A flexible architecture for modeling and simulation of diffusional association

Up to now, it is not possible to obtain analytical solutions for complex molecular association processes (e.g. Molecule recognition in Signaling or catalysis). Instead Brownian Dynamics (BD) simulations are commonly used to estimate the rate of diffusional association, e.g. to be later used in mesoscopic simulations. Meanwhile a portfolio of diffusional association (DA) methods have been developed that exploit BD. However, DA methods do not clearly distinguish between modeling, simulation, and experiment settings. This hampers to classify and compare the existing methods with respect to, for instance model assumptions, simulation approximations or specific optimization strategies for steering the computation of trajectories. To address this deficiency we propose FADA (Flexible Architecture for Diffusional Association) - an architecture that allows the flexible definition of the experiment comprising a formal description of the model in SpacePi, different simulators, as well as validation and analysis methods. Based on the NAM (Northrup-Allison-McCammon) method, which forms the basis of many existing DA methods, we illustrate the structure and functioning of FADA. A discussion of future validation experiments illuminates how the FADA can be exploited in order to estimate reaction rates and how validation techniques may be applied to validate additional features of the model

Transcriptome of iPSC-derived neuronal cells reveals a module of co-expressed genes consistently associated with autism spectrum disorder

Evaluation of expression profile in autism spectrum disorder (ASD) patients is an important approach to understand possible similar functional consequences that may underlie disease pathophysiology regardless of its genetic heterogeneity. Induced pluripotent stem cell (iPSC)-derived neuronal models have been useful to explore this question, but larger cohorts and different ASD endophenotypes still need to be investigated. Moreover, whether changes seen in this in vitro model reflect previous findings in ASD postmortem brains and how consistent they are across the studies remain underexplored questions. We examined the transcriptome of iPSC-derived neuronal cells from a normocephalic ASD cohort composed mostly of high-functioning individuals and from non-ASD individuals. ASD patients presented expression dysregulation of a module of co-expressed genes involved in protein synthesis in neuronal progenitor cells (NPC), and a module of genes related to synapse/neurotransmission and a module related to translation in neurons. Proteomic analysis in NPC revealed potential molecular links between the modules dysregulated in NPC and in neurons. Remarkably, the comparison of our results to a series of transcriptome studies revealed that the module related to synapse has been consistently found as upregulated in iPSC-derived neurons-which has an expression profile more closely related to fetal brain-while downregulated in postmortem brain tissue, indicating a reliable association of this network to the disease and suggesting that its dysregulation might occur in different directions across development in ASD individuals. Therefore, the expression pattern of this network might be used as biomarker for ASD and should be experimentally explored as a therapeutic target

Coarse Graining of Agent-Based Models and Spatio-Temporal Modeling of Spreading Processes

Agent-based models play a central role in modeling social spreading processes, in part because they allow detailed representation of interactions between individuals while integrating data on real-world processes. However, the resulting models are often too complex for a formal analysis and usually require high simulation e ort. In this thesis, based on general remarks on theoretical concepts such as stochastic dynamics and Markov processes, we have rst presented some new theoretical results on the e cient simulation and model reduction of agent-based models. Among these results are an event-based simulation algorithm for ABMs and a model reduction approach based on a projection of the state space and the utilization of convergence results to approximate agent-based models by less complex metapopulation models that can be simulated with much less e ort. Assuming metastability of the agent system, this approach preserves important model characteristics whith a low approximation error. In relation to this background a number of applications of agent-based models have been discussed. Of these, some are of fundamental structure, including a model to achieve global goals with local information, and others concern concrete spreading processes in prehistoric and contemporary societies. A focus among the applications is the spreading and development of culture and innovations in ancient times, both on a conceptual level and with reference to a concrete application case, the spread of the woolly sheep to Europe. In this context, the presented models have been developed through interdisciplinary cooperation and by taking into account archaeological, anthropological as well as geographical data in order to be able to depict the mobility and interactions of nomads, such as hunter-gatherers or shepherds, as realistically as possible. An important aspect that was discussed is the challenges posed by the prehistoric context, both in model parameterization and in validation and interpretation of the results. The comparison with current modeling scenarios is discussed with reference to the application area of epidemic spreading. Speci cally, the di erences in the assumptions about agent mobility and in the availability and reproducibility of data relevant to the model construction and analysis are highlighted. In the analysis of the models, we focused in particular on the identi cation of metastable processes through the application of clustering methods, including a novel approach that exploits the speci c structure of the agent-based models we have presented. Based on this analysis, possibilities for model reduction were discussed, which allow to generate additional data on macroscopic properties and mesoscopic structures of the models with low e ort. Especially, the generation of relevant statistics about critical transitions and other rare events is enabled by the reduced model complexity.Agentenbasierte Modelle spielen bei der Modellierung sozialer Ausbreitungsprozesse eine zentrale Rolle, da sie unter anderem die Interaktionen zwischen Individuen detailliert abbilden und Daten über reale Prozesse integrieren können. Die resultierenden Modelle sind jedoch häufig zu komplex für eine formale Analyse und in der Regel mit einem hohen Simulationsaufwand verbunden. In dieser Arbeit werden zunächst, aufbauend auf allgemeinen Ausführungen zu theoretischen Konzepten wie stochastischer Dynamik und Markov-Prozessen, einige neue theoretische Ergebnisse zur Simulation und Modellreduktion von agentenbasierten Modellen vorgestellt. Hervorzuheben ist dabei ein auf einer Zustandsraumprojektion basierender Ansatz zur Approximation agentenbasierter Modelle durch weniger komplexe Metapopulationsmodelle, die mit deutlich geringerem Aufwand simuliert werden können. Unter der Voraussetzung der Metastabilität bleiben dabei wichtige Modelleigenschaften bei geringem Approximationsfehler erhalten. In diesem Zusammenhang und im Anschluss daran werden eine Reihe von Anwendungen agentenbasierter Modelle diskutiert. Einige davon sind grundlegender Natur, darunter ein Modell zur Erreichung globaler Ziele mit lokalen Informationen, andere betreffen konkrete Ausbreitungsprozesse in prähistorischen und zeitgenössischen Gesellschaften. Ein Schwerpunkt unter den Anwendungsbereichen ist die Ausbreitung und Entwicklung von Kultur und Innovationen in der Antike, sowohl auf konzeptioneller Ebene als auch in Bezug auf einen konkreten Anwendungsfall, die Ausbreitung des Wollschafs nach Europa. Dabei wurden die vorgestellten Modelle in interdisziplinärer Kooperation und unter Berücksichtigung archäologischer, anthropologischer und geographischer Daten entwickelt, um die Mobilität und Interaktionen von Nomaden wie Jägern und Sammlern oder Hirten möglichst realitätsnah abbilden zu können. Ein wichtiger Aspekt, der diskutiert wird, sind die Herausforderungen, die sich aus dem prähistorischen Kontext sowohl für die Modellparametrisierung als auch für die Validierung und Interpretation der Ergebnisse ergeben. Der Vergleich mit aktuellen Modellierungsszenarien wird in Bezug auf das Anwendungsgebiet der Infektionsausbreitung diskutiert. Dabei werden insbesondere die Unterschiede in den Annahmen zur Mobilität der Agenten und in der Verfügbarkeit und Reproduzierbarkeit der für die Modellkonstruktion und -analyse relevanten Daten hervorgehoben. Bei der Analyse der Modelle liegt ein besonderer Schwerpunkt auf der Identifikation metastabiler Prozesse durch die Anwendung von Clusterverfahren, einschließlich eines neuartigen Ansatzes, der die besondere Struktur agentenbasierter Modelle ausnutzt. Darauf aufbauend werden Möglichkeiten der Modellreduktion diskutiert, die es erlauben, mit geringem Aufwand zusätzliche Daten über makroskopische Eigenschaften und mesoskopische Strukturen der Modelle zu erzeugen. Insbesondere die Generierung relevanter Statistiken über kritische Übergänge und andere seltene Ereignisse wird durch die geringere Modellkomplexität erst ermöglicht

GENERATION OF AUTHENTIC HUMAN NEOCORTICAL NEURONS FROM INDUCED PLURIPOTENT STEM CELLS TO INVESTIGATE 7Q11.23 GENE DOSAGE IMBALANCES

Questo lavoro di tesi ha avuto lo scopo di studiare lo sviluppo della neocorteccia umana ed i meccanisimi alla base della sua compromissione che risultano nell\u2019insorgenza di patologie del neurosviluppo mediante un\u2019analisi dei profili trascrizionali e della morfologia di neuroni neocorticali umani generati a partire da cellule staminali pluripotenti indotte (iPSCs). Data l\u2019importanza di basarsi su un paradigma di neurogenesi in vitro riproducibile e affidabile nel generare neuroni neocoritcali umani autentici, prima di adottare questo sistema modello per lo studio di patologie del neurosviluppo, nella prima fase di questa ricerca abbiamo eseguito un\u2019ampia caratterizzazione trascrizionale, molecolare e funzionale del protocollo di differenziamento. Le dinamiche trascrizionali che regolano il neurosviluppo in vitro sono state studiate effettuando esperimenti di RNA-sequencing sia a livello di popolazione che di singola cellula. In combinazione con diverse analisi bioinformatiche tra cui l\u2019analisi delle componeti principali (PCA), l\u2019analisi dei geni differenzialemtne espressi e l\u2019analisi WGCNA. L\u2019analisi dei profili trascrizionali \ue8 stata accompagnata da un\u2019ampia analisi di d\u2019immunocitochimica che ha permesso di confermare l\u2019identit\ue0 e lo stadio di sviluppo delle cellule in coltura. Inoltre, la maturit\ue0 funzionale dei neuroni derivati da iPSCs \ue8 stata ulteriormente confermata dalla loro capacit\ue0 di generare potenziali d\u2019azione, sostenere pattern di scarica complessi e sviluppare attivit\ue0 sinaptica spontanea eccitatoria ed inibitoria. Complessivamente, i risultati ottenuti da questo ampio e diversificato pannello di analisi hanno permesso di stabilitre la riproducibilit\ue0 del protocollo di differenziamento e la sua competenza nel generare con elevata efficienza principalmente neuroni neocorticali autentici. Successivamente abbiamo applicato questo protocollo di differenziamento neocorticale come sistema modello per studiare due patologie del neurosviluppo dovute alla delezione e duplicazione di una regione comprendente circa 1.5 - 1.8 Mb (megabasi) collacata sul braccio lungo (q) del cormosoma 7 nella banda 11.23. Duplicazioni e delezioni di questa regione sono di particolare interesse in quanto le due sindromi che ne risultano, rispettivamente la sindrome di Willams (WS) e la sindrome da duplicazione 7q11.23 (7q11DUP), presentano fenotipi cognitivi e comportamentali caratterizzati da profili simili e tratti simmetricamente opposti. La frequente comorbidit\ue0 della sindrome da duplicazione 7q11.23 con altre patologie del neurosviluppo come l\u2019autismo e la schizofrenia in contrasto con la sindrome di Williams che \ue8 una sindrome ben caraterizzata non associata ad altre patologie del neurosviluppo, rende lo studio dell\u2019 alterato dosaggio genico del locus 7q11.23 estremamente interessante per identificare con precisione i meccanismi molecolari caratteristici di ciascuna condizione clinica, condivisi da entrabme le sindromi e comuni anche ad altre patologie del neurosviluppo. A questo scopo, abbiamo generato diverse linee di iPS a partire da un ampio gruppo di individui, comprendente individui sani e pazienti affetti dalla sindrome di Williams (WS) e dalla sindrome di duplizazione 7q11.23, che sono poi state differenziate in neuroni neocorticali applicando il protocollo precedentemetne caraterizzato. Confermata l\u2019identit\ue0 e l\u2019autenticit\ue0 dei neuroni neocorticali generati da iPSCs, stiamo attualmente identificando i geni ed i meccanismi molecolari disregolati in specifici sottotipi di neuroni che abbiano la maggior rilvenza clinica. Inoltre, l\u2019analisi morfologica dei neuroni neocorticali umani ottenuti da pazienti WS e soggetti sani ha permesso di confermare nell\u2019uomo molte alterazioni morfologiche dei neuroni neocorticali osservate in un modello murino knockout per Dnajc30, un gene ancora funzionalmente non caraterizzato compreso nel locus 7q11.23.This research project has been aimed to investigate human neocortical development in healthy and diseased subjects by analyzing and comparing the transcriptional profiles and cellular morphologies of human neocortical cells derived from induced pluripotent stem cells (iPSCs). Given the importance to rely on a solid and highly reproducible iPSCs-based differentiation protocol that generates authentic neocortical neurons in vitro with high efficiency before applying it as a model system of human neurodevelopmental disorders, in the first phase of this study we performed a comprehensive transcriptional, cellular and physiological characterization of the in vitro neurodevelopmental paradigm. The transcriptional dynamics regulating in vitro neocortical development have been investigated by performing RNA-sequencing (RNA-seq) at both population and single- cell level in combination with several bioinformatics analyses including principal component analysis (PCA), differential gene expression analysis and weighted gene co-expression network analysis (WGCNA). The transcriptional results were corroborated by the widespread positivity for a selected panel of informative cell-fate and cell-stage specific markers detected through immunocytochemistry and the physiological maturity of our iPSCs-derived neocortical neurons was further confirmed by their ability to generate action potentials, develop complex firing patterns and sustain excitatory and inhibitory spontaneous synaptic activity. Overall, these results fully validated the reproducibility of the differentiation protocol and its efficiency and reliability in generating physiologically mature authentic neocortical neurons. Subsequently, we applied this extensively characterized neocortical differentiation paradigm to model in vitro two human neurodevelopmental disorders caused by symmetrical copy number variations (CNVs) of the Williams-Beuren syndrome chromosome region (WBSCR) located on the long arm (q) of chromosome 7 at position 11.23 (7q.11.23 locus). 7q11.23 CNVs are of special interest as the two disorders resulting from the deletion (Williams syndrome, WS) and duplication (7q.11.23 duplication syndrome, 7q11DUP) of this region exhibit cognitive and behavioral phenotypes marked by both similar features and symmetrically opposite traits. The association of 7q11DUP to complex neurodevelopmental disorders such as autism spectrum disorder and schizophrenia, while WS is a well-characterized syndrome without clear overlap to complex neurodevelopmental disorders make the study of this locus extremely interesting to identify the molecular mechanisms unique to each clinical condition, common to both syndromes and shared with other complex neurodevelopmental disorders. To this aim, we generated several iPSCs lines from a large cohort comprising WS individuals, 7q11DUP patients and healthy subjects and differentiated them into neocortical neurons by applying the previously in-depth characterized protocol. Having assessed the quality of our iPSCs-derived neocortical neurons, we are currently identifying neuronal subtypes specific genes and gene networks having the most statistically significant relationship to these disorders through single cell RNA-sequencing analysis. Furthermore, morphometric analysis of WS and control iPSCs-derived neocortical neurons has confirmed in humans many neuronal morphological abnormalities observed in a mouse knockout for Dnajc30, a previously uncharacterized gene contained in the 7q11.23 locus

Genetic vulnerability, environmental exposures and neurodevelopmental disorders : clinical insights and in-vitro consequences

An understanding of how different genetic backgrounds and environmental exposures interact and contribute to diverse medical conditions like neurodevelopmental disorders (NDDs), is key to better health outcomes. A considerable overlap exists in the underlying genetics and physiology, often leading to their co-diagnoses. There is a lack of robust biomarkers for ASD and ADHD. Furthermore, no efficient resource exists to evaluate potential gene-environment interactions during early human neurodevelopment. This thesis addressed these knowledge gaps through five clinical and in-vitro studies. Study I explored the utility of genetic information from exome sequencing in predicting intervention outcomes of a social skills group training (SSGT) clinical trial for ASD. A genetic score was developed for common and rare variants in relevant genetic pathways, followed by generating a predictive machine learning (ML) model for individual responses. Variant carriers demonstrated significantly less improvement after standard care at postintervention. A higher rare variant genetic score for synaptic transmission was linked to less efficacy after SSGT at follow-up, while an opposite effect was observed for regulation of transcription from RNA polymerase II. The ML model emphasised the importance of rare variants in predicting intervention outcomes. Study II deployed urine-based untargeted metabolomics to investigate ASD-related biomarkers in a twin cohort with ultra-high performance liquid chromatography and mass spectrometry (UHPLC-MS). For the first time, any associations with autistic traits were also evaluated. No metabolite was found to be significantly associated with ASD. Based on nominal significance, an elevation in phenylpyruvate and taurine, and a decline in carnitine were detected, amongst others. These were found to be enriched in the arginine and proline metabolism pathway. More nominally significant metabolites were associated with autistic traits, and indole-3-acetate was positively associated with autistic traits within twin pairs. Study III also utilised a twin cohort to detect urinary and faecal metabolites associated with ADHD using nuclear magnetic resonance (NMR) and UHPLC-MS, respectively. Males with ADHD had increased levels of urinary hippurate, a metabolite produced by microbial-host co-metabolism. Hippurate was also negatively associated with intelligence quotient (IQ) levels in males and differentially associated with faecal metabolites from the gut microbiome. ADHD faecal profiles were characterised by higher levels of 1-stearoyl-2-linoleoyl-snglycerol (SLG), flavine adenine dinucleotide (FAD) and 3,7-dimethylurate. Reduced levels of aspartate, xanthine, orotate and other metabolites were also detected. Study IV dissected the impact of six environmental factors (lead, valproic acid, bisphenol A, ethanol, fluoxetine and zinc deficiency) in human induced pluripotent stem cell (iPSC) derived neuronal progenitors after differentiation for 5 days using the fractional factorial experimental design (FFED) coupled with RNA-sequencing. This was followed by a stratified analytical approach. Several gene and pathway level changes, that were both convergent and divergent for the environmental factor exposures, were identified. Pathways related to synaptic function and lipid metabolism were significantly elevated by lead and fluoxetine, respectively. Furthermore, fluoxetine increased the levels of several fatty acids when validated with direct infusion electrospray ionisation mass spectrometry (ESI-MS). Study V evaluated the differential in-vitro effects of four commonly prescribed selectively serotonin reuptake inhibitors (SSRIs: fluoxetine, citalopram, sertraline and paroxetine) in iPSC-derived neuronal progenitors. Total reactive oxygen species (ROS) and adenosine triphosphate (ATP) levels were determined at day 5 and 28 of differentiation. Concurrently, untargeted metabolomics was performed using ESI-MS. Sertraline and paroxetine significantly decreased ROS and ATP levels. Sertraline mediated early metabolite changes at day 5, while both sertraline and paroxetine drove such effects at day 28. Combined effects were driven by LPC 18:0 and LPC 16:0. Overall, metabolites were enriched in phospholipid biosynthesis and amino acid metabolism pathways. In conclusion, this thesis highlighted that genetic information can be used as an indicator for ASD interventions, encouraging further exploration. Urine and faecal metabolites are potential biomarkers for ASD and ADHD, pending validation. A multiplexable resource for studying gene-environment interactions was developed, along with a rich dataset outlining molecular changes in ASD. Lastly, the thesis demonstrated that different SSRIs elicit both shared and unique in-vitro responses, with a need to evaluate probable in-utero effects. The findings can guide future clinical studies to generate greater insights into ASD, ADHD and other conditions with aberrant neurodevelopmental trajectories

Complexity, Emergent Systems and Complex Biological Systems:\ud Complex Systems Theory and Biodynamics. [Edited book by I.C. Baianu, with listed contributors (2011)]

An overview is presented of System dynamics, the study of the behaviour of complex systems, Dynamical system in mathematics Dynamic programming in computer science and control theory, Complex systems biology, Neurodynamics and Psychodynamics.\u

Surface variability of climate-relevant trace gases (N2O, CO2, CO) in the tropical eastern South Pacific Ocean

Given the climatic relevance of marine-derived trace gases, the investigation of their distribution and emissions from key oceanic regions is a crucial need in our efforts to better understand potential responses of the ocean and the overlying atmosphere to environmental changes such as warming and deoxygenation. Low-oxygen waters connected to coastal upwelling systems and the associated oxygen minimum zones(OMZ) are well-recognized strong sources of several trace gases. Our main goal during the M135-M138 cruises was to assess the distribution of different gases which are relevant for the biogeochemical cycling of carbon and nitrogen in the OMZ off Peru, as well as the spatial and temporal variability of their sea-air fluxes

Role of perinatal inflammation in preterm brain injury

Perinatal inflammation is associated with an increased risk of brain injury and neurodevelopmental impairment in preterm infants but the immune mediators driving this association are not well understood. This PhD thesis seeks to further characterise the inflammatory response associated with preterm birth, describe the relationship between perinatal inflammation and white matter development and explore the effect of specific inflammation-associated proteins on the development of human cortical neurons derived from induced pluripotent stem cells (iPSCs). In the first study, I investigated the inflammatory profile at birth in 55 very preterm infants, compared to 59 term-born controls and then used this profile to predict exposure to intrauterine inflammation in the preterm group. Preterm infants had a distinct pro-inflammatory profile in umbilical cord blood at delivery when compared to term-born controls and IL-8 was found to be the strongest predictor of intrauterine inflammation. In the second study, I investigated the association between specific inflammation-associated proteins and white matter microstructure in 71 very preterm infants using structural MRI and diffusion-weighted imaging of the brain. Elevated IL-8 in the first week of life was associated with white matter dysmaturation at term-equivalent age. Following this discovery, I investigated the effect of IL-8 on the maturation and morphology of iPSC-derived cortical neurons and found that exposure was associated with impaired neurite outgrowth. This thesis provides further evidence to support the role of inflammation in the aetiology of preterm brain injury and suggests that IL-8 dysregulation may link systemic inflammation with atypical cortical development and white matter disease in preterm infants