A Robust and Universal Metaproteomics Workflow for Research Studies and Routine Diagnostics Within 24 h Using Phenol Extraction, FASP Digest, and the MetaProteomeAnalyzer

The investigation of microbial proteins by mass spectrometry (metaproteomics) is a key technology for simultaneously assessing the taxonomic composition and the functionality of microbial communities in medical, environmental, and biotechnological applications. We present an improved metaproteomics workflow using an updated sample preparation and a new version of the MetaProteomeAnalyzer software for data analysis. High resolution by multidimensional separation (GeLC, MudPIT) was sacrificed to aim at fast analysis of a broad range of different samples in less than 24 h. The improved workflow generated at least two times as many protein identifications than our previous workflow, and a drastic increase of taxonomic and functional annotations. Improvements of all aspects of the workflow, particularly the speed, are first steps toward potential routine clinical diagnostics (i.e., fecal samples) and analysis of technical and environmental samples. The MetaProteomeAnalyzer is provided to the scientific community as a central remote server solution at www.mpa.ovgu.de.Peer Reviewe

Dynamic proteome profiling of individual proteins in human skeletal muscle after a high-fat diet and resistance exercise.

It is generally accepted that muscle adaptation to resistance exercise (REX) training is underpinned by contraction-induced, increased rates of protein synthesis and dietary protein availability. By using dynamic proteome profiling (DPP), we investigated the contribution of both synthesis and breakdown to changes in abundance on a protein-by-protein basis in human skeletal muscle. Age-matched, overweight males consumed 9 d of a high-fat, low-carbohydrate diet during which time they either undertook 3 sessions of REX or performed no exercise. Precursor enrichment and the rate of incorporation of deuterium oxide into newly synthesized muscle proteins were determined by mass spectrometry. Ninety proteins were included in the DPP, with 28 proteins exhibiting significant responses to REX. The most common pattern of response was an increase in turnover, followed by an increase in abundance with no detectable increase in protein synthesis. Here, we provide novel evidence that demonstrates that the contribution of synthesis and breakdown to changes in protein abundance induced by REX differ on a protein-by-protein basis. We also highlight the importance of the degradation of individual muscle proteins after exercise in human skeletal muscle.-Camera, D. M., Burniston, J. G., Pogson, M. A., Smiles, W. J., Hawley, J. A. Dynamic proteome profiling of individual proteins in human skeletal muscle after a high-fat diet and resistance exercise

Integrated Cycles for Urban Biomass as a Strategy to Promote a CO2-Neutral Society—A Feasibility Study

The integration of closed biomass cycles into residential buildings enables efficient resource utilization and avoids the transport of biowaste. In our scenario called Integrated Cycles for Urban Biomass (ICU), biowaste is degraded on-site into biogas that is converted into heat and electricity. Nitrification processes upgrade the liquid fermentation residues to refined fertilizer, which can be used subsequently in house-internal gardens to produce fresh food for residents. Our research aims to assess the ICU scenario regarding produced amounts of biogas and food, saved CO2 emissions and costs, and social–cultural aspects. Therefore, a model-based feasibility study was performed assuming a building with 100 residents. The calculations show that the ICU concept produces 21% of the annual power (electrical and heat) consumption from the accumulated biowaste and up to 7.6 t of the fresh mass of lettuce per year in a 70 m2 professional hydroponic production area. Furthermore, it saves 6468 kg CO2-equivalent (CO2-eq) per year. While the ICU concept is technically feasible, it becomes economically feasible for large-scale implementations and higher food prices. Overall, this study demonstrates that the ICU implementation can be a worthwhile contribution towards a sustainable CO2-neutral society and decrease the demand for agricultural land

Angiographic CT with intravenous administration of contrast medium is a noninvasive option for follow-up after intracranial stenting

Intracranial angioplasty and stenting (ICAS) is a therapeutic option in symptomatic intracranial atherosclerotic disease. Adequate follow-up examination is necessary to exclude in-stent restenosis. Conventional intraarterial digital subtraction angiography (ia-DSA) is the current gold standard, but it is an invasive technique and carries the risk of neurological complications. Angiographic CT (ACT) is a new technique that provides a volume dataset of the highest spatial resolution and high contrast resolution derived from a rotational acquisition of a c-arm-mounted flat-panel detector. The feasibility of ACT with intravenous administration of contrast medium (iv-ACT) for follow-up after ICAS is demonstrated. In two patients iv-ACT was performed as a follow-up examination 12 months after ICAS. High-resolution volume data from the rotational acquisitions were processed to provide delineation of the stent lumen as well as imaging of the brain parenchyma and vessels. In both patients the patency of the stent lumen was assessed successfully. In addition, all other brain vessels were displayed in a manner similar to their appearance on CT angiograms. The brain parenchyma was also adequately imaged in a manner similar to its appearance on CT images. We demonstrated the feasibility and diagnostic value of iv-ACT for follow-up imaging after ICAS. This new application has the potential to become the imaging method of choice after ICAS since it not only enables visualization of the patency of the stent lumen but also is minimally invasive and provides additional information about all brain arteries and the brain parenchyma

A Cognitive Model of an Epistemic Community: Mapping the Dynamics of Shallow Lake Ecosystems

We used fuzzy cognitive mapping (FCM) to develop a generic shallow lake ecosystem model by augmenting the individual cognitive maps drawn by 8 scientists working in the area of shallow lake ecology. We calculated graph theoretical indices of the individual cognitive maps and the collective cognitive map produced by augmentation. The graph theoretical indices revealed internal cycles showing non-linear dynamics in the shallow lake ecosystem. The ecological processes were organized democratically without a top-down hierarchical structure. The steady state condition of the generic model was a characteristic turbid shallow lake ecosystem since there were no dynamic environmental changes that could cause shifts between a turbid and a clearwater state, and the generic model indicated that only a dynamic disturbance regime could maintain the clearwater state. The model developed herein captured the empirical behavior of shallow lakes, and contained the basic model of the Alternative Stable States Theory. In addition, our model expanded the basic model by quantifying the relative effects of connections and by extending it. In our expanded model we ran 4 simulations: harvesting submerged plants, nutrient reduction, fish removal without nutrient reduction, and biomanipulation. Only biomanipulation, which included fish removal and nutrient reduction, had the potential to shift the turbid state into clearwater state. The structure and relationships in the generic model as well as the outcomes of the management simulations were supported by actual field studies in shallow lake ecosystems. Thus, fuzzy cognitive mapping methodology enabled us to understand the complex structure of shallow lake ecosystems as a whole and obtain a valid generic model based on tacit knowledge of experts in the field.Comment: 24 pages, 5 Figure

High-resolution 3D X-ray imaging of intracranial nitinol stents

Introduction To assess an optimized 3D imaging protocol for intracranial nitinol stents in 3D C-arm flat detector imaging. For this purpose, an image quality simulation and an in vitro study was carried out. Methods Nitinol stents of various brands were placed inside an anthropomorphic head phantom, using iodine contrast. Experiments with objects were preceded by image quality and dose simulations. We varied X-ray imaging parameters in a commercially interventional X-ray system to set 3D image quality in the contrast–noise–sharpness space. Beam quality was varied to evaluate contrast of the stents while keeping absorbed dose below recommended values. Two detector formats were used, paired with an appropriate pixel size and X-ray focus size. Zoomed reconstructions were carried out and snapshot images acquired. High contrast spatial resolution was assessed with a CT phantom. Results We found an optimal protocol for imaging intracranial nitinol stents. Contrast resolution was optimized for nickel–titanium-containing stents. A high spatial resolution larger than 2.1 lp/mm allows struts to be visualized. We obtained images of stents of various brands and a representative set of images is shown. Independent of the make, struts can be imaged with virtually continuous strokes. Measured absorbed doses are shown to be lower than 50 mGy Computed Tomography Dose Index (CTDI). Conclusion By balancing the modulation transfer of the imaging components and tuning the high-contrast imaging capabilities, we have shown that thin nitinol stent wires can be reconstructed with high contrast-to-noise ratio and good detail, while keeping radiation doses within recommended values. Experimental results compare well with imaging simulations