http://hdl.handle.net/1721.1/7629 2013-06-20T08:30:50Z http://hdl.handle.net/1721.1/78139 Human adaptation of avian influenza viruses Srinivasan, Karunya Human adaptation of avian influenza viruses pose an enormous public health challenge as the human population is predominantly naive to avian influenza antigens. As such, constant surveillance is needed to monitor the circulating avian strains. Of particular importance are strains belonging to H5N1, H7N7, H7N2 and H9N2 subtypes that continue to circulate in birds worldwide and have on occasions caused infections in humans. A key step in influenza human adaptation is the accumulation of substitutions/mutations in the viral coat glycoprotein, hemagglutinin (HA), that changes HA's binding specificity and affinity towards glycan receptors in the upper respiratory epithelia (referred to as human receptors). Unlike for the H1, H2, H3 and more recently H5 HA a correlation between the quantitative binding of HA to human receptors and respiratory droplet transmissibility has not been established for H9 and H7 subtypes. This thesis is a systematic investigation of determinants that mediate changes in HA-glycan receptor binding specificity, with focus on the molecular environments within and surrounding the glycan receptor binding site (RBS) of avian HAs, particularly the H9 and H7 subtypes. The glycan receptor binding properties of HA were studied using a combination of biochemical and molecular biology approaches including dose dependent glycan binding, human tissue staining and structural modeling. Using these complementary analyses, it is shown that molecular interactions between amino acids in and proximal to the RBS, including interactions between the RBS and the glycan receptor converge to provide high affinity binding of avian HA to human receptors. For the H9 HA [alpha]2-->6 glycan receptor-binding affinity of a mutant carrying Thr-189-->Ala amino acid change correlated with the respiratory droplet transmission in ferrets conferred by this change. Further, it was demonstrated for the first time that two specific mutations; Gln226-->Leu and Gly228-->Ser in glycan receptor-binding site of H7 HA substantially increase its binding affinity to human receptors. These approaches and findings contribute to a framework for monitoring the evolution of HA and the development of general rules that govern human adaption applicable to strains beyond ones currently under study. Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2012.; Cataloged from PDF version of thesis.; Includes bibliographical references. 2012-01-01T00:00:00Z http://hdl.handle.net/1721.1/78138 Stochastic gene expression during lineage specification of single T helper lymphocytes Fang, Miaoqing The adaptive immune system is an extraordinarily diverse inventory comprised of highly specialized cells, the differentiation of which requires numerous lineage specifications at various developmental stages. The precise control of immune cell differentiation and the delicate balance of their population composition are crucial for effective protection against infectious environmental agents, without triggering autoimmune responses or allergies. It is therefore important to understand at the molecular level in individual cells how lineage commitment is regulated. I explored the heterogeneous gene expression during the lineage specification of single T helper cells, by quantitatively measuring mRNA and protein levels. I have discovered a paradigm of cell lineage specification governed by the signaling interplay between extracellular cues and intracellular transcriptional factors, where the strength of extracellular signaling dominates over the intracellular signaling components. In the presence of extracellular cues, T helper cells stochastically acquire any intermediate Thl/Th2 states. The states of T helper cells can be gradually tuned by depriving availability of extracellular cytokines, which are produced stochastically by a small subpopulation of cells. When extracellular cues are removed, the weak intracellular signaling network reveals its effect, leading to classic mutual exclusion of antagonistic transcriptional factors. Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2012.; Cataloged from PDF version of thesis.; Includes bibliographical references (p. 118-125). 2012-01-01T00:00:00Z http://hdl.handle.net/1721.1/78137 Structure-function characterization and engineering of polysaccharides and antibodies with therapeutic activity Robinson, Luke (Luke Nathaniel) Proteins and polysaccharides are of growing importance as a source for novel therapeutic compounds and target a range of diseases, from cancer to infections from pathogens. However, owing to their large and complex structures, they face a unique set of challenges, compared to small molecules, in their discovery and development as safe, efficacious drugs. Towards addressing these challenges, we describe in this thesis the implementation of structure-function relationship approaches to characterize and engineer polysaccharides and antibodies to improve their therapeutic profiles. The plant polysaccharide pectin, when modified, has demonstrated significant anticancer activity in animal models and small-scale clinical trials. Its development has been hampered, however, due to its complex structure and lack of structure-activity correlates. Using an integrated approach, we engineer a modified pectin that exhibits significant in vivo anticancer activity, which we link to specific structural attributes and cellular functional mechanisms. These results improve our structure-function understanding of anticancer modified pectin, an important step towards the clinical use of this complex polysaccharide. Applying what we learned from pectin, we develop an integrated framework to identify a contaminant in batches of heparin, a polysaccharide anticoagulant drug, associated with an outbreak of allergic-type reactions in 2007-2008. Employing orthogonal analytical approaches to overcome challenges of characterizing structurally complex pharmaceutical heparin, we determine that the structurally related glycan, oversulfated chondroitin sulfate, is the major contaminant. We link its presence to activation of the contact pathway, thereby establishing a structure-function understanding of contaminated heparin and improving the safety profile of this polysaccharide drug. Transitioning knowledge gained from the structure-function characterization of polysaccharides, we engineer, by structure-based design, a broad spectrum neutralizing antibody to dengue virus, which yearly infects more than 200 million people, causing approximately 21,000 deaths. We incorporate complementary approaches of energetics and empirical informatics methods to rationally redesign an existing antibody for greater breadth and potency, resulting in an engineered antibody with binding to all four virus serotypes and good in vitro potency. Overall, this thesis provides important insights into structure-function approaches through the use of complementary methods to characterize and engineer therapeutic polysaccharides and antibodies. Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2012.; Cataloged from PDF version of thesis.; Includes bibliographical references. 2012-01-01T00:00:00Z http://hdl.handle.net/1721.1/78136 Engineered mRNA regulation using an inducible protein-RNA aptamer interaction Belmont, Brian J. (Brian Joshua) The importance and pervasiveness of naturally occurring regulation of RNA function in biology is increasingly being recognized. A common regulatory mechanism uses inducible protein-RNA interactions to shape diverse aspects of cellular RNA fate. Recapitulating this using a novel set of protein-RNA interactions is appealing given the potential to subsequently modulate RNA biology in a manner decoupled from normal cellular physiology. We describe a ligand-responsive protein-RNA interaction module that can be used to target a specific RNA for subsequent regulation. Using the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) method, RNA aptamers binding to the bacterial Tet Repressor protein (TetR) with low- to sub- nanomolar affinities were identified. This interaction is reversibly controlled by tetracycline in a manner analogous to the interaction of TetR with its cognate DNA operator. Aptamer minimization and mutational analyses support a functional role for conserved sequence and structural motifs in TetR binding. We illustrate the utility of this chemically-inducible RNA-protein interaction to directly regulate translation in both a prokaryotic and eukaryotic organism. By genetically encoding TetR-binding RNA elements into the 5'-untranslated region (5'-UTR) of a given mRNA, translation of a downstream coding sequence is directly controlled by TetR and tetracycline analogs. In endogenous and synthetic 5'-UTR contexts, this modular system efficiently regulates the expression of multiple target genes, and is sufficiently stringent to distinguish functional from nonfunctional RNA-TetR interactions. We also demonstrate engineering this TetR-aptamer module to regulate subcellular mRNA localization. This is efficiently achieved by fusing TetR to proteins natively involved in localizing endogenous transcripts, and genetically encoding TetR-binding RNA aptamers into the target transcript. Using this platform, we achieve tetracycline-regulated enhancement of target transcript subcellular localization. We also systematically examine some rules for successfully forward engineering this RNA localization system. Altogether, these results define and validate an inducible protein-RNA interaction module that incorporates desirable aspects of a ubiquitous mechanism for regulating RNA function in Nature and that can be used as a foundation for functionally and reversibly controlling multiple fates of RNA in cells. Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2012.; Cataloged from PDF version of thesis.; Includes bibliographical references (p. 114-131). 2012-01-01T00:00:00Z