Functional, clustered, feedforward, and mesoscale brain networks

The brain is a network spanning multiple scales from subcellular to macroscopic. In this thesis I present four projects studying brain networks at different levels of abstraction. The first involves determining a functional connectivity network based on neural spike trains and using a graph theoretical method to cluster groups of neurons into putative cell assemblies. In the second project I model neural networks at a microscopic level. Using diferent clustered wiring schemes, I show that almost identical spatiotemporal activity patterns can be observed, demonstrating that there is a broad neuro-architectural basis to attain structured spatiotemporal dynamics. Remarkably, irrespective of the precise topological mechanism, this behavior can be predicted by examining the spectral properties of the synaptic weight matrix. The third project introduces, via two circuit architectures, a new paradigm for feedforward processing in which inhibitory neurons have the complex and pivotal role in governing information flow in cortical network models. Finally, I analyze axonal projections in sleep deprived mice using data collected as part of the Allen Institute's Mesoscopic Connectivity Atlas. After normalizing for experimental variability, the results indicate there is no single explanatory difference in the mesoscale network between control and sleep deprived mice. Using machine learning techniques, however, animal classification could be done at levels significantly above chance. This reveals that intricate changes in connectivity do occur due to chronic sleep deprivation.

Biological activity of Pyrrole-Imidazole polyamides in vivo

This thesis focuses on biological activity of pyrrole-imidazole polyamides in vivo. The work presented includes experiments underlining sequence selectivity of these compounds in living cells and potential methods to improve it. A large fraction of this thesis is devoted to activity of Py-Im in murine models of cancer. We investigated the pharmacokinetics and biodistribution of two compounds – targeted to 5'-WGGWCW-3' and 5'-WTWCGW-3' sequences – and characterized their activity by measuring their effects on tumor growth, gene expression in vivo and in tissue culture, and their effects on physiology of tumors. The initial theoretical studies suggested that a large fraction of genomic sites are bound by Py-Im polyamides non-specifically and experimental data shows that the programmed binding sequence is not a sole determinant of the patterns of gene regulation. Despite the likely presence of non-specific effects of Py-Im polyamides in living cells, in vivo administration of Py-Im polyamides resulted in tolerable host toxicity and anti-tumor activity. Py-Im polyamide targeted to Estrogen Receptor Response Element showed downregulation of ER-driven gene expression in tumor cells, while the compound targeted to hypoxia response element reduced vascularization of tumors and their growth rate, induced apoptosis of cells in hypoxic areas and reduced expression of proangiogenic and prometastatic factors. Further studies, showed that polyamides distributed to many of the tested tissues and their FITC-conjugates showed nuclear uptake. The gene expression effects were also present in murine tissues, such as liver and kidneys, indicating a potential for use for Py-Im polyamides in non-cancerous diseases.