Auf dem Weg zu einer neuen Sicht auf metabolische Netzwerke: Automatische Rekonstruktion und ausgedehnte Rechenanalysen angewendet auf Dinoroseobacter shibae

The main focus of this thesis is on simulations of metabolic reactions taking place in a growing cell by the means of linear optimization. Additionally, we introduce novel tools assisting in the reconstruction of metabolic networks or in the interpretation of the simulation results. In particular, we automated large parts of the laborious reconstruction process and created a visualization method for genome-scale metabolic networks, which uses a generalized definition of branch points to focus on relevant metabolic context. We used these new methods to enable a rapid creation of a metabolic model of \dinoroseobactershibae and a large-scale computational analysis of the metabolic capabilities of this marine bacterium, which would not have been possible with the traditional metabolic modeling approach. In addition to a large variety of environmental conditions, we also studied plasmid and single gene knock-out mutants in our simulations. We analyzed our results with regard to energy metabolism and revealed among others a pronounced metabolic answer to the availability of light. Moreover, our results gave insight into the changing split-up of the DMSP flux to the cleavage and the demethylation pathway under the different conditions. In conclusion, this thesis provides a new view on metabolic networks by employing new approaches in the fields of metabolic reconstruction, computational analysis, and interpretation of flux distributions.Der Hauptschwerpunkt dieser Arbeit liegt auf Simulationen von metabolischen Reaktionen, die in einer wachsenden Zelle stattfinden, mit Hilfe von Methoden der linearen Optimierung. Zusätzlich führen wir neue Werkzeuge ein, die die Rekonstruktion von metabolischen Netzwerken oder die Interpretation der Simulationsergebnisse unterstützen. Insbesondere haben wir weite Teile des aufwändigen Rekonstruktionsprozesses automatisiert. Außerdem haben wir eine neue Visualisierungsmethode entwickelt, die eine verallgemeinerte Definition von Verzweigungspunkten verwendet um die Darstellung auf den relevanten metabolischen Kontext zu beschränken. Wir haben diese neuen Methoden benutzt um eine schnelle Erstellung eines metabolischen Modells von \dinoroseobactershibae und eine ausgedehnte Rechenanalyse der metabolischen Fähigkeiten dieses maritimen Bakteriums zu ermöglichen, die mit den traditionellen Ansätzen der metabolischen Modellierung nicht möglich gewesen wäre. Zusätzlich zu einer großen Vielfalt von Umweltbedingungen haben wir auch Plasmid- und Einzelgen-Deletionsmutanten mit unseren Simulationen untersucht. Wir haben unsere Ergebnisse im Hinblick auf den Energiestoffwechsel analysiert und unter Anderem eine deutliche metabolische Antwort auf die Verfügbarkeit von Licht aufgedeckt. Darüber hinaus gaben unsere Resultate Einsicht in die sich änderte Aufteilung des DMSP-Flusses in den Spaltungsweg und den Demethylierungsweg unter verschiedenen Bedingungen. Zusammenfassend erlaubt diese Arbeit einen neuen Blick auf metabolische Netzwerke in dem sie neue Ansätze in den Bereichen metabolische Rekonstruktion, computergestützte Analyse und Interpretation von Flussverteilungen aufzeigt

Atlas registration for edema-corrected MRI lesion volume in mouse stroke models

Lesion volume measurements with magnetic resonance imaging are widely used to assess outcome in rodent models of stroke. In this study, we improved a mathematical framework to correct lesion size for edema which is based on manual delineation of the lesion and hemispheres. Furthermore, a novel MATLAB toolbox to register mouse brain MR images to the Allen brain atlas is presented. Its capability to calculate edema-corrected lesion size was compared to the manual approach. Automated image registration performed equally well in in a mouse middle cerebral artery occlusion model (Pearson r=0.976, p=2.265e-11). Information encapsulated in the registration was used to generate maps of edema induced tissue volume changes. These showed discrepancies to simplified tissue models underlying the manual approach. The presented techniques provide biologically more meaningful, voxel-wise biomarkers of vasogenic edema after stroke

Atlas registration for edema-corrected MRI lesion volume in mouse stroke models

Lesion volume measurements with magnetic resonance imaging are widely used to assess outcome in rodent models of stroke. In this study, we improved a mathematical framework to correct lesion size for edema which is based on manual delineation of the lesion and hemispheres. Furthermore, a novel MATLAB toolbox to register mouse brain MR images to the Allen brain atlas is presented. Its capability to calculate edema-corrected lesion size was compared to the manual approach. Automated image registration performed equally well in in a mouse middle cerebral artery occlusion model (Pearson r=0.976, p=2.265e-11). Information encapsulated in the registration was used to generate maps of edema induced tissue volume changes. These showed discrepancies to simplified tissue models underlying the manual approach. The presented techniques provide biologically more meaningful, voxel-wise biomarkers of vasogenic edema after stroke

Double sampling of a faecal immunochemical test is not superior to single sampling for detection of colorectal neoplasia: a colonoscopy controlled prospective cohort study

<p>Abstract</p> <p>Background</p> <p>A single sampled faecal immunochemical test (FIT) has moderate sensitivity for colorectal cancer and advanced adenomas. Repeated FIT sampling could improve test sensitivity. The aim of the present study is to determine whether any of three different strategies of double FIT sampling has a better combination of sensitivity and specificity than single FIT sampling.</p> <p>Methods</p> <p>Test performance of single FIT sampling in subjects scheduled for colonoscopy was compared to double FIT sampling intra-individually. Test positivity of double FIT sampling was evaluated in three different ways: 1) "one of two FITs+" when at least one out of two measurements exceeded the cut-off value, 2) "two of two FITs+" when both measurements exceeded the cut-off value, 3) "mean of two FITs+" when the geometric mean of two FITs exceeded the cut-off value. Receiver operator curves were calculated and sensitivity of single and the three strategies of double FIT sampling were compared at a fixed level of specificity.</p> <p>Results</p> <p>In 124 of 1096 subjects, screen relevant neoplasia (SRN) were found (i.e. early stage CRC or advanced adenomas). At any cut-off, "two of two FITs+" resulted in the lowest and "one of two FITs+" in the highest sensitivity for SRN (range 35-44% and 42%-54% respectively). ROC's of double FIT sampling were similar to single FIT sampling. At specificities of 85/90/95%, sensitivity of any double FIT sampling strategy did not differ significantly from single FIT (p-values 0.07-1).</p> <p>Conclusion</p> <p>At any cut off, "one of two FITs+" is the most sensitive double FIT sampling strategy. However, at a given specificity level, sensitivity of any double FIT sampling strategy for SRN is comparable to single FIT sampling at a different cut-off value. None of the double FIT strategies has a superior combination of sensitivity and specificity over single FIT.</p

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

A metabolite-centric view on flux distributions in genome-scale metabolic models

BACKGROUND: Genome-scale metabolic models are important tools in systems biology. They permit the in-silico prediction of cellular phenotypes via mathematical optimisation procedures, most importantly flux balance analysis. Current studies on metabolic models mostly consider reaction fluxes in isolation. Based on a recently proposed metabolite-centric approach, we here describe a set of methods that enable the analysis and interpretation of flux distributions in an integrated metabolite-centric view. We demonstrate how this framework can be used for the refinement of genome-scale metabolic models. RESULTS: We applied the metabolite-centric view developed here to the most recent metabolic reconstruction of Escherichia coli. By compiling the balance sheets of a small number of currency metabolites, we were able to fully characterise the energy metabolism as predicted by the model and to identify a possibility for model refinement in NADPH metabolism. Selected branch points were examined in detail in order to demonstrate how a metabolite-centric view allows identifying functional roles of metabolites. Fructose 6-phosphate aldolase and the sedoheptulose bisphosphate bypass were identified as enzymatic reactions that can carry high fluxes in the model but are unlikely to exhibit significant activity in vivo. Performing a metabolite essentiality analysis, unconstrained import and export of iron ions could be identified as potentially problematic for the quality of model predictions. CONCLUSIONS: The system-wide analysis of split ratios and branch points allows a much deeper insight into the metabolic network than reaction-centric analyses. Extending an earlier metabolite-centric approach, the methods introduced here establish an integrated metabolite-centric framework for the interpretation of flux distributions in genome-scale metabolic networks that can complement the classical reaction-centric framework. Analysing fluxes and their metabolic context simultaneously opens the door to systems biological interpretations that are not apparent from isolated reaction fluxes. Particularly powerful demonstrations of this are the analyses of the complete metabolic contexts of energy metabolism and the folate-dependent one-carbon pool presented in this work. Finally, a metabolite-centric view on flux distributions can guide the refinement of metabolic reconstructions for specific growth scenarios

These 34 dynamics observables to have been used to characterize the dynasome.

<p>These 34 dynamics observables to have been used to characterize the dynasome.</p