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Bielow C.,Free University of Berlin | Bielow C.,MPI International | Ruzek S.,University of Salzburg | Huber C.G.,University of Salzburg | Reinert K.,Free University of Berlin
Journal of Proteome Research | Year: 2010

In electrospray ionization mass spectrometry (ESI-MS), peptide and protein ions are usually observed in multiple charge states. Moreover, adduction of the multiply charged species with other ions frequently results in quite complex signal patterns for a single analyte, which significantly complicates the derivation of quantitative information from the mass spectra. Labeling strategies targeting the MS1 level further aggravate this situation, as multiple biological states such as healthy or diseased must be represented simultaneously. We developed an integer linear programming (ILP) approach, which can cluster signals belonging to the same peptide or protein. The algorithm is general in that it models all possible shifts of signals along the m/z axis. These shifts can be induced by different charge states of the compound, the presence of adducts (e.g., potassium or sodium), and/or a fixed mass label (e.g., from ICAT or nicotinic acid labeling), or any combination of the above. We show that our approach can be used to infer more features in labeled data sets, correct wrong charge assignments even in high-resolution MS, improve mass precision, and cluster charged species in different charge states and several adduct types. © 2010 American Chemical Society.

Schubert S.,MPI International | Schubert S.,Meteorological Institute | Lucarini V.,Meteorological Institute | Lucarini V.,University of Reading
Quarterly Journal of the Royal Meteorological Society | Year: 2015

The classical approach for studying atmospheric variability is based on defining a background state and studying the linear stability of the small fluctuations around such a state. Weakly nonlinear theories can be constructed using higher order expansion terms. While these methods undoubtedly have great value for elucidating the relevant physical processes, they are unable to follow the dynamics of a turbulent atmosphere. We provide a first example of the extension of classical stability analysis to a nonlinearly evolving quasi-geostrophic flow. The so-called covariant Lyapunov vectors (CLVs) provide a covariant basis describing the directions of exponential expansion and decay of perturbations to the nonlinear trajectory of the flow. We use such a formalism to re-examine the basic barotropic and baroclinic processes of the atmosphere with a quasi-geostrophic beta-plane two-layer model in a periodic channel driven by a forced meridional temperature gradient ΔT. We explore three settings of ΔT, representative of relatively weak turbulence, well-developed turbulence and intermediate conditions. We construct the Lorenz energy cycle for each CLV describing the energy exchanges with the background state. A positive baroclinic conversion rate is a necessary but not sufficient condition for instability. Barotropic instability is present only for a few very unstable CLVs for large values of ΔT. Slowly growing and decaying hydrodynamic Lyapunov modes closely mirror the properties of the background flow. Following the classical necessary conditions for barotropic/baroclinic instability, we find a clear relationship between the properties of the eddy fluxes of a CLV and its instability. CLVs with positive baroclinic conversion seem to form a set of modes for constructing a reduced model of the atmospheric dynamics. © 2015 Royal Meteorological Society.

Rossi A.,Stowers Institute for Medical Research | Ross E.J.,Stowers Institute for Medical Research | Jack A.,MPI International | Sanchez Alvarado A.,Stowers Institute for Medical Research | Sanchez Alvarado A.,Howard Hughes Medical Institute
Gene | Year: 2014

Spliced leader (SL) trans-splicing is a biological phenomenon, common among many metazoan taxa, consisting in the transfer of a short leader sequence from a small SL RNA to the 5' end of a subset of pre-mRNAs. While knowledge of the biochemical mechanisms driving this process has accumulated over the years, the functional consequences of such post-transcriptional event at the organismal level remain unclear. In addition, the fact that functional analyses have been undertaken mainly in trypanosomes and nematodes leaves a somehow fragmented picture of the possible biological significance and evolution of SL trans-splicing in eukaryotes. Here, we analyzed the spatial expression of SL RNAs in the planarian flatworm Schmidtea mediterranea, with the goal of identifying novel developmental paradigms for the study of trans-splicing in metazoans. Besides the previously identified SL1 and SL2, S. mediterranea expresses a third SL RNA described here as SL3. While, SL1 and SL2 are collectively expressed in a broad range of planarian cell types, SL3 is highly enriched in a subset of the planarian stem cells engaged in regenerative responses. Our findings provide new opportunities to study how trans-splicing may regulate the phenotype of a cell. © 2013 Elsevier B.V.

Ahlswede J.,University of Hamburg | Hebel S.,University of Hamburg | Ross J.O.,University of Hamburg | Ross J.O.,MPI International | And 2 more authors.
Journal of Environmental Radioactivity | Year: 2013

Krypton-85 is mainly produced in nuclear reactors by fission of uranium and plutonium and released during chopping and dissolution of spent fuel rods in nuclear reprocessing facilities. As noble gas it is suited as a passive tracer for evaluation of atmospheric transport models. Furthermore, research is ongoing to assess its quality as an indicator for clandestine reprocessing activities. This paper continues previous efforts to compile a comprehensive historic emission inventory for krypton-85. Reprocessing facilities are the by far largest emitters of krypton-85. Information on sources and calculations used to derive the annual krypton-85 emission is provided for all known reprocessing facilities in the world. In addition, the emission characteristics of two plants, Tokai (Japan) and La Hague (France), are analysed in detail using emission data with high temporal resolution. Other types of krypton-85 sources are power reactors, naval reactors and isotope production facilities. These sources contribute only little or negligible amounts of krypton-85 compared to the large reprocessing facilities. Taking the decay of krypton-85 into account, the global atmospheric inventory is estimated to about 5500 PBq at the end of 2009. The correctness if the inventory has been proven by meteorological simulations and its error is assumed to be in the range of a few percent. © 2012 Elsevier Ltd.

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