Biochemical and Biomolecular Engineering Commons^™

Creation And Application Of Various Tools For The Reconstruction, Curation, And Analysis Of Genome-Scale Models Of Metabolism, Wheaton L. Schroeder

Department of Chemical and Biomolecular Engineering: Theses and Student Research

Systems biology uses mathematics tools, modeling, and analysis for holistic understanding and design of biological systems, allowing the investigation of metabolism and the generation of actionable hypotheses based on model analyses. Detailed here are several systems biology tools for model reconstruction, curation, analysis, and application through synthetic biology. The first, OptFill, is a holistic (whole model) and conservative (minimizing change) tool to aid in genome-scale model (GSM) reconstructions by filling metabolic gaps caused by lack of system knowledge. This is accomplished through Mixed Integer Linear Programming (MILP), one step of which may also be independently used as an additional curation …

A Gallium-Doped Cement For The Treatment Of Bone Cancers. The Effect Of Zno ↔ Ga2o3substitution Of An Ionomeric Glass Series On The Rheological, Mechanical, Ph And Ion-Eluting Properties Of Their Corresponding Glass Polyalkenoate Cements, Sunjeev Phull, Alireza Rahimnejad Yazdi, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

The primary treatment for patients suffering from bone cancers is resection of the tumor followed by reconstruction of the damaged bone. Despite the administration of post-operative chemotherapy, tumor recurrence continues to present itself as a severe complication leading to re-operation. Attempts to incorporate chemotherapeutic drugs into bone cements elicits local toxic effects on healthy bone, which could compromise implant fixation. Alternatively, the local administration of gallium (Ga) may prove to be more effective. This report considers the development of a Ga ionomeric glass series (0.48SiO₂-0.355ZnO-0.06CaO-0.08SrO-0.02P₂O₅-0.005Ta₂O₅, with 0.01-0.05 mol% substitution for …

Heparan Sulfate Proteoglycan Glypican‑1 And Pecam‑1 Cooperate In Shear‑Induced Endothelial Nitric Oxide Production, Anne Marie W. Bartosch, Rick Mathews, Marwa M. Mahmoud, Limary M. Cancel, Zahin S. Haq, John M. Tarbell

Publications and Research

This study aimed to clarify the role of glypican-1 and PECAM-1 in shear-induced nitric oxide production in endothelial cells. Atomic force microscopy pulling was used to apply force to glypican-1 and PECAM-1 on the surface of human umbilical vein endothelial cells and nitric oxide was measured using a fluorescent reporter dye. Glypican-1 pulling for 30 min stimulated nitric oxide production while PECAM-1 pulling did not. However, PECAM-1 downstream activation was necessary for the glypican-1 force-induced response. Glypican-1 knockout mice exhibited impaired flow-induced phosphorylation of eNOS without changes to PECAM-1 expression. A cooperation mechanism for the mechanotransduction of fluid shear stress …

Exploration Of The Sludge Biodiesel Pathway, Zachary Christman

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Wastewater sludge is an overlooked source of fat, oil, and grease (FOG) that could be converted into biodiesel. The United States produces about 8 million tons of sludge per year. The disposal cost for this amount of sludge is about 2 billion dollars. The widespread availability and low cost of sludge compared to other biodiesel raw materials make it an economical choice for a renewable fuel. Using sludge as a raw material can produce 25 to 30 mg per gram of fatty acid methyl ester (FAME); the main component of biodiesel. Sludge biodiesel has the potential of transforming a portion …

Elucidating Mechanisms And Genotypes Underlying Robust Phenotypes In Yarrowia Lipolytica, Caleb M. Walker

Doctoral Dissertations

Robustness is an important phenotype for bioenergy microbes to acquire but is difficult to engineer. Hence, tools for engineering microbial robustness are critical to unlock novel phenotypes for innovative bioprocessing strategies. The oleaginous yeast, Yarrowia lipolytica, is an exceptionally robust microbe that can tolerate stressful environments, assimilate a wide range of substrates, and produce high-value chemicals. In this doctoral dissertation, the impacts of systems biology and metabolic engineering to reveal mechanisms and identify genotypes- underlying robust phenotypes are addressed.

The first approach employs adaptive laboratory engineering to generate a platform strain by which to study superior robust mechanisms. This …

Engineering Modularity Of Ester Biosynthesis Across Biological Scales, Hyeongmin Seo

Doctoral Dissertations

Metabolic engineering and synthetic biology enable controlled manipulation of whole-cell biocatalysts to produce valuable chemicals from renewable feedstocks in a rapid and efficient manner, helping reduce our reliance on the conventional petroleum-based chemical synthesis. However, strain engineering process is costly and time-consuming that developing economically competitive bioprocess at industrial scale is still challenging. To accelerate the strain engineering process, modular cell engineering has been proposed as an innovative approach that harnesses modularity of metabolism for designing microbial cell factories. It is important to understand biological modularity and to develop design principles for effective implementation of modular cell engineering. In this …

Investigative Study Of Microalgal And Electrochemical Wastewater Treatment Systems And Modeling Of The Wafer-Enhanced Electrodeionization Using Supervised Learning, Humeyra Betul Ulusoy Erol

Graduate Theses and Dissertations

Wastewater has a serious impact on environment and public health due to its high concentration of nutrients and toxic contaminants. Without proper treatment, excess nutrients discharged in wastewater can cause a damage to the ecosystem such as undesirable pH shifts, cyanotoxin production, and low dissolved oxygen concentrations.

Main objectives of this dissertation work were to investigate i) the biofuel potential of P. cruentum when grown in swine wastewater, ii) the influence of four most commonly used ion exchange resins on the system efficiency and selectivity for the removal of sodium, calcium, and magnesium ions, and iii) the modeling of wafer-enhanced …

In Vivo Analysis Of A Proprietary Glass-Based Adhesive For Sternal Fixation And Stabilization Using Rabbit And Sheep Models, Cina Mehrvar, Emily Deignan, Mark Hurtig, Gideon Cohen, Paul Zalzal, Oleg Safir, Adel Alhalawani, Marcello Papini, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

Wire cerclage remains the standard method of care for sternal fixation, following median sternotomy, despite being beset with complications. An emerging treatment option has been to augment the wires with an adhesive. A patented ionomeric glass (mole fraction: SiO₂:0.48, ZnO:0.36, CaO:0.12, SrO:0.04) has been used to formulate GPC+, a glass polyalkenoate cement (GPC), by mixing it with poly(acrylic) acid (PAA) and de-ionized water. In a human cadaver study, this material, when applied with wire cerclage, was able to significantly reduce sternal instability. However, the material has yet to be tested in pertinent animal models. Here, after a series …

Mapping Three Dimensional Interactions Between Biomolecules And Electric Fields., Joseph Patrick Brian P.E.

Electronic Theses and Dissertations

Electroporation is a technique that induces the formation of open pores in cell membranes by the application of an electric field. Electroporation is widely practiced in research and clinical work for transfection of genetic sequences and drug molecule transport through the membrane barrier. However, a full theoretical explanation of the molecular mechanisms and thermodynamics responsible for pore formation, structure, and longevity does not yet exist. Advances in molecular dynamics simulations have enabled theoretical studies of electroporation with previously unobtainable fidelity spanning biologically relevant timescales. All-atom simulations utilizing the recently developed method of computational electrophysiology demonstrate that pore size correlates to …

Design Of An Undergraduate Laboratory Experiment Utilizing A Stirred-Tank, Jacketed Bioreactor, Brennen Middleton

Honors Theses

Bioreactors are utilized in many industries, such as the food, alternative fuel, and pharmaceutical industries, to design and manufacture products. Unlike the similar chemical batch reactors utilized in many chemical processing facilities, bioreactor utilization requires engineers to consider a wider range of operating conditions and parameters. This results in a more complex reaction system and controls network. Due to this, it is imperative for chemical and biomedical engineering students to not only understand the theory surrounding these reactor systems, but also understand how to properly design and perform operating procedures with these systems. Thus, it was determined to create an …

Engineered Switch Protein Inspired By Novel Protein Affinity Transition Mode, Liang Fang

Doctoral Dissertations

Many natural proteins involved in complex biological processes such as ligand binding and protein folding demonstrate multiple, allosterically-regulated conformational states, with protein activity regulated by effector molecules. The alpha L integrin and its inserted domain (I domain) is one example of such a protein. The binding of the effector molecule such as talin or filamin to the cytoplasmic domain of the integrin increases the binding affinity between I- domain and its ligand intercellular adhesion molecule-1, known as ICAM-1.There are multiple models attempting to describe the mechanism responsible for the change in binding affinity. According to research conducted by our lab, …

Development Of An Integrated Salt Cartridge-Reverse Electrodialysis (Red) Device To Increase Electrolyte Concentrations Of Human Blood Flow To Power Biomedical Devices, Caroline Campbell

Chemical Engineering Undergraduate Honors Theses

Emerging technologies in nanotechnology and biomedical sciences have led to an increase in biomedical implantable devices including cardiac pacemakers, artificial organs, drug pumps, and sensors. These devices require continuous stable and reliable power to operate, which creates the demand for the need to find a safe, reliable, and stable power source. A promising avenue for a power source for these devices is a miniaturized reverse electrodialysis (RED) biopower cell design that utilizes the salinity differences between bloodstreams that flow inside the human body. Initial results of the RED system demonstrate that higher gradient salinity differences between streams lead to a …

Growth Viability Assay Assessment For Disinfectant Screening, Paavana Jayaram

Electronic Thesis and Dissertation Repository

Disinfectant screening is an important step for manufacturing and approval of disinfectants. Screening helps identify the effectiveness, target microbe, minimum inhibitory concentration, and contact time. A standard screening test must be able to assess these parameters effectively over a broad range of formulations and microbes. Currently, there is no unified method to analyze disinfectants, a standard test is selected based on the application. This project aimed to identify a standard method that can be used over a broad range of microbes irrespective of disinfectant composition. Microbicidal activity of Hydrogen peroxide and Quaternary ammonium-based disinfectants was evaluated by Fluorescein diacetate (FDA), …

Metabolic Modeling Of Gas Fermentation For Renewable Fuel And Chemical Production, Xiangan Li

Doctoral Dissertations

Gas fermentation has emerged as a technologically and economically attractive option for producing renewable fuels and chemicals from carbon monoxide (CO) rich waste streams. As compared to traditional catalyst technologies, microbial systems have several advantages including operation near ambient temperature and pressure, high conversion efficiencies, robustness to gas impurities and high product yields that have motivated both fundamental research and commercial development. While microbial production of high-value products from waste gases is challenging because wild-type strains capable of gas consumption tend to synthesize these products at low yields, strategy like metabolically engineering the gas fermenting acetogens have been studied to …

Gagrank: Software For Glycosaminoglycan Sequence Ranking Using A Bipartite Graph Model, John D. Hogan, Jiandong Wu, Joshua A. Klein, Cheng Lin, Luis Carvalho, Joseph Zaia

Chemical and Biochemical Engineering Faculty Research & Creative Works

The Sulfated Glycosaminoglycans (GAGs) Are Long, Linear Polysaccharide Chains that Are Typically Found as the Glycan Portion of Proteoglycans. These GAGs Are Characterized by Repeating Disaccharide Units with Variable Sulfation and Acetylation Patterns Along the Chain. GAG Length and Modification Patterns Have Profound Impacts on Growth Factor Signaling Mechanisms Central to Numerous Physiological Processes. Electron Activated Dissociation Tandem Mass Spectrometry is a Very Effective Technique for Assigning the Structures of GAG Saccharides; However, Manual Interpretation of the Resulting Complex Tandem Mass Spectra is a Difficult and Time-Consuming Process that Drives the Development of Computational Methods for Accurate and Efficient Sequencing. …

Hydrothermal Synthesis And Structural Investigation Of A Crystalline Uranyl Borosilicate, Kristen A. Pace, Vladislav V. Klepov, Mark D. Smith, Travis Williams, Gregory Morrison, Jochen A. Lauterbach, Scott T. Misture, Hans Conrad Zur Loye

Faculty Publications

The relevance of multidimensional and porous crystalline materials to nuclear waste reme-diation and storage applications has motivated exploratory research focused on materials discovery of compounds, such as actinide mixed-oxoanion phases, which exhibit rich structural chemistry. The novel phase K1.8 Na1.2 [(UO2)BSi4 O12 ] has been synthesized using hydrothermal methods, rep-resenting the first example of a uranyl borosilicate. The three-dimensional structure crystallizes in the orthorhombic space group Cmce with lattice parameters a = 15.5471(19) Å, b = 14.3403(17) Å, c = 11.7315(15) Å, and V = 2615.5(6) Å3, and is composed of UO6 octahedra linked by [BSi4 O12 ]5− chains to …

Hydrothermal Synthesis And Structural Investigation Of A Crystalline Uranyl Borosilicate, Kristen A. Pace, Vladislav V. Klepov, Mark D. Smith, Travis Williams, Gregory Morrison, Jochen A. Lauterbach, Scott T. Misture, Hans Conrad Zur Loye

Faculty Publications

The relevance of multidimensional and porous crystalline materials to nuclear waste reme-diation and storage applications has motivated exploratory research focused on materials discovery of compounds, such as actinide mixed-oxoanion phases, which exhibit rich structural chemistry. The novel phase K1.8 Na1.2 [(UO2)BSi4 O12 ] has been synthesized using hydrothermal methods, rep-resenting the first example of a uranyl borosilicate. The three-dimensional structure crystallizes in the orthorhombic space group Cmce with lattice parameters a = 15.5471(19) Å, b = 14.3403(17) Å, c = 11.7315(15) Å, and V = 2615.5(6) Å3, and is composed of UO6 octahedra linked by [BSi4 O12 ]5− chains to …

Quantitative Pcr Of Small Nucleic Acids: Size Matters, Jay Min Lim, Rahul Tevatia, Ravi Saraf

Department of Chemical and Biomolecular Engineering: Faculty Publications

Quantitative dysregulation in small nucleic acids (NA), such as microRNA (miRNA), extracted from minimally invasive biopsies, such as, blood, stool, urine, nose, throat, are promising biomarker for diseases diagnosis and management. We quantify the effect of the extra step of poly(A) ligation for cDNA synthesis and small size of the NA on the limit of quantification (LOQ) of quantitative PCR (qPCR), the gold standard to measure copy number. It was discovered that for small NA, the cycle threshold, Ct that is proportional to −log[c], where [c] is the concentration of the target NA exhibits a sharp transition. The results indicate …

Photoluminescent Nanomaterials For Biosensing And Single Cell Analysis Applications, Khashayar Ramezani Bajgiran

LSU Doctoral Dissertations

The bioanalytical industry is projected to generate $36 billion by 2025, with the United States currently holding 80.9% of the consumers’ market. Among the bioanalytical platforms, point-of-care (POC) and point-of-use diagnosis (POU) have gained a lot of attention due to their emphasis on decentralized testing and providing low-cost solutions in resource-limited regions. While Traditional bioanalytical tools such as enzyme-linked immunosorbent assay and flow cytometry can sensitively detect biomolecules and screen single-cell response, they suffer from multiple drawbacks such as the high cost of antibodies and time-intensive procedures, which limit their ability to expand to POC/POU applications. Rapid developments in microtool …

Physical And Chemical Properties, Elemental Composition And Microbiological Purity Of Oil Extract Of Chamomile Flowers In Bitter Almond Oil, Khakim Tukhtaev, Sevara Khazratkulova

CHEMISTRY AND CHEMICAL ENGINEERING

The aim of the study was to obtain an oil extract with the participation of chamomile officinalis (Matrigaria Recutito) grown in the Tashkent region using bitter almond oil (Amygdalus communis L.). Its chromatographic and elemental analyzes have been carried out, its microbiological purity and physicochemical constants have been determined. For extraction, we used bitter almond oil obtained by cold pressing. Extraction of chamomile flowers in bitter almond oil was carried out by maceration in the ratio of raw material: solvent (1:10). Analysis of fatty acids in the fatty extract was carried out chromatographically. The fatty extract was found to contain …

Obtaining Of Bacterial Polysaccharides, Kulonov Abdulaziz, Mirzarakhmetova Dilbar, Turaeva Nigora

CHEMISTRY AND CHEMICAL ENGINEERING

The aim of this work was to develop a technology for obtaining bacterial exopolysaccharides. The problem was solved by using the bacterial strain Halovibrio variabilis UzAS3 as a polysaccharide producer. The optimal parameters of bacterial cultivation have been determined. A technological scheme for obtaining bacterial polysaccharides has been developed, which includes such stages as the cultivation of bacteria, the separation of bacterial biomass from the culture liquid, desalting, precipitation, washing and drying. The obtained results show that bacteria have a high potential for the yield of bacterial exopolysaccharides (7.1-9.5 mg/ml).

Development Of A Recombinant Brewing Yeast To Produce Beer From Hemp Extract (Cannabis Sativa L.), Mehmet Ugur Gulmen

Electronic Thesis and Dissertation Repository

The Cannabis industry is a rapidly-growing market in Canada. With the legalization of edible products in 2019, many cannabis-derived candies, baked goods, beverages appeared on shelves. Cannabis beer can be brewed by replacing barley with pretreated cannabis plant. However, using a traditional brewing yeast to brew cannabis beer will result in incomplete fermentation which will affect the beer’s composition and flavour because traditional brewing yeasts are not able to utilize xylose which is an abundant carbohydrate in lignocellulosic extracts. Using a recombinant strain of a brewing yeast and a xylose-fermenting yeast can overcome this issue. The work presented in this …

Bone Cement As A Local Chemotherapeutic Drug Delivery Carrier In Orthopedic Oncology: A Review, Sunjeev S. Phull, Alireza Rahimnejad Yazdi, Michelle Ghert, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

Metastatic bone lesions are common among patients with advanced cancers. While chemotherapy and radiotherapy may be prescribed immediately after diagnosis, the majority of severe metastatic bone lesions are treated by reconstructive surgery, which, in some cases, is followed by postoperative radiotherapy or chemotherapy. However, despite recent advancements in orthopedic surgery, patients undergoing reconstruction still have the risk of developing severe complications such as tumor recurrence and reconstruction failure. This has led to the introduction and evaluation of poly (methyl methacrylate) and inorganic bone cements as local carriers for chemotherapeutic drugs (usually, antineoplastic drugs (ANPDs)). The present work is a critical …

In Vitro Evaluation Of Novel Titania-Containing Borate Bioactive Glass Scaffolds, Romina Shafaghi, Omar Rodriguez, Anthony W. Wren, Loraine Chiu, Emil H. Schemitsch, Paul Zalzal, Stephen D. Waldman, Marcello Papini, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

Titanium-containing borate bioactive glass scaffolds (0, 5, 15, and 20 mol %, identified as BRT0, BRT1, BRT3, and BRT4) with a microstructure similar to that of human trabecular bone were prepared and evaluated in vitro for potential bone loss applications in revision total knee arthroplasty (rTKA). Methyl thiazolyl tetrazolium (MTT) cell viability assays of scaffold ion release extracts revealed that BRT0 scaffolds (0 mol % titanium) inhibited cell proliferation and activity at day 14. At day 30, all scaffold extracts decreased cell proliferation and activity significantly. However, live/dead cell assay results demonstrated that degradation products from all the scaffolds had …

The 3-O-Sulfation Of Heparan Sulfate Modulates Protein Binding And Lyase Degradation, Pradeep Chopra, Apoorva Joshi, Jiandong Wu, Weigang Lu, Tejabhiram Yadavalli, Margreet A. Wolfert, Deepak Shukla, Joseph Zaia, Geert Jan Boons

Chemical and Biochemical Engineering Faculty Research & Creative Works

Humans Express Seven Heparan Sulfate (HS) 3-O-Sulfotransferases that Differ in Substrate Specificity and Tissue Expression. Although Genetic Studies Have Indicated that 3-O-Sulfated HS Modulates Many Biological Processes, Ligand Requirements for Proteins Engaging with HS Modified by 3-O-Sulfate (3-OS) Have Been Difficult to Determine. in Particular, the Context in Which the 3-OS Group Needs to Be Presented for Binding is Largely Unknown. We Describe Herein a Modular Synthetic Approach that Can Provide Structurally Diverse HS Oligosaccharides with and Without 3-OS. the Methodology Was Employed to Prepare 27 Hexasaccharides that Were Printed as a Glycan Microarray to Examine Ligand Requirements of a …

A Microscale Approach To Investigate Breast Cancer Cellular Communication And Migration, Sharif Mohammad Mizanur Rahman

LSU Doctoral Dissertations

Metastatic breast cancer significantly decreases patient survival, with the majority of deaths caused by secondary metastasis. Cancer metastasis is a multi-step process that starts with the detachment of a cancer cell from the primary tumor and ends with establishing a secondary tumor at a distal location. This work's focus was to use an interdisciplinary microscale approach to study how cancer cells respond to neighboring cells and how they migrate in response to chemical gradients. Two distinct devices, a microfluidic device, and a 3D-printed plate insert, were developed to perform co-culture studies to elucidate the impact of ASCs on cancer cell …

Brownian Dynamics Of Interacting Anisotropic Magnetic Nanoparticles, Daniel Duke

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

Development Of Phagotrophic Algae-Based Process For Conversion Of Waste Organics To Algae Lipids As Potential Feedstock For Biofuel, Hannah Nelson

Williams Honors College, Honors Research Projects

Interest in sustainable feedstock for biofuel has encouraged research on the production of phagotrophic algae from bacteria using a two-staged continuous-flow system. Bacteria cultures were fed the content of a waste stream from The J.M. Smuckers Company containing high concentrations of sugar. In the design, the bacteria effluent overflowed into the algae tank which was kept at a set volume. Several methods were developed to assist in maintaining the system at steady state and minimize the impact from contaminants. A rigorous cleaning protocol was implemented for both tanks, effectively eliminating protozoa from the bacteria system. The protozoa were decreased in …

Effects Of Microporous Structure On The Enzymatic Conversion Of Biomass Using A Multiscale Model, Saketh Merugu

Dissertations, Master's Theses and Master's Reports

The generation of biofuels from lignocellulosic biomass involves innovative process technology that is being investigated worldwide. Enzymatic hydrolysis is a major step in the contemporary process of the generation of biofuels. Guided by pore size distribution measured using NMR cryoporometry, we developed pore-enzyme diffusion and adsorption models at the particle level coupled with a kinetic model for cellulose, cellobiose, and glucose production at flask level. By simulating these models in MATLAB, COMSOL, and Polymath software packages, we investigate the effects of various biomass particle-related parameters (particle dimensions, porosity, enzyme accessibility) on the characteristic time of enzyme diffusion and adsorption and …

Optimization Of Gelatin-Based Cellular Coating Of Msc For Myocardial Infarction Therapy, Kara Amelle Davis

Theses and Dissertations--Chemical and Materials Engineering

Cardiovascular disease remains the number one threat to American lives. During an acute myocardial infarction (AMI), blood flow is blocked and results in the formation of scar tissue. As the body’s immune system responds, inflammatory signaling causes an increase in both scar tissue size and the patient’s risk for further chronic heart failure. In order to reduce the risk of continued heart disease inflammatory signaling must be reduced. Stem cell therapies have the ability to alter the immune system’s pro-inflammatory signal. However, stem cell retention is limited due to blood flow shear. Gelatin methacrylate (GelMA) based coatings have been shown …