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The ORBi^lu Project

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	Browsing by title 0-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z or enter first few letters: OK Showing results 45421 to 45440 of 51566 2267 2268 2269 2270 2271 2272 2273 2274 2275 2276 2277 A systems biology investigation of neurodegenerative dementia reveals a pivotal role of autophagy Caberlotto, Laura; Nguyen, Thanh-Phuong in BMC Systems Biology (2014), 8(1), 65 Detailed reference viewed: 187 (5 UL) Systems Biology of Acidophile Biofilms for Efficient Metal Extraction Christel, Stephan; Dopson, Mark; Vera, Mario et al in Advanced Materials Research (2015), 1130 This European Union ERASysApp funded study will investigate one of the major drawbacks of bioleaching of the copper containing mineral chalcopyrite, namely the long lag phase between construction and ... [more ▼] This European Union ERASysApp funded study will investigate one of the major drawbacks of bioleaching of the copper containing mineral chalcopyrite, namely the long lag phase between construction and inoculation of bioleaching heaps and the release of dissolved metals. In practice, this lag phase can be up to three years and the long time period adds to the operating expenses of bioheaps for chalcopyrite dissolution. One of the major time determining factors in bioleaching heaps is suggested to be the speed of mineral colonization by the acidophilic microorganisms present. By applying confocal microscopy, metatranscriptomics, metaproteomics, bioinformatics, and computer modeling the authors aim to investigate the processes leading up to, and influencing the attachment of three moderately thermophilic sulfur-and/or iron-oxidizing model species: Acidithiobacillus caldus, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans. Stirred tank reactors containing chalcopyrite concentrate will be inoculated with these species in various orders and proportions and the effects on the lag phase and rates of metal release will be compared. Meanwhile, confocal microscopy studies of cell attachment to chalcopyrite mineral particles, as well as metatranscriptomics and metaproteomics of the formed biofilms will further increase understanding of the attachment process and help develop a model thereof. By fulfilling our goal to decrease the length of the lag phase of chalcopyrite bioleaching heaps we hope to increase their economic feasibility and therefore, industrial interest in bioleaching as a sustainable technology. [less ▲] Detailed reference viewed: 238 (14 UL) Systems biology of bacteria-host interactions Heinken, Almut Katrin ; Ravcheev, Dmitry ; Thiele, Ines in Nibali, Luigi; Henderson, Brian (Eds.) The Human Microbiota and Chronic Disease: Dysbiosis as a Cause of Human Pathology (2016) The aim of systems biology is to use computational methods to gain a complete, systems-level understanding of a cell, organism, or ecosystem. This chapter describes computational systems biology ... [more ▼] The aim of systems biology is to use computational methods to gain a complete, systems-level understanding of a cell, organism, or ecosystem. This chapter describes computational systems biology approaches and their applications to human gut microbiome research, with particular focus on constraint-based modeling. At heart of the Constraint-Based Modeling and Analysis (COBRA) approach are accurate, well-structured metabolic reconstructions based on the target organisms’ genome sequences. Such genome-scale reconstructions (GENREs) are constructed in a bottom-up manner and describe the target organism's metabolism. The availability of high-quality reconstructions of human metabolism and of other host organisms, enables the computational modeling of host-microbe interactions. Simulating host-microbe interactions is particularly valuable since it could be used to minimize the number of animal experiments. The discussed computational modeling approaches will be valuable tools for studying microbial dysbiosis and its impact on host metabolism. Common approaches for computational modeling include ordinary differential equation (ODE) and kinetic modeling [less ▲] Detailed reference viewed: 432 (12 UL) Systems biology of host-microbe metabolomics Heinken, Almut Katrin ; Thiele, Ines in Wiley Interdisciplinary Reviews. Systems Biology and Medicine (2015) The human gut microbiota performs essential functions for host and wellbeing, but has also been linked to a variety of disease states, e.g., obesity and type 2 diabetes. The mammalian body fluid and ... [more ▼] The human gut microbiota performs essential functions for host and wellbeing, but has also been linked to a variety of disease states, e.g., obesity and type 2 diabetes. The mammalian body fluid and tissue metabolomes are greatly influenced by the microbiota, with many health-relevant metabolites being considered “mammalian-microbial co-metabolites”. To systematically investigate this complex host-microbial co-metabolism, a systems biology approach integrating high-throughput data and computational network models is required. Here, we review established top-down and bottom-up systems biology approaches that have successfully elucidated relationships between gut microbiota-derived metabolites and host health and disease. We particularly focus on the constraint-based modeling and analysis approach, which enables the prediction of mechanisms behind metabolic host-microbe interactions on the molecular level. We illustrate that constraint-based models are a useful tool for the contextualization of metabolomic measurements and can further our insight into host-microbe interactions, yielding, e.g., in potential novel drugs and biomarkers. [less ▲] Detailed reference viewed: 402 (21 UL) Systems Biology of Microbiomes Wilmes, Paul Scientific Conference (2016, September) Detailed reference viewed: 101 (0 UL) Systems Biology through the Concept of Emergence Kolodkin, Alexey in Green, Sarah (Ed.) Philosophy of Systems Biology: Perspectives from Scientists and Philosophers (History, Philosophy and Theory of the Life Sciences) (2016) Detailed reference viewed: 258 (2 UL) Systems biology towards life in silico: mathematics of the control of living cells. Westerhoff, Hans V.; Kolodkin, Alexey ; Conradie, Riaan et al in Journal of Mathematical Biology (2009), 58(1-2), 7-34 Systems Biology is the science that aims to understand how biological function absent from macromolecules in isolation, arises when they are components of their system. Dedicated to the memory of Reinhart ... [more ▼] Systems Biology is the science that aims to understand how biological function absent from macromolecules in isolation, arises when they are components of their system. Dedicated to the memory of Reinhart Heinrich, this paper discusses the origin and evolution of the new part of systems biology that relates to metabolic and signal-transduction pathways and extends mathematical biology so as to address postgenomic experimental reality. Various approaches to modeling the dynamics generated by metabolic and signal-transduction pathways are compared. The silicon cell approach aims to describe the intracellular network of interest precisely, by numerically integrating the precise rate equations that characterize the ways macromolecules' interact with each other. The non-equilibrium thermodynamic or 'lin-log' approach approximates the enzyme rate equations in terms of linear functions of the logarithms of the concentrations. Biochemical Systems Analysis approximates in terms of power laws. Importantly all these approaches link system behavior to molecular interaction properties. The latter two do this less precisely but enable analytical solutions. By limiting the questions asked, to optimal flux patterns, or to control of fluxes and concentrations around the (patho)physiological state, Flux Balance Analysis and Metabolic/Hierarchical Control Analysis again enable analytical solutions. Both the silicon cell approach and Metabolic/Hierarchical Control Analysis are able to highlight where and how system function derives from molecular interactions. The latter approach has also discovered a set of fundamental principles underlying the control of biological systems. The new law that relates concentration control to control by time is illustrated for an important signal transduction pathway, i.e. nuclear hormone receptor signaling such as relevant to bone formation. It is envisaged that there is much more Mathematical Biology to be discovered in the area between molecules and Life. [less ▲] Detailed reference viewed: 212 (3 UL) Systems ecology of human-microbe interactions Wilmes, Paul Scientific Conference (2016, June) Detailed reference viewed: 98 (0 UL) Systems ecology of microbial pioneers in the gut Wilmes, Paul Presentation (2017, October) Detailed reference viewed: 100 (3 UL) Systems ecology of microbiome-human interactions: identifying which functions are key Wilmes, Paul Scientific Conference (2018, April) Detailed reference viewed: 117 (0 UL) Systems ecology of microbiomes Wilmes, Paul Scientific Conference (2018, December) Detailed reference viewed: 183 (9 UL) Systems ecology of microbiomes Wilmes, Paul Scientific Conference (2018, May) Detailed reference viewed: 130 (0 UL) Systems ecology of microbiomes: a new frontier of discovery in microbiology Wilmes, Paul Presentation (2017, August) Detailed reference viewed: 95 (0 UL) Systems Ecology of Microbiomes: A New Frontier of Discovery in Microbiology Wilmes, Paul Scientific Conference (2017, May) Detailed reference viewed: 108 (0 UL) Systems ecology of microbiomes: a new frontier of discovery in microbiology Wilmes, Paul Presentation (2017, August) Detailed reference viewed: 107 (0 UL) Systems ecology of microbiomes: a new frontier of discovery in microbiology Wilmes, Paul Scientific Conference (2017, September) Detailed reference viewed: 135 (1 UL) Systems Ecology of Microbiomes: A New Frontier of Discovery in Microbiology Wilmes, Paul Scientific Conference (2017, March) Detailed reference viewed: 131 (0 UL) Systems Ecology of microbiomes: function is key Wilmes, Paul Scientific Conference (2018, April) Detailed reference viewed: 115 (0 UL) Systems Ecology of microbiomes: identifying key functions Wilmes, Paul Scientific Conference (2018, August) Detailed reference viewed: 109 (0 UL) Systems ecology of the human microbiome Wilmes, Paul Scientific Conference (2018) Detailed reference viewed: 135 (5 UL) 2267 2268 2269 2270 2271 2272 2273 2274 2275 2276 2277

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