Cancer is one of the most pervasive health problems in the world today. Despite major advances in its treatment in recent decades, conventional therapies have seen limited success. Aggressive, drug-resistant cancer cells can reemerge after treatment, resulting in relapse. Immunotherapy, a strategy that utilizes a patient's own immune system to specifically destroy cancer cells, is a potential solution to this problem. Immunotherapy, however, is limited by multiple mechanisms of cancer-induced immunosuppression. One of the most important of these mechanisms is the induction of Treg, which are capable of suppressing multiple arms of the anti-cancer immune response. In the current study, we evaluated strategies to hinder the deleterious function of Treg on cancer immunotherapy. First, we determined that imatinib mesylate could inhibit Treg function in vivo and in vitro and increase the efficacy of dendritic cell-based immunization against an imatinib-resistant lymphoma. Then, searching for further methods to inhibit Treg, we found that Th-1 cells were capable of inhibiting Treg function and synergizing with a tumor lysate vaccine to treat leukemia. This process was dependent on IFN-γ secretion by the Th-1 cells. While investigating the influence of Th-1 on Treg and the resulting immunomodulatory effects of these cells in vivo, we discovered that they were capable of promoting the non-conventional direct tumor killing function of DC. We determined that Th-1 induce the cytotoxic function of bone marrow-derived DC generated with GM-CSF and IL-4 by a mechanism dependent on IFN-γ. Finally, because our results indicate that the antigen presenting function of KDC may depend upon their cytotoxic ability, and since DC generated with IL-15 have been reported to be more efficient APC than those generated with IL-4, we evaluated their ability to also function as direct tumor cell killers. We found that while IL-15 DC can indeed kill tumor cells, only LPS and not IFN-γ was capable of inducing this capability. These findings contribute to both arms of anti-cancer immunity by impairing immunosuppression with imatinib and Th-1, and promoting anti-tumor immunity with KDC. This double-pronged approach may contribute to further strategic advances in the field of cancer immunotherapy.

The transcription factor Interferon Regulatory Factor-1 (IRF-1) has been demonstrated to suppress tumour growth through the regulation of many anti-oncogenic genes. Pro- and anti-apoptotic factors, cell cycle control genes, DNA damage response genes and prometastatic factors are all under the control of IRF-1, which effects both transcriptional activation and repression. In addition to these cell autonomous tumour suppressor activities, IRF-1 is also a key regulator of the immune system and, as such, mediates immune surveillance of tumours. Numerous studies have confirmed that loss or mis-regulation of IRF-1 is a key factor in several different types of cancer. Despite strong evidence for the crucial role of IRF-1 in cancer, and frequent assertions that this protein warrants further investigation as a drug target, very little is known about its regulation. Furthermore, since recent studies have linked upregulation of IRF-1 to the development of autoimmune diseases, it is particularly important that drugs be able to decouple autoimmune and anti-cancer functions of IRF-1 to avoid harmful side effects. This thesis describes how phosphorylation of IRF-1 in its regulatory C-terminal Mf1 domain modulates transactivatory and tumour suppressor activity. Phosphospecific antibodies were developed as tools to study the C-terminal phosphorylation. Using these, it was shown that treatment of cells with Interferon-γ(IFN-γ) not only causes accumulation of IRF-1 protein, but also results in phosphorylation of IRF-1 at two sites in the C-terminal Mf1 domain. Phosphomimetic mutants demonstrated that these phosphorylations enhanced the transactivatory activity of IRF-1 at various promoters, but did not affect repressor activity. Gel shift assays revealed that dual phosphorylation of IRF-1 (IRF-1 D/D) promoted DNAbinding and suggested this was through increased interaction with the cofactor/histone acetylase p300 which induces a conformational change in IRF-1, favouring DNA-binding. Acetylation by p300 appears to be important although it is not yet clear whether this directly or indirectly affects IRF-1 activity. Since the tumour suppressor activity of IRF-1 is of particular interest, the effect of phosphorylation was examined in clonogenic and invasion assays. IRF-1 D/D more efficiently suppressed colony formation in both anchorage dependent and independent assays, and may improve inhibition of invasion in Transwell assays. Thus, cell treatment with the therapeutic agent IFN-γ nduces phosphorylation of IRF-1, resulting in enhanced DNA binding of IRF-1 through improved p300 binding. In cells the outcome is more effective tumour suppression and inhibition of metastasis.

The aim of environmental enrichment is to alter the environment of a captive animal in a way that results in improved mental and physical welfare. The technique has been utilised effectively for many years for captive mammals in a variety of settings. However, until now it has never been considered as a way of improving the welfare of aquatic animals such as fish. Fish that are used in regulatory toxicology studies are at present maintained solely in barren tank environments. Little is known about how these types of environments affect the well-being of the animals residing there and whether they impact either physiological heath or behavioural repertoire. This thesis aims to address this gap in the knowledge regarding the potential for environmental enrichment to improve the welfare of fish used in regulatory toxicology. More specifically it looks at two types of enrichment and the effects of these on the commonly used model species, the zebrafish (Danio rerio). The first type of enrichment studied was glass rod structures of varying heights provided to increase tank complexity and provide refuge. The glass structures did not produce any quantifiable benefits in unstressed fish and appeared to delay the formation of stable social hierarchies. When fish were stressed by a period of chasing, the presence of the glass rods appeared to reduce the magnitude of the cortisol response. Whilst this could be viewed as a potential benefit, it was felt that it would not outweigh the costs of this type of enrichment. The second type of enrichment studied was provision of airstones. Again, no clear evidence was found that fish in tanks with airstones experienced an improvement in welfare. The main observation was the vast increase in mortality in tanks containing these airstones, in particular, those of a smaller size. Regardless of the physiological cause underlying this result, this can only be viewed as a negative consequence and one that appears to rule out airstones as an effective form of enrichment for this species and strain of fish. It was also observed that both stress and the presence of enrichment influenced the absolute deviation from the mean in several endpoints. Since changes in endpoint variation will have effects both on the number of animals required to statistically measure environmentally relevant effects this is a factor that should be considered when researching methods of environmental enrichment. Finally, results from these studies suggest the possibility that laboratory zebrafish do not require the addition of environmental enrichment to tanks in order to promote maximum welfare. Furthermore, as considerable costs would be involved in implementing many types of enrichment (relating to manufacture, cleaning, incompatibility of results with previous studies etc.) it is likely that observed benefits would have to be both substantial and well established in order for changes in regulatory guidelines to take place. For a species such as zebrafish that are extremely easy to breed and maintain in the laboratory with minimal amounts of disease, social problems or mortalities, it may be that current conditions are satisfactory.

Among the tools available to enhance the rationality of policy formulation, Regulatory Impact Analysis (RIA) has captured the attention of many scholars for its potential to enhance the accountability and transparency of regulatory governance. Although almost all EU and OECD member states have adopted RIA, only a sub- set of small-n case comparative studies on institutional, political and administrative impact have been conducted. By filling this gap in the literature and proposing the rigorous operationalisation of concepts such as adoption, extent of implementation, and learning, this thesis ascertains the extent of interdependency among governments in their choices concerning an innovation of regulatory governance. Methodologically, the dissertation draws on a multi-method approach, consisting of qualitative analysis to track the process of institutionalisation, as well as event history analysis, based on a dataset covering thirty-eight countries from 1968 to 2006. The empirical findings show that diffusion is a multifaceted process. In the decision to adopt RIA, the role of the OECD in translating, packaging, and promoting such administrative innovation coexists with previous innovations and other administrative variables. Yet the impact of interdependency is marginal in the successive phases of implementation and evaluation. Earliness of adoption is the major predictor of the extent of implementation. There is little evidence of interaction and communication among adopters on the subject of their learning experience. On balance, this regulatory governance innovation is a domain of symbolic and rhetorical meanings that is not adequately supported by administrative capacity.

The regulatory gene for pyrimidine biosynthesis has been identified and designated pyrR. The pyrR gene product was purified to homogeneity and found to have a monomeric molecular mass of 19 kDa. The pyrR gene is located directly upstream of the pyrBC' genes in the pyrRBC' operon. Insertional mutagenesis of pyrR led to a 50- 70% decrease in the expression of pyrBC', pyrD, pyrE and pyrF while pyrC was unchanged. This suggests that PyrR is a positive activator. The upstream regions of the pyrD, pyrE and pyrF genes contain a common conserved 9 bp sequence to which the purified PyrR protein is proposed to bind. This consensus sequence is absent in pyrC but is present, as an imperfect inverted repeat separated by 11 bp, within the promoter region of pyrR. Gel retardation assays using upstream DNA fragments proved PyrR binds to the DNA of pyrD, pyrE, pyrF as well as pyrR. This suggests that expression of pyrR is autoregulated; moreover, a stable stem-loop structure was determined in the pyrR promoter region such that the SD sequence and the translation start codon for pyrR is sequestered. β-galactosidase activity from transcriptional pyrR::lacZ fusion assays, showed a two-fold in increase when expressed in a pyrR- strain compared to the isogenic pyrR+ strain. Thus, pyrR is negatively regulated while the other pyr genes (except pyrC) are positively activated by PyrR. That no regulation was seen for pyrC is in keeping with the recent discovery of a second functional pyrC that is not regulated in P. aeruginosa. Gel filtration chromatography shows the PyrR protein exists in a dynamic equilibrium, and it is proposed that PyrR functions as a monomer in activating pyrD, pyrE and pyrF and as a dimeric repressor for pyrR by binding to the inverted repeat. A related study discovered that the catabolite repression control (Crc) protein was indirectly involved in pyr gene regulation, and shown to negatively regulate expression of PyrR at the posttranscriptional level.

In spite of many efforts in the past, inference or reverse engineering of regulatory networks from microarray data remains an unsolved problem in the area of systems biology. Such regulatory networks play a critical role in cellular function and organization and are of interest in the study of a variety of disease areas and ecotoxicology to name a few. This dissertation proposes information theoretic methods/algorithms for inferring regulatory networks from microarray data. Most of the algorithms proposed in this dissertation can be implemented both on time series and multifactorial microarray data sets. The work proposed here infers regulatory networks considering the following six factors: (i) computational efficiency to infer genome-scale networks, (ii) incorporation of prior biological knowledge, (iii) choosing the optimal network that minimizes the joint network entropy, (iv) impact of higher order structures (specifically 3-node structures) on network inference (v) effects of the time sensitivity of regulatory interactions and (vi) exploiting the benefits of existing/proposed metrics and algorithms for reverse engineering using the concept of consensus of consensus networks. Specifically, this dissertation presents an approach towards incorporating knock-out data sets. The proposed method for incorporating knock-out data sets is flexible so that it can be easily adapted in existing/new approaches. While most of the information theoretic approaches infer networks based on pair-wise interactions this dissertation discusses inference methods that consider scoring edges from complex structures. A new inference method for building consensus networks based on networks inferred by multiple popular information theoretic approaches is also proposed here. For time-series datasets, new information theoretic metrics were proposed considering the time-lags of regulatory interactions estimated from microarray datasets. Finally, based on the scores predicted for each possible edge in the network, a probabilistic minimum description length based approach was proposed to identify the optimal network (minimizing the joint network entropy). Comparison analysis on in-silico and/or real time data sets have shown that the proposed algorithms achieve better inference accuracy and/or higher computational efficiency as compared with other state-of-the-art schemes such as ARACNE, CLR and Relevance Networks. Most of the methods proposed in this dissertation are generalized and can be easily incorporated into new methods/algorithms for network inference.

High-throughput technologies for measuring gene expression made inferring of the genome-wide Gene Regulatory Networks an active field of research. Reverse-engineering of systems of transcriptional regulations became an important challenge in molecular and computational biology. Because such systems model dependencies between genes, they are important in understanding of cell behavior, and can potentially turn observed expression data into the new biological knowledge and practical applications. In this dissertation we introduce a set of algorithms, which infer networks of transcriptional regulations from variety of expression profiles with superior accuracy compared to the state-of-the-art techniques. The proposed methods make use of ensembles of trees, which became popular in many scientific fields, including genetics and bioinformatics. However, originally they were motivated from the perspective of classification, regression, and feature selection theory. In this study we exploit their relative variable importance measure as an indication of the presence or absence of a regulatory interaction between genes. We further analyze their predictions on a set of the universally recognized benchmark expression data sets, and achieve favorable results in compare with the state-of-the-art algorithms.

The development and function of T helper (Th) cells and regulatory T cells (Tregs) are plastic processes that are regulated by cytokines. In our project we first analyzed the effect of different cytokines on the development of induced (i) Tregs. It has been demonstrated that iTregs arise from CD4+ CD25- T cells upon stimulation with alloantigen in the presence of transforming growth factor β (TGF-β). The development of these Tregs and their proliferation were inhibited by interleukin (IL)-4 and IL-12. The aquired results also demonstrated distinct responses of naturally occuring (n) Tregs and iTregs to the regulatory action of IL-4 and an opposite role of IL-4 in maintenance of nTregs and iTregs phenotype. An important role in the induction of T cell subsets may play also mesenchymal stem cells (MSCs) which can, under specific conditions, produce TGF-β and IL-6. Depending on the current production of TGF-β or IL-6, MSCs can qualitatively regulate the ration between Tregs and Th17 cells. Anti-inflammatory Tregs and pro-inflammatory Th17 cells are induced upon stimulation in the presence of TGF-β and TGF-β and IL-6, respectively. In addition to our previous work we studied the role of IL-12 in the development of Tregs and Th17 cells. It was shown that Treg and also Th17 cell differentiation was...

Regulatory T cells (Treg) are critical to the maintenance of immune tolerance, partly by controlling the unwanted activation of effector T cells (Teff) and thereby enhancing the resolution of autoimmune and allergic inflammation. Recent data suggest that Treg can specialize to better control different types of inflammation by using transcriptional machinery which controls differentiation and function of Teff. This thesis addresses questions related to the efficacious use of Treg, notably their ability to adopt distinct phenotypic profiles under different inflammatory contexts and their need to recognize antigen in the inflamed organ. Two differentially mediated mouse disease models were used in this project, namely Th1/Th17-mediated experimental autoimmune encephalomyelitis (EAE) as a model of multiple sclerosis and Th2-mediated allergic airways inflammation (AAI) as a model of asthma. A new model of rMOG-induced AAI was developed to specifically answer the questions on the importance of cell phenotype versus antigen-reactivity for the effective Treg-mediated suppression. It was demonstrated that Treg from the inflamed CNS in EAE had an upregulated expression of Th1 master regulator T-bet and Th1-associated chemokine receptor CXCR3, whereas Treg derived from the inflamed lung in AAI had an increased expression of Th2 master regulator GATA-3, lacked expression of T-bet and displayed decreased levels of CXCR3. This specialized and activated phenotype was restricted to tissue-derived Treg. The importance of appropriate Treg phenotype for effective suppression was suggested by the observed inability of CNS-derived Treg to inhibit AAI. A different Treg subset, TGF-β-induced Treg (iTreg), was shown to express high levels of T-bet and CXCR3, but not GATA-3 upon induction in vitro. iTreg effectively suppressed both Th1 and Th2 types of inflammation and the antigenreactivity was key to this. This thesis demonstrates that Treg are capable of acquiring a distinct phenotype corresponding with a CD4+ T cell response driving inflammatory disease and identifies antigen-reactivity as key to the efficacious suppression of inflammation. It also highlights substantial phenotypic differences between iTreg and naturally-occurring Treg which could be associated with different modes of suppression.

The Class Action Fairness Act of 2005 (CAFA) was signed into law on February 18, 2005. Prior to CAFA, plaintiffs found it easier for class action lawsuits to be tried in their preferred venue—state courts. Changes introduced by CAFA practically removed the majority of class action jurisdiction from state to federal courts. Since law and regulation might serve as an external corporate governance mechanism, an interesting question is whether CAFA has strengthened or weakened corporate governance. If CAFA improves corporate governance, associated marginal benefits would outweigh marginal costs. The opposite would be true if CAFA weakens corporate governance. This issue was hotly debated in the US Congress. The proponents argued that CAFA would reduce costs for the affected firms, while opponents argued the opposite. The main purpose of this paper is to examine which side of the debate is reflected in market reactions to various events that either enhanced or reduced the chances of the passage of CAFA. We identify the firms that are most likely to be affected by CAFA and find that the overall market reaction for these firms is positive when the likelihood of CAFA passage increases, while the reaction has been negative when the chance of its passage diminishes. We also hypothesize that firms that are more likely to be exposed to product liability litigation would experience a significantly higher (positive or negative) abnormal return than firms that are more likely to be involved in contract liability law suits. The results support this hypothesis. We also examine potential factors that might explain cross-sectional variations in abnormal returns and find that duality of Chairmanship and CEO has negative impact, while the