Open Access. Powered by Scholars. Published by Universities.®

Biomedical Engineering and Bioengineering Commons

Open Access. Powered by Scholars. Published by Universities.®

Articles 1 - 15 of 15

Full-Text Articles in Biomedical Engineering and Bioengineering

Fibrinogen, Factor Xiii And Fibronectin: A Biophysical And Kinetic Characterization Of Their Interactions, Frank Fabian Jun 2019

Fibrinogen, Factor Xiii And Fibronectin: A Biophysical And Kinetic Characterization Of Their Interactions, Frank Fabian

Chemical & Biomolecular Engineering Theses, Dissertations, & Student Research

The development of recombinant-based liquid fibrin tissue sealants having enhanced hemostatic and wound healing properties will involve understanding as yet not well characterized interactions between fibrinogen, fibrin (Fbn) factor XIII, thrombin and fibronectin. We study these phenomena in the context of comparing plasma derived fibrinogen to recombinant fibrinogen (rFI) produced in the milk of transgenic cows. An abundance of purified γγ and γγ’ FI subspecies enables detailed study of γγ or γγ’ biomonomer and their respective Fbn biopolymer formation as having different substrate behaviors of activated plasma derived factor XIII (pFXIIIa2b2). High pressure size exclusion (HPSEC) and ...


Comparative Kinetic Modeling Of Growth And Molecular Hydrogen Overproduction By Engineered Strains Of Thermotoga Maritima , Raghuveer Singh, Rahul Tevatia, Derrick White, Yasar Demirel, Paul H. Blum Jan 2019

Comparative Kinetic Modeling Of Growth And Molecular Hydrogen Overproduction By Engineered Strains Of Thermotoga Maritima , Raghuveer Singh, Rahul Tevatia, Derrick White, Yasar Demirel, Paul H. Blum

Chemical and Biomolecular Engineering -- All Faculty Papers

Thermotoga maritima is an anaerobic hyperthermophilic bacterium known for its high amounts of hydrogen (H2) production. In the current study, the kinetic modeling was applied on the engineered strains of T. maritima that surpassed the natural H2 production limit. The study generated a kinetic model explaining H2 overproduction and predicted a continuous fermentation system. A Leudking-Piret equation-based model predicted that H2 production by Tma200 (0.217 mol-H2 g–1-biomass) and Tma100 (0.147 mol-H2 g–1-biomass) were higher than wild type (0.096 mol-H2 g–1 -biomass) with reduced rates of ...


Uncoupling Fermentative Synthesis Of Molecular Hydrogen From Biomass Formation In Thermotoga Maritima, Raghuveer Singh, Derrick White, Yaşar Demirel, Robert Kelley, Kenneth Noll, Paul H. Blum Aug 2018

Uncoupling Fermentative Synthesis Of Molecular Hydrogen From Biomass Formation In Thermotoga Maritima, Raghuveer Singh, Derrick White, Yaşar Demirel, Robert Kelley, Kenneth Noll, Paul H. Blum

Chemical and Biomolecular Engineering -- All Faculty Papers

When carbohydrates are fermented by the hyperthermophilic anaerobe Thermotoga maritima, molecular hydrogen (H2) is formed in strict proportion to substrate availability. Excretion of the organic acids acetate and lactate provide an additional sink for removal of excess reductant. However, mechanisms controlling energy management of these metabolic pathways are largely unexplored. To investigate this topic, transient gene inactivation was used to block lactate production as a strategy to produce spontaneous mutant cell lines that overproduced H2 through mutation of unpredicted genetic targets. Single-crossover homologous chromosomal recombination was used to disrupt lactate dehydrogenase (encoded by ldh) with a truncated ldh ...


Genetic Code Expansion In Biochemical Investigations And Biomedical Applications, Nanxi Wang Apr 2017

Genetic Code Expansion In Biochemical Investigations And Biomedical Applications, Nanxi Wang

Student Research Projects, Dissertations, and Theses - Chemistry Department

Genetic code expansion provides a powerful tool for site-specific incorporation of unnatural amino acids (unAAs) with novel biochemical and physiological properties into proteins in live cells and organisms. To achieve this, a nonsense codon suppression system, which consists of an orthogonal aminoacyl-tRNA synthetase (aaRS) and tRNA pair that specifically decodes a nonsense codon (e.g., amber codon and quadruplet codon) with an unAA but do not “cross talk” with their endogenous counterparts, was established. This Ph.D. thesis presents our efforts on evolution and application of nonsense codon suppression systems for biochemical and biomedical investigations.

In Chapter 1, a brief ...


Characterization Of Molecular Communication Based On Cell Metabolism Through Mutual Information And Flux Balance Analysis, Zahmeeth Sayed Sakkaff Dec 2016

Characterization Of Molecular Communication Based On Cell Metabolism Through Mutual Information And Flux Balance Analysis, Zahmeeth Sayed Sakkaff

Computer Science and Engineering: Theses, Dissertations, and Student Research

Synthetic biology is providing novel tools to engineer cells and access the basis of their molecular information processing, including their communication channels based on chemical reactions and molecule exchange. Molecular communication is a discipline in communication engineering that studies these types of communications and ways to exploit them for novel purposes, such as the development of ubiquitous and heterogeneous communication networks to interconnect biological cells with nano and biotechnology-enabled devices, i.e., the Internet of Bio-Nano Things. One major problem in realizing these goals stands in the development of reliable techniques to control the engineered cells and their behavior from ...


Methanol And Dimethyl Ether From Renewable Hydrogen And Carbon Dioxide: Alternative Fuels Production And Life-Cycle Assessment, Michael J. Matzen, Yaşar Demirel Sep 2016

Methanol And Dimethyl Ether From Renewable Hydrogen And Carbon Dioxide: Alternative Fuels Production And Life-Cycle Assessment, Michael J. Matzen, Yaşar Demirel

Yasar Demirel Publications

In this work we investigate two renewably based alternative fuels; methanol and dimethyl ether. The ultimate feedstocks for production are wind-based electrolytic hydrogen and carbon dioxide captured from an ethanol fermentation process. Dimethyl ether production was modeled in ASPEN Plus using a previously simulated methanol production facility. The facilities use 18.6 metric tons (mt) of H2 and 138.4 mt CO2 per day. Methanol is produced at a rate 96.7 mt/day (99.5 wt%) and dimethyl ether is produced at a rate of 68.5 mt/day (99.6 wt%). A full comparative life-cycle assessment ...


Alginate Hydrogels As Three-Dimensional Scaffolds For In Vitro Culture Models Of Growth Plate Cartilage Development And Porcine Embryo Elongation, Taylor D. Laughlin Jul 2016

Alginate Hydrogels As Three-Dimensional Scaffolds For In Vitro Culture Models Of Growth Plate Cartilage Development And Porcine Embryo Elongation, Taylor D. Laughlin

Biological Systems Engineering--Dissertations, Theses, and Student Research

The establishment of in vitro culture models utilizes tissue engineering principles to design functional mimics of in vivo environments in vitro. Advantages for the use of in vitro culture models include ethical alleviation of animal models for therapeutic testing, cost efficiency, and a greater ability to study specific mechanisms via a systematic, ground-up approach to development. In this thesis, alginate hydrogels are utilized in the development of in vitro culture models of porcine embryo elongation and growth plate cartilage development. First, the effect of scaffold and modifications to the scaffold were explored in both projects. In order to modulate cell-scaffold ...


Sustained Cell Differentiation Of 2d H9 Human Embryonic Stem Cells Into Mesenchymal Stem Cells, Hannah M. Christian Apr 2016

Sustained Cell Differentiation Of 2d H9 Human Embryonic Stem Cells Into Mesenchymal Stem Cells, Hannah M. Christian

UCARE Research Products

This experiment consisted of the controlled differentiation of H9 embryonic stem cells to mesenchymal stem cells. Though this experiment was repeated twice and improvement was seen in these repetitions, the cells were only able to be partially differentiated. However, the morphology of the differentiated cells is similar to those of healthy adult mesenchymal stem cells.

The progression of the differentiation can be seen in the microscope slide photos below. Throughout the differentiation, there occurred a decrease in cell survival and reduction of cell growth, but an increase in mesenchymal stem cell morphology. Throughout the last week of the differentiation, very ...


Brain Tumor In A Dish: Glioma/Astrocyte Co-Cultures As A Model For In Vitro Studies, Erin Eickman, Christina Wilson, Srivatsan Kidambi Apr 2016

Brain Tumor In A Dish: Glioma/Astrocyte Co-Cultures As A Model For In Vitro Studies, Erin Eickman, Christina Wilson, Srivatsan Kidambi

UCARE Research Products

This study seeks to engineer an in vitro co-culture model to elucidate the role of glioma-astrocyte interactions on molecular changes in the tumor microenvironment. The use of patterned co-cultures created with polyelectrolyte multilayers and micromolding in capillaries will allow tthe investigation of cell-cell communication. This study will lead to better understanding of the role of healthy cells in cancer progression and potential treatment options.


Protein-Targeted Corona Phase Molecular Recognition, Gili Bisker, Juyao Dong, Hoyoung D. Park, Nicole M. Iverson, Jiyoung Ahn, Justin T. Nelson, Markita P. Landry, Sebastian Kruss, Michael S. Strano Jan 2016

Protein-Targeted Corona Phase Molecular Recognition, Gili Bisker, Juyao Dong, Hoyoung D. Park, Nicole M. Iverson, Jiyoung Ahn, Justin T. Nelson, Markita P. Landry, Sebastian Kruss, Michael S. Strano

Biological Systems Engineering: Papers and Publications

Corona phase molecular recognition (CoPhMoRe) uses a heteropolymer adsorbed onto and templated by a nanoparticle surface to recognize a specific target analyte. This method has not yet been extended to macromolecular analytes, including proteins. Herein we develop a variant of a CoPhMoRe screening procedure of single-walled carbon nanotubes (SWCNT) and use it against a panel of human blood proteins, revealing a specific corona phase that recognizes fibrinogen with high selectivity. In response to fibrinogen binding, SWCNT fluorescence decreases by >80% at saturation. Sequential binding of the three fibrinogen nodules is suggested by selective fluorescence quenching by isolated sub-domains and validated ...


Noninvasive Measurement Of Electrical Events Associated With A Single Chlorovirus Infection Of A Microalgal Cell, Seung-Woo Lee, Eun-Hee Lee, Gerhard Thiel, James L. Van Etten, Ravi Saraf Jan 2016

Noninvasive Measurement Of Electrical Events Associated With A Single Chlorovirus Infection Of A Microalgal Cell, Seung-Woo Lee, Eun-Hee Lee, Gerhard Thiel, James L. Van Etten, Ravi Saraf

Chemical and Biomolecular Engineering -- All Faculty Papers

Chlorovirus Paramecium bursaria chlorella virus 1 (PBCV-1) contains a viral-encoded K+ channel imbedded in its internal membrane, which triggers host plasma membrane depolarization during virus infection. This early stage of infection was monitored at high resolution by recording the cell membrane depolarization of a single Chlorella cell during infection by a single PBCV-1 particle. The measurement was achieved by depositing the cells onto a network of one-dimensional necklaces of Au nanoparticles, which spanned two electrodes 70 μm apart. The nanoparticle necklace array has been shown to behave as a single-electron device at room temperature. The resulting electrochemical field-effect transistor (eFET ...


Technoeconomics And Sustainability Of Renewable Methanol And Ammonia Productions Using Wind Power-Based Hydrogen, Michael J. Matzen, Mahdi H. Alhajji, Yasar Demirel Jan 2015

Technoeconomics And Sustainability Of Renewable Methanol And Ammonia Productions Using Wind Power-Based Hydrogen, Michael J. Matzen, Mahdi H. Alhajji, Yasar Demirel

Yasar Demirel Publications

This study analyzes and compares the economics and sustainability aspects of two hydrogenation processes for producing renewable methanol and ammonia by using wind-power based electrolytic hydrogen. Carbon dioxide from an ethanol plant is used for producing methanol, while the nitrogen is supplied by an Air Separation Unit (ASU) for producing ammonia. The capacities are 99.96 mt/day methanol and 1202.55 mt/day anhydrous ammonia. The methanol plant requires 138.37 mt CO2/day and 19.08 mt H2/day. The ammonia is synthesized by using 217.72 mt H2/day and 1009.15 mt N ...


Low Molecular Weight Glucosamine/L-Lactide Copolymers As Potential Carriers For The Development Of A Sustained Rifampicin Release System: Mycobacterium Smegmatis As A Tuberculosis Model, Jorge Ragusa Dec 2014

Low Molecular Weight Glucosamine/L-Lactide Copolymers As Potential Carriers For The Development Of A Sustained Rifampicin Release System: Mycobacterium Smegmatis As A Tuberculosis Model, Jorge Ragusa

Chemical & Biomolecular Engineering Theses, Dissertations, & Student Research

Tuberculosis, a highly contagious disease, ranks as the second leading cause of death from an infectious disease, and remains a major global health problem. In 2013, 9 million new cases were diagnosed and 1.5 million people died worldwide from tuberculosis. This dissertation aims at developing a new, ultrafine particle-based efficient antibiotic delivery system for the treatment of tuberculosis. The carrier material to make the rifampicin (RIF)-loaded particles is a low molecular weight star-shaped polymer produced from glucosamine (molecular core building unit) and L-lactide (GluN-LLA). Stable particles with a very high 50% drug loading capacity were made via electrohydrodynamic ...


Synthesis Of An Endothelial Cell Mimicking Surface Containing Thrombomodulin And Endothelial Protein C Receptor, Karl E. Kador Apr 2010

Synthesis Of An Endothelial Cell Mimicking Surface Containing Thrombomodulin And Endothelial Protein C Receptor, Karl E. Kador

Chemical & Biomolecular Engineering Theses, Dissertations, & Student Research

Synthetic materials for use in blood contacting applications have been studied for many years with limited success. One of the main areas of need for these materials is the design of synthetic vascular grafts for use in the hundreds of thousands of patients who have coronary artery bypass grafting, many without suitable veins for autologous grafts. The design of these grafts is constrained by two common modes of failure, the formation of intimal hyperplasia (IH) and thrombosis. IH formation has been previously linked to a mismatching of the mechanical properties of the graft and has been overcome by creating grafts ...


Simulation Of Corn Stover And Distillers Grains Gasification With Aspen Plus, Ajay Kumar, Hossein Noureddini, Yasar Demirel, David Jones, Milford Hanna Jan 2009

Simulation Of Corn Stover And Distillers Grains Gasification With Aspen Plus, Ajay Kumar, Hossein Noureddini, Yasar Demirel, David Jones, Milford Hanna

Yasar Demirel Publications

A model was developed to simulate the performance of a lab‐scale gasifier and predict the flowrate and composition of product from given biomass composition and gasifier operating conditions using Aspen Plus software. Mass balance, energy balance, and minimization of Gibbs free energy during the gasification were applied to determine the product gas composition. Carbon conversion efficiency and tar content were provided to the model as inputs as these could not be predicted by the model based on minimization of Gibbs free energy. Experiments for validation of the model were performed on a lab‐scale fluidized bed gasifier using corn ...