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Title: Incorporation of non-standard amino acids into proteins: challenges, recent achievements, and emerging applications
Creator: Jin, Xing, Park Oh-Jin, Hong, Seok Hoon
Date: 2019
Description: The natural genetic code only allows for 20 standard amino acids in protein translation, but genetic code reprogramming enables the...
Show moreThe natural genetic code only allows for 20 standard amino acids in protein translation, but genetic code reprogramming enables the incorporation of non-standard amino acids (NSAAs). Proteins containing NSAAs provide enhanced or novel properties and open diverse applications. With increased attention to the recent advancements in synthetic biology, various improved and novel methods have been developed to incorporate single and multiple distinct NSAAs into proteins. However, various challenges remain in regard to NSAA incorporation, such as low yield and misincorporation. In this review, we summarize the recent efforts to improve NSAA incorporation by utilizing orthogonal translational system optimization, cell-free protein synthesis, genomically recoded organisms, artificial codon boxes, quadruplet codons, and orthogonal ribosomes, before closing with a discussion of the emerging applications of NSAA incorporation.
Sponsorship: NIH R15AI130988
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Title: Undecanoic Acid, Lauric Acid, and N-Tridecanoic Acid Inhibit Escherichia coli Persistence and Biofilm Formation
Creator: Jin, Xing, Zhou, Jiacheng, Richey, Gabriella, Wang, Mengya, Hong, Sung Min Choi, Hong, Seok Hoon
Date: 2021
Description: Persister cell formation and biofilms of pathogens are extensively involved in the development of chronic infectious diseases. Eradicating...
Show morePersister cell formation and biofilms of pathogens are extensively involved in the development of chronic infectious diseases. Eradicating persister cells is challenging, owing to their tolerance to conventional antibiotics, which cannot kill cells in a metabolically dormant state. A high frequency of persisters in biofilms makes inactivating biofilm cells more difficult, because the biofilm matrix inhibits antibiotic penetration. Fatty acids may be promising candidates as antipersister or antibiofilm agents, because some fatty acids exhibit antimicrobial effects. We previously reported that fatty acid ethyl esters effectively inhibit Escherichia coli persister formation by regulating an antitoxin. In this study, we screened a fatty acid library consisting of 65 different fatty acid molecules for altered persister formation. We found that undecanoic acid, lauric acid, and N-tridecanoic acid inhibited E. coli BW25113 persister cell formation by 25-, 58-, and 44-fold, respectively. Similarly, these fatty acids repressed persisters of enterohemorrhagic E. coli EDL933. These fatty acids were all medium-chain saturated forms. Furthermore, the fatty acids repressed Enterohemorrhagic E. coli (EHEC) biofilm formation (for example, by 8-fold for lauric acid) without having antimicrobial activity. This study demonstrates that medium-chain saturated fatty acids can serve as antipersister and antibiofilm agents that may be applied to treat bacterial infections.
Sponsorship: NIH-R15AI130988; NSF REU-1757989
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Title: USING COMPUTATIONAL MOLECULAR MODELING TO STUDY TRANSPORT PROCESSES OF INTEREST IN SEPARATIONS
Creator: Wang,Xiaoyu
Date: 2020, 2020
Publisher: ProQuest
Description: Separation processes are widely used in chemical productions. The further development of membrane-based separation processes, compared with...
Show moreSeparation processes are widely used in chemical productions. The further development of membrane-based separation processes, compared with thermal separations, can lead to significant energy savings in chemical process industries. However, the main obstacle of experiments is that many separation processes are not well understood at the fundamental molecular level. In this dissertation, we use computational molecular modeling tools, mainly classical molecular dynamics (MD), to clarify molecular forces and provide detail at a molecular level, which can aid in the understanding of transport process and designing materials for a proposed application. In the first study, we investigated separation of water/alcohol vapor using zeolite membranes. Experimentally, the separation of water/isopropanol (IPA) mixtures shows a dramatic decrease in selectivity due to increase of IPA flux as the feed water concentration decrease when using the sodium A zeolite membrane. We used molecular dynamics simulations to help our experimental collaborators understand these puzzling results. The MD results reveal that the water molecules gather around the defect pores on the zeolite membrane, which stops the IPA from going through the membrane and has a positive effect on separation. Then, we studied the HPLC used to separate chiral drug mixtures. One popular chiral stationary phase, amylose tris(3,5-dimethylphenyl carbamate) (ADMPC), has been investigated using both experimental and computational methods; however, the dynamic nature of the interaction between enantiomers and ADMPC, as well as the solvent effects on the ADMPC-enantiomer interaction, are currently absent from the chiral recognition mechanism. We used MD simulations to model the ADMPC in different solvents to elucidate the chiral recognition mechanism from a new dynamic perspective. The ADMPC is found to hold the left-handed helical structure in both methanol and heptane/IPA (90/10); however, the ADMPC has a more extended average structure in heptane/IPA. We developed a model where the ADMPC atoms were restricted in the MD simulation. To better understand the molecular dynamic chiral recognition that provides the retention factor and the elution order in HPLC, we examined hydrogen bonding lifetimes, and mapped out ring-ring interactions between the drugs and the ADMPC. We discover several MD metrics related to hydrogen-bonding lifetimes and correlate them with HPLC results. One metric provides a prediction of the correct elution order 90%, and the ratios of these quantities for the enantiomers provide linear correlation (0.85 coefficient) with experimental retention factors. In the following study, we presented an improved model wherein multiple ADMPC polymer strands are coated on an amorphous silica slab. Using various MD techniques, we successfully coated ADMPCs onto the surface without losing the structural character of the backbone in the solvent. This model provides more opportunities for chiral molecules interacting with ADMPC, resulting in a better agreement compared with experiment when using the overall average metric. The new model also provides the possibility for drug molecules to interact with two polymer strands simultaneously, which is not possible in the previous single-strand model. For a better understanding of why some metrics are better predictors than others, we used charts of the distribution of hydrogen bonding lifetimes to display the information for various donor-acceptor pairs. The results are more consistent than the previous models and resolves the problematic cases of thalidomide and valsartan. Besides the membrane-based separations, immiscible liquid-liquid equilibrium states were also studied. We successfully predicted results based on MD simulations and showed comparable accuracy with experimental data. This method has applications in liquid-liquid extraction which is widely used in industrial separation process.
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Title: Modeling enantiomeric separations as an interfacial process using amylose tris(3,5-dimethylphenyl carbamate) (ADMPC) polymers coated on amorphous silica
Creator: Wang,Xiaoyu, Jameson, Cynthia, Murad, Sohail
Date: 2020, 2020-01-20
Publisher: ACS Langmuir
Description: In the present study, we present a model to predict the chiral separation results for drug enantiomers by ADMPC chiral stationary phase in...
Show moreIn the present study, we present a model to predict the chiral separation results for drug enantiomers by ADMPC chiral stationary phase in high performance liquid chromatography (HPLC) wherein multiple ADMPC polymer strands are coated on an amorphous silica slab. Both reactive and classical MD are used to prepare the surface. Using various MD techniques, we successfully coat ADMPCs onto the surface without losing the structural character of the backbone in the presence of the solvent system. Not only is this model more representative of the polymer surface on a solid support that is encountered by the enantiomers, it also provides more opportunities for chiral molecules interacting with ADMPC, resulting in a better agreement compared with experiment when we use overall average quantities as the metric. In our previous studies, we had used a single polymer strand of amylose tris(3,5-dimethylphenyl carbamate) (ADMPC) in the solvent system. The new model provides the possibility for large drug molecules to interact with two polymer strands at the same instant, which was not possible to model with only a single polymer strand in the solvent. For a better understanding of why some metrics are better predictors than others, we use charts of the distribution of hydrogen bonding lifetimes in this work to display the hydrogen-bonding information for various donor-acceptor pairs that contribute to the interaction events determining the relative retention times for the enantiomers. We also examine the contribution of the ring-ring interactions to the molecular recognition process and ultimately to differential retention of S and R enantiomers. The results using the new model are more consistent than the previous models and resolves the problematic case of two drugs, thalidomide and valsartan.
Sponsorship: The National Science Foundation (CBET 1545560)
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Title: Developing Adaptive and Predictive Modules for the Second Generation of Multivariable Insulin Delivery System for People with Type-1 Diabetes
Creator: Askari, Mohammad Reza
Date: 2023
Description: In this research, we are developing the second generation of multivariable automated insulin delivery system (mvAID) for people with Type 1...
Show moreIn this research, we are developing the second generation of multivariable automated insulin delivery system (mvAID) for people with Type 1 diabetes (T1D). AID system is improved by integrating missing data from sensors into the system, reconciling outliers in the data, and eliminating the effects of artifacts in signals from wearable devices. Behavioral patterns of individuals with T1D are captured by data-driven models. The model predictive control algorithm of the mvAID uses these patterns for making decisions and predicting glucose concentrations in the future more accurately. A pipeline algorithm is developed for removing noise and motion artifacts from wristband signals. Then, energy expenditure, physical activity, and acute psychological stress (APS) are estimated from wearable device signals to detect and quantify disturbances affecting the concentration of blood glucose concentration. Additionally, different modules were designed for predicting risky glycemic episodes and are used to build the second generation of the mvAID system. The techniques developed are tested with historical data sets from various clinical experiments and free-living data, and with simulations made by using our multivariable glucose, insulin and physiological variables simulator (mGIPsim).
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Title: Establishing Bisphenol A Degradation and Enhancing Microbial Fuel Cell Performance by Biofilm Optimization of Shewanella Oneidensis MR1
Creator: Zhou, Jiacheng
Date: 2023
Description: Bisphenol A (BPA) has been widely used as a plasticizer in the production of synthetic polymers, such as those used in food storage containers...
Show moreBisphenol A (BPA) has been widely used as a plasticizer in the production of synthetic polymers, such as those used in food storage containers and bottles. However, BPA interferes with endocrine systems, causing carcinogenicity, immunotoxicity, and embryotoxicity. Biological water treatment processes scarcely remove BPA, owing to the poor BPA degradability and efficiency of the applied microorganisms. Shewanella oneidensis has been studied and used for the biodegradation process in wastewater treatment because of its excellent extracellular electron transfer properties. In this work, we engineered S. oneidensis MR1 to enable BPA degradation by producing ferredoxin (Fdbisd) and cytochrome P450 (P450bisd) originating from Sphingomonas bisphenolicum AO1. The engineered S. oneidensis exhibited a higher BPA degradation efficiency than that of Escherichia coli producing the same enzymes. The endogenous ferredoxin and ferredoxin reductase of S. oneidensis participated in BPA degradation, and overexpression of mtrC, omcA, and So0521, which encode S. oneidensis cytochromes, decreased BPA. We developed BPA-degrading S. oneidensis biofilms. We measured these optimized BPA-degrading S. oneidensis biofilm in a single chamber microbial fuel cell formed on different carbon electrodes by morphology. Cyclic voltammetry and electrochemical impedance spectroscopy were measured to analyze the biofilm-electrode performance. The biofilm colonization was also measured by confocal laser scanning microscope and scanning electron microscope. And the developed microbial fuel cell was used to degrade BPA and the biofilm developed on different type of carbon anodes was identified. This study provides insights into biocatalyst utilization for the biological degradation of toxic organic compounds.
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Title: SEPARATING NOBLE GASES SUCH AS KRYPTON AND XENON FROM NUCLEAR POWER PLANTS OFF-GAS USING DD3R ZEOLITIC MEMBRANES: A COMPUTATIONAL MOLECULAR DYNAMICS STUDY
Creator: BASHMMAKH, BANDAR JAMAL S.
Date: 2021
Description: Noble gas fission products generated within nuclear power reactors, such as Kr and Xe, are currently discharged into the atmosphere. This...
Show moreNoble gas fission products generated within nuclear power reactors, such as Kr and Xe, are currently discharged into the atmosphere. This practice has a major economic drawback because of the high value associated with some of these gases. Zeolites, nanoporous materials suitable for gas separation processes, have become of major interest due to the potentially high selectivity for such separations. We have used nonequilibrium molecular dynamics to investigate the separation performance of DD3R framework zeolitic membranes (using LAMMPS software package) for such separations. Our studies have shown that the DD3R membrane shows promise for high selectivity ratios of Kr over Xe. The effects of pressure, temperature and pure vs. mixture gas feed conditions are studied in this work to understand at the molecular level the mechanisms of these (Kr/Xe) separations. MD runs show an agreement with most experimental trends in the permeation of Kr/Xe pure and mixed gases using DD3R zeolite with high separation factor, despite the absence of Xe complete permeation through the membrane because of MD timescale limitation, signaling much slower diffusion in comparison to Kr which is a desired trend in looking for high separation factors.
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Title: DEVELOPING FUSION BACTERIOCINS FOR ERADICATING PSEUDOMONAS AERUGINOSA BIOFILMS
Creator: An, Sungjun
Date: 2022
Description: The opportunistic pathogen Pseudomonas aeruginosa is a leading cause of morbidity and mortality in cystic fibrosis patients and...
Show moreThe opportunistic pathogen Pseudomonas aeruginosa is a leading cause of morbidity and mortality in cystic fibrosis patients and immunocompromised individuals. Due to its remarkable ability to resist antibiotics, eradicating P. aeruginosa has become increasingly difficult. As previously reported, we have successfully engineered a colicin-secretion system that kills target biofilm cells rapidly and selectively in multispecies biofilms as well as demonstrated the potential of using live microorganisms engineered to produce antimicrobial colicin protein to treat biofilm-associated infections. In this study,we constructed a fusion colicin-pyocin that could target P. aeruginosa by DNase activity of colicin E2. The newly engineered bacteriocin-secretion system upon the shift in target, maintained biofilm inhibition capacity. Both during biofilm formation and after its development, the system was able to suppress the P. aeruginosa biofilm. This result opened up the possibility that it could be used for novel live biotherapeutics. A further study was conducted to overcome the challenge of requiring an exogenous inducer. We applied the concept of Quorum-Sensing signal that recognize autoinducer as a trigger of fusion colicin-pyocin producing genetic circuit so that it automates the production and secretion of fusion colicin-pyocin as soon as the genetic circuit senses the target population growing. This study demonstrated that combining the domains of colicin and pyocin could broaden the genetic circuit target range, maintaining strain specificity, while employing the QS system could remove the fundamental problem of diffusion or degradation of extra compounds as they approach engineered cells.
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Title: COMPUTATIONAL FLUID DYNAMICS SIMULATION OF CARBON CAPTURE UNIT USING AN AMINE-BASED SOLID SORBENT
Creator: Esmaeili Rad, Farnaz
Date: 2021
Description: Carbon capture and sequestration (CCS) is one of the key technologies to reduce the emission of carbon dioxide, including that from exiting...
Show moreCarbon capture and sequestration (CCS) is one of the key technologies to reduce the emission of carbon dioxide, including that from exiting flue gas of fossil fuel-fired power plants. The goal of this project is the development of a computational fluid dynamics (CFD) model to predict the extent of CO2 capture in a circulating fluidized bed carbon capture unit using novel amine-based solid sorbents.In this study, first the hydrodynamics of the carbonation section of the carbon capture unit was investigated. Then, the performance of the amine-based solid sorbents toward capturing carbon dioxide from flue gas and the extent of CO2 adsorption in the carbonation section were studied. At the second stage of the study, the regeneration of the sorbents and desorption of carbon dioxide from carbonated solid sorbents in the regeneration section of the carbon capture unit was investigated. At the third stage of the study, the hydrodynamics of the entire loop of the integrated carbonation and regeneration sections were simulated. Two-dimensional non-reactive CFD simulations of the entire loop, including the carbonator, regenerator, and two loop-seal fluidized beds, were performed to study the details of the solid circulation in the system in a stable operational condition. At the fourth stage of the study, the effect of the carbonated solids’ residence time in the regeneration section was investigated by extending the regenerator fluidized bed height and adding to the volume of the system. Heated surfaces, which resembled heating coils in the regenerator cylinder, were also added to the system to investigate the effect of the temperature. The heated surface of the immersed coils in the bed provided sufficient energy for the endothermic regeneration reaction to keep the temperature of the bed at the desired temperature. Finally, the verified models of the carbonation section, the regenerations section, and non-reactive simulation of the CFB loop were used to simulate the entire circulating fluidized bed carbon capture unit, with an integrated carbonator and regenerator system using amine-based solid sorbents. The extent of CO2 capture in the carbonation section and desorption of carbon dioxide in the regeneration section were predicted. Our study showed the potential of continuous carbon capture by amine-based solid sorbents through the circulating fluidized bed CO2 capture unit.
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Title: DEVELOPMENT OF FULLY BIOCOMPATIBLE HYDROGEL NANOPARTICLE FORMULATIONS FOR CONTROLLED-RELEASE DELIVERY OF A WIDE VARIETY OF BIOMOLECULES
Creator: Borges, Fernando Tancredo Pereira
Date: 2020
Description: In recent years, our group has focused on the production of PEGDA-based hydrogel scaffolds and nanoparticles for drug delivery of small...
Show moreIn recent years, our group has focused on the production of PEGDA-based hydrogel scaffolds and nanoparticles for drug delivery of small molecules. However, with recent advances in modern therapeutic treatments, such as protein and genetic engineering, there is an increasing need for the development of drug delivery devices that would be able encapsulate larger molecules. Therefore, the goal of this thesis work was to develop a systematic way to produce fully biocompatible PEGDA-based hydrogel nanoparticle formulations that would be able to encapsulate any size molecule, ranging from small ionic molecules, to peptides and proteins, all the way to large nucleic acids, and deliver it in a controlled manner.The first of part of this work consisted of developing a stable and reproducible process for the production of hydrogel PPi-NPs. Initial studies were done in order to assess the influence of phosphate salts in the polymerization system and it was found that both monophosphate and polyphosphate salts significantly damper the NVP homo-polymerization kinetics, but do not affect the co-polymerization of NVP and PEGDA. Then, emulsion stability studies were done to determine whether phosphate salts affected the stability of the minimeulsion system used in the production of the nanoparticles. Cloud point measurements and droplet size screening measurements showed that by transitioning from a Pi-loaded emulsion system to a PPi-loaded emulsion system, the required HLB of the emulsion shifts by 1.5 points. Upon correction for that shift, a reproducible process for production of PPi-loaded nanoparticles was obtained. A parametric study was then performed to see how the different process parameters affected the different properties of the produced particles. The second part of the work consisted in developing a platform for encapsulation of large to very-large molecules within these hydrogel systems. A new set of equations was developed for better estimation of the interstitial space, available for encapsulation of molecules, of crosslinked polymers that used very high molecular weight crosslinkers and/or high amounts of crosslinker. Upon development of this new set of equations, hydrogel discs were made via photopolymerization in order to validate the equations. By introducing a third monomer, EGA, and varying the molecular weight and concentration of the crosslinker, hydrogels with a wide range of mesh dimensions from 25 to 700 were achieved. These gels were then used to encapsulate 4 different sample molecules of varying molecular weights and size. A new heuristic was developed for encapsulation of non-spherical molecules, where the aspect ratios of the molecule and of the polymer network are considered. By varying the size of the ratios of the dimensions of the hydrogel network to the dimensions of the molecule, significantly different release profiles of small molecules, peptides and oligonucleotides were obtained. Finally, in order to explore different administration routes, the process was transitioning into being fully biocompatible. The organic solvent previously used in the emulsion system was replaced by soybean oil and the surfactants were replaced by a food-grade surfactant, PGPR, to form Bio-Compatible Nanoparticle Emulsions (BCNEs). Qualitative release from the BCNEs was shown. A new method for quantitative measuring of release from BCNE was developed. Release from QK-BCNE was observed up to 46 days, which is unprecedented for sustained-release and revolutionary for the field. A BCNE spreadable ointment formulation was also developed.
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Title: Investigating anti-biofilm and anti-persister activities of natural compounds and antimicrobial proteins
Creator: Jin, Xing
Date: 2020
Description: Bacterial biofilm formation is frequently involved in the development of chronic infectious diseases. Inhibiting biofilms is challenging due...
Show moreBacterial biofilm formation is frequently involved in the development of chronic infectious diseases. Inhibiting biofilms is challenging due to their tolerance against conventional antibiotics which are not effective to penetrating biofilm matrix to kill the cells residing in biofilms. Metabolically dormant cells known as persisters are also not eradicated by antibiotic treatment. Therefore, novel antimicrobial drugs that can kill non-growing persisters or inhibit biofilms are needed urgently. Here, we investigate the anti-biofilm and anti-persister activities of new drug candidates including plant extracts, fatty acids and colicins. We firstly screened 50 different plant extracts on enterohemorrhagic E. coli and Listeria monocytogenes, and identified Cancavalia ensiformis-derived lectin Concanavalin A (ConA) inhibits biofilm formation of enterohemorrhagic E. coli and Listeria monocytogenes by binding to carbohydrates on bacterial cell surface. Biofilm results support that ConA lectin can be applied for developing anti-adherent and anti-biofilm agents to control biofilms. Also, fatty acids may be promising candidates as anti-persister or anti-biofilm agents, because some fatty acids exhibit antimicrobial effects. We screened a fatty acid library consisting of 65 different fatty acid molecules for altered persister formation. We found that undecanoic acid, lauric acid, and N-tridecanoic acid inhibited E. coli persister cell formation including enterohemorrhagic E. coli EDL933. These fatty acids were all medium chain saturated forms. Furthermore, the fatty acids repressed EHEC biofilm formation (for example, by 8-fold for lauric acid) without having antimicrobial activity. This study demonstrates that medium chain saturated fatty acids can serve as anti-persister and anti-biofilm agents that may be applied to treat bacterial infections. Colicins, a type of antimicrobial bacteriocins, are considered as a viable alternative of conventional antibiotics due to their unique cell killing mechanisms that can damage cells by pore-forming on the cell membrane, nuclease activity, and cell wall synthesis inhibition. In this study, we utilized cell-free protein synthesis to produce colicins with different modes of action. We optimized the production yield and activity of colicins in cell-free system. Also, we tested effect of cell-free produced colicins on persister cell formation and biofilm formation. We illustrated that colicins kill persister cells and biofilm cells. Moreover, colicins produced from the engineered probiotic E. coli cells, which can be used as a living medicine, specifically and significantly eradicate target biofilms without affecting other bacterial population. Colicins have great potential to be an antibiotic alternative, and engineered probiotic E. coli is a potential candidate for engineered bacterial therapeutics.
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Title: UTILIZING BACTERIAL INTERACTIONS TO CONTROL PATHOGENIC BIOFILM FORMATION
Creator: Fang, Kuili
Date: 2020
Description: Many chronic infections involve bacterial biofilms, which are difficult to eliminate using conventional antibiotic treatments. Biofilm...
Show moreMany chronic infections involve bacterial biofilms, which are difficult to eliminate using conventional antibiotic treatments. Biofilm formation is a result of dynamic intra- or inter-species interactions. However, the nature of molecular interactions between bacteria in multi-species biofilms are not well understood compared to those in mono-species biofilms. The first project (Chapter 3) investigated the ability of probiotic Escherichia coli Nissle 1917 (EcN) to outcompete the biofilm formation of pathogens including enterohemorrhagic E. coli (EHEC), Pseudomonas aeruginosa, Staphylococcus aureus, and S. epidermidis. When dual-species biofilms were formed, EcN inhibited the EHEC biofilm population by 14-fold compared to EHEC mono-species biofilms. This figure was 1,100-fold for S. aureus and 8,300-fold for S. epidermidis; however, EcN did not inhibit P. aeruginosa biofilms. In contrast, commensal E. coli did not exhibit any inhibitory effect toward other bacterial biofilms. We identified that EcN secretes DegP, a bifunctional (protease and chaperone) periplasmic protein, outside the cells and controls other biofilms. Although three E. coli strains tested in this study expressed degP, only the EcN strain secreted DegP outside the cells. The deletion of degP disabled the activity of EcN in inhibiting EHEC biofilms, and purified DegP directly repressed EHEC biofilm formation. Hence, probiotic E. coli outcompetes pathogenic biofilms via extracellular DegP activity during dual-species biofilm formation. Enterohemorrhagic Escherichia coli O157:H7 (EHEC) is a pathogen causing the outbreaks of hemorrhagic colitis. Conventional antibiotics treatment is not recommended for EHEC infection as antibiotics trigger Shiga toxin production of EHEC and aggravate hemolytic-uremic syndrome. EHEC biofilm formation is closely associated with its virulence expression. Previously, we identified that probiotic E. coli Nissle 1917 (EcN) secretes DegP resulting in the inhibition of EHEC biofilm formation in a dual culture. DegP is a serine protease exhibiting both proteolytic and chaperone functions and binds to outer membrane proteins (OMPs) of target cells. However, the extracellular function of DegP is not clear. We hypothesized that binding of DegP to OMPs of EHEC might inhibit EHEC biofilm formation by affecting the adhesion ability or changing biofilm-related gene regulations of EHEC. We constructed EHEC mutants lacking ompA, ompC, or ompF individually and in combination and assessed their biofilm formation in the presence of DegP-secreting EcN in the co-culture or by adding purified DegP. It was found that both ompA and ompC double deletion decreased EHEC single species biofilm, and also caused that DegP inhibited more EHEC biofilm (about 25 fold inhibition) than DegP inhibited EHEC wt biofilm (about 10 fold), indicating that OmpA and OmpC are more related to EHEC biofilm than OmpF, and OmpA and OmpC might deplete DegP inhibitory functions. On the other hand, DegP S210A, a DegP mutant lacking protease function, inhibited EHEC wt biofilm, indicating that DegP’s biofilm inhibition function is not from its protease activity. Additionally, EHEC transcription profiles in the presence of DegP showed that DegP up-regulated expressions of cellulose production related genes (csgD and bcsA) and motility related genes (flhD, qseB), which were all involved in EHEC biofilm inhibition, and down-regulated Shiga toxin 2 virulence gene (stx2). Besdies, DegP promoted EHEC cellulose production and motility, which is consistent with transcription profile, and Shiga toxin 2 production will be further tested. This study reveals a new function of DegP secreted by EcN in controlling biofilms and leads us to develop an alternative strategy to control biofilm-related infections. Foodborne pathogen Listeria monocytogenes biofilm formation renders these cells highly resistant to current sanitation methods, and probiotics may be a promising approach to the efficient inhibition of Listeria biofilms. In the Chapter 5 study, three Leuconostoc mesenteroides strains of lactic acid bacteria isolated from kimchi were shown to be effective probiotics for inhibiting Listeria biofilm formation. Biofilms of two L. monocytogenes serotypes, 1/2a (ATCC15313) and 4b (ATCC19115), in dual-species culture with each probiotic strain were decreased by more than 40-fold as compared with single-species Listeria biofilms; for instance, a reduction from 5.4 times 10^6 CFU/cm2 L. monocytogenes ATCC19115 in single-species biofilms to 1.1 times 10^5 CFU/cm2 in dual-species biofilms. Most likely, one of the Leuconostoc strains, L. mesenteroides W51, led to the highest Listeria biofilm inhibition without affecting the growth of L. monocytogenes. The cell-free supernatant from the L. mesenteroides W51 culture containing large protein molecules (> 30 kDa) also inhibited Listeria biofilms. These data indicate that Leuconostoc probiotics can be used to repress L. monocytogenes biofilm contamination on surfaces at food processing facilities.
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Title: Developing Advanced Materials for Carbon Dioxide Electroreduction to Value-Added Chemicals and Fuels
Creator: Esmaeilirad, Mohammadreza
Date: 2023
Description: Developing highly efficient electrocatalysts for the carbon dioxide reductionreaction (CO2RR) to value-added fuels and chemicals offers a...
Show moreDeveloping highly efficient electrocatalysts for the carbon dioxide reductionreaction (CO2RR) to value-added fuels and chemicals offers a feasible pathway for renewable energy storage and could help mitigate the ever-increasing carbon dioxide (CO2) emissions from human activities. Different catalysts are known to catalyze CO2RR in aqueous solutions. Most known catalysts are only capable of transferring 2 electrons with needed protons to CO2 producing either carbon monoxide (CO) or formic acid (HCOOH). Copper (Cu) is the only electrocatalytic material that converts CO2 into different types of hydrocarbon products. Additionally, owing to Cu’s natural abundance and low cost, it has been intensively studied for CO2RR for decades. However, the required high input energy (overpotential), low product selectivity towards valuable fuel products, and the lack of long-term stability remain major challenges for Cu-based catalysts. This work aims to develop new materials that produce hydrocarbons at lower overpotentials with higher rates and greater selectivity than current copper catalysts. By implementing a process referred to as the electrocatalyst discovery cycle iterations between predications, catalyst testing, and active site characterization allow for the rational design and discovery of new and improved electrocatalysts for CO2RR. This methodology led to the discovery of different heteroatomic catalysts as low overpotential catalysts for electroreduction of CO2 high energy density hydrocarbon products.
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