Suche
Ergebnisse
-
Controlled vocabularies and semantics in systems biology
(2011)Molecular Systems BiologyThe use of computational modeling to describe and analyze biological systems is at the heart of systems biology. Model structures, simulation descriptions and numerical results can be encoded in structured formats, but there is an increasing need to provide an additional semantic layer. Semantic information adds meaning to components of structured descriptions to help identify and interpret them unambiguously. Ontologies are one of the ...Journal Article -
Absolute quantification of microbial proteomes at different states by directed mass spectrometry
(2011)Molecular Systems BiologyOver the past decade, liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS) has evolved into the main proteome discovery technology. Up to several thousand proteins can now be reliably identified from a sample and the relative abundance of the identified proteins can be determined across samples. However, the remeasurement of substantially similar proteomes, for example those generated by perturbation experiments in systems ...Journal Article -
Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli
(2011)Molecular Systems BiologyDespite our increasing topological knowledge on regulation networks in model bacteria, it is largely unknown which of the many co‐occurring regulatory events actually control metabolic function and the distribution of intracellular fluxes. Here, we unravel condition‐dependent transcriptional control of Escherichia coli metabolism by large‐scale 13C‐flux analysis in 91 transcriptional regulator mutants on glucose and galactose. In contrast ...Journal Article -
The quantitative proteome of a human cell line
(2011)Molecular Systems BiologyThe generation of mathematical models of biological processes, the simulation of these processes under different conditions, and the comparison and integration of multiple data sets are explicit goals of systems biology that require the knowledge of the absolute quantity of the system's components. To date, systematic estimates of cellular protein concentrations have been exceptionally scarce. Here, we provide a quantitative description ...Journal Article -
Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics
(2011)Molecular Systems BiologyDecades of biochemical research have identified most of the enzymes that catalyze metabolic reactions in the yeast Saccharomyces cerevisiae. The adaptation of metabolism to changing nutritional conditions, in contrast, is much less well understood. As an important stepping stone toward such understanding, we exploit the power of proteomics assays based on selected reaction monitoring (SRM) mass spectrometry to quantify abundance changes ...Journal Article -
Quantification of mRNA and protein and integration with protein turnover in a bacterium
(2011)Molecular Systems BiologyBiological function and cellular responses to environmental perturbations are regulated by a complex interplay of DNA, RNA, proteins and metabolites inside cells. To understand these central processes in living systems at the molecular level, we integrated experimentally determined abundance data for mRNA, proteins, as well as individual protein half‐lives from the genome‐reduced bacterium Mycoplasma pneumoniae. We provide a fine‐grained, ...Journal Article -
Activin enhances skin tumourigenesis and malignant progression by inducing a pro-tumourigenic immune cell response
(2011)Nature CommunicationsActivin is an important orchestrator of wound repair, but its potential role in skin carcinogenesis has not been addressed. Here we show using different types of genetically modified mice that enhanced levels of activin in the skin promote skin tumour formation and their malignant progression through induction of a pro-tumourigenic microenvironment. This includes accumulation of tumour-promoting Langerhans cells and regulatory T cells in ...Journal Article -
No extension of quantum theory can have improved predictive power
(2011)Nature CommunicationsAccording to quantum theory, measurements generate random outcomes, in stark contrast with classical mechanics. This raises the question of whether there could exist an extension of the theory that removes this indeterminism, as suspected by Einstein, Podolsky and Rosen. Although this has been shown to be impossible, existing results do not imply that the current theory is maximally informative. Here we ask the more general question of ...Journal Article -
Measuring single-nanoparticle wetting properties by freeze-fracture shadow-casting cryo-scanning electron microscopy
(2011)Nature CommunicationsNanoparticles at fluid interfaces are central to a rapidly increasing range of cutting-edge applications, including drug delivery, uptake through biological membranes, emulsion stabilization and the fabrication of nanocomposites. Understanding nanoscale wetting is a challenging issue, still unresolved for individual nanoparticles, and is essential in designing nanoparticle-building blocks with controlled surface properties. The core ...Journal Article -
Missing transverse energy performance of the CMS detector
(2011)Journal of InstrumentationDuring 2010 the LHC delivered pp collisions with a centre-of-mass energy of 7 TeV. In this paper, the results of comprehensive studies of missing transverse energy as measured by the CMS detector are presented. The results cover the measurements of the scale and resolution for missing transverse energy, and the effects of multiple pp interactions within the same bunch crossings on the scale and resolution. Anomalous measurements of missing ...Journal Article