Finding wide tunnels in protein structures is an important problem in Structural Bioinformatics with applications in various areas such as drug design. Several algorithms have been proposed for finding wide tunnels in a fixed protein conformation. However, to the best of our knowledge, none of the existing work have considered widening the tunnel, i.e., finding a wider tunnel in an alternative conformation of the given structure. In this thesis we initiate this line of research by proposing a tunnel-widening algorithm which aims to make the tunnel wider by a slight local change in the structure of the protein. Given a fixed conformation of a protein with a point located inside it, we first describe an algorithm to identify the widest tunnel from that point to the outside environment of the protein. Then we try to make the tunnel wider by considering various alternative conformations of the protein. We only consider conformations whose energies are not much higher than the energy of the initial conformation. Among these alternative conformations we select the one with the widest tunnel. However, the alternative conformation with the widest tunnel might not be accessible from the initial structure. Thus, in the next step we develop three algorithms for finding a feasible transition pathway from the initial structure to the alternative conformation, i.e., a sequence of intermediate conformations between the initial structure and the alternative conformation such that the energy values of all these intermediate conformations are close to the energy of the initial structure. We evaluate our tunnel-finding and tunnel-widening algorithms on various proteins. Our experiments show that in most cases we can make the tunnel wider in an alternative conformation. However, there are cases in which we find a wider tunnel in an alternative conformation, but the energy value of the alternative conformation is much higher than the energy of the initial structure. We also implemented our three pathway-finding algorithms and tested them on various instances. Our experiments show that although in most cases we can find a feasible transition pathway, there are cases in which the alternative conformation has energy close to the initial structure, but our algorithms cannot find any feasible pathway from the initial structure to the alternative conformation. Furthermore, there is a trade-off between the running time and accuracy of the three pathway-finding algorithms.

Finding wide tunnels in protein structures is an important problem in Structural Bioinformatics with applications in various areas such as drug design. Several algorithms have been proposed for finding wide tunnels in a fixed protein conformation. However, to the best of our knowledge, none of the existing work have considered widening the tunnel, i.e., finding a wider tunnel in an alternative conformation of the given structure. In this thesis we initiate this line of research by proposing a tunnel-widening algorithm which aims to make the tunnel wider by a slight local change in the structure of the protein. Given a fixed conformation of a protein with a point located inside it, we first describe an algorithm to identify the widest tunnel from that point to the outside environment of the protein. Then we try to make the tunnel wider by considering various alternative conformations of the protein. We only consider conformations whose energies are not much higher than the energy of the initial conformation. Among these alternative conformations we select the one with the widest tunnel. However, the alternative conformation with the widest tunnel might not be accessible from the initial structure. Thus, in the next step we develop three algorithms for finding a feasible transition pathway from the initial structure to the alternative conformation, i.e., a sequence of intermediate conformations between the initial structure and the alternative conformation such that the energy values of all these intermediate conformations are close to the energy of the initial structure. We evaluate our tunnel-finding and tunnel-widening algorithms on various proteins. Our experiments show that in most cases we can make the tunnel wider in an alternative conformation. However, there are cases in which we find a wider tunnel in an alternative conformation, but the energy value of the alternative conformation is much higher than the energy of the initial structure. We also implemented our three pathway-finding algorithms and tested them on various instances. Our experiments show that although in most cases we can find a feasible transition pathway, there are cases in which the alternative conformation has energy close to the initial structure, but our algorithms cannot find any feasible pathway from the initial structure to the alternative conformation. Furthermore, there is a trade-off between the running time and accuracy of the three pathway-finding algorithms.

In recent years, several nations have adopted institutional framework laws, so-called Climate Change Acts (CCAs), as means to enforce Paris-compliant mitigation pathways. A key institutional feature to ensure policy stability and compliance with CCAs has been the establishment of independent advisory bodies, tasked with advising on mitigation targets and policy instruments, as well as the, monitoring and evaluation of target attainment. These advisory bodies are endowed with a crucial role in the long-term evaluation and planning process: examining how the low-carbon transition pathways might be achieved. Calling attention to the question of how transition pathways should be conceived and approached, whether it is in 'bio-physical' (climate science), 'techno- economic' (technology assessment/economics) or 'socio-technical' (socio-technical transition field) terms. Recent studies have indicated that a socio-technical transitions is increasingly framed as a question of removing carbon energy from various practices and infrastructures, challenging the dominant techno-economic approach of emissions reductions using carbon-pricing instruments. This thesis explores this challenge, drawing upon a case study of the establishment of the Swedish Climate Policy Council, by means of analyzing the process of institutionalization and how transition pathways are (re)produced discursively through the practices of climate policy evaluation and planning. The main findings of this thesis is that a cross-party consensus behind the Swedish CCA was formed around institutionalizing a 'bio-physical’ mitigation pathway, monitored and safeguarded by the Council which could assign 'political embarrassment' to governments failing to comply with the interim and long-term GHG mitigation targets. Beyond this consensus, the institutional design of the Council is the result of discursive struggles between actor-coalitions supporting techno-economic versus socio-technical transition pathways. However, the recently formed Council has come to challenge previously dominant techno-economic practices of forecasting cost-efficient emissions reductions. This has been accomplished by introducing a novel socio-technical approach to climate policy evaluation: the backcasting of interrelated technological and institutional shifts believed to be necessary in bringing about a low-carbon transition or transformation. Nevertheless, as this socio-technical practice primarily backcasts upon a number of key technological innovations, with limited changes to current industrial patterns of production and consumption, doubts are raised if this approach is to be considered as constitutive of transformative transition pathways.

Diese Arbeit beschäftigt sich mit Aerial Rivers („luftgetragenen Flüssen“), den bevorzugten Wegen des Flusses von Feuchte in der Atmosphäre. Ziel ist es, die Voraussetzung für deren Integration in aktuelle Paradigmen der Wasserwirtschaft zu schaffen. Im Mittelpunkt der Arbeit stehen Amazonien und die angrenzenden Gebiete, also Regionen der Erde, in denen sich derzeit der Landnutzungswandel mit am schnellsten vollzieht. Aus theoretischer Sicht wird das Wissen über die Verbindung zwischen Aerial Rivers und Oberflächenflüssen erweitert. Mit Hilfe eines Algorithmus zur Verfolgung des atmosphärischen Feuchtigkeitstransports werden die Auswirkungen von entferntem Landnutzungswandel in Windrichtung auf die Niederschlagsmenge einer Zielregion quantifiziert. Die räumliche Heterogenität des Einflusses der gesamten Quellevapotranspirationsfläche (precipitationsehed) auf die/den empfangene/n Niederschlagsmenge/Oberflächenabfluss der Zielregion wird untersucht und führt zur Identifizierung der „Most Influential Precipitationshed“ (MIP), der für Managementzwecke relevantesten Teilfläche. Ein Aerial River-Managementbeispiel für Santa Cruz (Bolivien) zeigt, dass die strategische Wiederaufforstung im MIP sowohl die Niederschlagsmenge als auch den empfangenen Oberflächenabfluss erhöht und 22%-59% des zukünftigen Wasserbedarfszuwachses einer schnell wachsenden Stadt decken kann. Weiterhin werden sozio-technische Regime entlang von Aerial Rivers, die zu Extremereignissen wie Megadürren beitragen können, mit Hilfe der sozialwissenschaftlichen Methode der Multi-Level-Perspektive (MLP) untersucht. Ursachen wie Bodenpolitik und Marktinterventionen in Brasilien und Bolivien steuern weit entfernte kolumbianische Energieregime und deren Wandel. Aerial Rivers sind also zentral für zukünftiges Gewässermangement einschließlich Wasserkraft; ihr Management erfordert jedoch eine ganzheitliche Betrachtung der gesellschaftlichen Schnittstellen über administrative Grenzen und Sektoren hinweg. / Aerial rivers are the preferential pathways of moisture flows in the atmosphere. They connect the atmosphere, the water system, and the land system. This thesis aims to provide knowledge for integration of aerial rivers into management of these systems. It focuses on Amazonia and adjacent areas, which collectively experience some of the most rapid land use change on the planet. This thesis further develops three key aspects (theoretical, technical, and societal) of knowledge concerning aerial rivers. From a theoretical aspect, it advances the knowledge of connection between aerial rivers and surface rivers. Using a moisture tracking algorithm, the impact from upwind land use change via aerial rivers on target regions’ runoff reception is quantified. Spatial heterogeneity in the influence of the precipitationshed on runoff reception of the target region is found, implying a need to determine the most influential precipitationshed (MIP) for management purposes. From a technical aspect, the work demonstrates an aerial river management example for a rapidly growing city. It is shown that strategic reforestation in the MIP can increase both rainfall and runoff reception and secure 22%-59% of a rapidly growing city’s future water needs. Finally, the work explores the societal aspect of aerial river management. Socio-technical regimes along aerial rivers contributing to extreme events of mega-drought were traced through the social scientific method of multi-level perspective. It reveals that the source regimes such as land policy and market interventions in Brazil and Bolivia govern remote Colombian energy regimes and their transitions through aerial rivers. These findings show that aerial rivers are relevant and viable options for the development of future water resources - including hydropower - but their management will require a holistic consideration of the various societal interfaces as they cross jurisdictional boundaries and sectors.

Glioma, the tumor of glial cells, is one of the common types of primary central nervous system (CNS) neoplasms. Astrocytoma is the most common of all gliomas and originates from astrocytic glial cells. Astrocytoma tumors belong to two main categories: benign tumors, comprising of grade I Pilocytic astrocytoma and malignant tumors which diffusely infiltrate throughout the brain parenchyma. Diffusely infiltrating astrocytomas are graded into diffuse astrocytoma (DA; grade II), anaplastic astrocytoma (AA; grade III) and glioblastoma (GBM; grade IV) in the order of increasing malignancy. Patients with grade II astrocytoma have a median survival time of 6 to 8 years after surgical intervention. While the more aggressive grade III (AA) and grade IV (GBM) are together called malignant astrocytomas, the treatment protocols and length of survival are distinctly different between these grades. The median survival time for grade III patients is 2 to 3 years whereas patients with grade IV have a median survival of 12-15 months. GBMs have been further divided into primary GBM and secondary GBM on the basis of clinical and histopathological criteria. Primary GBM presents in an acute de novo manner with no evidence of an antecedent lower grade tumor and it accounts for >90% of all GBMs. In contrast, secondary GBM results from the progressive malignant transformation of a grade II or grade III astrocytoma. The current WHO grading system of astrocytomas is based on the histopathological characteristics of the underlying tumor tissue. Diagnoses by pathologists are dependent on specific histologic features: increased mitosis, nuclear atypia, microvascular proliferation and/or necrosis, which associate with biologically aggressive behaviour (WHO 2007). Though grading based on histology is largely reproducible and well accepted, subjectivity involved and substantial disagreement between pathologists has remained a major concern. Because of inherent sampling problems (mainly due to tumor location in the brain) and inadequate sample size available for histological evaluation, there exists a very high possibility of error in grading. Recent studies have attempted to characterize the molecular basis for the histological and prognostic differences between grade III and grade IV astrocytoma. While reports have shown the grade specific profile of gene expression, there is no molecular signature that can accurately classify grade III and grade IV astrocytoma samples. In the current work, we have identified molecular signatures for the accurate classification of grade III and grade IV astrocytoma patients by using transcriptome and miRNome data. The receptor tyrosine kinase pathway is known to be overexpressed in 88% of glioblastoma patients. The expression and activation of the receptors is reported to be deregulated by events like amplification and activating mutations. The aberrant expression of RTKs could also be due to the deregulation of miRNAs, which, in the untransformed astrocytes regulate and fine-tune the levels of the RTKs. In the current study, we have identified that tumor suppressor miRNA miR-219-5p regulates RTK pathway by targeting EGFR and PDGFRα. Part I. Transcriptome approach: Identification of a 16-gene signature for classification of malignant astrocytomas In order to obtain a more robust molecular classifier to accurately classify grade III and grade IV astrocytoma samples, we used transcriptome data from microarray study previously performed in our laboratory. The differential regulation of 175 genes identified from microarray was validated in a cohort of grade III and grade IV patients by real-time qRT-PCR. In order to identify the classification signature that can classify grade III and grade IV astrocytoma samples, we used the expression data of 175 genes for performing Prediction Analysis of Microarrays (PAM) in the training set of grade III and grade IV astrocytoma samples. PAM analysis identified the most discriminatory 16-gene expression signature for the classification of grade III and grade IV astrocytoma. The Principal Component Analysis (PCA) of 16-genes astrocytoma patient samples revealed that the expression of 16-genes could classify grade III and grade IV astrocytoma samples into two separate clusters. In the training set, the 16-gene signature was able to classify grade III and grade IV patients with an accuracy rate of 87.9% as tested by additional analysis of Cross-Validated probability by PAM. The 16-gene signature obtained in the training set was validated in the test set with diagnostic accuracy of 89%. We further validated the 16-gene signature in three independent cohorts of patient samples from publicly available databases: GSE1993, GSE4422 and TCGA datasets and the classification signature got validated with accuracy rates of 88%, 92% and 99% respectively. To address the discordance in grading between 16-gene signature and histopathology, we looked at the clinical features (age and survival) and molecular markers (CDKN2A loss, EGFR amplification and p53 mutation) that differ substantially between grade III and grade IV in discordant grade III and grade IV samples. The grading done by 16-gene signature correlated with known clinical and molecular markers that distinguish grade III and grade IV proving the utility of the 16-gene signature in the molecular classification of grade III and grade IV. In order to identify the pathways that 16 genes of the classification signature could regulate, we performed protein-protein interaction network and subsequently pathway analysis. The pathways with highest significance were ECM (extracellular matrix) and focal adhesion pathways, which are known to be involved in the epithelial to mesenchymal transition (EMT), correlating well with the aggressive infiltration of grade IV tumors. In addition to accurately classifying the grade III and grade IV samples, the 16-gene signature also demonstrated that genes involved in epithelial-mesenchymal transition play key role in distinguishing grade III and grade IV astrocytoma samples. Part II. miRNome approach microRNAs (miRNAs) have emerged as one of the important regulators of the interaction network that controls various cellular processes. miRNAs are short non-coding RNAs (mature RNA being 21-22nt long) that regulate the target mRNA by binding mostly in the 3’ UTR bringing about either translational repression or degradation of the target. miRNAs are shown to play key roles in cell survival, proliferation, apoptosis, migration, invasion and various other characteristic features that get altered in human cancers. miRNAs are characterized to have oncogenic or tumor suppressor role and the aberrant expression of miRNAs is reported in multiple human cancer types. Part A. Genome-wide expression profiling identifies deregulated miRNAs in malignant astrocytoma With an aim to identify the role of miRNAs in the development of in malignant astrocytoma, we performed a large-scale, genome-wide microRNA (miRNA) (n=756) expression profiling of 26 grade IV astrocytoma, 13 grade III astrocytoma and 7 normal brain samples. Using Significance Analysis of Microarrays (SAM), we identified several differentially regulated miRNAs between control normal brain and malignant astrocytoma, grade III and grade IV astrocytoma, grade III astrocytoma and grade IV secondary GBM, progressive pathway and de novo pathway of GBM development and also between primary and secondary GBM. Importantly, we identified a most discriminatory 23-miRNA expression signature, by using PAM, which precisely distinguished grade III from grade IV astrocytoma samples with an accuracy of 90%. We re-evaluated the grading of discordant samples by histopathology and identified that one of the discordant grade III samples had areas of necrosis and it was reclassified as grade IV GBM. Similarly, out of two discordant grade IV samples, one sample had oligo component and it was reclassified as grade III mixed oligoastrocytoma. Thus, after the revised grading, the prediction accuracy increased from 90% to 95%. The differential expression pattern of nine miRNAs was further validated by real-time RT-PCR in an independent set of malignant astrocytomas (n=72) and normal samples (n=7). Inhibition of two glioblastoma-upregulatedmiRNAs (miR-21 and miR-23a) and exogenous overexpression of two glioblastoma-downregulatedmiRNAs (miR-218 and miR-219-5p) resulted in reduced soft agar colony formation but showed varying effects on cell proliferation and chemosensitivity. Thus, we have identified the grade specific expression of miRNAs in malignant astrocytoma and identified a miRNA expression signature to classify grade III astrocytoma from grade IV glioblastoma. In addition, we have demonstrated the functional relevance of miRNA modulation and thus showed the miRNA involvement and their importance in astrocytoma development. Part B. miR-219-5p inhibits the receptor tyrosine kinase pathway by targeting mitogenic receptor kinases in glioblastoma The receptor tyrosine kinase (RTK) pathway, being one of the important growth promoting pathways, is known to be deregulated in 88% of the patients with glioblastoma. In order to understand the role of miRNAs in regulating the RTK pathway, we undertook a screening procedure to identify the potential miRNAs that could target different members of the RTK pathway. From the screening study involving bioinformatical prediction of miRNAs and subsequent experimental validation by modulation of miRNA levels in glioma cell lines, we identified miR-219-5p as a candidate miRNA. The overexpression of miR-219-5p reduced the protein levels of both EGFR and PDGFRα. We confirmed the binding of miR-219-5p to the 3’ UTRs by using reporter plasmids. We also confirmed the specificity of miR-219-5p binding sites in the 3’ UTR of EGFR by site directed mutagenesis of binding sites which abrogated the miRNA-UTR interaction. The expression of miR-219-5p was significantly downregulated in grade III as well as in grade IV astrocytoma samples in the miRNA microarray experiment and we further validated the downregulation in an independent cohort of grade III and grade IV astrocytoma patients by real-time qRT-PCR. The ectopic overexpression of miR-219-5p in glioma cell lines inhibited cell proliferation, colony formation, anchorage independent growth and the migration of glioma cells. In addition, overexpression of miR-219-5p decreased MAPK and PI3K pathways, in concordance with its ability to target EGFR and PDGFRα. Additionally, for the further characterization of miR-219-5p – EGFR interaction and its effect on MAPK and PI3K pathways, we used U87 glioma cells that stably overexpress wild-type EGFR and constitutively active ΔEGFR (both lacking 3’-UTR and thus being insensitive to miR-219-5p overexpression) along with U87 parental cells. In these cell lines with the overexpression of EGFR lacking 3’-UTR, miR-219-5p was unable to inhibit - MAPK and PI3K pathways and also glioma cell migration suggesting that these effects were indeed because of its ability to target EGFR. Further, in the glioblastoma patient cohort (TCGA dataset), we found significant negative correlation between EGFR protein levels, both total EGFR and phospho EGFR and miR-219-5p levels in the glioblastoma tissue samples suggesting a role of miR-219-5p in increasing the protein levels of EGFR in glioblastoma. In summary, we have identified and characterized miR-219-5p as the RTK regulating tumor suppressor miRNA in glioblastoma.