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Biomedical Engineering and Bioengineering Commons

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Full-Text Articles in Biomedical Engineering and Bioengineering

Computational Protein Design For Peptide-Directed Bioconjugation, Joseph Gabriel Plaks Jan 2019

Computational Protein Design For Peptide-Directed Bioconjugation, Joseph Gabriel Plaks

Chemical & Biological Engineering Graduate Theses & Dissertations

Proteins enable living organisms to perform many of their critical functions, having been applied over evolutionary time to solve problems of overwhelming diversity and complexity. Protein engineering seeks to deploy these versatile molecules in addressing problems of human concern and would benefit from innovations that improve protein utilization in unnatural environments as well as from increased predictive capability in protein design.

Bioconjugation facilitates the use of proteins in unnatural environments by permitting the attachment of molecules, such as polymers, that can modulate protein stability, solubility, and activity and by mediating protein immobilization. We initially explored this propensity of bioconjugation by ...


Engineering Bacterial Gene Expression: Applications Towards Biofuels And Antibiotic Resistance, Peter Britton Otoupal Jan 2018

Engineering Bacterial Gene Expression: Applications Towards Biofuels And Antibiotic Resistance, Peter Britton Otoupal

Chemical & Biological Engineering Graduate Theses & Dissertations

Nature is rarely static. Organisms live in diverse and stressful environments that necessitate rapid response strategies for survival. Microorganisms have responded to this by evolving bet-hedging, wherein they exhibit constitutively heterogeneous gene expression to maximize fitness across numerous background. The goal of this thesis is to “hijack” this phenomenon using novel gene expression engineering techniques to alter how bacteria respond to their environments, in order to address pressing societal concerns.

This begins with a systematic exploration of how bacterial gene expression naturally responds to antibiotics and biofuels. This reveals promising gene candidates for targeted manipulation, for which a library of ...


In Situ Designer Lipid Production: Integration Of Novel Characteristics And Behaviors Into Synthetic Cell Membranes, Danielle S. Konetski Jan 2018

In Situ Designer Lipid Production: Integration Of Novel Characteristics And Behaviors Into Synthetic Cell Membranes, Danielle S. Konetski

Chemical & Biological Engineering Graduate Theses & Dissertations

This thesis investigated the coupling of lysolipids and functionalized tails for in situ formation of synthetic liposomes designed to enable specific characteristics or behaviors in applications ranging from drug delivery to the advancement of artificial cell development. Copper-catalyzed Azide-Alkyne Cycloaddition (CuAAC) mediated lipid coupling was improved via incorporation of a photoinitiation system. Here, photo-CuAAC enabled spatiotemporal control over liposome assembly, an over 400-fold increase in formation density, and control over the maximal cross-sectional area of the liposomes formed.

Thiol-Michael mediated lipid coupling was enabled using thiol-functionalized lysolipids and acrylate tails where phospholipids were produced over 48 hours with approximate 90 ...


Modeling And Designing Genetic Devices Using Transcriptional Interference In Escherichia Coli, Antoni Escalas Bordoy Jan 2018

Modeling And Designing Genetic Devices Using Transcriptional Interference In Escherichia Coli, Antoni Escalas Bordoy

Chemical & Biological Engineering Graduate Theses & Dissertations

Microorganisms inhabit every extreme location of our planet. In their journey through the ages, they have been able to incredibly adapt to a myriad of different environmental conditions. A key mechanism for their success has been their ability to respond to environmental and nutritional changes through regulatory programs primarily encoded at the transcriptional level. This adaptability to new environments is what encourages scientists to believe in engineering a biological revolution that will transform our lives due to its potential to result in innovative approaches for bioremediation, sustainable energy production, and biomedical therapies. This thesis explores the potential of the phenomenon ...


Connecting Protein Structure And Dynamics On Biomaterials With The Foreign Body Response, David Faulon Marruecos Jan 2018

Connecting Protein Structure And Dynamics On Biomaterials With The Foreign Body Response, David Faulon Marruecos

Chemical & Biological Engineering Graduate Theses & Dissertations

The harsh environment of the foreign body response (FBR) has the potential to negatively impact the implantations of biomaterials in the body. The FBR is initiated by inflammatory cells that recognize the material as foreign through surface-adsorbed proteins. When proteins interact with surfaces, they can unfold and expose epitopes that may be recognized by immune cells and trigger a series of reactions. Importantly, the presentation of unfolded proteins is directly influenced by the highly dynamic and heterogeneous behavior of proteins in near-surface environments, as well as by the physicochemical features of the underlying surface. Such behavior is the result of ...


Improved Methods For Understanding Sparse, Multi-Dimensional, High Throughput Sequencing Data, Sophie J. Weiss Jan 2015

Improved Methods For Understanding Sparse, Multi-Dimensional, High Throughput Sequencing Data, Sophie J. Weiss

Chemical & Biological Engineering Graduate Theses & Dissertations

Tremendous advances in genetic and sequencing technology are enabling unprecedented insight into human disease, forensics, and cellular mechanisms, to name a few. Conclusions drawn from these studies are strongly influenced by the interpretation of their associated massive data sets. The goal of this thesis is to understand, develop, and apply algorithms to help overcome common ecological and biological sequencing study challenges: contamination, differences in sampling efforts, a very large amount of zeroes, and compositionality.

We use simulations and experimental data to understand how different matrix normalization strategies mitigate the effects of the aforementioned challenges on downstream analyses, particularly principal coordinate ...


The Role Of Matrix Properties In Directing Valvular Interstitial Cell Phenotype, Kelly Marie Pollock Mabry Jan 2015

The Role Of Matrix Properties In Directing Valvular Interstitial Cell Phenotype, Kelly Marie Pollock Mabry

Chemical & Biological Engineering Graduate Theses & Dissertations

This thesis presents the development of hydrogel platforms to study the fibroblast-to-myofibroblast transition in valvular interstitial cells (VICs). These systems were used to characterize the effects of extracellular matrix cues on VICs, as well as the synergies between mechanical and biochemical signals. First, the impact of culture platform on VIC phenotype was assessed by culturing VICs in peptide-functionalized poly(ethylene glycol) hydrogels (2D and 3D) and comparing them to those cultured on tissue culture polystyrene (TCPS). Expression of the myofibroblast marker α-smooth muscle actin (αSMA), as well as by a global analysis of the transcriptional profiles1 demonstrated that TCPS ...


Real-Time Single-Molecule Observations Of Proteins At The Solid-Liquid Interface, Blake Brianna Langdon Jan 2014

Real-Time Single-Molecule Observations Of Proteins At The Solid-Liquid Interface, Blake Brianna Langdon

Chemical & Biological Engineering Graduate Theses & Dissertations

Non-specific protein adsorption to solid surfaces is pervasive and observed across a broad spectrum of applications including biomaterials, separations, pharmaceuticals, and biosensing. Despite great interest in and considerable literature dedicated to the phenomena, a mechanistic understanding of this complex phenomena is lacking and remains controversial, partially due to the limits of ensemble-averaging techniques used to study it. Single-molecule tracking (SMT) methods allow us to study distinct protein dynamics (e.g. adsorption, desorption, diffusion, and intermolecular associations) on a molecule-by-molecule basis revealing the protein population and spatial heterogeneity inherent in protein interfacial behavior. By employing single-molecule total internal reflection fluorescence microscopy ...