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The Modern Phosphorus Sustainability Movement
(2013)SustainabilitySince the “peak phosphorus” concept emerged in 2007, concerns about the future availability of phosphate rock have funneled into a growing number of actions, often in the form of new and innovative platforms focusing on phosphorus sustainability. This trend seems to continue on different levels and in different formats, which makes the landscape of activities increasingly blurred and complex. This article considers the emerging phase of ...Journal Article -
Global climate targets and future consumption level: An evaluation of the required GHG intensity
(2013)Environmental Research LettersDiscussion and analysis on international climate policy often focuses on the rather abstract level of total national and regional greenhouse gas (GHG) emissions. At some point, however, emission reductions need to be translated to consumption level. In this article, we evaluate the implications of the strictest IPCC representative concentration pathway for key consumption categories (food, travel, shelter, goods, services). We use IPAT ...Journal Article -
Dissecting specific and global transcriptional regulation of bacterial gene expression
(2013)Molecular Systems BiologyGene expression is regulated by specific transcriptional circuits but also by the global expression machinery as a function of growth. Simultaneous specific and global regulation thus constitutes an additional—but often neglected—layer of complexity in gene expression. Here, we develop an experimental‐computational approach to dissect specific and global regulation in the bacterium Escherichia coli. By using fluorescent promoter reporters, ...Journal Article -
Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast
(2013)Molecular Systems BiologyThe diauxic shift in Saccharomyces cerevisiae is an ideal model to study how eukaryotic cells readjust their metabolism from glycolytic to gluconeogenic operation. In this work, we generated time‐resolved physiological data, quantitative metabolome (69 intracellular metabolites) and proteome (72 enzymes) profiles. We found that the diauxic shift is accomplished by three key events that are temporally organized: (i) a reduction in the ...Journal Article -
Transcriptional regulation is insufficient to explain substrate‐induced flux changes in Bacillus subtilis
(2013)Molecular Systems BiologyOne of the key ways in which microbes are thought to regulate their metabolism is by modulating the availability of enzymes through transcriptional regulation. However, the limited success of efforts to manipulate metabolic fluxes by rewiring the transcriptional network has cast doubt on the idea that transcript abundance controls metabolic fluxes. In this study, we investigate control of metabolic flux in the model bacterium Bacillus ...Journal Article -
Timescales and bottlenecks in miRNA-dependent gene regulation
(2013)Molecular Systems BiologyMiRNAs are post‐transcriptional regulators that contribute to the establishment and maintenance of gene expression patterns. Although their biogenesis and decay appear to be under complex control, the implications of miRNA expression dynamics for the processes that they regulate are not well understood. We derived a mathematical model of miRNA‐mediated gene regulation, inferred its parameters from experimental data sets, and found that ...Journal Article -
Targeted proteomics reveals strain-specific changes in the mouse insulin and central metabolic pathways after a sustained high-fat diet
(2013)Molecular Systems BiologyThe metabolic syndrome is a collection of risk factors including obesity, insulin resistance and hepatic steatosis, which occur together and increase the risk of diseases such as diabetes, cardiovascular disease and cancer. In spite of intense research, the complex etiology of insulin resistance and its association with the accumulation of triacylglycerides in the liver and with hepatic steatosis remains not completely understood. Here, ...Journal Article -
Biomedically relevant circuit-design strategies in mammalian synthetic biology
(2013)Molecular Systems BiologyThe development and progress in synthetic biology has been remarkable. Although still in its infancy, synthetic biology has achieved much during the past decade. Improvements in genetic circuit design have increased the potential for clinical applicability of synthetic biology research. What began as simple transcriptional gene switches has rapidly developed into a variety of complex regulatory circuits based on the transcriptional, ...Journal Article -
Effects of environmental variation and spatial distance on Bacteria, Archaea and viruses in sub-polar and arctic waters
(2013)The ISME JournalWe investigated the influence of environmental parameters and spatial distance on bacterial, archaeal and viral community composition from 13 sites along a 3200-km long voyage from Halifax to Kugluktuk (Canada) through the Labrador Sea, Baffin Bay and the Arctic Archipelago. Variation partitioning was used to disentangle the effects of environmental parameters, spatial distance and spatially correlated environmental parameters on prokaryotic ...Journal Article -
A closed-loop synthetic gene circuit for the treatment of diet-induced obesity in mice
(2013)Nature CommunicationsDiet-induced obesity is a lifestyle-associated medical condition that increases the risk of developing cardiovascular disease, type 2 diabetes and certain types of cancer. Here we report the design of a closed-loop genetic circuit that constantly monitors blood fatty acid levels in the setting of diet-associated hyperlipidemia and coordinates reversible and adjustable expression of the clinically licensed appetite-suppressing peptide ...Journal Article