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Investigations Of Prokaryotic Defense Systems, Hannah Domgaard 2022 Utah State University

Investigations Of Prokaryotic Defense Systems, Hannah Domgaard

All Graduate Theses and Dissertations

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 ...


Correlating The Macrostructural Variations Of An Ion Gel With Its Carbon Dioxide Sorption Capacity, Tung Nguyen,, Mona Bavarian, Siamak Nejati 2022 University of Nebraska-Lincoln

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

Chemical and Biomolecular Engineering -- All Faculty Papers

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 ...


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 2022 Louisiana State University Health Sciences Center

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

Chemical and Biomolecular Engineering -- All Faculty Papers

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 ...


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 2022 University of Nebraska-Lincoln

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

Chemical and Biomolecular Engineering -- All Faculty Papers

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 ...


Teb 406 Reflection, Ryan Alfonso Falcon 2022 Western University

Teb 406 Reflection, Ryan Alfonso Falcon

Undergraduate Student Research Internships Conference

Slides for a non-exhaustive reflection on my work in summer


Improving The Crystal Habit Of Rufinamide, Peter M. Sadaka 2022 Western University

Improving The Crystal Habit Of Rufinamide, Peter M. Sadaka

Undergraduate Student Research Internships Conference

This research was developed by utilizing the knowledge gathered and learned about crystallization through my USRI project. The goal was to improve the crystal habit of a selected drug from the many that were available in the lab. To choose this, we looked at all of them and chose the drug with the worst habit and then began working. It was created by organizing my findings for each week and then making it all much more concise for the form of a simple presentation that most could understand.


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 2022 University of Manchester

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

Chemical and Biomolecular Engineering -- All Faculty Papers

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 ...


A Rapid And Ultra-Sensitive Biosensing Platform Based On Tunable Dielectrophoresis For Robust Poc Applications, Yu Jiang 2022 University of Tennessee, Knoxville

A Rapid And Ultra-Sensitive Biosensing Platform Based On Tunable Dielectrophoresis For Robust Poc Applications, Yu Jiang

Doctoral Dissertations

With the ongoing pandemic, there have been increasing concerns recently regarding major public health issues such as abuse of organophosphorus compounds, pathogenic bacterial infections, and biosecurity in agricultural production. Biosensors have long been considered a kernel technology for next-generation diagnostic solutions to improve food safety and public health. Significant amounts of effort have been devoted to inventing novel sensing mechanisms, modifying their designs, improving their performance, and extending their application scopes. However, the reliability and selectivity of most biosensors still have much to be desired, which holds back the development and commercialization of biosensors, especially for on-site and point-of-care (POC ...


Elucidating Mammalian Cellular Responses To The Uptake Of Nanoparticles (Nps), Pathogens, And Lipoproteins: Similarities And Differences, Monireh Asoudeh 2022 University of Tennessee, Knoxville

Elucidating Mammalian Cellular Responses To The Uptake Of Nanoparticles (Nps), Pathogens, And Lipoproteins: Similarities And Differences, Monireh Asoudeh

Doctoral Dissertations

Soft poly-ethylene-glycol (PEG)-based soft nanoparticles (NPs) including cylindrical (CNPs) micelles, spherical (SNPs) micelles, and lipid bilayer vesicles (LNPs) are thought to be treated as foreign objects by mammalian phagocytes. If this hypothesis is true, NPs should trigger a proinflammatory, autophagic phenotype that is similar to the one seen when macrophages phagocytose pathogens or when macrophage surface expressed proteins bind pathogen surface factors such as lipopolysaccharide (LPS). Here, we show that macrophage responses to the above NPs are almost completely unique from those triggered by group A streptococcus (GAS) pathogens (JRS4 cells) and LPS. Instead, macrophages treat these soft NPs ...


Scale Up Of A Novel Method To Maximize Malonyl-Coa In Escherichia Coli, Clifford Harris LeBlanc IV 2022 Louisiana State University and Agricultural and Mechanical College

Scale Up Of A Novel Method To Maximize Malonyl-Coa In Escherichia Coli, Clifford Harris Leblanc Iv

LSU Master's Theses

The instability of oil’s price along with its limited availability and impact on the environment motivate the search for an alternative feedstock that can sustain the profitability of chemical companies. Industrial biotechnology can promote renewable sources of energy and products by using microorganisms to produce a wide range of chemical compounds. The three-carbon metabolite, malonyl-CoA, can serve as a precursor to a variety of industrial chemicals. The major hurdle with using malonyl-CoA in industry is that its intracellular concentration in Escherichia Coli is very low. Previous attempts to increase the intracellular level of malonyl-CoA have ranged from genetic engineering ...


Improving The Biocompatibility Of The Bio-Inorganic Interface For Enhanced Photosystem I-Based Biophotovoltaic Device Performance, Alexandra H. Teodor 2022 University of Tennessee, Knoxville

Improving The Biocompatibility Of The Bio-Inorganic Interface For Enhanced Photosystem I-Based Biophotovoltaic Device Performance, Alexandra H. Teodor

Doctoral Dissertations

The world’s energy demands are projected to increase by nearly 50% by the year 2040, and consumption of carbon-based fuels continues to release greenhouse gases such as carbon dioxide and methane into the atmosphere. This has been causally linked with climate change and increased extreme weather events, which has been further linked to adverse health outcomes and negative effects on biodiversity, food security, and increased disease transmission. Clearly, there is a need for a sustainable, carbon-free, and cost-effective method of energy production to meet growing energy production demands. The sun irradiates Earth’s surface annually with ~80,000 terawatts ...


Crowd Control: Regulating The Spatial Organization Of Biopolymers And Gene Expression By Macromolecular Crowding, Gaurav Chauhan 2022 University of Tennessee, Knoxville

Crowd Control: Regulating The Spatial Organization Of Biopolymers And Gene Expression By Macromolecular Crowding, Gaurav Chauhan

Doctoral Dissertations

The intracellular environment is crowded with macromolecules that can occupy a significant fraction of the cellular volume. This can give rise to attractive depletion interactions that impact the conformations and interactions of biopolymers, as well as their interactions with confining surfaces. We used computer simulations to study the effects of crowding on biologically-inspired models of polymers. We showed that crowding can lead to attractive interactions between two flexible ring polymers, and we further characterized the adsorption of both flexible and semiflexible polymers onto confining surfaces. These results indicate that crowding-induced depletion interactions could play a role in the spatial organization ...


Interactions Between Soft Nanoparticles And Mammalian Cells, Mitchell Raith 2022 University of Tennessee, Knoxville

Interactions Between Soft Nanoparticles And Mammalian Cells, Mitchell Raith

Doctoral Dissertations

Nanoparticles have been of interest to the pharmaceutical industry since the 1980s. The first FDA approved nanoparticle-based therapies included liposomal anesthesia agents. Since then, the amount of FDA-approved nanoparticle therapies remains low. This is because nanoparticle-patient interactions can be very complex and are not well understood. Complicating factors also include increasing obesity rates among the patient population and many small animal pre-clinical trials are completed with healthy, lean animals. The biochemical differences between lean and obese patients prevents early studies from accurately predicting nanoparticle clinical behaviors. Many nanoparticles fail in trails. In this thesis, I aimed to uncover how nanoparticles ...


Isolation And Production Of Tandem Collagen Binding Domain From Clostridial Collagenase Colg And Developments In C1q Reagent Production For Future Molecule Characterization Work, Stephanie Beitle 2022 University of Arkansas, Fayetteville

Isolation And Production Of Tandem Collagen Binding Domain From Clostridial Collagenase Colg And Developments In C1q Reagent Production For Future Molecule Characterization Work, Stephanie Beitle

Chemical Engineering Undergraduate Honors Theses

This thesis covers a two part project: the production methods to create a double collagen binding domain molecule with a growth factor for wound healing applications and the development of a new in-house production method for isolating C1q from bovine blood. The wound healing molecule was created using transformation, sonication, and purification before being tested via electrophoresis SDS page and Western blots to confirm the molecule’s presence. The C1q in-house production method utilizes an ultrafiltration flow cell rather than dialysis at a critical point in the process, allowing for researchers to not only be able to use a single ...


Drug-Facilitated Sexual Assault At The University Of Arkansas, Barrett Weidman 2022 University of Arkansas, Fayetteville

Drug-Facilitated Sexual Assault At The University Of Arkansas, Barrett Weidman

Chemical Engineering Undergraduate Honors Theses

This work was written to fulfill two main purposes. First, to help survivors of Drug-Facilitated Sexual Assault (DFSA) process their experience by compiling the toxicological, pharmacological, and distribution of the three most used date-rape drugs. Second, to gauge the knowledge and interest of University of Arkansas students regarding drug impairments, sexual assault education, and bystander intervention training. A survey was conducted for the latter and revealed that 91.6% of students believe the University’s existing sexual assault prevention education and bystander intervention training have room for improvement. Also, 37.1% of students who have received this education report that ...


Mixed Pet Plastics Waste To Dimethyl Terephthalate & Ethylene Glycol, Chelsea Cao, Hyuck Choi, Christopher Kline, Shannon Zhang 2022 University of Pennsylvania

Mixed Pet Plastics Waste To Dimethyl Terephthalate & Ethylene Glycol, Chelsea Cao, Hyuck Choi, Christopher Kline, Shannon Zhang

Senior Design Reports (CBE)

Polyethylene terephthalate (PET) plastic is integral to our everyday lives. As the primary plastic used in food and beverage packaging and synthetic textiles (PET Resin Association, 2015), PET is produced in North America at a rate of 3.1 million tons per year. However, as of 2015, only 26.6% of the PET produced is being recycled per year (PET Resin Association, 2015). Thus, the accumulation of PET waste has become a significant environmental concern. To address this problem, this report proposes a methanolysis plant using technology from Eastman Chemical Company (Sharpe et al., 2020) to depolymerize 100,000 metric ...


Co2 And Ch4 To Liquids Via Low-Thermal Plasma, Nathaniel Hess, Brandon Burghardt, Caitlyn McCloskey 2022 University of Pennsylvania

Co2 And Ch4 To Liquids Via Low-Thermal Plasma, Nathaniel Hess, Brandon Burghardt, Caitlyn Mccloskey

Senior Design Reports (CBE)

This process uses a low-thermal plasma reactor to convert carbon dioxide, natural gas, and water vapor into acetic acid, waste liquid, and flue gas. The plant requires co-location with a corn ethanol plant for carbon dioxide feed and for the disposal of liquid waste (made primarily of ethanol and methanol) as an ethanol additive. The acetic acid is the target liquid product for this process. The flue gas has significant energy value and may also be sold. In the best case scenario, the plant achieves a 33.78% internal rate of return with a $27,000,000 net present value ...


Replacing Conventional Pfas Water Treatment By Gac With Plasma Treatment To Improve Sustainability, Isabel Gutierrez, Ryan Lam 2022 University of Pennsylvania

Replacing Conventional Pfas Water Treatment By Gac With Plasma Treatment To Improve Sustainability, Isabel Gutierrez, Ryan Lam

Senior Design Reports (CBE)

Per and poly-fluoroalkylated substances (PFAS) are carcinogenic compounds which make their way into water systems and are difficult to remove. Currently, PFAS is removed from drinking water at an industrial scale using granular activated carbon (GAC), a solid particulate which removes PFAS from water through adsorption. However, in recent years, a new method utilizing a plasma reactor to mineralize the PFAS has been designed and tested at small scales. This project aims to increase the scale of existing plasma reactor designs to treat the same volumes of water that traditional GAC plants are capable of treating. A specific well in ...


Cellular Agriculture, Christina Kim, Amanda Kishun, Fahmida Lubna 2022 University of Pennsylvania

Cellular Agriculture, Christina Kim, Amanda Kishun, Fahmida Lubna

Senior Design Reports (CBE)

Cellular agriculture is a field of biotechnology focused on the production of animal products using cells grown in vitro . Traditional meat production consumes vast amounts of water, arable land, and feed crops, as well as driving deforestation, emitting large amounts of greenhouse gases, and creating large potential reservoirs for zoonotic diseases. As the global demand for meat increases, continuing to scale up the industry for slaughtered meat could have disastrous consequences for the environment. Growing cells in bioreactors creates the potential to drastically decrease land requirements, feed requirements, and other environmental impacts. For example, hindgut fermentation of feed, the main ...


Natural Gas Conversion Into Clean Hydrogen And Carbon For Li-Ion Battery Electrodes Using Renewable Energy, Skylar Cannon, Sydney Levine, Adam Ritter 2022 University of Pennsylvania

Natural Gas Conversion Into Clean Hydrogen And Carbon For Li-Ion Battery Electrodes Using Renewable Energy, Skylar Cannon, Sydney Levine, Adam Ritter

Senior Design Reports (CBE)

The global green hydrogen market, set to increase 54% by 2030, was valued at 1.83 billion USD in 2021 (Precedence Research, 2022). Making use of the recent availability and affordability of solar energy as well as the high demand for green hydrogen, major strides have been made in the decarbonization of the commodity chemicals industry. Traditionally energy intensive processes, such as steam methane reforming (SMR) for the production of hydrogen and natural gas fired furnaces (NGFF) for the production of carbon black, can be replaced with alternative renewable electricity powered processes. This project proposes one such process in which ...


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