly, we used empirical species–individual rela- tionships (SIRs) to test the pre-existing hypothesis that environmental filtering i
  • Journal article
    Field KJ, Cameron DD, Leake JR, Tille S, Bidartondo MI, Beerling DJet al., 2012,

    Contrasting arbuscular mycorrhizal responses of vascular and non-vascular plants to a simulated Palaeozoic CO(2) decline.

    , Nature Communications, Vol: 3

    The arbuscular mycorrhizal (AM) fungal symbiosis is widely hypothesized to have promoted the evolution of land plants from rootless gametophytes to rooted sporophytes during the mid-Palaeozoic (480-360 Myr, ago), at a time coincident with a 90% fall in the atmospheric CO(2) concentration ([CO(2)](a)). Here we show using standardized dual isotopic tracers ((14)C and (33)P) that AM symbiosis efficiency (defined as plant P gain per unit of C invested into fungi) of liverwort gametophytes declines, but increases in the sporophytes of vascular plants (ferns and angiosperms), at 440 p.p.m. compared with 1,500 p.p.m. [CO(2)](a). These contrasting responses are associated with larger AM hyphal networks, and structural advances in vascular plant water-conducting systems, promoting P transport that enhances AM efficiency at 440 p.p.m. [CO(2)](a). Our results suggest that non-vascular land plants not only faced intense competition for light, as vascular land floras grew taller in the Palaeozoic, but also markedly reduced efficiency and total capture of P as [CO(2)](a) fell.
  • Journal article
    Lawrence D, Fiegna F, Behrends V, Bundy JG, Phillimore AB, Bell T, Barraclough TGet al., 2012,

    Species interactions alter evolutionary responses to a novel environment.

    , PLoS Biol, Vol: 10

    Studies of evolutionary responses to novel environments typically consider single species or perhaps pairs of interacting species. However, all organisms co-occur with many other species, resulting in evolutionary dynamics that might not match those predicted using single species approaches. Recent theories predict that species interactions in diverse systems can influence how component species evolve in response to environmental change. In turn, evolution might have consequences for ecosystem functioning. We used experimental communities of five bacterial species to show that species interactions have a major impact on adaptation to a novel environment in the laboratory. Species in communities diverged in their use of resources compared with the same species in monocultures and evolved to use waste products generated by other species. This generally led to a trade-off between adaptation to the abiotic and biotic components of the environment, such that species evolving in communities had lower growth rates when assayed in the absence of other species. Based on growth assays and on nuclear magnetic resonance (NMR) spectroscopy of resource use, all species evolved more in communities than they did in monocultures. The evolutionary changes had significant repercussions for the functioning of these experimental ecosystems: communities reassembled from isolates that had evolved in polyculture were more productive than those reassembled from isolates that had evolved in monoculture. Our results show that the way in which species adapt to new environments depends critically on the biotic environment of co-occurring species. Moreover, predicting how functioning of complex ecosystems will respond to an environmental change requires knowing how species interactions will evolve.
  • Journal article
    Banks-Leite C, Ewers RM, Pimentel RG, Metzger JPet al., 2012,

    Decisions on Temporal Sampling Protocol Influence the Detection of EcologicalPatterns

    , Biotropica, Vol: 44, Pages: 378-385
  • Journal article
    Banks-Leite C, Ewers RM, Metzger JP, 2012,

    The confounded effects of habitat disturbance at the local, patch and landscapescale on understorey birds of the Atlantic Forest: Implications for thedevelopment of landscape-based indicators

    , Ecological Indicators
  • Journal article
    Martensen AC, Ribeiro MC, Banks-Leite C, Prado PI, Metzger JPet al., 2012,

    Associations of Forest Cover, Fragment Area, and Connectivity with Neotropical Understory Bird Species Richness and Abundance

    , Conservation Biology, Vol: 6, Pages: 1100-1111
  • Journal article
    Lira PK, Ewers RM, Banks-Leite C, Pardini R, Metzger JPet al., 2012,

    Evaluating the legacy of landscape history: extinction debt and species credit in bird and small mammal assemblages in the Brazilian Atlantic Forest

    , Journal of Applied Ecology, Pages: 1325-1333
  • Journal article
    Gendrel AV, Apedaile A, Coker H, Termanis A, Zvetkova I, Godwin J, Tang YA, Huntley D, Montana G, Taylor S, Giannoulatou E, Heard E, Stancheva I, Brockdorff Net al., 2012,

    Smchd1-dependent and -independent pathways determine developmental dynamics of CpG island methylation on the inactive X chromosome.

    , Developmental Cell, Vol: 23, Pages: 265-279
  • Journal article
    Foster K, Bell T, 2012,

    Competition, Not Cooperation, Dominates Interactions among Culturable Microbial Species

    , Current Biology, Vol: 22, Pages: 1845-1850

    Microbial cells secrete numerous enzymes, scavenging molecules, and signals that can promote the growth and survival of other cells around them [ [1], [2], [3] and [4]]. This observation is consistent with the evolution of cooperation within species [5], and there is now an increasing emphasis on the importance of cooperation between different microbial species [ [4], [5] and [6]]. We lack, however, a systematic test of the importance of mutually positive interactions between different species, which is vital for assessing the commonness and importance of cooperative evolution in natural communities. Here, we study the extent of mutually positive interaction among bacterial strains isolated from a common aquatic environment. Using data collected from two independent experiments evaluating community productivity across diversity gradients, we show that (1) in pairwise species combinations, the great majority of interactions are net negative and (2) there is no evidence that strong higher-order positive effects arise when more than two species are mixed together. Our data do not exclude the possibility of positive effects in one direction where one species gains at the expense of another, i.e., predator-prey-like interactions. However, these do not constitute cooperation and our analysis suggests that the typical result of adaptation to other microbial species will be competitive, rather than cooperative, phenotypes.
  • Journal article
    Gravel D, Bell T, Barbera C, Combe M, Pommier T, Mouquet Net al., 2012,

    Phylogenetic constraints on ecosystem functioning

    , Nature Communications, Vol: 3

    There is consensus that biodiversity losses will result in declining ecosystem functioning if species have different functional traits. Phylogenetic diversity has recently been suggested as a predictor of ecosystem functioning because it could approximate the functional complementarity among species. Here we describe an experiment that takes advantage of the rapid evolutionary response of bacteria to disentangle the role of phylogenetic and species diversity. We impose a strong selection regime on marine bacterial lineages and assemble the ancestral and evolved lines in microcosms of varying lineage and phylogenetic diversity. We find that the relationship between phylogenetic diversity and productivity is strong for the ancestral lineages but brakes down for the evolved lineages. Our results not only emphasize the potential of using phylogeny to evaluate ecosystem functioning, but also they warn against using phylogenetics as a proxy for functional diversity without good information on species evolutionary history
  • Journal article
    Pageon SV, Rudnicka D, Davis DM, 2012,

    Illuminating the dynamics of signal integration in Natural Killer cells

    , FRONTIERS IN IMMUNOLOGY, Vol: 3, ISSN: 1664-3224
  • Conference paper
    Hardner CM, Peace C, Vithanage V, Carroll B, Turnbull C, McConchie Cet al., 2012,

    Genetic Resources and Improvement in Macadamia

    , 1st International Symposium on Wild Relatives of Subtropical and Temperate Fruit and Nut Crops, Publisher: INT SOC HORTICULTURAL SCIENCE, Pages: 253-262, ISSN: 0567-7572
  • Journal article
    Mallarino R, Abzhanov A, 2012,

    Paths Less Traveled: Evo-Devo Approaches to Investigating Animal Morphological Evolution

    , ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY, VOL 28, Vol: 28, Pages: 743-763, ISSN: 1081-0706
  • Journal article
    Luo YQ, JT Randerson, G Abramowitz, C Bacour, E Blyth, N Carvalhais, P Ciais, D Dalmonech, JB Fisher, R Fisher, P Friedlingstein, K Hibbard, F Hoffman, D Huntzinger, CD Jones, C Koven, D Lawrence, DJ Li, M Mahecha, SL Niu, R Norby, SL Piao, X Qi, P Peylin, IC Prentice, W Riley, M Reichstein, C Schwalm, YP Wang, J Xia, S Zaehle and XH Zhouet al., 2012,

    A framework for benchmarking land models

    , . Biogeosciences, Vol: 9, Pages: 3587-3874
  • Journal article
    Luo YQ, Randerson JT, Abramowitz G, Bacour C, Blyth E, Carvalhais N, Ciais P, Dalmonech D, Fisher JB, Fisher R, Friedlingstein P, Hibbard K, Hoffman F, Huntzinger D, Jones CD, Koven C, Lawrence D, Li DJ, Mahecha M, Niu SL, Norby R, Piao SL, Qi X, Peylin P, Prentice IC, Riley W, Reichstein M, Schwalm C, Wang YP, Xia JY, Zaehle S, Zhou XHet al., 2012,

    A framework for benchmarking land models

    , BIOGEOSCIENCES, Vol: 9, Pages: 3857-3874, ISSN: 1726-4170
    • Cite
    • Citations: 216
  • Journal article
    Antkowiak M, Torres-Mapa ML, McGinty J, Chahine M, Bugeon L, Rose A, Finn A, Moleirinho S, Okuse K, Dallman M, French P, Harding SE, Reynolds P, Gunn-Moore F, Dholakia Ket al., 2012,

    Towards gene therapy based on femtosecond optical transfection

    , BIOPHOTONICS: PHOTONIC SOLUTIONS FOR BETTER HEALTH CARE III, Vol: 8427, ISSN: 0277-786X
  • Journal article
    O'Gorman EJ, Pichler DE, Adams G, Benstead JP, Cohen H, Craig N, Cross WF, Demars BOL, Friberg N, Gislason GM, Gudmundsdottir R, Hawczak A, Hood JM, Hudson LN, Johansson L, Johansson MP, Junker JR, Laurila A, Manson JR, Mavromati E, Nelson D, Olafsson JS, Perkins DM, Petchey OL, Plebani M, Reuman DC, Rall BC, Stewart R, Thompson MSA, Woodward Get al., 2012,

    Impacts of Warming on the Structure and Functioning of Aquatic Communities: Individual-to Ecosystem-Level Responses

    , ADVANCES IN ECOLOGICAL RESEARCH, VOL 47: GLOBAL CHANGE IN MULTISPECIES SYSTEMS, PT 2, Vol: 47, Pages: 81-176, ISSN: 0065-2504
  • Book chapter
    Hagen M, Kissling WD, Rasmussen C, De Aguiar MAM, Brown LE, Carstensen DW, Alves-Dos-Santos I, Dupont YL, Edwards FK, Genini J, Guimaraes PR, Jenkins GB, Jordano P, Kaiser-Bunbury CN, Ledger ME, Maia KP, Darcie Marquitti FM, Mclaughlin O, Morellato LPC, O'Gorman EJ, Trojelsgaard K, Tylianakis JM, Vidal MM, Woodward G, Olesen JMet al., 2012,

    Biodiversity, Species Interactions and Ecological Networks in a Fragmented World

    , ADVANCES IN ECOLOGICAL RESEARCH, VOL 46: GLOBAL CHANGE IN MULTISPECIES SYSTEMS, PT 1, Editors: Jacob, Woodward, Publisher: ELSEVIER ACADEMIC PRESS INC, Pages: 89-210, ISBN: 978-0-12-396992-7
  • Journal article
    Bodi Z, Zhong S, Mehra S, Song J, Graham N, Li H, May S, Fray RGet al., 2012,

    Adenosine methylation in <i>Arabidopsis</i> mRNA is associated with the 3′ end and reduced levels cause developmental defects

    , FRONTIERS IN PLANT SCIENCE, Vol: 3, ISSN: 1664-462X
  • Journal article
    Wang H, Prentice IC, Ni J, 2012,

    Primary production in forests and grasslands of China: contrasting environmental responses of light- and water-use efficiency models

    , BIOGEOSCIENCES, Vol: 9, Pages: 4689-4705, ISSN: 1726-4170
    • Cite
    • Citations: 10

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