Mathematical Analysis and Modeling of Signaling Networks

Mathematical models are in focus of modern systems biology and increasingly important to understand and manipulate complex biological systems. At the same time, new and improved techniques in metabolomics and proteomics enhance the ability to measure cellular states and molecular concentrations. In consequence, this leads to important biological insights and novel potential drug targets. Model development in systems biology can be described as an iterative process of model refinement to match the observed properties. The resulting research cycle is based on a well-defined initial model and requires careful model revision in each step. {As an initial step, a stoichiometry-based mathematical model of the muscarinic acetylcholine receptor subtype 2 (M2 receptor)-induced signaling in Chinese hamster ovary (CHO) cells was derived. To validate the obtained initial model based on spatially accessible, not neces-sarily time-resolved data, the novel constrained flux sampling (CFS) is proposed in this work. The thus verified static model was then translated into a dynamical system based on ordinary differential equations (ODEs) by incorporating time-dependent experimental data. To learn from the errors of systems biological models, the dynamic elastic-net (DEN), a novel approach based on optimal control theory, is proposed in this thesis. Next, the Bayesian dy-namic elastic-net (BDEN), a systematic, fully algorithmic method based on the Markov chain Monte Carlo method was derived, which allows to detect hidden influences as well as missed reactions in ODE-based models. The BDEN allows for further validation of the developed M2 receptor-induced signaling pathway and thus provides evidence for the completeness of the obtained dynamical system. This thesis introduces the first comprehensive model of the M2 receptor-induced signaling in CHO cells. Furthermore, this work presents several novel algorithms to validate and correct static and dynamic models of biological systems in a semi-automatic manner. These novel algorithms are expected to simplify the development of further mathematical models in systems biology.Mathematische Modellierung und Analyse von Signalnetzwerken Mathematische Modelle stehen im Zentrum der modernen Systembiologie und werden immer wichtiger, um komplexe biologische Systeme verstehen und manipulieren zu können. Gleichzeitig erweitern neue und verbesserte Verfahren der Metabolomik und Proteomik die Möglichkeiten, Zellzustände und Molekülkonzentrationen zu bestimmen. Dies ermöglicht die Gewinnung neuer und wichtiger biologischer Erkenntnisse und die Identifizierung neuer potentieller Ansatzpunkte für medizinische Wirkstoffe. Die Modellentwicklung in der Systembiologie kann als ein iterativer Prozess der permanenten Modellverbesserung beschrieben werden, der das Ziel hat, die beobachteten Eigenschaften korrekt wiederzugeben. Der resultierende Modellierungskreislauf basiert auf einem klar bestimmten Anfangsmodell und erfordert das sorgfältige Anpassen des Modells in jedem einzelnen Modellierungsschritt. In einem ersten Schritt wurde ein auf stöchiometrischen Daten basierendes mathematisches Modell für die durch den muskarinischen Acetylcholinrezeptor des Subtyps 2 (M2-Rezeptor) induzierte Signalübertragung in CHO-Zellen aufgestellt. Zur Validierung des ursprünglichen Modells auf der Grundlage von räumlich erfassbaren, nicht notwendigerweise zeitaufgelösten Daten wird in dieser Arbeit das neu entwickelte Constrained Flux Sampling (CFS) vorgestellt. Das auf diese Weise verifizierte statische Modell wurde dann unter Einbeziehung zeitabhängiger experimenteller Messdaten in ein dynamisches Modell basierend auf gewöhnlichen Differentialgleichungen (DGL) umgewandelt. Um aus den mathematischen Unsicherheiten systembiologischer Modelle zu lernen, wird in dieser Arbeit das Dynamic Elastic-Net (DEN) eingeführt, ein neuer Ansatz basierend auf der Theorie der optimalen Steuerungen. Als nächster Schritt wurde das Bayesian Dynamic Elastic-Net (BDEN) entwickelt, eine systematische, vollständig algorithmische Methode basierend auf dem Markov-Chain-Monte-Carlo-Verfahren, die es erlaubt, sowohl verborgene Einflussfaktoren als auch übersehene Reaktionen in DGL-basierten Modellen aufzuspüren. Das BDEN ermöglicht die weitere Validierung des durch den M2-Rezeptor induzierten Signalwegs und liefert so den Beweis für die Vollständigkeit des modellierten dynamischen Systems. In dieser Arbeit wird das erste vollständige Modell für den durch den M2-Rezeptor induzierten Signalweg in CHO-Zellen eingeführt. Des Weiteren werden in dieser Arbeit verschiedene neue Algorithmen zur halbautomatischen Validierung und Korrektur statischer und dynamischer Modelle biologischer Systeme vorgestellt. Es wird erwartet, dass diese neuen Algorithmen die Entwicklung weiterer mathematischer Modelle in der Systembiologie stark vereinfachen

Using personalized support & school-based study groups to increase teachers’ participation in MOOCs

There is little doubt that online training formats and Massive Open Online Courses (MOOCs) in particular have the potential to increase accessibility for training educators and address some challenges reported by teachers in being able to access relevant professional development (OECD, 2019). However, pre-pandemic data shows that participation in online training is not yet widespread amongst teachers (OECD, 2019). This paper therefore explores two mechanisms that could potentially increase teachers’ participation in MOOCs: an offer of personalized support during a MOOC and the provision of school-based study groups. Evidence of the implementation of a personalized support in field trials has demonstrated substantial impact on teachers’ participation in MOOCs, with 42% of the test group completing a series of MOOCs versus only 32% of the control group. Results from a small pilot program focusing on the use of school-based study groups are more tentative but suggest that a school-based blended learning model that makes use of study groups has the potential to increase participation in MOOCs by engaging teachers who would not have previously considered enrolling to a MOOC and building teachers’ competence and confidence levels so that they are able to start and complete a MOOC

Nachhaltigkeit im industriellen Umfeld

Im Rahmen der Lehrveranstaltung "Nachhaltigkeit im industriellen Umfeld" im Masterstudiengang Umwelt- und Verfahrenstechnik der Hochschulen Konstanz und Ravensburg-Weingarten fand im Dezember 2016 eine studentische Fachkonferenz statt. Die Studierenden entwickelten in Einzelarbeit oder als Zweierteam Konferenzbeiträge zu folgenden Themen: - Spannendes aus dem Bereich der Energieerzeugung und der Grauen Energie - Aspekte der Kreislaufwirtschaft - Ökosysteme - ihre Belastung und Erhalt - Spezifische Wirtschaftszweige und Nachhaltigkeit Die Ergebnisse der studentischen Fachkonferenz zur „Nachhaltigkeit im industriellen Umfeld“ werden in der vorliegenden Publikation präsentiert

Adenovirus-Mediated Transfer of the CFTR Gene to Lung of Nonhuman Primates: Biological Efficacy Study

Overview summary Recombinant adenoviruses hold tremendous promise for gene therapies of lung disease in cystic fibrosis (CF). An evaluation of the feasibility and safety of this technology in nonhuman primates is critical in the design of clinical protocols. In a series of two papers, Wilson and colleagues describe an extensive study in baboons designed to evaluate the feasibility and safety of direct instillation of CF transmembrane conductance regulator (CFTR)-expressing adenoviruses into the airway. This paper by Engelhardt et al., addresses the biological efficacy of E1-deleted adenoviruses for gene therapy of CF lung disease.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/63146/1/hum.1993.4.6-759.pd

Evidence for a regulatory role of Cullin-RING E3 ubiquitin ligase 7 in insulin signalling

Dysfunctional regulation of signalling pathways downstream of the insulin receptor plays a pivotal role in the pathogenesis of insulin resistance and type 2 diabetes. In this study we report both in vitro and in vivo experimental evidence for a role of Cullin-RING E3 ubiquitin ligase 7 (CRL7) in the regulation of insulin signalling and glucose homeostasis. We show that Cul7−/− mouse embryonic fibroblasts displayed enhanced AKT and Erk MAP kinase phosphorylation upon insulin stimulation. Depletion of CUL7 by RNA interference in C2C12 myotubes led to increased activation of insulin signalling pathways and cellular glucose uptake, as well as a reduced capacity of these cells to execute insulin-induced degradation of insulin receptor substrate 1 (IRS1). In vivo, heterozygosity of either Cul7 or Fbxw8, both key components of CRL7, resulted in elevated PI3 kinase / AKT activation in skeletal muscle tissue upon insulin stimulation when compared to wild-type controls. Finally, Cul7+/− or Fbxw8+/− mice exhibited enhanced insulin sensitivity and plasma glucose clearance. Collectively, our findings point to a yet unrecognized role of CRL7 in insulin-mediated control of glucose homeostasis by restraining PI3 kinase / AKT activities in skeletal muscle cells

Analysis of delayed surgical treatment and oncologic outcomes in clinical stage I non-small cell lung cancer

Importance: The association between delayed surgical treatment and oncologic outcomes in patients with non-small cell lung cancer (NSCLC) is poorly understood given that prior studies have used imprecise definitions for the date of cancer diagnosis. Objective: To use a uniform method to quantify surgical treatment delay and to examine its association with several oncologic outcomes. Design, Setting, and Participants: This retrospective cohort study was conducted using a novel data set from the Veterans Health Administration (VHA) system. Included patients had clinical stage I NSCLC and were undergoing resection from 2006 to 2016 within the VHA system. Time to surgical treatment (TTS) was defined as the time between preoperative diagnostic computed tomography imaging and surgical treatment. We evaluated the association between TTS and several delay-associated outcomes using restricted cubic spline functions. Data analyses were performed in November 2021. Exposure: Wait time between cancer diagnosis and surgical treatment (ie, TTS). Main Outcomes and Measures: Several delay-associated oncologic outcomes, including pathologic upstaging, resection with positive margins, and recurrence, were assessed. We also assessed overall survival. Results: Among 9904 patients who underwent surgical treatment for clinical stage I NSCLC, 9539 (96.3%) were men, 4972 individuals (50.5%) were currently smoking, and the mean (SD) age was 67.7 (7.9) years. The mean (SD) TTS was 70.1 (38.6) days. TTS was not associated with increased risk of pathologic upstaging or positive margins. Recurrence was detected in 4158 patients (42.0%) with median (interquartile range) follow-up of 6.15 (2.51-11.51) years. Factors associated with increased risk of recurrence included younger age (hazard ratio [HR] for every 1-year increase in age, 0.992; 95% CI, 0.987-0.997; P = .003), higher Charlson Comorbidity Index score (HR for every 1-unit increase in composite score, 1.055; 95% CI, 1.037-1.073; P \u3c .001), segmentectomy (HR vs lobectomy, 1.352; 95% CI, 1.179-1.551; P \u3c .001) or wedge resection (HR vs lobectomy, 1.282; 95% CI, 1.179-1.394; P \u3c .001), larger tumor size (eg, 31-40 mm vs \u3c10 mm; HR, 1.209; 95% CI, 1.051-1.390; P = .008), higher tumor grade (eg, II vs I; HR, 1.210; 95% CI, 1.085-1.349; P \u3c .001), lower number of lymph nodes examined (eg, ≥10 vs \u3c10; HR, 0.866; 95% CI, 0.803-0.933; P \u3c .001), higher pathologic stage (III vs I; HR, 1.571; 95% CI, 1.351-1.837; P \u3c .001), and longer TTS, with increasing risk after 12 weeks. For each week of surgical delay beyond 12 weeks, the hazard for recurrence increased by 0.4% (HR, 1.004; 95% CI, 1.001-1.006; P = .002). Factors associated with delayed surgical treatment included African American race (odds ratio [OR] vs White race, 1.267; 95% CI, 1.112-1.444; P \u3c .001), higher area deprivation index [ADI] score (OR for every 1 unit increase in ADI score, 1.005; 95% CI, 1.002-1.007; P = .002), lower hospital case load (OR for every 1-unit increase in case load, 0.998; 95% CI, 0.998-0.999; P = .001), and year of diagnosis, with less recent procedures more likely to have delay (OR for each additional year, 0.900; 95% CI, 0.884-0.915; P \u3c .001). Patients with surgical treatment within 12 weeks of diagnosis had significantly better overall survival than those with procedures delayed more than 12 weeks (HR, 1.132; 95% CI, 1.064-1.204; P \u3c .001). Conclusions and Relevance: Using a more precise definition for TTS, this study found that surgical procedures delayed more than 12 weeks were associated with increased risk of recurrence and worse survival. These findings suggest that patients with clinical stage I NSCLC should undergo expeditious treatment within that time frame

Correlation functions quantify super-resolution images and estimate apparent clustering due to over-counting

We present an analytical method to quantify clustering in super-resolution localization images of static surfaces in two dimensions. The method also describes how over-counting of labeled molecules contributes to apparent self-clustering and how the effective lateral resolution of an image can be determined. This treatment applies to clustering of proteins and lipids in membranes, where there is significant interest in using super-resolution localization techniques to probe membrane heterogeneity. When images are quantified using pair correlation functions, the magnitude of apparent clustering due to over-counting will vary inversely with the surface density of labeled molecules and does not depend on the number of times an average molecule is counted. Over-counting does not yield apparent co-clustering in double label experiments when pair cross-correlation functions are measured. We apply our analytical method to quantify the distribution of the IgE receptor (Fc{\epsilon}RI) on the plasma membranes of chemically fixed RBL-2H3 mast cells from images acquired using stochastic optical reconstruction microscopy (STORM) and scanning electron microscopy (SEM). We find that apparent clustering of labeled IgE bound to Fc{\epsilon}RI detected with both methods arises from over-counting of individual complexes. Thus our results indicate that these receptors are randomly distributed within the resolution and sensitivity limits of these experiments.Comment: 22 pages, 5 figure

You Can?t Win If You Don?t Fight: The Role of Regime Type in Counterinsurgency Outbreaks and Outcomes

What effect, if any, does democracy have on outcomes of counterinsurgency wars? Previous studies have provided inconclusive answers mainly because of the challenges involved in testing the question empirically: First, insurgencies are not accidental and the anticipated outcomes also affect whether they break out in the first place. Second, regimes are non-random and their determinants can also affect insurgency incidence and its outcomes. Moreover, different aspects of democracy can have opposite effects on the government's chances of winning. I address these challenges by conducting a critical test to distinguish between different causal mechanisms. I find that domestic institutions that are associated with public goods provision make insurgency onsets less likely. I also show that once we control for this selection effect, domestic political institutions do not influence insurgency outcomes

Do red deer stags (Cervus elaphus) use roar fundamental frequency (F0) to assess rivals?

It is well established that in humans, male voices are disproportionately lower pitched than female voices, and recent studies suggest that this dimorphism in fundamental frequency (F0) results from both intrasexual (male competition) and intersexual (female mate choice) selection for lower pitched voices in men. However, comparative investigations indicate that sexual dimorphism in F0 is not universal in terrestrial mammals. In the highly polygynous and sexually dimorphic Scottish red deer Cervus elaphus scoticus, more successful males give sexually-selected calls (roars) with higher minimum F0s, suggesting that high, rather than low F0s advertise quality in this subspecies. While playback experiments demonstrated that oestrous females prefer higher pitched roars, the potential role of roar F0 in male competition remains untested. Here we examined the response of rutting red deer stags to playbacks of re-synthesized male roars with different median F0s. Our results show that stags’ responses (latencies and durations of attention, vocal and approach responses) were not affected by the F0 of the roar. This suggests that intrasexual selection is unlikely to strongly influence the evolution of roar F0 in Scottish red deer stags, and illustrates how the F0 of terrestrial mammal vocal sexual signals may be subject to different selection pressures across species. Further investigations on species characterized by different F0 profiles are needed to provide a comparative background for evolutionary interpretations of sex differences in mammalian vocalizations