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Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carry out a community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluate the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, laboratory-assembled human intestinal model and a human fecal sample. We observe that variability at the peptide level is predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappear at the protein group level. While differences are observed for predicted community composition, similar functional profiles are obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-laboratory studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.
MYCN is a transcription factor that is aberrantly expressed in many tumor types and is often correlated with poor patient prognosis. Recently, several lines of evidence pointed to the fact that oncogenic activation of MYC family proteins is concomitant with reprogramming of tumor cells to cope with an enhanced need for metabolites during cell growth. These adaptions are driven by the ability of MYC proteins to act as transcriptional amplifiers in a tissue-of-origin specific manner. Here, we describe the effects of MYCN overexpression on metabolic reprogramming in neuroblastoma cells. Ectopic expression of MYCN induced a glycolytic switch that was concomitant with enhanced sensitivity towards 2-deoxyglucose, an inhibitor of glycolysis. Moreover, global metabolic profiling revealed extensive alterations in the cellular metabolome resulting from overexpression of MYCN. Limited supply with either of the two main carbon sources, glucose or glutamine, resulted in distinct shifts in steady-state metabolite levels and significant changes in glutathione metabolism. Interestingly, interference with glutamine-glutamate conversion preferentially blocked proliferation of MYCN overexpressing cells, when glutamine levels were reduced. Thus, our study uncovered MYCN induction and nutrient levels as important metabolic master switches in neuroblastoma cells and identified critical nodes that restrict tumor cell proliferation.
MACC1 is a prognostic and predictive metastasis biomarker for more than 20 solid Cancer entities. However, its role in cancer metabolism is not sufficiently explored. Here, we report on how MACC1 impacts the use of glucose, glutamine, lactate, pyruvate and fatty acids and show the comprehensive analysis of MACC1-driven metabolic networks. We analyzed concentrationdependent changes in nutrient use, nutrient depletion, metabolic tracing employing 13C-labeled substrates, and in vivo studies. We found that MACC1 permits numerous effects on cancer
metabolism. Most of those effects increased nutrient uptake. Furthermore, MACC1 alters metabolic pathways by affecting metabolite production or turnover from metabolic substrates. MACC1 supports use of glucose, glutamine and pyruvate via their increased depletion or altered distribution within metabolic pathways. In summary, we demonstrate that MACC1 is an important regulator of metabolism in cancer cells.
Molecular machines are a key component in the vision of molecular nanotechnology and have the potential to transport molecular species and cargo on surfaces. The motion of such machines should be triggered remotely, ultimately allowing a large number of molecules to be propelled by a single source, with light being an attractive stimulus. Here, we report upon the photoinduced translation of molecular machines across a surface by characterizing single molecules before and after illumination. Illumination of molecules containing a motor unit results in an enhancement in the diffusion of the molecules. The effect vanishes if an incompatible photon energy is used or if the motor unit is removed from the molecule, revealing that the enhanced motion is due to the presence of the wavelength-sensitive motor in each molecule.
Inelastic incoherent neutron time-of flight scattering was employed to measure the low frequency density of states for a series of addition polynorbornenes with bulky side groups. The rigid main chain in combination with the bulky side groups give rise to a microporosity of these polymers in the solid state. The microporosity characterized by the BET surfaces area varies systematically in the considered series. Such materials have some possible application as active separation layer in gas separation membranes.
All investigated materials show excess contributions to the Debye type density of states characteristic for glasses known as Boson peak. The maximum position of the Boson peak shifts to lower frequency values with increasing microporosity. Data for PIM-1 and Matrimid included for comparison are in good agreement to this dependency. This result supports the sound wave interpretation of the Boson peak.
A thorough characterization of base materials is the prereq- uisite for further research. In this paper, the characterization data of the reference materials (CEM I 42.5 R, limestone pow- der, calcined clay and a mixture of these three components) used in the second funding phase of the priority program 2005 of the German Research Foundation (DFG SPP 2005) are presented under the aspects of chemical and min- eralogical composition as well as physical and chemical properties. The data were collected based on tests performed by up to eleven research groups involved in this cooperative program.
The first hard X-ray beamline at BESSY II will be installed by BAM and PTB at a superconducting 7 T wavelength shifter. The main optical elements of the beamline are a Double-Multilayer-Monochromator and a Double-Crystal-Monochromator. The two devices can be used separately or in-line. Main applications of monochromatic radiation with photon energies up to 50 keV are X-ray fluorescence analysis, micro-computed tomography, X-ray topography, detector calibration and reflectometry. Calculable undispersed radiation up to 200 keV will be available for radiometric applications.
The first hard x-ray beamline at BESSY II has been installed by BAM and PTB at a superconducting 7 T wavelength shifter. The main optical elements of the beamline are a double-multilayer monochromator and a double-crystal monochromator. Depending on the application, the two devices are used separately or in-line. The main applications of the monochromatic radiation with photon energies up to 60 keV are x-ray fluorescence analysis, micro computed tomography, x-ray topography, detector calibration and reflectometry. Calculable undispersed radiation up to 200 keV is available for radiometric applications.