The mathematical model of Schizosaccharomyces pombe : Batch and repeated batch simulations.

Mathematical models are playing an important part in the current developments in engineering, science and biotechnology. Within this field the most fashionable and representative organisms are the ones who are genetically and physiologically tractable. Since the fission yeast Schizosaccharomyces pombe plays a role model among them and its behaviour has medical, genetic and industrial links (related to cancer research, metabolic pathways and beer production), this makes it a particularly interesting organism for study. This dissertation presents the first physiological model ever developed for the yeast S. pombe. The model allows for the simulation and prediction of batch and repeated batch experiments which are an important engineering tool in terms of optimization of industrial processes improving yield in bioreactors by predicting precise values of harvest fraction (HF) and dilution cycle times (DCT). The model has been developed within the generic modelling framework of CelCyMUS (Cell Cycle Model University of Surrey). As part of the research being carried out CelCyMUS has been up-dated by introducing the new Fortran 95 features and utilities in order to exploit its powerful new features and to keep the generic model in pace with technological software advancements. The model is a one-dimensional age-based population balance for the fission yeast S. pombe. It includes the four typical phases (S, G2, M and G1) with the G2 phase divided into two phases (G2A, G2B) and two checkpoints that govern the movement of cells between G1 and S, and G2B and M phases. The transitions (movement of cells between phases) are determined by a probability function related to the consumption of glucose. The G2B-M transition is also dependent on cell size, but since individual growth of cells is related to the consumption of the carbon source (in this case glucose), cell size is dependent upon the amount of glucose consumed per cell. The model also includes a phase for cells facing starvation before going into a meiotic cycle, with some chance of coming back to the mitotic cycle, and a death phase that accounts for cells dying with no chance of recovering at all. Parameters in the S. pombe model have been gathered from experimental data in batch culture reported in literature. Data generated from this specific model have been compared with data from experiments (Fotuhi, 2002) in batch and repeated batch cultures of S. pombe following the behaviour of population balance, consumption of nutrients, and production of metabolites. The new code was tested by successftilly reproducing data from mm-321 hybridoma cell line, the first specific model of a cell line developed in CelCyMUS. As a new feature a model of mass transfer has been incorporated in the generic framework. This mass transfer module accounts for interactions of metabolites (oxygen and carbon dioxide) in the gas and liquid phase of bioreactors. The new S. pombe model was fitted to the experiments of Creanor (1992) on synchronised cultures where the consumption of oxygen was being measured. Such experiments identify two points (G2B and G1) where the rate of oxygen uptake increased in the cycle, doubling the consumption at the end of every cycle. With the model fitted to experimental results in synchronised cultures of S. pombe the model was then used to simulate desynchronised cultures. S. pombe was successfully tested when reproducing experimental data generated by Fotuhi (2002) in S.pombe for batch and repeated batch bioreactors. The S. pombe model was able to simulate cell number, oxygen and glucose consumption. Carbon dioxide and ATP production were predicted by the model however there was no experimental data to compare with. Now that the S. pombe model has been tested against experimental data it will be applied in a model-based observer strategy for the online control of bioreactors

Dynamic modelling reveals the separable contributions to achieving correct spindle orientation in a noisy system

The mechanisms by which the mammalian mitotic spindle is guided to a predefined orientation through microtubule-cortex interactions have recently received considerable interest, but there has been no dynamic model that describes spindle movements toward the preferred axis in human cells. Here, we develop a dynamic model based on stochastic activity of cues anisotropically positioned around the cortex of the mitotic cell and we show that the mitotic spindle does not reach equilibrium before chromosome segregation. Our model successfully captures the characteristic experimental behavior of noisy spindle rotation dynamics in human epithelial cells, including a weak underlying bias in the direction of rotation, suppression of motion close to the alignment axis, and the effect of the aspect ratio of the interphase cell shape in defining the final alignment axis. We predict that the force exerted per cue has a value that minimizes the deviation of the spindle from the predefined axis. The model has allowed us to systematically explore the parameter space around experimentally relevant configurations, and predict the mechanistic function of a number of established regulators of spindle orientation, highlighting how physical modeling of a noisy system can lead to functional biological understanding. We provide key insights into measurable parameters in live cells that can help distinguish between mechanisms of microtubule and cortical-cue interactions that jointly control the final orientation of the spindle.This work was supported by Cancer Research UKThis is the author accepted manuscript. The final version is available from Elsevier via http://dx.doi.org/10.1016/j.bpj.2015.08.01

An Agent-based model of stem and cancer cell interaction

Advancements in tissue engineering combined with the disease seeking nature of stem cells have provided new grounds for targeted therapy of cancer. However the discrepancies found in existing literature on the role of un-modified stem cells at tumour sites (Klopp et al. 2011), indicates the need for further research. In vitro approaches provide an insight into actual cell behaviour under given conditions. However these methods are limited by factors such as cost, time and technological advancements in available protocols. In silico tools provide means for quantitative analysis of accumulated data in addition to exploring scenarios and queries otherwise impossible to create in the lab. However these tools can lack in accuracy and realistic correlation with actual biological behaviour. The combination of both in vitro and in silico methods results in a powerful tool that compensates for the limitations of both approaches. An agent-based model (ABM) is a bottom-up approach that uses information regarding cell behaviour at the single cell level to generate emergent cell population results. Through the development of an agent-based model, the resulting effects of known and hypothesised rules regarding individual cell characteristics and cell-to-cell interactions will be simulated. Where possible, the model rules will be informed and the final model predictions validated using results and observations obtained from cell culture experiments run simultaneously, allowing for a one-to-one mapping of in vitro and in silico results. Computational modelling coupled with cell culture experiments will provide an insight into the mechanisms behind stem cell and cancer cell interactions, taking us one step closer to using stem cells as a method of cancer treatment

TAPBPR: a new player in the MHC class I presentation pathway.

In order to provide specificity for T cell responses against pathogens and tumours, major histocompatibility complex (MHC) class I molecules present high-affinity peptides at the cell surface to T cells. A key player for peptide loading is the MHC class I-dedicated chaperone tapasin. Recently we discovered a second MHC class I-dedicated chaperone, the tapasin-related protein TAPBPR. Here, we review the major steps in the MHC class I pathway and the TAPBPR data. We discuss the potential function of TAPBPR in the MHC class I pathway and the involvement of this previously uncharacterised protein in human health and disease.C.H was supported by a Wellcome Trust PhD Studentship (Grant 089563) and L.H.B was funded by a Wellcome Trust Career Development Fellowship (Grant 085038).This is the author accepted manuscript. The final published version is available via Wiley at http://onlinelibrary.wiley.com/doi/10.1111/tan.12538/abstract;jsessionid=3D6AF64F5BD8C64E84634A4303842BE2.f04t01

A systems biology approach to DNA damage repair

PhD ThesisThe presence of DNA double-stranded breaks in a mammalian cell typically activates the Non-Homologous End Joining (NHEJ) pathway to repair the damage and signal to downstream systems that govern cellular decisions such as apoptosis or senescence. The signalling system also stimulates effects such as the generation of reactive oxygen species (ROS) which in turn feed back into the damage response. Although the overall process of NHEJ is well documented, and much is known about downstream processes that together constitute the DNA damage response (DDR), we know little of the dynamics and how the system operates as a whole. To further our understanding of this we have constructed computational models which integrate current knowledge of the DNA repair process and key downstream signalling systems. The models are coded in Systems Biology Mark-up Language and BioNetGen Language and are quantified as far as possible with experimental data generated within our own laboratories or otherwise gathered from the literature. They are designed to simulate the observed stochastic dynamics of repair by DNA Protein Kinase (DNA-PK) dependent NHEJ (D-NHEJ) and back-up NHEJ mechanisms (B-NHEJ) following damage induced by gamma irradiation in human fibroblasts and the response this causes in the p53-p21 senescence signalling pathway. We have used the models to investigate a number of issues relevant to the study of ageing cells. Our work suggests that this observed heterogeneity in the repair of DNA damage foci that is influenced by levels of damage cannot be explained solely by inherent stochasticity in the NHEJ system. We find that the presence of multiple repair mechanisms and the modulation of key repair factors by oxidation along with further damage inducing feedback triggered by p53 and changes brought about by cellular processes such as senescence all play a cumulative role in causing the differences between stressed and unstressed cells. Our model highlights the importance of Ku oxidation which leads to increased Ku dissociation rates from DNA damage foci and shifts in favour of the less efficient B-NHEJ system. Furthermore we have utilised the model to investigate the role that various levels of DNA damage and repair have on the maintenance of the important p53 oscillations in a cell. We find that, contrary to the current view, p53 levels are affected by temporal dynamics of DNA damage and have used our model to inform the design of further experimental work to investigate the effect of iii maintained low levels of DNA damage induced by frequent low pulses of γ irradiation on the p53 mediated DDR

Genetic predisposition to mosaic Y chromosome loss in blood.

Mosaic loss of chromosome Y (LOY) in circulating white blood cells is the most common form of clonal mosaicism1-5, yet our knowledge of the causes and consequences of this is limited. Here, using a computational approach, we estimate that 20% of the male population represented in the UK Biobank study (n = 205,011) has detectable LOY. We identify 156 autosomal genetic determinants of LOY, which we replicate in 757,114 men of European and Japanese ancestry. These loci highlight genes that are involved in cell-cycle regulation and cancer susceptibility, as well as somatic drivers of tumour growth and targets of cancer therapy. We demonstrate that genetic susceptibility to LOY is associated with non-haematological effects on health in both men and women, which supports the hypothesis that clonal haematopoiesis is a biomarker of genomic instability in other tissues. Single-cell RNA sequencing identifies dysregulated expression of autosomal genes in leukocytes with LOY and provides insights into why clonal expansion of these cells may occur. Collectively, these data highlight the value of studying clonal mosaicism to uncover fundamental mechanisms that underlie cancer and other ageing-related diseases.This research has been conducted using the UK Biobank Resource under application 9905 and 19808. This work was supported by the Medical Research Council [Unit Programme number MC_UU_12015/2]. Full study-specific and individual acknowledgements can be found in the supplementary information

Kinetochore Structural Plasticity and its Regulation in <i>Saccharomyces cerevisiae</i>

The kinetochore is a multi-protein complex that connects the chromosome with microtubule and pulls the chromosome during chromosome segregation. In yeast, a single kinetochore assembles on a Cse4 nucleosome and attaches to a single microtubule, making it an ideal system for studying the architecture of kinetochore-microtubule interaction, function, and regulation. The inner kinetochore assembles on the centromere and anchors the outer kinetochore that attaches to the dynamic microtubule. The interplay between the kinetochore structure and microtubule dynamics in a living cell has not been studied. I have used a combination of in-house developed quantitative microscopy, genetic techniques and mathematical simulation in the budding yeast, S.cerevisiae, to elucidate a novel structural transition of the kinetochore. During anaphase, the microtubule undergoes rapid depolymerization. Kinetochore tracking of microtubule during this phase is critical for chromosome segregation, but how this tracking is achieved is not well understood. A combination of FRAP and photoconversion on kinetochore proteins have revealed that the kinetochore consists of highly dynamic sub-modules and stable sub-modules. I show that microtubule dynamics significantly affect the dynamic kinetochore sub-modules but not the stable ones. Mathematical modeling of microtubule dynamics and kinetochore attachment has revealed the importance of kinetochore structural transition for microtubule attachment. In addition, I have discovered that kinetochore structural transitions are regulated by known metaphase-anaphase specific pathways. Scm3 is the chaperone responsible for assembling the centromeric nucleosome that contains a specific histone variant Cse4. I helped to identify and characterize a new chaperone for Cse4. I demonstrated that recombinant yCAF-1 can promote the assembly of Cse4 nucleosomes in vitro and at non-centromeric positions, causing problems for chromatin-based processes. In summary, my thesis work has significantly contributed to our understanding of centromere and kinetochore function in budding yeast. I speculate that many of the findings will inform our perspectives on centromere and kinetochore function in higher eukaryotes

Contribution to the evaluation and optimization of passengers' screening at airports

Security threats have emerged in the past decades as a more and more critical issue for Air Transportation which has been one of the main ressource for globalization of economy. Reinforced control measures based on pluridisciplinary research and new technologies have been implemented at airports as a reaction to different terrorist attacks. From the scientific perspective, the efficient screening of passengers at airports remain a challenge and the main objective of this thesis is to open new lines of research in this field by developing advanced approaches using the resources of Computer Science. First this thesis introduces the main concepts and definitions of airport security and gives an overview of the passenger terminal control systems and more specifically the screening inspection positions are identified and described. A logical model of the departure control system for passengers at an airport is proposed. This model is transcribed into a graphical view (Controlled Satisfiability Graph-CSG) which allows to test the screening system with different attack scenarios. Then a probabilistic approach for the evaluation of the control system of passenger flows at departure is developped leading to the introduction of Bayesian Colored Petri nets (BCPN). Finally an optimization approach is adopted to organize the flow of passengers at departure as best as possible given the probabilistic performance of the elements composing the control system. After the establishment of a global evaluation model based on an undifferentiated serial processing of passengers, is analyzed a two-stage control structure which highlights the interest of pre-filtering and organizing the passengers into separate groups. The conclusion of this study points out for the continuation of this theme

Ethnic identity, political identity and ethnic conflict: simulating the effect of congruence between the two identities on ethnic violence and conflict

This thesis outlines and presents an alternative hypothetical process to the emergence of ethnic conflict. Ethnic conflicts, rather than being dependent upon pre-existing 'ancient hatreds', are instead the result of a congruence between ethnic and political identity which grants individuals the ability to use ethnicity to identify and eliminate political threats. This hypothesis is formed by the examination of three case studies of ethnic conflict: Lebanon, Northern Ireland and Croatia. This hypothesis is then formalised and tested using an agent based simulation in which agent interactions are dependent upon ethnic and political identity and the congruence between the two. As predicted there was a strong positive correlation between how accurately ethnic identity reflected political identity and the level of ethnically motivated violence in the simulation, although the relationship was not linear. Furthermore the effect of a shift in congruence was found to be roughly comparable to the effect of initialising agents with a moderate level of pre-existing ethnic antagonism