Bio-inspired optimization & sampling technique for side-chain packing in MCCE

The prediction of proteins' conformation helps to understand their exhibited functions, allows for modeling and allows for the possible synthesis of the studied protein. Our research is focused on a sub-problem of protein folding known as side-chain packing. Its computational complexity has been proven to be NP-Hard. The motivation behind our study is to offer the scientific community a means to obtain faster conformation approximations for small to large proteins over currently available methods. As the size of proteins increases, current techniques become unusable due to the exponential nature of the problem. We investigated the capabilities of a hybrid genetic algorithm / simulated annealing technique to predict the low-energy conformational states of various sized proteins and to generate statistical distributions of the studied proteins' molecular ensemble for pKa predictions. Our algorithm produced errors to experimental results within .acceptable margins and offered considerable speed up depending on the protein and on the rotameric states' resolution used.

Cellular Mechanisms of Resveratrol's Interaction with Mitochondrial Reactive Oxygen Species Metabolism

Resveratrol, a polyphenol found naturally in red wines, has attracted great interest in both the scientific community and the general public for its reported ability to protect against many of the diseases facing Western society today. While the purported health effects of resveratrol are well characterized, details of the cellular mechanisms that give rise to these observations are unclear. Here, the mitochondrial antioxidant enzyme Mn superoxide dismutase (MnSOD) was identified as a proximal target of resveratrol in vitro and in vivo. MnSOD protein and activity levels increase significantly in cultured cells treated with resveratrol, and in the brain tissue of mice given resveratrol in a high fat diet. Preventing the increase in MnSOD levels eliminates two of resveratrol’s more interesting effects in the context of human health: inhibition of proliferative cell growth and cytoprotection. Thus, the induction of MnSOD is a critical step in the molecular mechanism of resveratrol. Mitochondrial morphology is a malleable property that is capable of impeding cell cycle progression and conferring resistance against stress induced cell death. Using confocal microscopy and a novel ‘cell free’ fusion assay it was determined that concurrent with changes in MnSOD protein levels, resveratrol treatment leads to a more fused mitochondrial reticulum. This observation may be important to resveratrol’s ability to slow proliferative cell growth and confer cytoprotection. Resveratrol's biological activities, including the ability to increase MnSOD levels, are strikingly similar to what is observed with estrogen treatment. Resveratrol fails to increase MnSOD levels, slow proliferative cell growth and confer cytoprotection in the presence of an estrogen receptor antagonist. Resveratrol's effects can be replicated with the specific estrogen receptor beta agonist diarylpropionitrile, and are absent in myoblasts lacking estrogen receptor beta. Four compounds that are structurally similar to resveratrol and seven phytoestrogens predicted to bind to estrogen receptor beta were screened for their effects on MnSOD, proliferative growth rates and stress resistance in cultured mammalian cells. Several of these compounds were able to mimic the effects of resveratrol on MnSOD levels, proliferative cell growth and stress resistance in vitro. Thus, I hypothesize that resveratrol interacts with estrogen receptor beta to induce the upregulation of MnSOD, which in turn affects cell cycle progression and stress resistance. These results have important implications for the understanding of RES’s biological activities and potential applications to human health.

Educating for Community Resilience: How the Work of Thomas Homer-Dixon and JohnDewey's Pattern of Inquiry Can Help Us Prepare for the Ecological and Social Challenges of the 21st Century

Scientists have overwhelmingly concluded that global warming occurs as a consequence of human activities and that climate change, combined with the depletion of resources, could have catastrophic consequences for the human civilization later this century. However, in political circles and in the public sphere these conclusions are not taken seriously, or they are laid aside for future generations to deal with; at the same time, significant efforts are being deployed to discredit the scientific evidence. In this thesis I have studied the positions of climate scientists as well as those of climate change deniers, and I also examined how their points of view are likely to impact the interests and habits of corporations and citizens. The work of Thomas Homer-Dixon was used as an important source for analyzing the complex interaction between our natural, economic, and social systems, and John Dewey's pattern of inquiry provided the theoretical foundation for an analysis of the current crisis and its possible solutions. No concerted action to deal with climate change has yet been taken by the leaders of the Western world; I corroborated data from four reliable sources (Hansen, 2009; IPCC, 2007; Lynas, 2007; Steffen, 2011) regarding several development scenarios and their likely consequences on greenhouse gas emissions, and I concluded that a future temperature increase of more than 2°C appears now as unavoidable. In the light of this conclusion I argue that education for increasing the resilience of smaller communities is a realistic alternative that can offer some hope in dealing with the challenges ahead.