Thesis (M. Eng.)--Massachusetts Institute of Technology, Biological Engineering Division, 2007. / Includes bibliographical references (p. 51-53). / Neurodegenerative diseases typically affect a limited number of specific neuronal subtypes, and the death of these neurons causes permanent loss of a specific motor function. Efforts to restore function would require regenerating the affected cells, but progress is limited by a narrow understanding of the mechanisms that underlie the generation of these neurons from their progenitor cells. In order to prevent neuronal degeneration and potentially repair or regenerate the damaged motor output circuitry, it will be necessary to understand the molecular and genetic factors that control, direct, and enhance differentiation, axonal projection and connectivity. While techniques are available to separate specific populations of neurons once they are fully-differentiated, current methods make it nearly impossible to monitor or control the development of a neural precursor in standard open culture. To carry out directed differentiation experiments effectively, it will be critical to control how signals are introduced to the cells. In this study, we present a microfluidic system to address the limitations of previous research. / (cont.) The device is capable of generating a controlled gradient of chemoattractant or growth factor of interest and directing axonal growth through an extra-cellular matrix material. Once the cells have grown into the device, signals and gradients can be applied directly to either the cell bodies or the axons. This device will serve as a platform technology for future experimentation with biomaterial scaffolds for neural tissue engineering, drug design or testing, and eventually directed differentiation of neural precursor cells. / by Johanna Varner. / M.Eng.

Thesis (S.M. in Toxicology)--Massachusetts Institute of Technology, Biological Engineering Division, 2002. / Includes bibliographical references (leaf 23, 1st group). / A formal series of conditions of lifetime genetic risk of cancer is explored, and algebra is provided for applications in human population genetics. Risks are considered in terms of alleles necessary and/or sufficient for carcinogenesis. Alleles are first classified with respect to their effects on reproductive fitness, and then in terms of their potential effects on carcinogenic pathways. The algebraic formulations for a series of genetic possibilities: monogenic, multigenic, and polygenic, are provided. It is expected that technology will be developed to identify and enumerate rare inherited alleles in large general and cancer proband populations. / by Helen Banava. / S.M.in Toxicology

Thesis (Ph. D.)--Massachusetts Institute of Technology, Biological Engineering Division, 2007. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references (leaves 112-127). / 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 or protein for new function. This thesis presents methods for the analysis and design of rationally and evolutionarily designed molecules and focuses on applying these methods to make protein and small molecule changes more strategically. First, electrostatic analysis of a series of small molecule neuraminidase inhibitors was used to demonstrate that charge optimization improves the electrostatic component of the binding free energy, despite changes in binding mode and discrete chemical constraints. Additionally, chemical changes suggested by charge optimization frequently corresponded to tighter-binding inhibitors, indicating that this technique would be useful for the design of future inhibitors. Second, computational sequence and structure analysis were used to study the PDZ3-CRIPT binding interaction and a method for sequence analysis was developed to locate residues important for binding specificity. Third, computational analysis of the horseradish peroxidase active site suggested five positions as candidates for mutation, and further studies of new mutant enzymes let to ideas for the improvement of computational enzyme design procedures. Finally, both computational protein design techniques and a model of the evolutionary process were used to study the efficiency of evolution as a tool for creating new proteins in the laboratory. We identified sequences that serve as better evolutionary starting points that others and provide a general framework for considering the impact of protein structure on the allowed sequence space and therefore on the challenges that each protein presents to evolutionary protein engineering procedures. / by Kathryn Anne Armstrong. / Ph.D.

Thesis (Ph. D. in Bioengineering)--Massachusetts Institute of Technology, Biological Engineering Division, 2003. / Includes bibliographical references. / Emerging medical technologies for effective and lasting repair of articular cartilage include delivery of cells or cell-seeded scaffolds to a defect site to initiate de novo tissue regeneration. Biocompatible scaffolds assist in providing a template for cell distribution and extracellular matrix accumulation in a three-dimensional geometry. In these studies, a self-assembling peptide hydrogel is evaluated as a potential scaffold for cartilage repair using a model bovine cell source. A seeding technique is developed for 3-D encapsulation of chondrocytes in a peptide hydrogel. The chondrocyte-seeded peptide hydrogel was then evaluated cellular activities in vitro under standard culture conditions and also when subjected to dynamic compression. During 4 weeks of culture in vitro, chondrocytes seeded within the peptide hydrogel retained their morphology and developed a cartilage-like ECM rich in proteoglycans and type II collagen, indicative of a stable chondrocyte phenotype. Time dependent accumulation of this ECM was paralleled by increases in material stiffness, indicative of deposition of mechanically-functional neo-tissue. Culture of chondrocyte-seeded peptide hydrogels in ITS-supplemented medium was investigated as an alternative to high serum culture. Low serum (0.2%), ITS-supplemented medium was found to maintain high levels of cell division and extracellular matrix synthesis and accumulation, as seen in high serum culture. Furthermore, low serum, ITS medium induced minimal chondrocyte de-differentiation on the surface of the hydrogel. This is in contrast to high serum culture, where surface de-differentiation and subsequent proliferation led to a 5-10 cell thick layer that stained positive for type I collagen. / (cont.) The effects of dynamic compression of chondrocyte-seeded peptide hydrogels were evaluated over long-term culture. A non-continuous loading protocol was identified in which proteoglycan, but not protein, synthesis increased over static, free-swelling culture. Increases in GAG matrix accumulation were observed after at least 8 days of loading, while hydroxyproline accumulation was unaffected by dynamic compression. These data demonstrated dynamic compression differentially regulated the synthesis of proteoglycans. Analysis of GAG loss to the medium indicated peak proteoglycan catabolism occurred immediately after the initiation of loading. This phenomenon was further explored using a modified loading protocol that increased GAG loss to the medium. Peak GAG loss to the medium was 2-fold higher than previously observed, resulting in GAG accumulation values significantly less than controls. Hydroxyproline accumulation was minimally affected by loading, demonstrating that dynamic compression also differentially regulated the catabolism of proteoglycans. Proteoglycan catabolism was not predominantly due to physical disruption accumulated extracellular matrix or loss of newly-synthesized molecules. Instead, the presence of MMPs in the medium that coincided with GAG loss suggest a potential enzymatic mechanism. These results demonstrate the potential of a self-assembling peptide hydrogel as a scaffold for the synthesis and accumulation of a true cartilage-like extracellular matrix ... / John D. Kisiday. / Ph.D.in Bioengineering

Thesis (M. Eng.)--Massachusetts Institute of Technology, Biological Engineering Division, 2008. / Includes bibliographical references (leaves 57-62). / Implantable, controlled release drug delivery devices offer several advantages over systemic oral administration routes and immediate drug release treatments including direct therapy to target organ, more continuous maintenance of plasma and tissue drug levels and the potential for reduced side effects or toxicity. Urology has emerged as a unique field in which minimally invasive implantation techniques are available and such devices could provide improved beneficial therapies over conventional treatments. Urological indications for which localized drug therapy is already being advocated and investigated are highly suitable for treatment with implantable controlled release devices. This thesis describes the in vitro performance evaluation of an implantable, bio-resorbable device that can provide localized drug therapy of ciprofloxacin (CIP) to the seminal vesicle and nearby prostate gland for treatment of chronic prostatitis (CP). The device functions as an elementary osmotic pump (EOP) to release CIP for a period of 2-3 weeks after implantation in the seminal vesicle (SV) through transrectal needle injection or cystoscopic methods. The device is composed of an elastomeric, resorbable polymer cast in a tubular geometry with solid drug powder packed into its core and a micromachined release orifice drilled through its wall. Drug release experiments were performed to determine the effective release rate from a single orifice and the range of orifice size in which osmotic-controlled zero-order release was the dominant mechanism of drug delivery from the device. Device stability and function in an alkaline environment of similar pH to that of the SVs and infected prostate gland was also assessed in vitro. The device was found to function well in both de-ionized water and NaOH pH-8 solution with a sustained zero-order release rate of 2.47 ± 0.29 jtg/hr when fabricated with an orifice of diameter 100-150pm. / by Irene S. Tobias. / M.Eng.

Thesis (M. Eng.)--Massachusetts Institute of Technology, Biological Engineering Division, 2004. / Includes bibliographical references (leaves 91-93). / This work describes the integration of novel microfabrication techniques for vascular tissue engineering applications in the context of a novel biodegradable elastomer. The field of tissue engineering and organ regeneration has been born out of the high demand for organ transplants. However, one of the critical limitations in regeneration of vital organs is the lack of an intrinsic blood supply. This work expands on the development of microfluidic scaffolds for vascular tissue engineering applications by employing microfabrication techniques. Unlike previous efforts, this work focuses on fabricating this scaffolds from poly(glycerol-sebacate) (PGS), a novel biodegradable elastomer with superior mechanical properties. The transport properties of oxygen and carbon dioxide in PGS were measured through a series of time-lag diffusion experiments. The results of these measurements were used to calculate a characteristic length scale for oxygen diffusion limits in PGS scaffolds. Microfluidic scaffolds were then produced using fabrication techniques specific for PGS. Initial efforts have resulted in solid PGS-based scaffolds with biomimetic fluid flow and capillary channels on the order of 10 microns in width. These scaffolds have also been seeded with endothelial cells and perfused continuously in culture for up to 14 days resulting in partially confluent channels. More complex fabrication techniques were also demonstrated. A novel electrodeposition technique was used in the fabrication of biomimetic microfluidic masters. Thin-walled devices were also synthesized to accommodate the relatively low gas permeability of PGS. / by Christopher John Bettinger. / M.Eng.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Biological Engineering Division, 2008. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references (leaves 180-203). / 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 area of synthetic biology: metabolic engineering. Abstraction is used to compile a desired system function, reprogramming bacterial odor, to devices with human-defined function, then to biological parts, and finally to genetic sequences. Standardization is used to make the process of engineering a multi-component system easier. I then focus on devices that implement digital information processing through transcriptional regulation in Escherichia coli. For simplicity, I limit the discussion to a particular type of device, a transcriptional inverter, although much of the work applies to other devices as well. First, I discuss basic issues in transcriptional inverter design. Identification of key metrics for evaluating the quality of a static device behavior allows informed device design that optimizes digital performance. Second, I address the issue of ensuring that transcriptional devices work in combination by presenting a framework for developing standards for functional composition. The framework relies on additional measures of device performance, such as error rate and the operational demand the device places on the cellular chassis, in order to proscribe standard device signal thresholds. Third, I develop an experimental, proof-of-principle implementation of a transcriptional inverter based on a synthetic transcription factor derived from a zinc finger DNA binding domain and a leucine zipper dimerization domain. Zinc fingers and leucine zippers offer a potential scalable solution to the challenge of building libraries of transcription-based logic devices for arbitrary information processing in cells. / (cont.) Finally, I extend the principle of physical composition standards from parts and devices to the vectors that propagate those parts and devices. The new vectors support the assembly of biological systems. Taken together, the work helps to advance the transformation of biological system design from an ad hoc, artisanal craft to a more predictable, engineering discipline. / by Reshma P. Shetty. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Biological Engineering Division, 2008. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references (p. 165-176). / The aim of my thesis is to help enable the engineering of biological systems that behave in a predictable manner. Well-established techniques exist to engineer systems that behave as expected. Here, I apply such techniques to two aspects of the engineering of biological systems. First, I address the design and construction of standard biological devices in a manner that facilitates reuse in higher-order systems. I describe the design and construction of an exemplar device, an engineered cell-cell communication receiver using standard biological parts (refined genetic objects designed to support physical and functional composition). I adopt a conventional framework for describing the behavior of engineered devices and use the adopted framework to design and interpret experiments that describe the behavior of the receiver. The output of the device is the activity of a promoter reported in units of Polymerases Per Second (PoPS), a common signal carrier. Second, I begin to address the coupling that exists between engineered biological systems and the host cell, or chassis. I propose that the coupling between engineered biological systems and the cellular chassis might be reduced if fewer resources were shared between the system and the chassis. I describe the construction of cellular chassis expressing both T7 RNA polymerases (RNAP) and orthogonal ribosomes that are unused by the chassis but are available for use by an engineered system. I implement a network in which the orthogonal ribosomal RNA and the gene encoding T7 RNAP are transcribed by T7 RNAP. In turn, the orthogonal ribosomes translate the T7 RNAP message. In addition, the T7 RNAP and orthogonal ribosomes express a repressor that inhibits transcription of both the T7 RNAP and orthogonal ribosomes. / (cont.) As a result, the orthogonal RNAP and ribosomes are auto-generating and self-regulating. The provision of resources unused by the cellular chassis and dedicated to an engineered biological system forms the beginnings of a biological virtual machine. / by Bartholomew Canton. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Biological Engineering Division, 2008. / Includes bibliographical references (leaves 100-112). / 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 influencing protein-biomolecule binding interactions is important both for fundamental knowledge and as a foundation for therapeutic applications and biotechnology. This thesis presents two applications of computational modeling to study protein-biomolecule binding in different contexts. First, we sought to characterize effects of applied mechanical force on protein structural and biochemical properties. Despite growing experimental evidence of force-regulated cell behavior, the molecular mechanisms involved in force sensing and transmission are still largely unknown. We adapted a free energy method to directly compute the change in binding affinity upon force application. Our simulations demonstrated that differential responses in the bound and unbound state of a protein-ligand complex can lead to graded force-modulation of binding affinity. Application to a prototypical protein system - the helical bundle complex of a paxillin fragment bound to the FAT domain of focal adhesion kinase (FAK) revealed several structural mechanisms responsible. Second, we used computational methods to design individual mutations computed to improve binding affinity of an antibody-small molecule complex with relevance to cancer treatment. Our calculations suggested several beneficial mutations for experimental characterization. The work illustrates the value of computational modeling for understanding protein-biomolecule interactions with application to therapeutic development and advances in biotechnology. / by Aurore Zyto. / Ph.D.

Thesis (M. Eng.)--Massachusetts Institute of Technology, Biological Engineering Division, 2006. / "September 2006." / Includes bibliographical references (p. 141-147). / Nonviral vector research and development has been stunted by a lack of knowledge and understanding of how vectors are trafficked within the cell. Research currently involves mass screenings of different combinations of vector components without a true understanding of how each component interacts with the target cell. Few tools are currently available for scientists to quantitatively examine these vector-to-cell interactions or determine the rate limiting steps within the gene delivery pathway. Thus, researchers cannot fully optimize the vector design to reach maximal delivery efficiency. This project seeks to address this issue by modifying a density gradient electrophoresis (DGE) device originally developed on Mel Juso cells to segregate primary rat hepatocyte lysate into nuclear, early endosomal, late endosomal/lysosomal, and cytoplasmic fractions. We found that according to the Horseradish Peroxidase assay, late endosomes and lysosomes consistently localize to fractions 11-13 and early endosomes in fractions 18 to 21. There was minimal labeling in fractions 14 through 17 demonstrating that separation of the organelles was achieved. With this higher resolution fractionation, movement through the endosomal pathway can be studied in greater detail. / (cont.) The rates with which each vector moves from outside of the cell into the early endosome, to the late endosome, to the cytoplasm and into the nucleus can be quantified. The steps affected by specific modifications to the vector design and the vector properties most important for delivery efficiency can be identified. As vectors are sorted differently in different cell types, this DGE device will allow researchers to gain insight of the cell-specific sorting mechanisms. Ultimately, DGE can aid design of vectors that reach delivery efficiencies comparable to viruses and tailor the vectors to the tissue of interest. / by Jennifer Fang. / M.Eng.