Metabolic Engineering For Biocatalyst Robustness To Organic Inhibitors, 2019 Iowa State University
Metabolic Engineering For Biocatalyst Robustness To Organic Inhibitors, Liam Royce, Laura R. Jarboe
Chemical and Biological Engineering Publications
Microbial production of biorenewable fuels and chemicals is often limited by inhibition of the biocatalyst, either by increasing concentrations of the product compound or by contaminant compounds in the biomass‐derived sugars. This inhibition can interfere with economically viable production. Here we discuss typical mechanisms of inhibition and methods for improving biocatalyst robustness. Inhibition often takes the form of inhibition of enzyme activity, depletion of cofactor pools, and membrane damage; methods are discussed for mitigating each of these types of inhibition. Various evolutionary schemes have been developed and implemented on a variety of inhibitory compounds, including butanol, acetic acid, furfural ...
Methanogens, Plausible Extraterrestrial Life Forms On Mars, And Their Tolerance To Increasing Concentrations Of Illite Clay, 2018 University of Arkansas, Fayetteville
Methanogens, Plausible Extraterrestrial Life Forms On Mars, And Their Tolerance To Increasing Concentrations Of Illite Clay, Chandler Kern
Biological Sciences Undergraduate Honors Theses
Methanogens, some of Earth’s most primitive prokaryotic organisms, are candidates for possible life forms capable of inhabiting Mars. Specifically, four different species (Methanobacterium formicicum, Methanococcus maripaludis, Methanosarcina barkeri, Methanothermobacter wolfeii) were analyzed for their tolerance to the presence of illite clay. Illite is a crystalline mineral that has been identified from regions of Mars’s surface. Results indicated that all four species grew with some success in the illite at different concentrations. This experimentation with methanogens’ abilities to survive and reproduce in the presence of illite allows for a more accurate understanding of the potential capability of microbial growth ...
Dissecting The Mechanism Of Action Of A Novel Antifungal Peptide, 2018 University of Arkansas, Fayetteville
Dissecting The Mechanism Of Action Of A Novel Antifungal Peptide, Cody Bullock
Theses and Dissertations
There is an urgent need for novel treatments for Candida infections. The utility of antimicrobial peptides for antifungal therapy has garnered interest in recent years. One promising family of peptides is the Histatins, a family of naturally-occurring peptides secreted into the oral cavity that display antimicrobial activity. Histatin 5 is a twenty-four amino acid peptide with strong antifungal activity. Studies from our laboratory have identified a small histatin-derived peptide, KM29, that yields fungicidal activity 10-fold greater than Histatin 5 against multiple Candida species. Our laboratory has focused on understanding the mechanism of action of KM29 to further develop it as ...
A Broad Spectrum Racemase In Pseudomonas Putida Kt2440 Plays A Key Role In Amino Acid Catabolism, 2018 University of California - San Francisco
A Broad Spectrum Racemase In Pseudomonas Putida Kt2440 Plays A Key Role In Amino Acid Catabolism, Atanas D. Radkov, Luke A. Moe
Plant and Soil Sciences Faculty Publications
The broad-spectrum amino acid racemase (Alr) of Pseudomonas putida KT2440 preferentially interconverts the L- and D-stereoisomers of Lys and Arg. Despite conservation of broad-spectrum racemases among bacteria, little is known regarding their physiological role. Here we explore potential functional roles for Alr in P. putida KT2440. We demonstrate through cellular fractionation that Alr enzymatic activity is found in the periplasm, consistent with its putative periplasm targeting sequence. Specific activity of Alr is highest during exponential growth, and this activity corresponds with an increased accumulation of D-Lys in the growth medium. An alr gene knockout strain (Δalr) was generated and ...
Inefficient Metabolism Of The Human Milk Oligosaccharides Lacto-N-Tetraose And Lacto-N-Neotetraose Shifts Bifidobacterium Longum Subsp. Infantis Physiology, 2018 University of Massachusetts, Amherst
Inefficient Metabolism Of The Human Milk Oligosaccharides Lacto-N-Tetraose And Lacto-N-Neotetraose Shifts Bifidobacterium Longum Subsp. Infantis Physiology, Ezgi Ozcan, David Sela
Open Access Articles
Human milk contains a high concentration of indigestible oligosaccharides, which likely mediated the coevolution of the nursing infant with its gut microbiome. Specifically, Bifidobacterium longum subsp. infantis (B. infantis) often colonizes the infant gut and utilizes these human milk oligosaccharides (HMOs) to enrich their abundance. In this study, the physiology and mechanisms underlying B. infantis utilization of two HMO isomers lacto-N-tetraose (LNT) and lacto-N-neotetraose (LNnT) was investigated in addition to their carbohydrate constituents. Both LNT and LNnT utilization induced a significant shift in the ratio of secreted acetate to lactate (1.7-2.0) in contrast to the catabolism of their ...
Identification Of A Tola Protein Binding Site For Bacterial Toxins, 2018 Bowling Green State University
Identification Of A Tola Protein Binding Site For Bacterial Toxins, Monica Ferrante
Group A colicins are proteinaceous bacteriocins encoded by plasmids that exploit the cellular envelope protein TolA to translocate the cell wall barrier and cellular envelope of the bacterium Escherichia coli. These colicins offer protocols for studying certain protein-protein interactions involved in such membrane transport functions. Previous experimentations suggest the carboxyl-terminal domain of TolA protein contains specific amino acid binding regions required for the translocation of group A colicins into E. coli. The amino acid sequence of this domain varies between E. coli and other gram-negative bacterial species. It has been suggested that this diversity could be utilized to identify specific ...
Bioprospecting Deep-Sea Actinobacteria For Novel Anti-Infective Natural Products, 2018 Florida Atlantic University
Bioprospecting Deep-Sea Actinobacteria For Novel Anti-Infective Natural Products, Dongbo Xu, Linna Han, Chunhui Li, Qi Cao, Duolong Zhu, Nolan H. Barrett, Dedra Harmody, Jing Chen, Haining Zhu, Peter J. Mccarthy, Xingmin Sun, Guojun Wang
Molecular and Cellular Biochemistry Faculty Publications
The global prevalence of drug resistance has created an urgent need for the discovery of novel anti-infective drugs. The major source of antibiotics in current clinical practice is terrestrial actinobacteria; the less-exploited deep-sea actinobacteria may serve as an unprecedented source of novel natural products. In this study, we evaluated 50 actinobacteria strains derived from diverse deep water sponges and environmental niches for their anti-microbial activities against a panel of pathogens including Candida albicans, Clostridium difficile, Staphylococcus aureus, and methicillin-resistant S. aureus (MRSA), and Pseudomonas aeruginosa. More than half of the tested strains (27) were identified as active in at least ...
Predator-By-Environment Interactions Mediate Bacterial Competition In The Dictyostelium Discoideum Microbiome, 2018 Washington University in St Louis
Predator-By-Environment Interactions Mediate Bacterial Competition In The Dictyostelium Discoideum Microbiome, R Fredrik Inglis, Odion Asikhia, Erica Ryu, David C. Queller, Joan E. Strassmann
Biology Faculty Publications & Presentations
Interactions between species and their environment play a key role in the evolution of diverse communities, and numerous studies have emphasized that interactions among microbes and among trophic levels play an important role in maintaining microbial diversity and ecosystem functioning. In this study, we investigate how two of these types of interactions, public goods cooperation through the production of iron scavenging siderophores and predation by the social amoeba Dictyostelium discoideum, mediate competition between two strains of Pseudomonas fluorescens that were co-isolated from D. discoideum. We find that although we are able to generally predict the competitive outcomes between strains based ...
The Effect Of Alcohol On Pfk1 Gene Expression And Feeding Activity In Tetrahymena Thermophila, Evelyn Sowers, Alex Skoulis
Carroll College Student Undergraduate Research Festival
The purpose of this experiment was to test whether alcohol induces starvation conditions in Tetrahymena thermophila. Prior research has shown that exposure to alcohol results in decreases in both the frequency of feeding and overall growth. For this experiment, it was hypothesized that these effects are due to a lack of energy available in the organism for feeding. This hypothesis was tested by monitoring food vacuole formation and expression of the PFK-1 gene in Tetrahymena that were exposed to alcohol. The PFK-1 gene was chosen because its encoded protein plays an essential role in cellular metabolism. For the experiment, control ...
The Effects Of Salt Concentration On Tetrahymena Thermophila Growth And Crp1 Gene Expression, Anna Sapone, Rachel Tremaine,, Katie Mchugh
Carroll College Student Undergraduate Research Festival
The use of salt to remove ice from roads has resulted in increased salinity in many freshwater lakes in North America. For this project, we wanted to explore how environmental salt concentrations influence the rate of growth of Tetrahymena thermophila and expression of the CRP1 gene. We hypothesized that if the sodium concentration is increased in the media, Tetrahymena growth would decrease and expression of the CRP1 gene would increase. The CRP1 gene encodes a protein that helps regulate calcium concentrations within a cell based on the concentration of sodium ions. The media of the experimental group was treated with ...
Investigating Phenotypic And Genetic Variation In Quorum Sensing In Natural Isolates Of The Model Yeast, Saccharomyces Cerevisiae, 2018 College of William and Mary
Investigating Phenotypic And Genetic Variation In Quorum Sensing In Natural Isolates Of The Model Yeast, Saccharomyces Cerevisiae, Benedict Lenhart
Undergraduate Honors Theses
Microbes can enact massive change to themselves and their environment through the process of quorum sensing (QS). Through the chemical and metabolic processes of QS, microbes can determine the concentration of cooperative cells in their environment, and if a “quorum” is reached, alter genetic expression to modify microbe behavior and take advantage of resources. Often this altered behavior involves cooperative formations, as is the case of yeast strains like Saccharomyces Cerevisiae. This vastly abundant microbe serves as a convenient and effective model organism for studies examing microbial communication, as well as model for developing treatments for related-yeast Candida albicans infections ...
Use Of Elispot Assay To Study Hbs-Specific B Cell Responses In Vaccinated And Hbv Infected Humans, 2018 Nanjing University
Use Of Elispot Assay To Study Hbs-Specific B Cell Responses In Vaccinated And Hbv Infected Humans, Chen Tian, Yuxin Chen, Yong Liu, Shixia Wang, Yang Li, Guiyang Wang, Juan Xia, Xiang-An Zhao, Rui Huang, Shan Lu, Chao Wu
Open Access Articles
Hepatitis B surface antibody (HBsAb) plays a critical role in protecting against infection of hepatitis B virus (HBV) and were extensively studied in literature. At the same time, the status of hepatitis B surface antigen (HBs)-specific B cells in both vaccinated and HBV infected people received limited attention. In the current study, we adopted a highly specific B-cell Enzyme Linked ImmunoSpot (ELISpot) assay to analyze HBs-specific B cells in various clinical settings: healthy individuals with the history of HBV vaccination before and after receiving an extra HBV vaccine boost, people chronically infected with HBV (CHB) in various clinical stages ...
Insights Into Key Gene Regulatory Networks In Borrelia Burgdorferi, 2018 University of Kentucky
Insights Into Key Gene Regulatory Networks In Borrelia Burgdorferi, William Kenneth Arnold
Theses and Dissertations--Microbiology, Immunology, and Molecular Genetics
Gene regulatory networks are composed of interconnected regulatory nodes created by regulatory factors of multiple types. All organisms finely tune gene expression in order to adapt to and survive within their current niche. Obligate parasitic bacteria are under extreme pressure to quickly and appropriately adapt their gene regulatory programs in order to survive within their given host. Borrelia burgdorferi is one such organism and persists in nature by alternating between two hosts; Ixodes spp. ticks and small vertebrate animals. These two hosts represent drastically different environments; requiring a unique gene regulatory program to survive and transmit between them. Microbiologists have ...
Hydrogen Stress And Syntrophy Of Hyperthermophilic Heterotrophs And Methanogens, 2018 University of Massachusetts Amherst
Hydrogen Stress And Syntrophy Of Hyperthermophilic Heterotrophs And Methanogens, Begum Topcuoglu
Approximately 1 giga ton (Gt, 1015 g) of CH4 is formed globally per year from H2, CO2, and acetate through methanogenesis, largely by methanogens growing in syntrophic association with anaerobic microbes that hydrolyze and ferment biopolymers. However, our understanding of methanogenesis in hydrothermal regions of the subseafloor and potential syntrophic methanogenesis at thermophilic temperatures is nascent. This dissertation shows that thermophilic H2 syntrophy can support methanogenesis within natural microbial assemblages at hydrothermal vents and that it can be an important alternative energy source for thermophilic autotrophs in marine geothermal environments. This dissertation also elucidates H ...
Emergence Of New Metabolic Pathways In Escherichia Coli, 2018 University of Colorado, Boulder
Emergence Of New Metabolic Pathways In Escherichia Coli, Michael Kristofich
Undergraduate Honors Theses
Catalytic promiscuity provides a starting point for the evolution of new enzymes. Taking this concept further, a series of promiscuous enzymes may assemble to form the basis of a new metabolic pathway (termed “serendipitous pathway”) that may emerge and become more efficient in adapting bacterial cells that require it to grow. The Copley lab at the University of Colorado at Boulder has been observing genetic changes that improve growth of Escherichia coli cells that lack the essential gene pdxB. These genetic changes are believed to improve the flux of metabolites through one or more serendipitous pathways that make up for ...
The Bi-Directional Relationship Between Gut Microbiota And Autoimmunity, 2018 Eastern Washington University
The Bi-Directional Relationship Between Gut Microbiota And Autoimmunity, Trevor O. Kirby
EWU Masters Thesis Collection
Humans serve as a major reservoir for a vast number of microbiota. These microbes have evolved symbiotic relationships with humans due to their close proximity with their host. As a result, the immune system adapts to the microbiota thus modulating immunological function. Autoimmunity is a state in which there are aberrant immune responses produced against host tissue. Intestinal bacteria are directly impacted by instances of inflammation brought on by autoimmunity. The complicated nature between autoimmunity and bacterial modulation demonstrates a bi-directional relationship. Here, we utilize experimental autoimmune encephalomyelitis, a model for multiple sclerosis, to explore the bi-directional relationship that disease ...
Molecular Classification And Uv Tolerance Of Pigmented Antarctic Extremophiles, 2017 University of Tennessee, Knoxville
Molecular Classification And Uv Tolerance Of Pigmented Antarctic Extremophiles, Aaron M. Perry
University of Tennessee Honors Thesis Projects
No abstract provided.
Anaerobic Oxidation Of Ethane, Propane, And Butane By Marine Microbes: A Mini Review, 2017 Washington University in St. Louis
Anaerobic Oxidation Of Ethane, Propane, And Butane By Marine Microbes: A Mini Review, Rajesh Singh, Michael S. Guzman, Arpita Bose
Biology Faculty Publications & Presentations
The deep ocean and its sediments are a continuous source of non-methane short-chain alkanes (SCAs) including ethane, propane, and butane. Their high global warming potential, and contribution to local carbon and sulfur budgets has drawn significant scientific attention. Importantly, microbes can use gaseous alkanes and oxidize them to CO2, thus acting as effective biofilters. A relative decrease of these gases with a concomitant 13C enrichment of propane and n-butane in interstitial waters vs. the source suggests microbial anaerobic oxidation. The reported uncoupling of sulfate-reduction (SR) from anaerobic methane oxidation supports their microbial consumption. To date, strain BuS5 ...
Tumor Necrosis Factor Dynamically Regulates The Mrna Stabilome In Rheumatoid Arthritis Fibroblast-Like Synoviocytes, 2017 Hospital for Special Surgery
Tumor Necrosis Factor Dynamically Regulates The Mrna Stabilome In Rheumatoid Arthritis Fibroblast-Like Synoviocytes, Konstantinos Loupasakis, David Kuo, Upneet K. Sokhi, Christopher Sohn, Bethany Syracuse, Eugenia G. Giannopoulou, Sung Ho Park, Hyelim Kang, Gunnar Rätsch, Lionel B. Ivashkiv, George D. Kalliolias
Publications and Research
During rheumatoid arthritis (RA), Tumor Necrosis Factor (TNF) activates fibroblast-like synoviocytes (FLS) inducing in a temporal order a constellation of genes, which perpetuate synovial inflammation. Although the molecular mechanisms regulating TNF-induced transcription are well characterized, little is known about the impact of mRNA stability on gene expression and the impact of TNF on decay rates of mRNA transcripts in FLS. To address these issues we performed RNA sequencing and genome-wide analysis of the mRNA stabilome in RA FLS. We found that TNF induces a biphasic gene expression program: initially, the inducible transcriptome consists primarily of unstable transcripts but progressively switches ...
Candida And Pseudomonas Interact To Enhance Mucosal Infection In Transparent Zebrafish, 2017 The University of Maine
Candida And Pseudomonas Interact To Enhance Mucosal Infection In Transparent Zebrafish, Audrey C. Bergeron
Electronic Theses and Dissertations
Polymicrobial communities exist throughout the human body and include both fungi and bacteria. During disease, cross-kingdom interactions among bacteria, fungi, and/or the immune system can alter virulence and lead to complex polymicrobial infections. The fungus C. albicans is among the most commonly isolated fungi in the context of fungal-bacterial co-infections and is often accompanied by the bacterium P. aeruginosa at a variety of sites throughout the body including mucosal tissues such as the lung. In vitro, C. albicans and P. aeruginosa have a cyclic, bi-directional, and largely antagonistic relationship, but these interactions do not account for the role of ...