Biochemical and Biomolecular Engineering Commons^™

Computational And Experimental Determination Of The Mixing Efficiency Of A Microfluidic Serpentine Micromixer, Siril Arockiam

Theses

In microfluidics, efficiency and mixing time are the greatest disadvantages. These parameters hinder the application of microfluidic devices for biochemical and immunological assays. However, once these disadvantages have been overcome by optimizing the parameters of the microfluidic device, it becomes the important analytical tool. In this experiment, various designs of microfluidic devices have been both simulated using COMSOL software, and experimentally verified to obtain the optimized parameter such as depth and velocity for better mixing efficiency. The COMSOL model has been validated by comparing the results with fluorescent images data of the experiment. The microfluidic device is built with Adhesive …

Removal Of Organic Material In Free Water Surface Gravel Bed Filters, Aloyce Mayo

Tanzania Journal of Engineering and Technology (TJET)

The removal of organic material in free surface gravel bed filters was investigated and modelled. Two pilot wetland units of 7.5m x 1.5m x 0.7m were constructed adjacent to the University of Dar es Salaam waste stabilization ponds to receive maximum organic and hydraulic loading rates of less than 185 kg/ha/d and 110 l/m2/d, respectively. These units received wastewater of domestic characteristics from primary stabilization pond. The entire depth of 0.7 m of the wetland units were packed with gravel of size 8 ~ 25 mm and porosity of 35%. Samples were collected from the influent and effluent of wetland …

The Role Of Catalytic Residue PKA On The Hydrolysis/Transglycosylation Partition In Family 3 Β-Glucosidases, Inacrist Geronimo, Christina M. Payne, Mats Sandgren

Chemical and Materials Engineering Faculty Publications

β-Glucosidases (βgls) primarily catalyze the hydrolysis of the terminal glycosidic bond at the non-reducing end of β-glucosides, although glycosidic bond synthesis (called transglycosylation) can also occur in the presence of another acceptor. In the final reaction step, the glucose product or another substrate competes with water for transfer to the glycosyl-enzyme intermediate. The factors governing the balance between the two pathways are not fully known; however, the involvement of ionizable residues in binding and catalysis suggests that their pK_a may play a role. Through constant pH molecular dynamics simulations of a glycoside hydrolase Family 3 (GH3) βgl, we …

Reducing Biomass Recalcitrance By Heterologous Expression Of A Bacterial Peroxidase In Tobacco (Nicotiana Benthamiana), Ayalew Ligaba-Osena, Bertrand Hankoua, Kay Dimarco, Robert Pace, Mark Crocker, Jesse Mcatee, Nivedita Nagachar, Ming Tien, Tom L. Richard

Center for Applied Energy Research Faculty and Staff Publications

Commercial scale production of biofuels from lignocellulosic feed stocks has been hampered by the resistance of plant cell walls to enzymatic conversion, primarily owing to lignin. This study investigated whether DypB, the lignin-degrading peroxidase from Rodococcus jostii, depolymerizes lignin and reduces recalcitrance in transgenic tobacco (Nicotiana benthamiana). The protein was targeted to the cytosol or the ER using ER-targeting and retention signal peptides. For each construct, five independent transgenic lines were characterized phenotypically and genotypically. Our findings reveal that expression of DypB in the cytosol and ER does not affect plant development. ER-targeting increased protein accumulation, and …

Nanoparticle-Based Plasmonic Transduction For Modulation Of Electrically Excitable Cells, Parveen Bazard, Robert D. Frisina, Joseph P. Walton, Venkat R. Bhethanabotla

Chemical and Biochemical Engineering Faculty Research & Creative Works

There is a compelling need for the development of new sensory and neural prosthetic devices which are capable of more precise point stimulation. Current prosthetic devices suffer from the limitation of low spatial resolution due to the non-specific stimulation characteristics of electrical stimulation, i.e., the spread of electric fields generated. We present a visible light stimulation method for modulating the firing patterns of electrically excitable cells using surface plasmon resonance phenomena. In in-vitro studies using gold (Au) nanoparticle-coated nanoelectrodes, we show that this method (substrate coated with nanoparticles) has the potential for incorporating this new technology into neural stimulation prosthetics, …

Peptoid-Modified Bicelles As Surrogate Cell Membranes For Membrane Protein Sensors And Analytics, Helya Najafi

Graduate Theses and Dissertations

Membrane-affiliated interactions are significant in understanding cell function, detecting biomarkers to diagnose disease, and in testing the efficiency of new therapeutic targets. Model membrane systems have been developed to study membrane proteins, allowing for stable protein structure and maintaining native activity. Bicelles, disc-shaped lipid bilayers created by combining long- and short-chain phospholipids, are the model membrane system of focus in this study. Bicelles are accessible from both sides and have a wide size range, which make them attractive for studying membrane proteins without affecting function. In this work, bicelles were functionalized with two peptoids to alter the edge and face …

High-Throughput Droplet Barcoding And Automated Image Analysis In Microfluidic Droplet Trapping Array, Manibarathi Vaithiyanathan

LSU Master's Theses

Molecularly-targeted therapeutics and personalized medicine have dramatically increased the median survival rate of patients suffering from cancer. However, cellular heterogeneity and the personalized nature of cancer have resulted in the limited success of single drug treatments which has led to the use of multiple therapeutic combinations. This has required the development of new analytical methods capable of multiplexed high-throughput screening (HTS) technologies necessary to identify is single or multi-agent therapies are effective in ex vivo samples like liquid biopsies. Droplet microfluidic devices have garnered significant interest to facilitate high-throughput, single cell analysis of heterogeneous populations. However, these devices are still …

Titanium Addition Influences Antibacterial Activity Of Bioactive Glass Coatings On Metallic Implants, Omar Rodriguez, Wendy Stone, Emil H. Schemitsch, Paul Zalzal, Stephen Waldman, Marcello Papini, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

In an attempt to combat the possibility of bacterial infection and insufficient bone growth around metallic, surgical implants, bioactive glasses may be employed as coatings. In this work, silica-based and borate-based glass series were synthesized for this purpose and subsequently characterized in terms of antibacterial behavior, solubility and cytotoxicity. Borate-based glasses were found to exhibit significantly superior antibacterial properties and increased solubility compared to their silica-based counterparts, with BRT0 and BRT3 (borate-based glasses with 0 and 15 mol% of titanium dioxide incorporated, respectively) outperforming the remainder of the glasses, both borate and silicate based, in these respects. Atomic Absorption Spectroscopy …

Potency And Cytotoxicity Of A Novel Gallium-Containing Mesoporous Bioactive Glass/Chitosan Composite Scaffold As Hemostatic Agents, Sara Pourshahrestani, Ehsan Zeimaran, Nahrizul Adib Kadri, Nicola Gargiulo, Hassan Mahmood Jindal, Sangeetha Vasudevaraj Naveen, Shamala Devi Sekaran, Tunku Kamarul, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

Chitosan-based hemostats are promising candidates for immediate hemorrhage control. However, they have some disadvantages and require further improvement to achieve the desired hemostatic efficiency. Here, a series of 1% Ga2O3-containing mesoporous bioactive glass-chitosan composite scaffolds (Ga-MBG/CHT) were constructed by the lyophilization process and the effect of various concentrations of Ga-MBG (10, 30, and 50 wt %) on the hemostatic function of the CHT scaffold was assessed as compared to that of Celox Rapid gauze (CXR), a current commercially available chitosan-coated hemostatic gauze. The prepared scaffolds exhibited >79% porosity and showed increased water uptake compared to that in CXR. The results …

Advancement Of Oxygen Biosensor In Escherichia Coli, Caitlyn Meiser

Rose-Hulman Undergraduate Research Publications

Microbial biosensors can be used to provide information about the cells’ environment in large-scale fermentations. In this project an oxygen sensitive biosensor is being developed in Escherichia coli to determine what kind of conditions cells are growing in: aerobic or anaerobic. This project specifically studies expression from the fumarate and nitrate reductase (FNR) promoter (P_FNR) under aerobic and anaerobic conditions. In fluorescence experiments, the expression levels of green fluorescent protein (GFP) were used to quantify the effectiveness of the P_FNR in the DH5α, MG1655 and BL21 strains of E. coli. The negative control of the experiments, …

Effects Of Filtration Conditions On Clearance Of Bacteriophage, Rigen Te

Graduate Theses and Dissertations

Virus Clearance is one of the major challenges in biopharmaceutical industry, especially in the manufacturing of drugs. U.S. Food and Drug Administration (FDA) recommends using several model bacteriophages as surrogates of pathogenic mammalian virus for process validation. In this work, two bacteriophages were tested against 30 kDa, 100 kDa, 300 kDa polyethersulfone (PES) membranes to investigate the effects of pore size on virus clearance. Virus particles were spiked into the protein feed solutions containing bovine serum albumin (BSA) or lysozyme at different concentrations. Besides protein concentration, the effects of feed pH on the filtration performance and virus rejection were also …

Peptoid-Based Microsphere Coatings For Use As Tunable Biocompatible Interfaces, German Raul Perez Bakovic

Graduate Theses and Dissertations

The pursuit of sensitive, non-invasive, and cost efficient diagnostic tools for early stage disease detection have led to the development of sophisticated biosensor technologies for proteomic studies. As these markers increase in complexity, the role of support substrates grows increasingly important. Limitations in existing support substrates include the potential for increased sensitivity, binding specificity, and bio-stability. Ideal support substrates need to provide biocompatible and bioresistant surfaces, that offer high surface areas for binding, and enables the incorporation of diverse chemistries. The use of peptoids as the basis for the deposition of uniform microsphere coatings offers a mean to the attainment …

Identification Of Developmental Stage And Anatomical Fraction Contributions To Cell Wall Recalcitrance In Switchgrass, Jacob D. Crowe, Nicholas Feringa, Sivakumar Pattathil, Brian Merritt, Cliff Foster, Dayna Dines, Rebecca Ong, David B. Hodge

Department of Chemical Engineering Publications

Background

Heterogeneity within herbaceous biomass can present important challenges for processing feedstocks to cellulosic biofuels. Alterations to cell wall composition and organization during plant growth represent major contributions to heterogeneity within a single species or cultivar. To address this challenge, the focus of this study was to characterize the relationship between composition and properties of the plant cell wall and cell wall response to deconstruction by NaOH pretreatment and enzymatic hydrolysis for anatomical fractions (stem internodes, leaf sheaths, and leaf blades) within switchgrass at various tissue maturities as assessed by differing internode.

Results

Substantial differences in both cell wall composition …

Raman Spectral Variation For Human Fingernails Of Postmenopausal Women Is Dependent On Fracture Risk And Osteoporosis Status, J. R. Beattie, M. C. Caraher, N. M. Cummins, O. M. O'Driscoll, R. Eastell, S. H. Ralston, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

Patients diagnosed with osteoporosis have reported loss of fingernail resilience as the disease progresses. Keratin is the predominant protein in human nail tissue, and its structure has been postulated to be different in fingernails clipped from subjects who have sustained fragility fractures and those who have not, which may offer a window into the donor's bone health. This study was designed to qualify these differences, which may lead to the development of a novel screening tool for fracture risk. Raman spectroscopy was used to measure the fingernails of 633 postmenopausal women who presented at six fracture clinics located across the …

Common Treatments And Procedures Used For Fractures Of The Distal Radius And Scaphoid: A Review, Basel A. Khader, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

The distal radius and the scaphoid are the most commonly injured carpal bones among both active adults and the osteoporotic elderly. The purpose of surgical treatment is to restore form and function to the wrist. Depending on the nature of the fracture, either topical procedures or invasive surgery can be applied. This article critiques the treatments currently used for fixation of wrist fractures in order to drive the development of new materials to improve patient outcomes.

An Expedited, Regiospecific Para-Bromination Of Activated Aryls, Kathryn E. Dudley

Masters Theses & Specialist Projects

Electrophilic Aromatic Substitution (EAS) is one of the most frequently used aryl substitution methods. Aside from the fact that most EAS reactions require an acid and an oxidizer to proceed, the reactions involving activated aryls typically produce a mixture of ortho- and para- products as well as an ortho-/para- disubstituted product. Regiospecificity in aromatic substitution is key in the production of many compounds in a variety of disciplines. Since EAS is one of the most often used substitution methods, it is extremely important to develop an efficient method for regiospecific substitutions. Previous research developed a method of ortho-substitution by using …

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

Department of Chemistry: Dissertations, Theses, and Student Research

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 overview of …

A Novel Tantalum-Containing Bioglass. Part I. Structure And Solubility, Adel Mf Alhalawani, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

Bio glasses are employed for surgical augmentation in a range of hard tissue applications. Tantalum is a bioactive and biocompatible transition metal that has been used as an orthopedic medical device. It has a range of biological and physical properties that make its incorporation into ionic form into bioactive glass systems promising for various clinical applications. The work herein reports the characterization and properties of novel tantalum-containing glasses. A series of glasses based on the system 48SiO₂-(36-X)ZnO-6CaO-8SrO-2P₂O₅-XTa₂O₅ with X varying from 0 mol% (TA0) to 0.5 mol% (TA2) were synthesized. The …

Characterization And Fracture Property Of Different Strontium-Containing Borate-Based Glass Coatings For Ti6al4v Substrates, Yiming Li, Ali Matinmanesh, Declan J. Curran, Emil H. Schemitsch, Paul Zalzal, Marcello Papini, Anthony W. Wren, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

This work considered the effect of increasing Strontium ion (Sr²⁺) content on the structure of a series of glasses based on the B₂O₃-P₂O₅-CaCO₃-Na₂CO₃-TiO₂-SrCO₃ series and their resultant fracture toughness when coated onto a surgical metal substrate. Six glasses with increasing Sr²⁺ content (0 to 25 mol%) were synthesized and subsequently characterized by X-ray Diffraction (XRD), Differential Thermal Analysis (DTA) and both Magic Angle Spinning Nuclear Magnetic Resonance (MAS-NMR) and Raman Spectroscopy. These techniques confirmed that increased Sr²⁺ content induced …

High-Density Non-Fouling Bioactive Coatings: Development And Characterization, Bonan Yu, Ramya Raman, Karl Schlike

Biomedical Engineering Western Regional Conference

No abstract provided.

Molecular Modeling Of Antibody-Antigen Binding Near Solid Surfaces, Derek Bush, Thomas Knotts

Biomedical Engineering Western Regional Conference

Antibody microarrays are biosensors that have the potential to revolutionize molecular detection in medicine, scientific research, and national defense. However, current microarrays are not widely used due to problems including poor reproducibility and signal quality, unbalanced antibody performance, and cross-reactivity. Prior work in the area focused mainly on the stability of the antibody alone and not its affinity for its antigen. This presentation shows results of using molecular simulation to determine how different types of surfaces affect antigen binding to surface-tethered antibodies. The results offer an unprecedented, molecular-level view into these protein-protein-surface interactions and how to drive binding to occur.

A Novel Tantalum-Containing Bioglass. Part Ii. Development Of A Bioadhesive For Sternal Fixation And Repair, Adel Mf Alhalawani, Cina Mehrvar, Wendy Stone, Stephen D. Waldman, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

With over a million median sternotomy surgeries performed worldwide every year, sternal wound complications have posed a serious risk to the affected patients. A rigid therapeutic sternal fixation device has therefore become a necessity. In this work, the incorporation of up to 0.5 mol% of tantalum pentoxide (Ta₂O₅), in exchange for zinc oxide (ZnO), into the SiO₂-ZnO-CaO-SrO-P₂O₅ glass system is presented. The effect of Ta incorporation on the physical, chemical and biological properties of the glass polyalkenoate cements (GPCs) prepared from them have been presented in this manuscript. The data obtained …

Novel Experimental Method For The Determination Of The Minimum Agitation Speed For Solids Suspension In Flat-Bottomed Stirred Tank Reactors, Shriarjun Shastry

Theses

Knowledge of the minimum agitation speed, Njs, required to suspend finely divided solids in vessels stirred by an impeller is a critical parameter to properly operate industrial tanks in a large number of industrial operations. The most common experimental approach to measure N_js is that of Zwietering’s (Chem. Eng. Sci., 1958, 8, 244-253), consisting of visually inspecting the tank bottom and visually determining the impeller agitation speed at which the solids are observed to rest on the tank bottom for no more than 1-2 seconds before being swept away. This method is quite reliable, but a method …

Engineering A Fluorescent Protease Sensor For In Vivo Protein Detection, Thomas C. Kinard

Honors Scholar Theses

This report details the results of an ongoing project to engineer a mutant form of Red Fluorescent Protein (RFP) variant mCherry that acts as a real-time in vivo protease sensor. The sought-after mutant only becomes fluorescent when exposed to Tobacco Etch Virus (TEV) Protease, this system’s model protease. This will be accomplished via the insertion of the TEV Protease Recognition Site (TEV-PRS) in such a position that, before cleavage, will prevent the protein from folding to fluorescent conformation, but upon cleavage, will allow for fluorescent conformation to occur. The cylindrical structure of the protein, composed of beta-pleated sheets, contains “loops” …

Development And Validation Of A Kinetic Model For Enzymatic Hydrolysis Using Candida Rugosa Lipase, Ammar Jamie, Ali Alshami, Zuhair O. Maliabari, Muataz A. Ateih

Chemical Engineering Faculty Publications

Biochemical processing involving enzymatic catalysis of hydrolysis reactions of oils and fats must overcome significant technological barriers before the full benefits of the technology can be realized. Owing to their selectivity and mild reaction conditions, lipases are becoming increasingly important as biocatalysts provided that their kinetics and optimum reaction conditions are well-understood. In this study we report on the development and validation of a kinetic model for the degradation of oils using Candida rugosa lipase, from which a better understanding of the influence of different reaction conditions on hydrolysis kinetics is elucidated. Variations of reaction temperature, mixing speed, enzyme loading …

Selection Criteria For Miscible-Gases To Enhance Oil Recovery In Unconventional Reservoirs Of North America, Dheiaa Alfarge, Mingzhen Wei, Baojun Bai, Mortadha Alsaba

Geosciences and Geological and Petroleum Engineering Faculty Research & Creative Works

Unconventional resources have played a significant role in changing oil industry plans recently. Shale formations in North America such as Bakken, Niobrara, and Eagle Ford have huge oil in place, 100-900 billion barrels of oil in Bakken only. However, the predicted primary recovery is still low as 5-10%. Therefore, seeking for techniques to enhance oil recovery in these complex plays is inevitable. In this paper, two different approaches have been integrated to investigate the feasibility of three different miscible gases which are CO₂, lean gases, and rich gases. Firstly, numerical simulation methods of compositional models have been incorporated …

Optimizing Injector-Producer Spacing For Co2 Injection In Unconventional Reservoirs Of North America, Dheiaa Alfarge, Mingzhen Wei, Baojun Bai, Abdullah Almansour

Geosciences and Geological and Petroleum Engineering Faculty Research & Creative Works

Shale oil reservoirs such as Bakken, Niobrara, and Eagle Ford have become the main target for oil and gas investors as conventional formations started to deplete and diminish in number. These reservoirs have a huge oil potential; however, the predicted primary oil recovery is still low as average of 7.5 %. Carbon dioxide (CO₂) flooding has been a controversial approach to increase oil recovery in these poor-quality formations. This study investigated the effect of injector-producer spacing, in range of 925-1664 ft, on CO₂ performance in these plays by using numerical simulation methods. CO₂ utilization value under …

Novel Environmentally Benign Hydrogel: Nano-Silica Hybrid Hydrolyzed Polyacrylamide/ Polyethyleneimine Gel System For Conformance Improvement In High Temperature High Salinity Reservoir, Liping Ma, Shitou Wang, Yifu Long, Changqian Zhu, Hongbin Yang, Tangying Yang, Xiaochun Liu, Xiaorong Li, Baojun Bai, Wanli Kang

Geosciences and Geological and Petroleum Engineering Faculty Research & Creative Works

In order to address the conformance problem in high temperature and high salinity/hardness reservoir, an environmentally benign in-situ gel was developed based on hydrolyzed polyacrylamide (HPAM) and polyethyleneimine (PEI). Moreover, silica nanoparticle (SNP) was embedded to improve the performance of HPAM/PEI gel. To achieve the optimum formulation of HPAM/PEI-SNP gel, a comprehensive investigation was first conducted with the respect of gelation time, gel strength, and thermal stability. In addition, the particle size of SNP was determined by Dynamic Light Scatter (DLS) and the microstructure of HPAM/ PEI-SNP gel was characterized via Scanning Electron Microscopy (SEM). The optimum formulation, containing the …

Protein Release Study Using Heparin Modified Methacrylamide Chitosan Hydrogels, Dakotah G. Cox

Williams Honors College, Honors Research Projects

This study was performed to improve the release of proteins from hydrogels in order to increase their effectiveness in treating spinal cord injuries. Heparin, which has the ability to bind to proteins and slow their release, underwent methacrylation, was added to prepared methacrylamide chitosan (MAC) solutions with a model protein (SDF-1α) and photopolymerized to create MAC-heparin hydrogels. Varying weight percentages of methacrylated heparin were tested in order to determine the optimal amount needed to improve the release profile. The pure MAC hydrogels and gels with 10 wt% heparin had a rapid release of the SDF-1α (>23% and >29%, respectively, …

Integrating Microgels And Low Salinity Waterflooding To Improve Conformance Control In Fractured Reservoirs, Ali Alhuraishawy, Mingzhen Wei, Baojun Bai, Abdullah Almansour

Geosciences and Geological and Petroleum Engineering Faculty Research & Creative Works

The recovery from fractured reservoirs is usually low. The areal heterogeneity is one result of the fractured reservoir. Low salinity waterflooding (LSWF) and preformed particle gel (PPG) have recently investigated by some researchers. The main objective of this study was to determine whether the combining technologies can improve conformance control in fractured sandstone reservoirs. Semi-transparent five-spot models made of sandstone cores and acrylic plates were built. The effect of low salinity waterflooding on oil recovery was studied. Models were designed with three parallel open fractures. Sodium chloride (1.0, 0.1, 0.01, and 0.001 wt. % NaCl) were used for brine flooding …