Biochemical and Biomolecular Engineering Commons^™

Post-Translational Modifications And Age-Related Hearing Loss, Parveen Bazard, Jennifer Pineros, Alejandro A. Acosta, Mark Thivierge, Lauren R. Paganella, Samuel Zucker, Freyda L. Mannering, Shrikar Modukuri, Xiaoxia Zhu, Robert D. Frisina, Bo Ding

Chemical and Biochemical Engineering Faculty Research & Creative Works

Post-translational modifications (PTMs) affect nearly all systems of the human body due to their role in protein synthesis and functionality. These reversible and irreversible modifications control the structure, localization, activity, and properties of proteins. For this reason, PTMs are essential in regulating cellular processes and maintaining homeostasis. Diseases such as Alzheimer's, cardiovascular disease, diabetes, cancer, and many others have been linked to dysfunctions of PTMs. Recent research has also shown that irregularities in PTMs can be linked to hearing loss, including age-related hearing loss (ARHL) – the number one communication disorder and one of the top neurodegenerative diseases in our …

Metabolic Engineering Of Yarrowia Lipolytica For Enhanced Peroxisomal Production Of Polyhydroxyalkanoates, Michael Spagnuolo

All Dissertations

Traditional chemical processes are made inefficient by the generation of side products and reactions that fail to reach completion. Bioprocesses, on the other hand, lose product potential due to the necessity of growing the organism required to produce the desired compounds. The field of metabolic engineering often seeks to alter this balance between product formation and cell growth to generate more product from the same quantity of feed (reagent). In addition to balance, such organisms may also be engineered to produce the desired products from nontraditional substrates, such as waste compounds. In resource-poor environments, the ability to produce a wanted …

Investigations Of Prokaryotic Defense Systems, Hannah Domgaard

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Bacteria are constantly threatened with infection by mobile genetic elements (MGE) such as bacteriophage and plasmids. Bacteriophage and plasmids require the bacteria's cellular infrastructure to replicate their genomes. Rampant replication can lead to cell death which is one reason why bacteria have developed a diverse array of immune systems to prevent or limit infection. This thesis studies three types of bacterial immune systems, type IV-A CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeat –CRISPR associated), type V-A2 CRISPR-Cas systems, and Wadjet systems.

The type IV-A system lies adjacent to a dinG-like helicase gene. Research has shown that this system can target …

Enhancing Human Schwann Cells Reparative Behavior Using Heparin/Collagen Layer-By-Layer Coatings, Luis Carlos Pinzon-Herrera

Graduate Theses and Dissertations

When a peripheral nerve injury (PNI) occurs, the gold standard for tissue regeneration is the use of autografts. However, due to the secondary effects produced by multiple surgeries involved in the removal and implantation of autografts for very small lesions, it is possible to replace them with the use of Nerve Guide Conduits (NGCs). However, NGCs are limited to short lesions (less than 1 cm). This limitation is caused by the absence of compounds in the extracellular matrix (ECM) that autografts can provide. Since much of the regenerative process takes place on the NGC surface, our work aims to modify …

Life Cycle Assessment Of Novel Electrochemical Struvite Recovery In Municipal Wastewater Treatment At The Plant And U.S. Watershed Scales, Karla Morrissey

Graduate Theses and Dissertations

As the supply of phosphorus decreases, nutrient recovery in municipal wastewater treatment has become an important area of research. Recovery methods for phosphorus-containing fertilizers, such as struvite, and other products are currently being developed and assessed for their efficiency and economic feasibility. Potential environmental impacts from nutrient recovery are also being assessed as design for the environment is important, especially with regards to the eutrophying potential of phosphorus in phosphorus-limited freshwater aquatic systems. Life cycle assessment (LCA) is a tool that can be used to estimate potential environmental impacts of a product or service focusing on its entire life cycle. …

In Vitro Models For The Study Of Liver Biology And Diseases: Advances And Limitations, Savneet Kaur, Srivatsan Kidambi, Martí Ortega-Ribera, Le Thi Thanh Thuy, Natalia Nieto, Victoria C. Cogger, Wei-Fen Xie, Frank Tacke, Jordi Gracia-Sancho

Department of Chemical and Biomolecular Engineering: Faculty Publications

In vitro models of liver (patho)physiology, new technologies, and experimental approaches are progressing rapidly. Based on cell lines, induced pluripotent stem cells or primary cells derived from mouse or human liver as well as whole tissue (slices), such in vitro single- and multicellular models, including complex microfluidic organ-on-a-chip systems, provide tools to functionally understand mechanisms of liver health and disease. The International Society of Hepatic Sinusoidal Research (ISHSR) commissioned this working group to review the currently available in vitro liver models and describe the advantages and disadvantages of each in the context of evaluating their use for the study of …

Genetic Code Expansion In Pseudomonas Putida Kt2440, Xinyuan He, Tian Gao, Yan Chen, Kun Liu, Jiantao Guo, Wei Niu

Department of Chemical and Biomolecular Engineering: Faculty Publications

Pseudomonas putida KT2440 is an emerging microbial chassis for bio-based chemical production from renewable feedstocks and environmental bioremediation. However, tools for studying, engineering, and modulating protein complexes and biosynthetic enzymes in this organism are largely underdeveloped. Genetic code expansion for the incorporation of unnatural amino acids (unAAs) into proteins can advance such efforts and, furthermore, enable additional controls of biological processes of the strain. In this work, we established the orthogonality of two widely used archaeal tRNA synthetase and tRNA pairs in KT2440. Following the optimization of decoding systems, four unAAs were incorporated into proteins in response to a UAG …

Characterizations And Potential Recovery Pathways Of Phosphate Mines Waste Rocks, Amine El Mahdi Safhi, Hicham Amar, Yahya El Berdai, Mustapha El Ghorfi, Yassine Taha, Rachid Hakkou, Muthanna H. Al-Dahhan, Mostafa Benzaazoua

Chemical and Biochemical Engineering Faculty Research & Creative Works

The Phosphate Ore Production is Steadily Increasing Due to its High Demand for Agriculture, Medicine, and Others. Ore Extraction Generates a Considerable Quantity of Waste Rocks that Are Generally Stocked in Piles. the Current Research Aims to Investigate the Characterization of Phosphate Mine Waste Rocks (PMWR) Generated in Benguerir, Morocco Mine Site. as a Part of a Wide Project Aiming to Recycle Those Stockpiles, Sensor-Based Ore Sorting Will Be Employed to Separate the Different Lithologies. as a Prior Investigation Before Implementing This Technology, Two Samples of 25 Tons from the Destoning and Screening PMWR Piles Were Sampled and Submitted to …

Ab Initio Insight Into The Electrolysis Of Water On Basal And Edge (Fullerene C20) Surfaces Of 4 Å Single-Walled Carbon Nanotubes, Zhen Jiang, Nadia N. Intan, Qiong Yang

Department of Chemical and Biomolecular Engineering: Faculty Publications

The extreme surface reactivity of 4 Å single-walled carbon nanotubes (SWCNTs) makes for a very promising catalytic material, however, controlling it experimentally has been found to be challenging. Here, we employ ab initio calculations to investigate the extent of surface reactivity and functionalization of 4 Å SWCNTs. We study the kinetics of water dissociation and adsorption on the surface of 4 Å SWCNTs with three different configurations: armchair (3,3), chiral (4,2) and zigzag (5,0). We reveal that out of three different configurations of 4 Å SWCNTs, the surface of tube (5,0) is the most reactive due to its small HOMO–LUMO …

Correlating The Macrostructural Variations Of An Ion Gel With Its Carbon Dioxide Sorption Capacity, Tung Nguyen,, Mona Bavarian, Siamak Nejati

Department of Chemical and Biomolecular Engineering: Faculty Publications

We report on a direct correlation between the macroscale structural variations and the gas sorption capacities of an ion gel. Here, we chose 1-ethyl-3-methylimidazolium bis(trifluoromethyl sulfonyl)imide ([Emim][TF₂N]) and poly(vinylidene fluoride)-co-hexafluoropropylene (PVDF-HFP) as the ionic liquid and host polymer, respectively. The CO₂ sorption in the thin films of the IL-polymer was measured using the gravimetric method. The results of our experiment showed that the trend in CO₂ uptake of these mixtures was nonlinearly correlated with the content of IL. Here, we highlight that the variations in the molecular structure of the polymers were the main reason behind …

Wetting Of Paper Towels: A Method To Determine The Two-Dimensional Absorption Capacity, Hossein Abedsoltan

Chemical and Biochemical Engineering Faculty Research & Creative Works

This study proposes a method to determine the two-dimensional absorption capacity of paper towels. Individual plies were tested to minimize the effects of transverse wicking on wetting. The method involves arbitrary point source injection of liquid into the towel surface while recording microscopic images of the wetted areas. The samples were selected from the main manufacturing processes: conventional wet pressing and through-air drying. Wetting graphs that illustrate the dynamic and static wetting behaviors were generated. The driving force was found to have a negligible effect on the maximum wetted area. The maximum wetted area and the paper grammage were used …

Electrophilic Aldehyde 4-Hydroxy-2-Nonenal Mediated Signaling And Mitochondrial Dysfunction, Sudha Sharma, Papori Sharma, Tara Bailey, Susmita Bhattarai, Utsab Subedi, Chloe Miller, Hosne Ara, Srivatsan Kidambi, Hong Sun, Manikandan Panchatcharam, Sumitra Miriyala

Department of Chemical and Biomolecular Engineering: Faculty Publications

Reactive oxygen species (ROS), a by-product of aerobic life, are highly reactive molecules with unpaired electrons. The excess of ROS leads to oxidative stress, instigating the peroxidation of polyunsaturated fatty acids (PUFA) in the lipid membrane through a free radical chain reaction and the formation of the most bioactive aldehyde, known as 4-hydroxynonenal (4-HNE). 4-HNE functions as a signaling molecule and toxic product and acts mainly by forming covalent adducts with nucleophilic functional groups in proteins, nucleic acids, and lipids. The mitochondria have been implicated as a site for 4-HNE generation and adduction. Several studies clarified how 4-HNE affects the …

Film-Terminated Fibrillar Microstructures With Improved Adhesion On Skin-Like Surfaces, Gabriela Moreira Lana, Xuan Zhang, Christian Müller, René Hensel, Eduard Arzt

Chemical and Biochemical Engineering Faculty Research & Creative Works

Adhesives for interaction with human skin and tissues are needed for multiple applications. Micropatterned dry adhesives are potential candidates, allowing for a conformal contact and glue-free adhesion based on van der Waals interactions. In this study, we investigate the superior adhesion of film-terminated fibrillar microstructures (fibril diameter, 60 μm; aspect ratio, 3) in contact with surfaces of skin-like roughness (Rz 50 μm). Adhesion decays only moderately with increasing roughness, in contrast to unstructured samples. Sinusoidal model surfaces adhere when their wavelengths exceed about four fibril diameters. The film-terminated microstructure exhibits a saturation of the compressive force during application, implying a …

Fabricating 3-Dimensional Human Brown Adipose Microtissues For Transplantation Studies, Ou Wang, Li Han, Haishuang Lin, Mingmei Tian, Shuyang Zhang, Bin Duan, Soonkyu Chung, Chi Zhang, Xiaojun Lian, Yong Wang, Yuguo Lei

Department of Chemical and Biomolecular Engineering: Faculty Publications

Transplanting cell cultured brown adipocytes (BAs) represents a promising approach to prevent and treat obesity (OB) and its associated metabolic disorders, including type 2 diabetes mellitus (T2DM). However, transplanted BAs have a very low survival rate in vivo. The enzymatic dissociation during the harvest of fully differentiated BAs also loses significant cells. There is a critical need for novel methods that can avoid cell death during cell preparation, transplantation, and in vivo. Here, we reported that preparing BAs as injectable microtissues could overcome the problem. We found that 3D culture promoted BA differentiation and UCP-1 expression, and the optimal initial …

Prototype Catalytic Membrane Reactor For Dimethyl Ether Synthesis Via Co2hydrogenation, Qiaobei Dong, Weiwei L. Xu, Xiao Fan, Huazheng Li, Naomi Klinghoffer, Travis Pyrzynski, Howard S. Meyer, Xinhua Liang, Miao Yu, Shiguang Li

Chemical and Biochemical Engineering Faculty Research & Creative Works

Dimethyl ether (DME) has become attractive as a potential environmentally friendly substitute for diesel and liquefied petroleum gas (LPG) due to its similar properties to those of LPG, high cetane number, but less carbon emissions. In this work, we developed a novel prototype-scale catalytic membrane reactor to synthesize DME directly from CO₂and renewable H₂, which could address the environmental and fuel security issues in a cost-effective way. This membrane reactor was equipped with superior hydrophilic NaA zeolite membranes and bifunctional Cu-ZnO-ZrO₂-Al₂O₃/HZSM-5 catalysts. The effects of the reaction temperature and gas …

Reduced Building Energy Consumption By Combined Indoor Co2 And H2o Composition Control, Anshuman Sinha, Harshul Thakkar, Fateme Rezaei, Yoshiaki Kawajiri, Matthew J. Realff

Chemical and Biochemical Engineering Faculty Research & Creative Works

Rapid growth in global energy consumption has raised concern on the environmental impacts such as ozone layer depletion and climate change. Enclosed space, such as commercial buildings, accounts for about 40% of global energy consumption and the demand is constantly increasing due to increasing population, urbanization, and economic development. The energy demands in the building sector calls for strategic measures to develop energy efficient technologies. This paper presents a strategy to decrease energy demands inside buildings by proposing a ventilation system which regulates the enclosed air quality resulting in reduced air conditioning. The system consists of multiple adsorption beds with …

Atomic Layer Deposited Pt/Tio2-Sio2 And Pt/Zro2-Sio2 For Sequential Adsorption And Oxidation Of Vocs, Busuyi O. Adebayo, Han Yu, Ali A. Rownaghi, Xinhua Liang, Fateme Rezaei

Chemical and Biochemical Engineering Faculty Research & Creative Works

In this work, Pt nanoparticles were loaded on SiO₂, TiO₂-thin-film-modified SiO₂ (TiO₂-SiO₂), or ZrO₂-thin-film-modified SiO₂ (ZrO₂-SiO₂) particles and the composites were investigated for sequential adsorption and desorption/catalytic oxidation of benzene. The SiO₂ was prepared via sol–gel method, while TiO₂-SiO₂ and ZrO₂-SiO₂ were synthesized via atomic layer deposition (ALD) thin film coating of TiO₂ or ZrO₂ on SiO₂ particles substrate. In the sequential capture-reaction tests, the materials were first exposed to ca. 500 ppmv benzene …

Ionic Liquid Pilocarpine Analog As An Antiglaucoma Drug Candidate, Juan Wang, Boxuan Li, Jing Tang, Li Qiu, Xin Qiao, Na Xu, Hu Yang

Chemical and Biochemical Engineering Faculty Research & Creative Works

Ionic liquid pilocarpine analog [Pilo-OEG]Cl, the first-of-its-kind ionic liquid antiglaucoma drug candidate, is synthesized and reported. To synthesize [Pilo-OEG]Cl, pilocarpine was reacted with the oligo-polyethylene glycol chloride, 2-[2-(2-chloroethoxy)ethoxy] ethanol, to form an ionic liquid molecule with an imidazole cation and a chloride anion. The chemical structure of [Pilo-OEG]Cl was confirmed with 1H NMR spectroscopy. Compared with pilocarpine (Pilo) and pilocarpine hydrochloride (PiloHCl), [Pilo-OEG]Cl has improved structural stability according to pH measurements and LC-MS analysis. The corneal permeability coefficient of [Pilo-OEG]Cl is 2-fold higher than that of Pilo and 8-fold higher than that of PiloHCl. [Pilo-OEG]Cl does not show apparent toxicity …

Estimating Flashpoints Of Fuels And Chemical Compounds Using Hybrid Machine-Learning Techniques, Farid Amirkhani, Amir Dashti, Hossein Abedsoltan, Amir H. Mohammadi, Abdoulmohammad Gholamzadeh Chofreh, Feybi Ariani Goni, Jiří Jaromír Klemeš

Chemical and Biochemical Engineering Faculty Research & Creative Works

Flashpoint of organic materials is a crucial physical property in industrial applications and laboratory experiments, which provides information on safety standards and needed precautions in handling various organic materials. Proposed methods to determine the flashpoint of an organic material suffer from dependency on other physical properties of the chemical or demand complicated calculations which are time-consuming. In this work, a direct system model is proposed to anticipate the flashpoints of organic materials for a wide range of chemical compounds. The following models of genetic algorithm-adaptive neuro-fuzzy inference system, the least-squares version of the support vector machine, particle swarm optimization-adaptive neuro-fuzzy …

Nonordered Dendritic Mesoporous Silica Nanoparticles As Promising Platforms For Advanced Methods Of Diagnosis And Therapies, S. Malekmohammadi, Riaz Ur Rehman Mohammed, H. Samadian, A. Zarebkohan, A. García-Fernández, G. R. Kokil, F. Sharifi, J. Esmaeili, M. Bhia, M. Razavi, M. Bodaghi, T. Kumeria, R. Martínez-Máñez

Department of Chemical and Biomolecular Engineering: Faculty Publications

Dendritic mesoporous silica nanoparticles (DMSNs) are a new generation of porous materials that have gained great attention compared to other mesoporous silicas due to attractive properties, including straightforward synthesis methods, modular surface chemistry, high surface area, tunable pore size, chemical inertness, particle size distribution, excellent biocompatibility, biodegradability, and high pore volume compared with conventional mesoporous materials. The last years have witnessed a blooming growth of the extensive utilization of DMSNs as an efficient platform in a broad spectrum of biomedical and industrial applications, such as catalysis, energy harvesting, biosensing, drug/gene delivery, imaging, theranostics, and tissue engineering. DMSNs are considered great …