Biochemical and Biomolecular Engineering Commons^™

Development Of An In Vitro Platform For The Exploration Of Skeletal Muscle Cell Mechanobiology, Sydney Spradlin

Biomedical Engineering Undergraduate Honors Theses

Muscles have the natural ability to regenerate when damaged. This works to keep the body functioning, unless this ability is overwhelmed. Volumetric muscle loss (VML) occurs when a substantial amount of a muscles mass is lost. This leads to the development of scar tissue, and often a loss of function. In order to find a solution for this condition, in vitro models are needed to explore the mechanobiology of skeletal muscle cells. Two platforms were developed in this study, to explore 3 factors: orientation, strain, and supporting structure. One platform used fibronectin stamped lanes on PDMS to encourage cell growth …

Development Of A Novel Bioactive Glass Suitable For Osteosarcoma-Related Bone Grafts, Alireza Rahimnejad Yazdi, Lawrence Torkan, Stephen D. Waldman, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

In this study, zinc borate-based glasses with increasing gallium content (0, 2.5, 5, 10, and 15 wt % Ga) were synthesized and their effect on the viability and proliferation of preosteoblasts and osteosarcoma cancer cells were investigated. Methyl thiazolyl tetrazolium (MTT) cell viability assays using glass degradation extracts revealed that the extracts from glasses with lower Ga contents could enhance the viability of preosteoblasts, while extracts from the glass composition with 15 wt % Ga caused statistically significant reduction of their viability. MTT cell viability assays using the extracts and osteosarcoma cells showed that only extracts from the glass composition …

Injectable Glass Polyalkenoate Cements: Evaluation Of Their Rheological And Mechanical Properties With And Without The Incorporation Of Lidocaine Hydrochloride, P. Niranjan, A. Alhalawani, S. Phull, I. Beniluz, B. Krishnan, P. Zalzal, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

Lidocaine hydrochloride is used as an anesthetic in many clinical applications. This short communication investigates the effect of complete substitution of lidocaine hydrochloride for deionized (DI) water on the physico-chemical properties of two novel glass polyalkenoate cements. Substituting DI water with lidocaine hydrochloride resulted in cements with shorter working times but comparable setting times and mechanical properties. Fourier transform infrared spectroscopy confirmed that the setting reaction in cements containing DI water and lidocaine hydrochloride was completed within 24 h, post cement preparation and maturation. Further, it was explained that lidocaine hydrochloride binds to poly(acrylic) acid (PAA) due to electrostatic forces …

The Effect Of Mg²⁺ Incorporation Into The Glass Phase Of Zinc-Based Glass Polyalkenoate Cements, Basel A. Khader, Omar Rodriguez, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

The suitability of glass polyalkenoate cements (GPCs) as injectable adhesives in orthopedics have been compromised by the presence of aluminum (Al), a component in the glass phase of all commercial GPCs. There has been considerable work on the development of Al-free GPCs which can be formulated based on calcium (Ca) zinc (Zn) silicate (Si) glasses. These materials, in terms of biocompatibility and mechanical properties, have potential for orthopedics. However, many of these experimental Al-free GPCs have setting times shorter than 60 s, restricting clinical applications. Here, the authors incorporate Magnesium (Mg) into the glass phase of Al-free GPCs in an …

Raman Spectroscopy Predicts The Link Between Claw Keratin And Bone Collagen Structure In A Rodent Model Of Oestrogen Deficiency, M. Clare Caraher, Antonia Sophocleous, J. Renwick Beattie, Olive O'Driscoll, Niamh M. Cummins, Orlaith Brennan, Fergal J. O'Brien, Stuart H. Ralston, Steven E.J. Bell, Mark R. Towler, Aymen I. Idris

Chemical and Biochemical Engineering Faculty Research & Creative Works

Osteoporosis is a common disease characterized by reduced bone mass and an increased risk of fragility fractures. Low bone mineral density is known to significantly increase the risk of osteoporotic fractures; however, the majority of non-traumatic fractures occur in individuals with a bone mineral density too high to be classified as osteoporotic. Therefore, there is an urgent need to investigate aspects of bone health, other than bone mass, that can predict the risk of fracture. Here, we successfully predicted association between bone collagen and nail keratin in relation to bone loss due to oestrogen deficiency using Raman spectroscopy. Raman signal …

A Preliminary Evaluation Of The Ability Of Keratotic Tissue To Act As A Prognostic Indicator Of Hip Fracture Risk, J. Renwick Beattie, Diane Feskanich, M. Clare Caraher, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

Studies have shown that Raman spectroscopic analysis of fingernail clippings can help differentiate between post-menopausal women who have and who have not suffered a fracture. However, all studies to date have been retrospective in nature, comparing the proteins in nails sourced from women, post-fracture. The objective of this study was to investigate the potential of a prospective test for hip fracture based on spectroscopic analysis of nail tissue. Archived toenail samples from post-menopausal women aged 50 to 63 years in the Nurses' Health Study were obtained and analysed by Raman spectroscopy. Nails were matched case-controls sourced from 161 women; 82 …

The Impact Of Gallium Content On Degradation, Bioactivity, And Antibacterial Potency Of Zinc Borate Bioactive Glass, Alireza Rahimnejad Yazdi, Lawrence Torkan, Wendy Stone, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

Zinc borate glasses with increasing gallium content (0, 2.5, 5, 10, and 15 Wt % Ga) were synthesized and their degradation, bioactivity in simulated body fluid (SBF), and antibacterial properties were investigated. ICP measurements showed that increased gallium content in the glass resulted in increased gallium ion release and decreased release of other ions. Degradability declined with the addition of gallium, indicating the formation of more symmetric BO₃ units with three bridging oxygens and asymmetric BO₃ units with two bridging oxygens in the glass network as the gallium content in the series increased. The formation of amorphous Ca-P …

Development Of Entubulation Strategies For Treating Central Nervous System Injuries, Ivy Brosch

Williams Honors College, Honors Research Projects

According to the McKnight Brain Institute, at least 10,000 people annually in the USA suffer from a central nervous system (CNS) injury. These injuries can cause serve disabilities including paralysis. Due to the complexity of the spinal cord, it is common that potential CNS treatments are first applied to an optic nerve crush (ONC) model in rats. Two proposed treatments were employed; one where nerve growth factor (NGF) was immobilized to a chitosan substrate to stimulate axonal regeneration, and the other using pentadecafluorooctanoyl chloride modified methacrylamide chitosan (MAC(Ali15)F) hydrogel to enhance local oxygenation. The two different treatments were formed into …

Molded Features In Pdms For Fabricating Bacterial Cellulose For Various Geometries, Mitchell Habegger

Williams Honors College, Honors Research Projects

The purpose of producing features on bacterial cellulose (BC) is to facilitate the elongation and alignment for cells, in this case Normal Human Dermal Fibroblast (NHDF) cells. The elongated cells have applications in wound healing, tissue engineering, disease diagnostics, and many other fields. Experiments were run to test the effectiveness of transferring features to BC sheets from features induced by fracturing on polydimethylsiloxane (PDMS) and those duplicated from molds with existing features. The features were duplicated to BC sheets by either air drying or Guided Assembly-Based Biolithography (GAB). The research results showed that fracture inducing on PDMS produced very small …

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 …

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 …

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 …

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.

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 …

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 …

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” …

Sugar Versus Lipid For Sustainable Biofuels, Yaşar Demirel

Yaşar Demirel Publications

Introduction

First‐generation biofuels, namely, ethanol and biodiesel, have led to far reaching impact on the peoples’ life world‐wide.[1] However, they inter-fere with the food supply chain and may not be sustainable although some of the biomass are converted to biofuels after those biomasses have met the human needs. Still, the first‐generation–based biofuels have proved that sugar and lipid platforms can be an answer to energy security and global warming concerns without the need for new infrastructure for feedstock delivery as well as for biomass‐to‐biofuel conversion tech-nologies. At the same time, we are discovering and assessing the long‐term environmental im-plications on …

Surface Enabled Lab-On-A-Chip (Loc) Device For Protein Detection And Separation, Zhichao Wang

Dissertations, Master's Theses and Master's Reports

Sensitive and selective chemical/biological detection/analysis for proteins is essential for applications such as disease diagnosis, species phenotype identification, product quality control, and sample examination. Lab-on-a-chip (LOC) device provides advantages of fast analysis, reduced amount of sample requirements, and low cost, to magnificently facilitate protein detection research. Isoelectric focusing (IEF) is a strong and reliable electrophoretic technique capable of discerning proteins from complex mixtures based on the isoelectric point (pI) differences. It has experienced plenty of fruitful developments during previous decades which has given it the capability of performing with highly robust and reproducible analysis. This progress has made IEF devices …

Fabrication Of Flexible, Biofunctional Architectures From Silk Proteins, Ramendra K. Pal

Theses and Dissertations

Advances in the biomedical field require functional materials and processes that can lead to devices that are biocompatible, and biodegradable while maintaining high performance and mechanical conformability. In this context, a current shift in focus is towards natural polymers as not only the structural but also functional components of such devices. This poses material-specific functionalization and fabrication related questions in the design and fabrication of such systems. Silk protein biopolymers from the silkworm show tremendous promise in this regard due to intrinsic properties: mechanical performance, optical transparency, biocompatibility, biodegradability, processability, and the ability to entrap and stabilize biomolecules. The unique …

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

School of Computing: Dissertations, Theses, 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 the …

Subcellular And In-Vivo Nano-Endoscopy, Surya Venkatasekhar Cheemalapati, John Winskas, Hao Wang, Karthik Konnaiyan, Arseny Zhdanov, Alison Roth, Swamy Rakesh Adapa, Andrew Deonarine, Rays H. Y. Jiang, Anna Pyayt

Chemical, Biological and Materials Engineering Faculty Publications

Analysis of individual cells at the subcellular level is important for understanding diseases and accelerating drug discovery. Nanoscale endoscopes allow minimally invasive probing of individual cell interiors. Several such instruments have been presented previously, but they are either too complex to fabricate or require sophisticated external detectors because of low signal collection efficiency. Here we present a nanoendoscope that can locally excite fluorescence in labelled cell organelles and collect the emitted signal for spectral analysis. Finite Difference Time Domain (FDTD) simulations have shown that with an optimized nanoendoscope taper profile, the light emission and collection was localized within ~100 nm. …

Materials And Techniques Used In Cranioplasty Fixation: A Review, Basel A. Khader, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

Cranioplasty is the surgical repair of a deficiency or deformity of the skull. The purpose of cranioplasty is to provide protection for the brain following cranial surgery, and to offer relief to psychological disadvantages while increasing social performance. There are several materials that had been used for cranioplasty, but an ideal product has yet to be developed, hence the ongoing research into biologic and non-biologic alternatives to the existing materials. This article critiques the products currently used for cranioplasty in order to facilitate the development of new materials, which can improve patient outcomes.

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

Yaşar 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 (cradle-to-grave) of both fuels was conducted to investigate …

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

Department of Agricultural and 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 …

Hydrothermal Synthesis And Characterisation Of Bioactive Glass-Ceramic Nanorods, Ehsan Zeimaran, Sara Pourshahrestani, Seyed Farid Seyed Shirazi, Belinda Pingguan-Murphy, Nahrizul Adib Kadri, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

In this study fabrication of rod-like bioactive glass-ceramics (BGCs) using hydrothermal treatment based on a sol-gel precursor is reported for the first time. BGCs with composition 58 wt% SiO₂, 33 wt% CaO and 9 wt% P₂O₅ were synthesized in different thermal conditions (200 and 220 °C) and characterised with regard to morphology, chemical composition and crystallinity. The bioactivity of the materials was assessed by immersion in simulated body fluid for up to 7 days. The results revealed that as the reaction temperature increased from 200 to 220 °C, the diameter of rods was reduced from …