Les cellules T régulatrices (Treg) jouent un rôle important dans différentes infections chroniques comme le VIH. Lors de l’infection chronique par le VIH, une augmentation du nombre de ces cellules limite la réponse des cellules T effectrices spécifiques du virus mais permet également le contrôle de la très forte activation du système immunitaire. La régulation de l’activité suppressive des Treg constitue une voie importante pour le développement d’un vaccin, l’efficacité de la surveillance tumorale et l’auto-immunité. Dans ce travail, nous avons étudié différents mécanismes de régulation des Treg chez les patients infectés par le VIH et sujets sains. Le but de mon travail a été d’étudier les mécanismes impliqués dans les fonctions suppressives des Treg et de leur régulation. Nous nous sommes particulièrement intéressés au rôle de Notch sur la sensibilité des cellules T effectrices à la fonction suppressive des Treg, en montrant que l’activation de Notch rendait les cellules T effectrices plus sensibles à l’action suppressive des Treg, et ceci même en présence d’un très faible nombre de Treg. Nous avons démontré que certains ligands de Notch, tels que DL-4 et Jagged-1 mais non DL-1, régulent l’effet inhibiteur des Treg sur les cellules T effectrices par une surexpression de TGFβ-RII et à la phosphorylation de Smad3. Le rôle important de l’enzyme CD39 dans la fonction suppressive des Treg a été décrit, mais peu d’études ont démontré son rôle dans l’infection par le VIH. Nous avons montré que les Treg de patients infectés par le VIH experiment plus fortement le CD39, et que leur effet suppresseur était inhibé en utilisant un anticorps monoclonal anti-CD39 et maintenu en utilisant un agoniste de l’adénosine. Nous avons également montré que le polymorphisme du gène CD39, associé à une plus faible expression de CD39, était corrélé à une plus lente progression de la maladie. Nos résultats montrent non seulement les mécanismes impliqués dans l’activité suppressive des Treg lors de l’infection par le VIH, mais constituent une approche intéressante pour en modifier les fonctions. Enfin, nous avons recherché l’effet de l’IL-7 sur le phénotype des Treg et l’expression de molécules impliquées dans leur fonction suppressive. Nos résultats montrent deux effets synergique de l’IL-7 sur les Treg mémoires: diminution de l’expression de CD39 à leur surface induisant une diminution de leur fonction suppressive, et surexpression du récepteur à l’ATP induisant un phénotype Th17. L’administration d’IL-7 in vivo chez des patients infectés par le VIH a confirmé la modification de phénotype des Treg en Th17 et notamment une surexpression du facteur de transcription spécifique des Th17, RORγt. En conclusion, notre travail apporte de nouvelles connaissances sur les mécanismes impliqués dans les fonctions inhibitrices des Treg et comment moduler ces fonctions. Ceci pourrait avoir un impact clinique direct, soit dans le traitement de maladies associées à un dysfonctionnement des Treg (infections chroniques virales, sclérose multiple, diabète de type 1, arthrite rhumatoide et lupus érythémateux), soit dans les stratégies vaccinales. / T regulatory cells (Treg cells) play an important role during various chronic infections like HIV. Increase in Treg cell number during chronic phase limit the HIV specific T effector cell response but may control exaggerated activation of the immune system. Modulation of regulatory T cell (Treg cells) suppression has important implications for vaccine development, the effectiveness of tumor surveillance, and the emergence of autoimmunity. Here we studied various mechanisms of Treg cells modulation in HIV+ patients and healthy subjects. The aim of my work was to decipher some aspects of the mechanisms involved in Treg cell mediated suppressive effects and the modulation of Treg cell suppressive effects in healthy subjects and HIV- infected patients.We have extended knowledge on the role of Notch in Treg/Effectors T cells cross talk. Here we focused our interest on the role of Notch pathway on the sensitivity of effectors T cells to Treg cell-mediated suppression, showing that Notch activation may significantly increase the sensitivity of effector cells to Treg cells even at a low ratio. We demonstrated that Notch ligands DL-4 and Jagged-1, but not DL-1 modulate significantly the suppressive effect of Treg cells on effectors T cells through an up regulation of TGF-RII expression and the phosphorylated form of Smad3 protein.A critical role of CD39 has been described for Treg cells in general but only a few studies have analyzed its role in HIV infection. We showed an increase in CD39 expression on Treg cells in a cohort of HIV- infected patients. Treg cells inhibitory effects were relieved by CD39 down modulation using an antiCD39 monoclonal antibody and this suppressive effect was reproduced on effector CD8+ T cells by an adenosine agonist. We found that CD39 gene polymorphism associated with a lower CD39 expression correlated with slower progression to AIDS. Our results shows not only the mechanism by which Treg cell suppression occurs during HIV infection but also provide an attractive approach to modify Treg cell functions.Finally, we have investigated the role of IL-7 on the phenotype of Treg cells and expression of molecules involved in the suppressive functions of these cells. Our results show that IL-7 exerts two synergistic effects on memory Treg cells. It decreases their suppressive effect by decreasing CD39 expression and increases ATP receptor leading to a switch towards a Th17 phenotype. In vivo administration of IL-7 tipped the balance towards a higher expression of RORγT in PBMCs from HIV infected patients.In conclusion our study bring new findings in the mechanisms involved in Treg cell mediated suppression and the way to modulate these cells which could have direct clinical impact either in the treatment of diseases associated with Treg cell dysregulation (chronic viral infections, autoimmune disorders like multiple sclerosis, type 1 diabetes, rheumatoid arthritis, and systemic lupus erthematosus) or during vaccination.

Tissue-resident memory T cells (TRM) are a non-circulating subset of memory that are maintained at sites of pathogen entry and mediate optimal protection against reinfection. Lung TRM can be generated in response to respiratory infection or vaccination, however, the molecular pathways involved in CD4+TRM establishment have not been defined. Here, we performed transcriptional profiling of influenza-specific lung CD4+TRM following influenza infection to identify pathways implicated in CD4+TRM generation and homeostasis. Lung CD4+TRM displayed a unique transcriptional profile distinct from spleen memory, including up-regulation of a gene network induced by the transcription factor IRF4, a known regulator of effector T cell differentiation. In addition, the gene expression profile of lung CD4+TRM was enriched in gene sets previously described in tissue-resident regulatory T cells. Up-regulation of immunomodulatory molecules such as CTLA-4, PD-1, and ICOS, suggested a potential regulatory role for CD4+TRM in tissues. Using loss-of-function genetic experiments in mice, we demonstrate that IRF4 is required for the generation of lung-localized pathogen-specific effector CD4+T cells during acute influenza infection. Influenza-specific IRF4−/− T cells failed to fully express CD44, and maintained high levels of CD62L compared to wild type, suggesting a defect in complete differentiation into lung-tropic effector T cells. This finding identifies IRF4 as an important regulator of CD4+TRM generation in response to respiratory infection. Furthermore, comparing whole transcriptome profiling of mouse and human lung memory T cell subsets, we define a lung CD4+TRM gene signature common to mice and humans. IRF4 protein was specifically up-regulated in lung CD4+TRM but not in circulating memory subsets, in both humans and mice previously infected with influenza. This result suggest that high expression of IRF4 contributes to a cross-species conserved molecular pathway of long term maintenance of CD4+TRM in the lung. Overall, our findings confirm lung CD4+TRM as a unique memory T cell subset regulated by tissue-specific transcription factors. These results have important implications in focusing future studies of tissue resident memory T cells to factors with translational potential. Importantly, by determining the lung CD4+TRM gene signature common to mice and humans, we motivate future genetic studies that could lead to the complete identification of the mechanisms of TRM maintenance in humans.

Ceramide sind biologisch aktive Sphingolipide, die verschiedene zelluläre Signalwege regulieren, meist im Zusammenhang mit der Induktion von Apoptose oder der Regulation des Zellzyklus. Darüber hinaus wurde in der Literatur beschrieben, dass Ceramide die Zytoskelettdynamik unterschiedlicher Zelltypen beeinflussen, die Bedeutung von Ceramiden für die Funktion von T-Zellen wurde allerdings bisher wenig untersucht. In der vorliegenden Arbeit konnte gezeigt werden, dass die exogene Akkumulation von Ceramiden ebenso wie die Generierung von Ceramiden durch bSMase die Adhärenz von T-Zellen an FN bzw. ICAM-1 beeinträchtigt. Des Weiteren konnte eine verminderte T-Zell-Polarisierung auf FN sowie eine reduzierte Chemotaxis und Motilität ceramidmodifizierter T-Zellen in Antwort auf SDF-1 nachgewiesen werden. In Übereinstimmung mit der Unfähigkeit ceramidmodifizierter Zellen morphologisch zu polarisieren wird ferner die Relokalisation von Oberflächenmolekülen und intrazellulärer Proteine durch die Akkumulation von Ceramiden gestört. Überdies konnte in dieser Arbeit gezeigt werden, dass Ceramide mit dem Aktivierungsstatus von Akt und ERM-Proteinen interferieren, da eine verminderte stimulationsabhängige Phosphorylierung von Akt und ERM-Proteinen in ceramidmodifizierten Zellen nachgewiesen wurde. Ein wesentlicher Schritt im Verlauf der T-Zell-Aktivierung ist die Ausbildung einer immunologischen Synapse mit dendritischen Zellen. In dieser Arbeit konnte gezeigt werden, dass, obwohl ceramidreiche Membrandomänen von der Kontaktstelle ausgeschlossen werden, Konjugatfrequenz und Architektur der IS durch die Induktion von Ceramiden nicht beeinflusst werden, da eine normale Verteilung von CD3 und des MTOC beobachtet wurde. Allerdings wird die Funktionalität der Konjugate durch die Induktion von Ceramiden beeinträchtigt. Ceramidmodifizierte Zellen waren nur eingeschränkt in der Lage Orai1 und Stim1 zur Kontaktfläche mit DCs zu translozieren. In Übereinstimmung mit diesen Befunden wurde auch ein verminderter Calcium-Einstrom sowie eine verminderte Proliferation infolge der Akkumulation von Ceramiden detektiert. Zusammenfassend konnte in dieser Arbeit gezeigt werden, dass Ceramide wesentliche Prozesse im Verlauf der T-Zell-Aktivierung beeinflussen, so dass die pathogeninduzierte Generierung von Ceramiden einen möglichen Mechanismus darstellt, die Funktion von T-Zellen zu beeinträchtigen. / Ceramides are sphingolipids regulating various signalling pathways mainly associated with the induction of apoptosis and cell cycle arrest. Besides their established role in these processes several lines of evidence suggest that ceramides also regulate cytoskeletal dynamics in non-hematopoietic cells, but their role in T lymphocyte function has not yet been addressed. In this study we show that accumulation of membrane ceramides affects several processes required for accurate T cell function. Treatment of T cells with bSMase or exogenously added ceramides interfered with T cell adhesion to FN and ICAM-1 as well as T cell polarisation, chemotaxis and motility in response to SDF-1. In line with the impairment to morphologically polarise, relocation of surface receptors as well as intracellular signalling molecules was also impaired upon ceramide treatment of T cells. Moreover, increase in cellular ceramide levels interfered with cellular signalling pathways as revealed by reduced phosphorylation levels of Akt and ERM proteins. T cell activation requires the formation of an IS with DCs. In this study we could show, that ceramides, although excluded from the DC/T cell interface, do not interfere with conjugate frequency or synapse organisation, since a normal distribution of CD3 and the MTOC was observed. Nevertheless, ceramide generation interfered with the translocation of Orai1 and Stim1 to the interface and in line with this observation a reduced calcium-influx in T cells was detected upon bSMase exposure. In addition to the decrease in cytosolic calcium levels ceramides also reduced the ability of T cells to proliferate in response to CD3/CD28 stimulation. Therefore the induction of ceramides by certain pathogens, including MV, might be a possible mechanism to interfere with essential processes required for T cell activation.

A persistência de células T de memória funcionais é importante para garantir uma imunidade protetora na infecção pelo Vírus da Imunodeficiência Humana (HIV). As células T de memória têm sido subdivididas em memória central (TCM), memória efetora (TEM) e memória efetora altamente diferenciada (TEMRA) com base na expressão de moléculas de superfície como CCR7 e CD45RA, e na capacidade de produzir citocinas e proliferar. Recentemente, identificamos 18 peptídeos derivados de seqüências do consenso B do HIV-1, ligadores de múltiplas moléculas HLA-DR e amplamente reconhecidos por linfócitos T de sangue periférico de pacientes infectados pelo HIV. Diante disso e considerando a importância das células T de memória na manutenção da resposta imune específica, nosso objetivo foi caracterizar fenotípica e funcionalmente as subpopulações de células T de memória de indivíduos infectados pelo HIV envolvidas no reconhecimento in vitro desses epitopos. Foram incluídos 14 indivíduos controles sadios e 61 pacientes HIV+ com contagem de linfócitos T CD4+ maior que 250 células/mm3. Os pacientes HIV+ foram divididos em seis diferentes grupos clínicos de acordo com o estágio da infecção, carga viral (CV) plasmática e uso de terapia anti-retroviral (ART): não progressores por longo tempo (LTNP), avirêmicos em uso de ART (AV-ART), virêmicos em uso de ART (VI-ART), virêmicos sem uso de ART (VI sem ART), virêmicos recéminfectados sem uso de ART (VI-RI) e controladores. Células mononucleares do sangue periférico dos indivíduos do estudo foram estimuladas com o conjunto de peptídeos do HIV-1 e com um conjunto de peptídeos do Citomegalovírus (CMV). A freqüência de células de memória produtoras de IFN- e IL-2 e a proliferação celular antígeno-específica foram detectadas por citometria de fluxo de multiparâmetros. Nossos resultados mostraram que o conjunto de peptídeos do HIV-1 foi capaz de ativar subpopulações funcionais de memória TCM, TEM e TEMRA secretoras de IFN- e IL-2 em 100% dos pacientes HIV+ dos diferentes grupos clínicos. O conjunto de peptídeos do HIV-1 também induziu proliferação das subpopulações de linfócitos T de memória. As freqüências de TEMRA CD4+IFN-+, TEMRA CD4+IFN-+ total, TCM CD8+IFN-+, TCM CD8+IFN-+ total, TEM CD8+IFN-+, TEM CD8+IFN-+ total e TEMRA CD8+IFN-+ correlacionaram-se negativamente com a carga viral do HIV em pacientes virêmicos. Esses dados sugerem que essas subpopulações de memória funcionais são importantes no controle da viremia. Comparando as respostas HIV e CMVespecíficas observamos freqüências mais elevadas de células T de memória produtoras de IL-2, IFN-/IL-2 e IFN- em respostas ao pool de peptídeos do HIV. Esses dados sugerem que esse conjunto de peptídeos derivados de seqüências do HIV-1 ativa respostas polifuncionais de subpopulações de linfócitos T de memória. Nossos resultados mostraram que o conjunto de peptídeos do HIV-1 foi capaz de estimular diferentes subpopulações distintas de linfócitos T de memória produtores de IFN-, IFN-,/IL-2 e IL-2 de indivíduos em diferentes estágios da infecção pelo HIV e sugerem o envolvimento de subpopulações de memória funcionais no controle da viremia. Estes achados fortalecem a possibilidade de uso desses peptídeos em uma formulação vacinal bem-sucedida em humanos / The persistence of functional memory T cell is important to ensure a protective immunity to Human Immunodeficiency Virus (HIV) infection. Memory T cells have been subdivided into central memory (TCM), effector memory (TEM) and highly differentiated effector memory (TEMRA) based on the expression of surface molecules such as CCR7 and CD45RA, and the ability to produce cytokines and proliferate. Recently, we identified 18 peptides derived from B consensus sequences of HIV-1 that bind to multiple HLA-DR molecules and are widely recognized by peripheral blood T lymphocytes from HIV-infected patients. Given this and considering the importance of memory T cells in the maintenance of specific immune response, our objective was to characterize phenotypic and functionally memory T cell subsets from HIV-infected individuals involved in the recognition of these epitopes in vitro. The study included 14 healthy control subjects and 61 HIV+ patients with CD4+ lymphocytes counts higher than 250 cells/mm3. The HIV+ patients were divided into six different clinical groups according to the stage of infection, plasma viral load (VL) and antiretroviral therapy use (ART): long-term non-progressors (LTNP), aviremic under ART (AV-ART), viremic under ART (VI-ART), viremic without using ART (VI without ART), recently infected viremic without using ART (VI-RI) and controllers. Peripheral blood mononuclear cells from study subjects were stimulated with HIV-1 peptide pool and with a cytomegalovirus (CMV) peptide pool. The frequencies of IFN- and IL-2 producing memory cells and antigenspecific cell proliferation were detected by multiparametric flow cytometry. Our results showed that the HIV-1 set of peptides was able to activate TCM, TEM and TEMRA functional memory subsets that secrete IFN- and IL-2 in 100% of the HIV patients from the different clinical groups. The HIV-1 set of peptides also induced memory T lymphocyte subsets proliferation. TEMRA CD4+IFN-+, total TEMRA CD4+IFN-+, TCM CD8+IFN-+, total TCM CD8+IFN-+, total TEM CD8+IFN-+, TEM CD8+IFN-+ and TEMRA CD8+IFN- + frequencies negatively correlated with HIV viral load in viremic patients. These data suggest that these functional memory subsets are important to control the viremia. When comparing the HIV and CMV-specific responses we observed higher frequencies of IL-2, IFN-/IL-2 and IFN- producing memory T cells in response to HIV peptide pool. These data suggest that this set of HIV sequence derived peptides activates polyfunctional response of memory T lymphocyte subsets. Our results showed that the HIV-1 peptide set was able to stimulate different IFN-, IFN-/IL-2 e IL-2 producing memory T lymphocytes from individuals in different stages of HIV infection and suggest the involvement of functional memory subsets in the control of viremia. These findings strengthen the possibility of using these peptides in a successful vaccine formulation in humans

University of Macau / Institute of Chinese Medical Sciences

Near-Earth Asteroids (NEAs) can provide useful resources in terms of feedstock for spacecraft propellant, crew logistic support and a range of useful metals. The possibility of capturing small NEAs using low energy transfers would therefore be of significant scientific and commercial interest. Although NEAs may make close approaches to the Earth, and so represent a potential impact threat, the exploitation of their resources has long been proposed as a necessary element for future space exploration. The objective of the research presented in this thesis is to develop methodologies for the trajectory design of capturing NEAs in the neighbourhood of the Earth. Firstly aimed at capturing NEAs around the Earth-Moon L2 point, a new type of lunar asteroid capture is defined, termed direct capture. In this capture strategy, the transfer trajectory for capturing an NEA into the Earth-Moon system is modelled in the Sun-Earth-Moon restricted four-body. A Lambert arc in the Sun-asteroid two-body problem is used as an initial guess and a differential corrector used to generate the transfer trajectory from the asteroid’s initial obit to the stable manifold associated with Earth-Moon L2 point. The direct asteroid capture strategy requires a shorter flight time compared to an indirect asteroid capture strategy, which couples capture in the Sun-Earth circular restricted three-body problem and subsequent transfer to the Earth-Moon circular restricted three-body problem. Finally, the direct and indirect asteroid capture strategies are also applied to consider capture of asteroids at the triangular libration points in the Earth-Moon system. As ideal locations for space science missions and candidate gateways for future crewed interplanetary missions, the Sun-Earth libration points L1 and L2 are also preferred locations for the captured asteroids. Therefore, the concept of coupling together a flyby of the Earth and then capturing small NEAs onto Sun–Earth L1 or L2 periodic orbits is proposed. A periapsis map is then employed to determine the required perigee of the Earth flyby. Moreover, depending on the perigee distance of the flyby, Earth flybys with and without aerobraking are investigated to design a transfer trajectory capturing a small NEA from its initial orbit to the stable manifolds associated with Sun-Earth L1 and L2 periodic orbits. NEA capture strategies using an Earth flyby with and without aerobraking both have the potential to be of lower cost in terms of energy requirements than a direct NEA capture strategy without the Earth flyby. Moreover, NEA capture with an Earth flyby also has the potential for a shorter flight time compared to the NEA capture strategy without the Earth flyby. Following by this work, a more general analysis of aerobraking is undertaken and the low energy capture of near-Earth asteroids into bound orbits around the Earth using aerobraking is then investigated. Two asteroid capture strategies utilizing aerobraking are defined, termed single-impulse capture and bi-impulse capture, corresponding to two approaches to raising the perigee height of the captured asteroid’s orbit after the aerobraking manoeuvre. A Lambert arc in the Sun-asteroid two-body problem is again used as an initial estimate for the transfer trajectory to the Earth and then a global optimization is undertaken, using the total transfer energy cost and the retrieved asteroid mass ratio (due to ablation) as objective functions. It is shown that aerobraking can in principle enable candidate asteroids to be captured around the Earth with, in some cases, extremely low energy requirements. The momentum exchange theory is also applied to the capture of small near-Earth asteroids into bound periodic orbits at the Sun-Earth L1 and L2 points. A small asteroid is first manoeuvred to engineer a flyby with a larger asteroid. Two strategies are then considered: when the small asteroid approaches the vicinity of the large asteroid, it will either impact the large asteroid or connect to it with a tether. In both strategies, momentum exchange can be used to effect the capture of one of the asteroids. Then, a two-impulse Lambert arc is utilized to design a post-encounter transfer trajectory to the stable manifolds of the Sun-Earth L1 or L2 points. By investigating the outcome of the impact on the small asteroid, or the tension of the tether, the maximum velocity increment available using these momentum exchange strategies is investigated. Again the capture strategies using momentum exchange in principle have the potential to deliver low-energy capture of asteroids. The methods presented in this thesis are intended to be used as a preliminary analysis for these asteroid capture strategies. Although some significant practical challenges remain, the transfer in the CRTBP models can serve as a good approximation for the trajectory in a more accurate dynamical model.

Adoptive cell transfer (ACT) has garnered significant interest in recent years within the medical field due to its potential in providing an effective form of personalized medicine for patients suffering from a wide range of chronic illnesses, including but not limited to cancer. By leveraging the patient’s own cells as the therapeutic agent, concerns over patient compatibility and adverse reactions are significantly reduced. Central to this therapy is the ability to optimize cell quantity and cell activation in order to produce a more robust infusion to the patient. This thesis focuses on two main aspects. The first is the materials synthesis and development of a novel platform for the ex vivo expansion of human T cells for ACT, while the second aims to elucidate the underlying structural mechanics of this platform. This platform, which consists of an electrospun mesh of micron and sub-micron diameter poly (dimethyl siloxane)-based fibers, aims to maintain the high surface-area to volume ratio characteristic of the current clinical gold standard. This also simultaneously allows for effective leveraging of T cell mechanosensing, a phenomenon previously discovered by our lab that is the ability of a human T cell to respond differently to surface mechanical cues. By modulating the concentration of poly (ε-caprolactone) in these fibers, a biocompatible polymer, the mesh mechanical rigidity was varied: this effectively allowed for the leverage of T cell mechanosensing by maintaining a low and tunable Young’s modulus throughout. Additionally, safety concerns involving transfusion of the expansion platform into the patient were addressed by having a single continuous substrate instead of an array of disjoint ferromagnetic beads. Our results thus far indicate that this soft mesh platform can produce upwards of 5.6-12.5 times more T cells in healthy patients than the clinical gold standard while maintaining comparable levels of cellular activation and phenotypic distributions as measured through IFNγ secretion and expression of surface proteins CD107b, CD45RO, and CCR7, respectively. Additionally, this platform demonstrates the ability to produce improved expansion of exhausted (PD-1high) T cells from CLL patients compared to the clinical gold standard across all analyzed Rai stages. Finally, experiments have shown our platform to be scalable to produce clinically relevant levels of cells (> 50 million) from a given starting population, thus indicating its potential in adaptation in larger scale in vitro systems. The currently demonstrated capabilities of our mesh platform thus hold significant promise in the clinical development and adoption of ACT, as well as the development of larger scale in vitro systems. In order to elucidate the underlying structural mechanics of our platform, quantitative AFM studies have indicated a force-dependency in rigidity measurement, thus indicating that standard Hertzian contact models and their derivatives (DMT, Sneddon, etc.), may not be ideal in calculating the rigidity of this material. In order to better model the effective Young’s modulus (E_eff) of the mesh and account for cantilever beam-bending type mechanical deformation, a modification of Euler-Bernoulli theory was established. This mathematical model was subsequently used to correlate fiber geometry parameters to bending stiffness, thus allowing for us to estimate E_eff for a range of meshes. Subsequent T cell expansions and comparison of data to previous expansions on planar surfaces provided verification of our model.

No description available.

Change is an inescapable aspect of natural and artificial systems, and adaptation is central to their resilience. Optimization problems are no exception to this maxim. Indeed, viability of businesses depends heavily on their effectiveness in responding to a change in the myriad of optimization problems they entail. Changes in optimization problems usually are result of change in the objective function and/or number of variables and/or constraints. Such optimization problems are denoted as dynamic optimization problems (DOPs) in the literature. Despite the large body of literature on DOPs and algorithms in this domain, there are still noticeable gaps between real-world DOPs and academic research. The first objective of this thesis is investigating DOPs to identify any class of DOPs or any DOPs' characteristics that are common in practical situation but have not been studied by the researchers. In this thesis, two important gaps are identified, namely considering switching cost in DOPs and large-scale DOPs. Both are common in many real-world dynamic problem but a few research investigated them in the past. In an attempt to bridge these gaps, this thesis makes the following contributions: First, this thesis considers the impact of cost for changing solutions after environmental changes. In fact, changing solutions in real-world problems is costly. Furthermore, larger changes have higher cost and need more resources such as time, human resources and energy. Thus, lack of switching cost consideration in most previous algorithms makes them unsuitable for many of real-world DOPs. In this thesis, different scenarios of DOPs with switching cost are investigated, their challenges are identified, and the performance of the state-of-the-art methods are investigated for solving them. Contributions include developing a novel robust optimization over time (ROOT) framework, a novel adaptive method for maximizing efficiency by changing or keeping solutions after environmental changes, and a novel multi-objective and time-linkage based method for minimizing switching cost. Second, this thesis investigates large-scale DOPs. Up to now, little attention has been given to the scalability of DOPs. Indeed, the dimension of typical DOPs studied in the literature hardly exceeds twenty. In this thesis, the challenges of large-scale DOPs are studied, then the efficiency of the current methods are investigated for solving them. Moreover, this thesis proposes a novel cooperative coevolution algorithm based on a multi-population approach which benefits from a new resource allocation method for DOPs with high-dimensional search space. All the proposed methods in this thesis use particle swarm optimization as the core optimizer embedded in a multi-population framework. The performance of the proposed methods are compared with state-of-the-art methods on a wide range of problem instances generated by the state-of-the-art and the proposed DOP benchmarks. The comparison results indicate the superiority of the proposed methods.

The thymus is the primary lymphoid organ responsible for the development and maturation of T lymphocytes (aka T-cells) in vertebrates. The complex architecture of the thymic microenvironment orchestrates the formation of a diverse and self-tolerant T-cell repertoire capable of supporting the development and maintenance of a functional immune system. The main component of this microenvironment, the thymic epithelium, is crucially required to direct thymus organogenesis and homeostasis, and to mediate T-cell repertoire development and selection. The thymic epithelial progenitor cells (TEPCs) from which the mature thymus develops originate from the endoderm of the 3rd pharyngeal pouch by embryonic day 9 in mouse development (or early week 6 in human embryos). Expression of the transcription factor FOXN1 is required to drive TEPCs differentiation in each thymic epithelial lineage (TEC), while the absence of functional FOXN1 causes athymia. Moreover, forced expression of Foxn1 in mouse embryonic fibroblasts (MEFs) converts these MEFs into TECs that can support the development of a normal thymic system. Despite the great therapeutic potential that TEPCs present in regenerative medicine, there is currently no detailed model describing regulation of the TEPC state and its differentiation into cortical (c) and medullary (m) TECs, or explaining the dominant role of FOXN1 in the thymic epithelial system. Comparative transcriptomics analysis in conjunction with pathway enrichment analysis of the developing TEPCs could reveal the signalling pathways that regulate the early TEPC state and progression into differentiation. Additionally, integrative bioinformatics analysis of transcriptomics and genomics datasets could identify the functional networks that are directly regulated by FOXN1 during early TEC progression. In this thesis I provide, for the first time, an in silico model explaining fetal TEPC differentiation into the functionally distinct TEC lineages, in the cellular, molecular and signalling contexts of thymus early development. Furthermore, I present evidence which suggests that FOXN1 could be a pioneer factor, capable of fully establishing the transcriptional programme that underpins thymic epithelial cell identity and function. Finally, in this thesis, I introduce the development of an interactive thymic-specific database that provides a platform for easy access, analysis and integration of curated bioinformatics datasets.