Browsing Biological Engineering - Ph.D. / Sc.D. by Subject "Biological Engineering Division."
Now showing items 1-20 of 91
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Analysis of sequence-selective guanine oxidation by biological agents
(Massachusetts Institute of Technology, 2008)Oxidatively damaged DNA has been strongly associated with cancer, chronic degenerative diseases and aging. Guanine is the most frequently oxidized base in the DNA, and generation of a guanine radical cation (G'") as an ... -
Analysis of the structural changes caused by positive DNA supercoiling
(Massachusetts Institute of Technology, 2007)The procession of helix-tracking enzymes along a DNA molecule results in the formation of supercoils in the DNA, with positive supercoiling (overwinding) generated ahead of the enzyme, and negative supercoiling (underwinding) ... -
An apparatus for high throughput muscle cell experimentation
(Massachusetts Institute of Technology, 2006)The cardiac ventricular muscle cell (myocyte) is a key experimental system for exploring the mechanical properties of the diseased and healthy heart. The myocyte experimental model provides a higher level of physiological ... -
Applying engineering principles to the design and construction of transcriptional devices
(Massachusetts Institute of Technology, 2008)The aim of this thesis is to consider how fundamental engineering principles might best be applied to the design and construction of engineered biological systems. I begin by applying these principles to a key application ... -
Bayesian network models of biological signaling pathways
(Massachusetts Institute of Technology, 2006)Cells communicate with other cells, and process cues from their environment, via signaling pathways, in which extracellular cues trigger a cascade of information flow, causing signaling molecules to become chemically, ... -
Biophysical characterization of high affinity engineered single chain Fv antibody fragments
(Massachusetts Institute of Technology, 2004)High affinity antibody binding interactions are important for both pharmaceutical and biotechnological uses. However, designing higher affinity interactions has remained difficult. Both high affinity interactions from ... -
Cartilage mechanobiology : the effects of loading on the fine structure and function of chondroitin sulfate glycosaminoglycans
(Massachusetts Institute of Technology, 2005)Chondroitin sulfate is a critical component of articular cartilage due to its contribution to the tissue's resistance to compressive deformation. Alterations in the biosynthesis of this molecule over time could impact the ... -
Cartilage response to in vitro models of injury in combination with growth factor and antioxidant treatments
(Massachusetts Institute of Technology, 2008)Approximately one in five Americans is affected by arthritis, making it one of the most prevalent diseases and the leading cause of disability in the United States. Post-traumatic arthritis occurs after joint injury (e.g., ... -
Chondrocyte gene expression and intracellular signaling pathways in cartilage mechanotransduction
(Massachusetts Institute of Technology, 2005)Chondrocytes respond to in vivo mechanical loads by regulating the composition of the cartilage extracellular matrix. This study utilized three loading protocols that span the range of forces and flows induced by in vivo ... -
Chondrocyte response to in vitro mechanical injury and co-culture with joint capsule tissue
(Massachusetts Institute of Technology, 2005)Acute traumatic joint injury in young adults leads to an increased risk for the development of osteoarthritis (OA) later in life irrespective of surgical intervention to stabilize the injured joint. Although the mechanism ... -
Cisplatin cytotoxicity associated with tetracycline resistance determinants in Escherichia coli
(Massachusetts Institute of Technology, 2005)Tetracyclines, a broad-spectrum class of antibiotics, were discovered in the late 1940s, and became widely used because of their important advantages: they are inexpensive, safe, demonstrate good oral absorption, and are ... -
Computational modeling of protein-biomolecule interactions with application to mechanotransduction and antibody maturation
(Massachusetts Institute of Technology, 2008)Cell survival, growth, differentiation, migration, and communication all depend on the appropriate combination of specific interactions between proteins and biomolecules. Therefore, understanding the molecular mechanisms ... -
Computational structure-based modeling and analysis with application to rational and evolutionary molecular engineering
(Massachusetts Institute of Technology, 2007)The design and development of new proteins and small molecules has considerable practical application in medicine, industry, and basic science. Frequently, progress in this area is made by altering an existing small molecule ... -
Control of flow and oxygen in a 3-D perfused micro-environment fosters balanced survival of hepatocyte-non-parenchymal cell co-cultures
(Massachusetts Institute of Technology, 2007)Creating a physiologically relevant in vitro liver model requires reproducing the cellular heterogeneity of in vivo liver in a functional state. However differentiated sinusoidal endothelial cells (SECs), marked by SE-1 ... -
Deoxyribose oxidation chemistry and endogenous DNA adducts
(Massachusetts Institute of Technology, 2006)Endogenous and exogenous oxidants react with cellular macromolecules to generate a variety of electrophiles that react with DNA produce cytotoxic and mutagenic adducts. One source of such electrophiles is deoxyribose in ... -
Design principles of mammalian signaling networks : emergent properties at modular and global scales
(Massachusetts Institute of Technology, 2008)This thesis utilizes modeling approaches rooted in statistical physics and physical chemistry to investigate several aspects of cellular signal transduction at both the modular and global levels. Design principles of ... -
Development and characterization of an in vitro culture system as a physiological model for chronic Hepatitis B infection
(Massachusetts Institute of Technology, 2007)Human Hepatitis B virus (HBV) is the prototype member of the family Hepadnaviridae that consists of enveloped, partially double stranded DNA viruses that specifically target hepatocytes for viral replication. Although a ... -
Development of a collagen gel sandwich hepatocyte bioreactor for detecting hepatotoxicity of drugs and chemicals
(Massachusetts Institute of Technology, 2004)Understanding the hepatotoxicity of drugs and chemicals is essential for progress in academic research, medical science and in the development of new pharmaceuticals. Studying hepatotoxicity in vitro is a challenging task ... -
Development of an analytical method to quantify the oxidative deoxyribose damage product 3'-phosphoglycolaldehyde induced by radiation, iron and peroxynitrite
(Massachusetts Institute of Technology, 2004)Deoxyribose oxidation in DNA forms strongly electrophilic terminal blocking groups and abasic sites capable of stopping polymerases, forming DNA-protein crosslinks and nucleobase adducts. These threats to the genetic ... -
Development of mass spectrometry based technologies for quantitative cell signaling phosphoproteomics : the epidermal growth factor receptor family as a model system
(Massachusetts Institute of Technology, 2007)Ligand binding to cell surface receptors initiates a cascade of signaling events regulated by dynamic phosphorylation on a multitude of pathway proteins. Quantitative features, including intensity, timing, and duration of ...
