TY - JOUR A1 - Tang, Kam W. A1 - Gladyshev, Michail I. A1 - Dubovskaya, Olga P. A1 - Kirillin, Georgiy A1 - Grossart, Hans-Peter T1 - Zooplankton carcasses and non-predatory mortality in freshwater and inland sea environments JF - Journal of plankton research N2 - Zooplankton carcasses are ubiquitous in marine and freshwater systems, implicating the importance of non-predatory mortality, but both are often overlooked in ecological studies compared with predatory mortality. The development of several microscopic methods allows the distinction between live and dead zooplankton in field samples, and the reported percentages of dead zooplankton average 11.6 (minimum) to 59.8 (maximum) in marine environments, and 7.4 (minimum) to 47.6 (maximum) in fresh and inland waters. Common causes of non-predatory mortality among zooplankton include senescence, temperature change, physical and chemical stresses, parasitism and food-related factors. Carcasses resulting from non-predatory mortality may undergo decomposition leading to an increase in microbial production and a shift in microbial composition in the water column. Alternatively, sinking carcasses may contribute significantly to vertical carbon flux especially outside the phytoplankton growth seasons, and become a food source for the benthos. Global climate change is already altering freshwater ecosystems on multiple levels, and likely will have significant positive or negative effects on zooplankton non-predatory mortality. Better spatial and temporal studies of zooplankton carcasses and non-predatory mortality rates will improve our understanding of this important but under-appreciated topic. KW - carbon flux KW - inland waters KW - lakes KW - live KW - dead sorting KW - non-predatory mortality KW - zooplankton carcasses Y1 - 2014 U6 - https://doi.org/10.1093/plankt/fbu014 SN - 0142-7873 SN - 1464-3774 VL - 36 IS - 3 SP - 597 EP - 612 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Beck, Jan A1 - Ballesteros-Mejia, Liliana A1 - Buchmann, Carsten M. A1 - Dengler, Jürgen A1 - Fritz, Susanne A. A1 - Gruber, Bernd A1 - Hof, Christian A1 - Jansen, Florian A1 - Knapp, Sonja A1 - Kreft, Holger A1 - Schneider, Anne-Kathrin A1 - Winter, Marten A1 - Dormann, Carsten F. T1 - What's on the horizon for macroecology? JF - Ecography : pattern and diversity in ecology ; research papers forum N2 - Over the last two decades, macroecology the analysis of large-scale, multi-species ecological patterns and processes has established itself as a major line of biological research. Analyses of statistical links between environmental variables and biotic responses have long and successfully been employed as a main approach, but new developments are due to be utilized. Scanning the horizon of macroecology, we identified four challenges that will probably play a major role in the future. We support our claims by examples and bibliographic analyses. 1) Integrating the past into macroecological analyses, e.g. by using paleontological or phylogenetic information or by applying methods from historical biogeography, will sharpen our understanding of the underlying reasons for contemporary patterns. 2) Explicit consideration of the local processes that lead to the observed larger-scale patterns is necessary to understand the fine-grain variability found in nature, and will enable better prediction of future patterns (e.g. under environmental change conditions). 3) Macroecology is dependent on large-scale, high quality data from a broad spectrum of taxa and regions. More available data sources need to be tapped and new, small-grain large-extent data need to be collected. 4) Although macroecology already lead to mainstreaming cutting-edge statistical analysis techniques, we find that more sophisticated methods are needed to account for the biases inherent to sampling at large scale. Bayesian methods may be particularly suitable to address these challenges. To continue the vigorous development of the macroecological research agenda, it is time to address these challenges and to avoid becoming too complacent with current achievements. Y1 - 2012 U6 - https://doi.org/10.1111/j.1600-0587.2012.07364.x SN - 0906-7590 SN - 1600-0587 VL - 35 IS - 8 SP - 673 EP - 683 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Cencil, Ugo A1 - Nitschke, Felix A1 - Steup, Martin A1 - Minassian, Berge A. A1 - Colleoni, Christophe A1 - Ball, Steven G. T1 - Transition from glycogen to starch metabolism in Archaeplastida JF - Trends in plant science N2 - In this opinion article we propose a scenario detailing how two crucial components have evolved simultaneously to ensure the transition of glycogen to starch in the cytosol of the Archaeplastida last common ancestor: (i) the recruitment of an enzyme from intracellular Chlamydiae pathogens to facilitate crystallization of alpha-glucan chains; and (ii) the evolution of novel types of polysaccharide (de)phosphorylating enzymes from preexisting glycogen (de)phosphorylation host pathways to allow the turnover of such crystals. We speculate that the transition to starch benefitted Archaeplastida in three ways: more carbon could be packed into osmotically inert material; the host could resume control of carbon assimilation from the chlamydial pathogen that triggered plastid endosymbiosis; and cyanobacterial photosynthate export could be integrated in the emerging Archaeplastida. KW - evolution of plastids KW - starch and glycogen metabolism KW - polyglucan debranching reactions KW - starch and glycogen (de)phosphorylation KW - Chlamydia-like bacteria KW - Lafora disease Y1 - 2014 U6 - https://doi.org/10.1016/j.tplants.2013.08.004 SN - 1360-1385 VL - 19 IS - 1 SP - 18 EP - 28 PB - Elsevier CY - London ER - TY - JOUR A1 - Krause, Sascha A1 - Le Roux, Xavier A1 - Niklaus, Pascal A. A1 - Van Bodegom, Peter M. A1 - Lennon, Jay T. A1 - Bertilsson, Stefan A1 - Grossart, Hans-Peter A1 - Philippot, Laurent A1 - Bodelier, Paul L. E. T1 - Trait-based approaches for understanding microbial biodiversity and ecosystem functioning JF - Frontiers in microbiology N2 - In ecology, biodiversity-ecosystem functioning (BEE) research has seen a shift in perspective from taxonomy to function in the last two decades, with successful application of trait-based approaches. This shift offers opportunities for a deeper mechanistic understanding of the role of biodiversity in maintaining multiple ecosystem processes and services. In this paper, we highlight studies that have focused on BEE of microbial communities with an emphasis on integrating trait-based approaches to microbial ecology. In doing so, we explore some of the inherent challenges and opportunities of understanding BEE using microbial systems. For example, microbial biologists characterize communities using gene phylogenies that are often unable to resolve functional traits. Additionally, experimental designs of existing microbial BEE studies are often inadequate to unravel BEE relationships. We argue that combining eco-physiological studies with contemporary molecular tools in a trait-based framework can reinforce our ability to link microbial diversity to ecosystem processes. We conclude that such trait-based approaches are a promising framework to increase the understanding of microbial BEE relationships and thus generating systematic principles in microbial ecology and more generally ecology. KW - functional traits KW - ecosystem function KW - ecological theory KW - study designs KW - microbial diversity Y1 - 2014 U6 - https://doi.org/10.3389/fmicb.2014.00251 SN - 1664-302X VL - 5 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Kissling, W. D. A1 - Dormann, Carsten F. A1 - Groeneveld, Juergen A1 - Hickler, Thomas A1 - Kühn, Ingolf A1 - McInerny, Greg J. A1 - Montoya, Jose M. A1 - Römermann, Christine A1 - Schiffers, Katja A1 - Schurr, Frank Martin A1 - Singer, Alexander A1 - Svenning, Jens-Christian A1 - Zimmermann, Niklaus E. A1 - O'Hara, Robert B. T1 - Towards novel approaches to modelling biotic interactions in multispecies assemblages at large spatial extents JF - Journal of biogeography N2 - Aim Biotic interactions within guilds or across trophic levels have widely been ignored in species distribution models (SDMs). This synthesis outlines the development of species interaction distribution models (SIDMs), which aim to incorporate multispecies interactions at large spatial extents using interaction matrices. Location Local to global. Methods We review recent approaches for extending classical SDMs to incorporate biotic interactions, and identify some methodological and conceptual limitations. To illustrate possible directions for conceptual advancement we explore three principal ways of modelling multispecies interactions using interaction matrices: simple qualitative linkages between species, quantitative interaction coefficients reflecting interaction strengths, and interactions mediated by interaction currencies. We explain methodological advancements for static interaction data and multispecies time series, and outline methods to reduce complexity when modelling multispecies interactions. Results Classical SDMs ignore biotic interactions and recent SDM extensions only include the unidirectional influence of one or a few species. However, novel methods using error matrices in multivariate regression models allow interactions between multiple species to be modelled explicitly with spatial co-occurrence data. If time series are available, multivariate versions of population dynamic models can be applied that account for the effects and relative importance of species interactions and environmental drivers. These methods need to be extended by incorporating the non-stationarity in interaction coefficients across space and time, and are challenged by the limited empirical knowledge on spatio-temporal variation in the existence and strength of species interactions. Model complexity may be reduced by: (1) using prior ecological knowledge to set a subset of interaction coefficients to zero, (2) modelling guilds and functional groups rather than individual species, and (3) modelling interaction currencies and species effect and response traits. Main conclusions There is great potential for developing novel approaches that incorporate multispecies interactions into the projection of species distributions and community structure at large spatial extents. Progress can be made by: (1) developing statistical models with interaction matrices for multispecies co-occurrence datasets across large-scale environmental gradients, (2) testing the potential and limitations of methods for complexity reduction, and (3) sampling and monitoring comprehensive spatio-temporal data on biotic interactions in multispecies communities. KW - Community ecology KW - ecological networks KW - global change KW - guild assembly KW - multidimensional complexity KW - niche theory KW - prediction KW - species distribution model KW - species interactions KW - trait-based community modules Y1 - 2012 U6 - https://doi.org/10.1111/j.1365-2699.2011.02663.x SN - 0305-0270 VL - 39 IS - 12 SP - 2163 EP - 2178 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Becher, Matthias A. A1 - Osborne, Juliet L. A1 - Thorbek, Pernille A1 - Kennedy, Peter J. A1 - Grimm, Volker T1 - Towards a systems approach for understanding honeybee decline - a stocktaking and synthesis of existing models JF - Journal of applied ecology : an official journal of the British Ecological Society N2 - 1. The health of managed and wild honeybee colonies appears to have declined substantially in Europe and the United States over the last decade. Sustainability of honeybee colonies is important not only for honey production, but also for pollination of crops and wild plants alongside other insect pollinators. A combination of causal factors, including parasites, pathogens, land use changes and pesticide usage, are cited as responsible for the increased colony mortality. 2. However, despite detailed knowledge of the behaviour of honeybees and their colonies, there are no suitable tools to explore the resilience mechanisms of this complex system under stress. Empirically testing all combinations of stressors in a systematic fashion is not feasible. We therefore suggest a cross-level systems approach, based on mechanistic modelling, to investigate the impacts of (and interactions between) colony and land management. 3. We review existing honeybee models that are relevant to examining the effects of different stressors on colony growth and survival. Most of these models describe honeybee colony dynamics, foraging behaviour or honeybee - varroa mite - virus interactions. 4. We found that many, but not all, processes within honeybee colonies, epidemiology and foraging are well understood and described in the models, but there is no model that couples in-hive dynamics and pathology with foraging dynamics in realistic landscapes. 5. Synthesis and applications. We describe how a new integrated model could be built to simulate multifactorial impacts on the honeybee colony system, using building blocks from the reviewed models. The development of such a tool would not only highlight empirical research priorities but also provide an important forecasting tool for policy makers and beekeepers, and we list examples of relevant applications to bee disease and landscape management decisions. KW - Apis mellifera KW - colony decline KW - feedbacks KW - integrated model KW - multiple stressors KW - predictive systems ecology KW - review Y1 - 2013 U6 - https://doi.org/10.1111/1365-2664.12112 SN - 0021-8901 VL - 50 IS - 4 SP - 868 EP - 880 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Block, Benjamin D. A1 - Denfeld, Blaize A. A1 - Stockwell, Jason D. A1 - Flaim, Giovanna A1 - Grossart, Hans-Peter A1 - Knoll, Lesley B. A1 - Maier, Dominique B. A1 - North, Rebecca L. A1 - Rautio, Milla A1 - Rusak, James A. A1 - Sadro, Steve A1 - Weyhenmeyer, Gesa A. A1 - Bramburger, Andrew J. A1 - Branstrator, Donn K. A1 - Salonen, Kalevi A1 - Hampton, Stephanie E. T1 - The unique methodological challenges of winter limnology JF - Limnology and Oceanography: Methods N2 - Winter is an important season for many limnological processes, which can range from biogeochemical transformations to ecological interactions. Interest in the structure and function of lake ecosystems under ice is on the rise. Although limnologists working at polar latitudes have a long history of winter work, the required knowledge to successfully sample under winter conditions is not widely available and relatively few limnologists receive formal training. In particular, the deployment and operation of equipment in below 0 degrees C temperatures pose considerable logistical and methodological challenges, as do the safety risks of sampling during the ice-covered period. Here, we consolidate information on winter lake sampling and describe effective methods to measure physical, chemical, and biological variables in and under ice. We describe variation in snow and ice conditions and discuss implications for sampling logistics and safety. We outline commonly encountered methodological challenges and make recommendations for best practices to maximize safety and efficiency when sampling through ice or deploying instruments in ice-covered lakes. Application of such practices over a broad range of ice-covered lakes will contribute to a better understanding of the factors that regulate lakes during winter and how winter conditions affect the subsequent ice-free period. Y1 - 2018 U6 - https://doi.org/10.1002/lom3.10295 SN - 1541-5856 VL - 17 IS - 1 SP - 42 EP - 57 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Bertilsson, Stefan A1 - Burgin, Amy A1 - Carey, Cayelan C. A1 - Fey, Samuel B. A1 - Grossart, Hans-Peter A1 - Grubisic, Lorena M. A1 - Jones, Ian D. A1 - Kirillin, Georgiy A1 - Lennon, Jay T. A1 - Shade, Ashley A1 - Smyth, Robyn L. T1 - The under-ice microbiome of seasonally frozen lakes JF - Limnology and oceanography N2 - Compared to the well-studied open water of the "growing" season, under-ice conditions in lakes are characterized by low and rather constant temperature, slow water movements, limited light availability, and reduced exchange with the surrounding landscape. These conditions interact with ice-cover duration to shape microbial processes in temperate lakes and ultimately influence the phenology of community and ecosystem processes. We review the current knowledge on microorganisms in seasonally frozen lakes. Specifically, we highlight how under-ice conditions alter lake physics and the ways that this can affect the distribution and metabolism of auto-and heterotrophic microorganisms. We identify functional traits that we hypothesize are important for understanding under-ice dynamics and discuss how these traits influence species interactions. As ice coverage duration has already been seen to reduce as air temperatures have warmed, the dynamics of the under-ice microbiome are important for understanding and predicting the dynamics and functioning of seasonally frozen lakes in the near future. Y1 - 2013 U6 - https://doi.org/10.4319/lo.2013.58.6.1998 SN - 0024-3590 SN - 1939-5590 VL - 58 IS - 6 SP - 1998 EP - 2012 PB - Wiley CY - Waco ER - TY - JOUR A1 - Sicard, Adrien A1 - Lenhard, Michael T1 - The selfing syndrome a model for studying the genetic and evolutionary basis of morphological adaptation in plants JF - Annals of botany N2 - Background In angiosperm evolution, autogamously selfing lineages have been derived from outbreeding ancestors multiple times, and this transition is regarded as one of the most common evolutionary tendencies in flowering plants. In most cases, it is accompanied by a characteristic set of morphological and functional changes to the flowers, together termed the selfing syndrome. Two major areas that have changed during evolution of the selfing syndrome are sex allocation to male vs. female function and flower morphology, in particular flower (mainly petal) size and the distance between anthers and stigma. Scope A rich body of theoretical, taxonomic, ecological and genetic studies have addressed the evolutionary modification of these two trait complexes during or after the transition to selfing. Here, we review our current knowledge about the genetics and evolution of the selfing syndrome. Conclusions We argue that because of its frequent parallel evolution, the selfing syndrome represents an ideal model for addressing basic questions about morphological evolution and adaptation in flowering plants, but that realizing this potential will require the molecular identification of more of the causal genes underlying relevant trait variation. KW - Evolution KW - selfing syndrome KW - autogamy KW - pollen-to-ovule ratio KW - flower size KW - herkogamy KW - quantitative trait loci KW - self-incompatibility Y1 - 2011 U6 - https://doi.org/10.1093/aob/mcr023 SN - 0305-7364 SN - 1095-8290 VL - 107 IS - 9 SP - 1433 EP - 1443 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Sharma, Tripti A1 - Dreyer, Ingo A1 - Riedelsberger, Janin T1 - The role of K+ channels in uptake and redistribution of potassium in the model plant Arabidopsis thaliana JF - Frontiers in plant science N2 - Potassium (K+) is inevitable for plant growth and development. It plays a crucial role in the regulation of enzyme activities, in adjusting the electrical membrane potential and the cellular turgor, in regulating cellular homeostasis and in the stabilization of protein synthesis. Uptake of K+ from the soil and its transport to growing organs is essential for a healthy plant development. Uptake and allocation of K+ are performed by K+ channels and transporters belonging to different protein families. In this review we summarize the knowledge on the versatile physiological roles of plant K+ channels and their behavior under stress conditions in the model plant Arabidopsis thaliana. KW - plant potassium channel KW - Shaker KW - TPK KW - K-ir-like KW - Arabidopsis thaliana KW - voltage-dependent KW - voltage-independent Y1 - 2013 U6 - https://doi.org/10.3389/fpls.2013.00224 SN - 1664-462X VL - 4 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Yokoyama, Kenichi A1 - Leimkühler, Silke T1 - The role of FeS clusters for molybdenum cofactor biosynthesis and molybdoenzymes in bacteria JF - Biochimica et biophysica acta : Molecular cell research N2 - The biosynthesis of the molybdenum cofactor (Moco) has been intensively studied, in addition to its insertion into molybdoenzymes. In particular, a link between the assembly of molybdoenzymes and the biosynthesis of FeS clusters has been identified in the recent years: 1) the synthesis of the first intermediate in Moco biosynthesis requires an FeS-cluster containing protein, 2) the sulfurtransferase for the dithiolene group in Moco is also involved in the synthesis of FeS clusters, thiamin and thiolated tRNAs, 3) the addition of a sulfido-ligand to the molybdenum atom in the active site additionally involves a sulfurtransferase, and 4) most molybdoenzymes in bacteria require FeS clusters as redox active cofactors. In this review we will focus on the biosynthesis of the molybdenum cofactor in bacteria, its modification and insertion into molybdoenzymes, with an emphasis to its link to FeS cluster biosynthesis and sulfur transfer. (C) 2014 Elsevier B.V. All rights reserved. KW - Molybdenum-iron-iron-sulfur cluster KW - Molybdenum cofactor KW - tRNA KW - Sulfur transfer KW - L-Cysteine desulfurase Y1 - 2015 U6 - https://doi.org/10.1016/j.bbamcr.2014.09.021 SN - 0167-4889 SN - 0006-3002 VL - 1853 IS - 6 SP - 1335 EP - 1349 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Zupok, Arkadiusz A1 - Iobbi-Nivol, Chantal A1 - Mejean, Vincent A1 - Leimkühler, Silke T1 - The regulation of Moco biosynthesis and molybdoenzyme gene expression by molybdenum and iron in bacteria JF - Metallomics : integrated biometal science N2 - Bacterial molybdoenzymes are key enzymes involved in the global sulphur, nitrogen and carbon cycles. These enzymes require the insertion of the molybdenum cofactor (Moco) into their active sites and are able to catalyse a large range of redox-reactions. Escherichia coli harbours nineteen different molybdoenzymes that require a tight regulation of their synthesis according to substrate availability, oxygen availability and the cellular concentration of molybdenum and iron. The synthesis and assembly of active molybdoenzymes are regulated at the level of transcription of the structural genes and of translation in addition to the genes involved in Moco biosynthesis. The action of global transcriptional regulators like FNR, NarXL/QP, Fur and ArcA and their roles on the expression of these genes is described in detail. In this review we focus on what is known about the molybdenum- and iron-dependent regulation of molybdoenzyme and Moco biosynthesis genes in the model organism E. coli. The gene regulation in E. coli is compared to two other well studied model organisms Rhodobacter capsulatus and Shewanella oneidensis. Y1 - 2019 U6 - https://doi.org/10.1039/c9mt00186g SN - 1756-5901 SN - 1756-591X VL - 11 IS - 10 SP - 1602 EP - 1624 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Sengupta, Saswati A1 - Chattopadhyay, Madhab K. A1 - Grossart, Hans-Peter T1 - The multifaceted roles of antibiotics and antibiotic resistance in nature JF - Frontiers in microbiology N2 - Antibiotics are chemotherapeutic agents, which have been a very powerful tool in the clinical management of bacterial diseases since the 1940s. However, benefits offered by these magic bullets have been substantially lost in subsequent days following the widespread emergence and dissemination of antibiotic-resistant strains. While it is obvious that excessive and imprudent use of antibiotics significantly contributes to the emergence of resistant strains, antibiotic resistance is also observed in natural bacteria of remote places unlikely to be impacted by human intervention. Both antibiotic biosynthetic genes and resistance-conferring genes have been known to evolve billions of years ago, long before clinical use of antibiotics. Hence it appears that antibiotics and antibiotics resistance determinants have some other roles in nature, which often elude our attention because of overemphasis on the therapeutic importance of antibiotics and the crisis imposed by the antibiotic resistance in pathogens. In the natural milieu, antibiotics are often found to be present in sub-inhibitory concentrations acting as signaling molecules supporting the process of quorum sensing and biofilm formation. They also play an important role in the production of virulence factors and influence host-parasite interactions (e.g., phagocytosis, adherence to the target cell, and so on). The evolutionary and ecological aspects of antibiotics and antibiotic resistance in the naturally occurring microbial community are little understood. Therefore, the actual role of antibiotics in nature warrants in-depth investigations. Studies on such an intriguing behavior of the microorganisms promise insight into the intricacies of the microbial physiology and are likely to provide some lead in controlling the emergence and subsequent dissemination of antibiotic resistance. This article highlights some of the recent findings on the role of antibiotics and the genes that confer resistance to antibiotics in nature. KW - antibiotics KW - sub-inhibitory concentration KW - quorum sensing KW - virulence KW - stress response KW - antibiotic resistance KW - antibiotic paradox Y1 - 2013 U6 - https://doi.org/10.3389/fmicb.2013.00047 SN - 1664-302X VL - 4 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Paolini, Alessio A1 - Abdelilah-Seyfried, Salim T1 - The mechanobiology of zebrafish cardiac valve leaflet formation JF - Current opinion in cell biology : review articles, recommended reading, bibliography of the world literature N2 - Over a lifetime, rhythmic contractions of the heart provide a continuous flow of blood throughout the body. An essential morphogenetic process during cardiac development which ensures unidirectional blood flow is the formation of cardiac valves. These structures are largely composed of extracellular matrix and of endocardial cells, a specialized population of endothelial cells that line the interior of the heart and that are subjected to changing hemodynamic forces. Recent studies have significantly expanded our understanding of this morphogenetic process. They highlight the importance of the mechanobiology of cardiac valve formation and show how biophysical forces due to blood flow drive biochemical and electrical signaling required for the differentiation of cells to produce cardiac valves. Y1 - 2018 U6 - https://doi.org/10.1016/j.ceb.2018.05.007 SN - 0955-0674 SN - 1879-0410 VL - 55 SP - 52 EP - 58 PB - Elsevier CY - London ER - TY - JOUR A1 - Kaplan, Aaron A1 - Harel, Moshe A1 - Kaplan-Levy, Ruth N. A1 - Hadas, Ora A1 - Sukenik, Assaf A1 - Dittmann-Thünemann, Elke T1 - The languages spoken in the water body (or the biological role of cyanobacterial toxins) JF - Frontiers in microbiology N2 - Although intensification of toxic cyanobacterial blooms over the last decade is a matter of growing concern due to bloom impact on water quality, the biological role of most of the toxins produced is not known. In this critical review we focus primarily on the biological role of two toxins, microcystins and cylindrospermopsin, in inter- and intra-species communication and in nutrient acquisition. We examine the experimental evidence supporting some of the dogmas in the field and raise several open questions to be dealt with in future research. We do not discuss the health and environmental implications of toxin presence in the water body. KW - aoa KW - cylindrospermopsin KW - microcystin KW - cyr KW - mcy Y1 - 2012 U6 - https://doi.org/10.3389/fmicb.2012.00138 SN - 1664-302X VL - 3 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Nickerson, David A1 - Atalag, Koray A1 - de Bono, Bernard A1 - Geiger, Joerg A1 - Goble, Carole A1 - Hollmann, Susanne A1 - Lonien, Joachim A1 - Mueller, Wolfgang A1 - Regierer, Babette A1 - Stanford, Natalie J. A1 - Golebiewski, Martin A1 - Hunter, Peter T1 - The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable JF - Interface focus N2 - Reconstructing and understanding the Human Physiome virtually is a complex mathematical problem, and a highly demanding computational challenge. Mathematical models spanning from the molecular level through to whole populations of individuals must be integrated, then personalized. This requires interoperability with multiple disparate and geographically separated data sources, and myriad computational software tools. Extracting and producing knowledge from such sources, even when the databases and software are readily available, is a challenging task. Despite the difficulties, researchers must frequently perform these tasks so that available knowledge can be continually integrated into the common framework required to realize the Human Physiome. Software and infrastructures that support the communities that generate these, together with their underlying standards to format, describe and interlink the corresponding data and computer models, are pivotal to the Human Physiome being realized. They provide the foundations for integrating, exchanging and re-using data and models efficiently, and correctly, while also supporting the dissemination of growing knowledge in these forms. In this paper, we explore the standards, software tooling, repositories and infrastructures that support this work, and detail what makes them vital to realizing the Human Physiome. KW - Human Physiome KW - standards KW - repositories KW - service infrastructure KW - reproducible science KW - managing big data Y1 - 2016 U6 - https://doi.org/10.1098/rsfs.2015.0103 SN - 2042-8898 SN - 2042-8901 VL - 6 SP - 57 EP - 61 PB - Royal Society CY - London ER - TY - JOUR A1 - Leimkühler, Silke A1 - Wuebbens, Margot M. A1 - Rajagopalan, K. V. T1 - The history of the discovery of the molybdenum cofactor and novel aspects of its biosynthesis in bacteria JF - Coordination chemistry reviews N2 - The biosynthesis of the molybdenum cofactor in bacteria is described with a detailed analysis of each individual reaction leading to the formation of stable intermediates during the synthesis of molybdopterin from GTP. As a starting point, the discovery of molybdopterin and the elucidation of its structure through the study of stable degradation products are described. Subsequent to molybdopterin synthesis, the molybdenum atom is added to the molybdopterin dithiolene group to form the molybdenum cofactor. This cofactor is either inserted directly into specific molybdoenzymes or is further modified by the addition of nucleotides to molybdopterin phosphate group or the replacement of ligands at the molybdenum center. KW - Molybdenum cofactor KW - Molybdopterin KW - Precursor Z KW - Molybdopterin guanine dinucleotide cofactor KW - Urothione KW - Dithiolene group Y1 - 2011 U6 - https://doi.org/10.1016/j.ccr.2010.12.003 SN - 0010-8545 VL - 255 IS - 9-10 SP - 1129 EP - 1144 PB - Elsevier CY - Lausanne ER - TY - JOUR A1 - Pearson, Leanne A. A1 - Dittmann, Elke A1 - Mazmouz, Rabia A1 - Ongley, Sarah E. A1 - Neilan, Brett A. T1 - The genetics, biosynthesis and regulation of toxic specialized metabolites of cyanobacteria JF - Harmful algae N2 - The production of toxic metabolites by cyanobacterial blooms represents a significant threat to the health of humans and ecosystems worldwide. Here we summarize the current state of the knowledge regarding the genetics, biosynthesis and regulation of well-characterized cyanotoxins, including the microcystins, nodularin, cylindrospermopsin, saxitoxins and antitoxins, as well as the lesser-known marine toxins (e.g. lyngbyatoxin, aplysiatoxin, jamaicamides, barbamide, curacin, hectochlorin and apratoxins). (C) 2015 Elsevier B.V. All rights reserved. KW - Cyanobacteria KW - Cyanotoxins KW - Specialized metabolites KW - Genetics KW - Biosynthesis KW - Regulation Y1 - 2016 U6 - https://doi.org/10.1016/j.hal.2015.11.002 SN - 1568-9883 SN - 1878-1470 VL - 54 SP - 98 EP - 111 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Haack, Timm A1 - Abdelilah-Seyfried, Salim T1 - The force within: endocardial development, mechanotransduction and signalling during cardiac morphogenesis JF - Development : Company of Biologists N2 - Endocardial cells are cardiac endothelial cells that line the interior of the heart tube. Historically, their contribution to cardiac development has mainly been considered from a morphological perspective. However, recent studies have begun to define novel instructive roles of the endocardium, as a sensor and signal transducer of biophysical forces induced by blood flow, and as an angiocrine signalling centre that is involved in myocardial cellular morphogenesis, regeneration and reprogramming. In this Review, we discuss how the endocardium develops, how endocardial-myocardial interactions influence the developing embryonic heart, and how the dysregulation of blood flowresponsive endocardial signalling can result in pathophysiological changes. KW - Endocardium KW - Cardiac development KW - Hemodynamics KW - Bmp KW - Kruppel-like factor 2 KW - Vegf KW - Mechanotransduction KW - Zebrafish KW - Mouse Y1 - 2016 U6 - https://doi.org/10.1242/dev.131425 SN - 0950-1991 SN - 1477-9129 VL - 143 SP - 373 EP - 386 PB - Company of Biologists Limited CY - Cambridge ER - TY - JOUR A1 - Baumann, Otto A1 - Walz, Bernd T1 - The blowfly salivary gland - A model system for analyzing the regulation of plasma membrane V-ATPase JF - Journal of insect physiology N2 - Vacuolar H+-ATPases (V-ATPases) are heteromultimeric proteins that use the energy of ATP hydrolysis for the electrogenic transport of protons across membranes. They are common to all eukaryotic cells and are located in the plasma membrane or in membranes of acid organelles. In many insect epithelia, V-ATPase molecules reside in large numbers in the apical plasma membrane and create an electrochemical proton gradient that is used for the acidification or alkalinization of the extracellular space, the secretion or reabsorption of ions and fluids, the import of nutrients, and diverse other cellular activities. Here, we summarize our results on the functions and regulation of V-ATPase in the tubular salivary gland of the blowfly Calliphora vicina. In this gland, V-ATPase activity energizes the secretion of a KCl-rich saliva in response to the neurohormone serotonin (5-HT). Because of particular morphological and physiological features, the blowfly salivary glands are a superior and exemplary system for the analysis of the intracellular signaling pathways and mechanisms that modulate V-ATPase activity and solute transport in an insect epithelium. KW - Vacuolar-type H+-ATPase KW - Insect epithelia KW - Reversible assembly KW - cAMP KW - Phosphorylation KW - Calliphora vicina Y1 - 2012 U6 - https://doi.org/10.1016/j.jinsphys.2011.11.015 SN - 0022-1910 VL - 58 IS - 4 SP - 450 EP - 458 PB - Elsevier CY - Oxford ER -