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Redirection Of Skn-1 Abates The Negative Metabolic Outcomes Of A Perceived Pathogen Infection, James D. Nhan, Christian D. Turner, Sarah M. Anderson, Chia-An Yen, Hans M. Dalton, Hilary K. Cheesman, Dana L. Ruter, Nandhitha Uma Naresh, Cole M. Haynes, Alexander A. Soukas, Read Pukkila-Worley, Sean P. Curran 2019 University of Southern California

Redirection Of Skn-1 Abates The Negative Metabolic Outcomes Of A Perceived Pathogen Infection, James D. Nhan, Christian D. Turner, Sarah M. Anderson, Chia-An Yen, Hans M. Dalton, Hilary K. Cheesman, Dana L. Ruter, Nandhitha Uma Naresh, Cole M. Haynes, Alexander A. Soukas, Read Pukkila-Worley, Sean P. Curran

Open Access Articles

Early host responses toward pathogens are essential for defense against infection. In Caenorhabditis elegans, the transcription factor, SKN-1, regulates cellular defenses during xenobiotic intoxication and bacterial infection. However, constitutive activation of SKN-1 results in pleiotropic outcomes, including a redistribution of somatic lipids to the germline, which impairs health and shortens lifespan. Here, we show that exposing C. elegans to Pseudomonas aeruginosa similarly drives the rapid depletion of somatic, but not germline, lipid stores. Modulating the epigenetic landscape refines SKN-1 activity away from innate immunity targets, which alleviates negative metabolic outcomes. Similarly, exposure to oxidative stress redirects SKN-1 activity away from ...


Investigation Of Microbiota In Health And Disease Of Poultry, Bishnu Adhikari 2019 University of Arkansas, Fayetteville

Investigation Of Microbiota In Health And Disease Of Poultry, Bishnu Adhikari

Theses and Dissertations

The microbiotas play vital roles in health and diseases of both humans and animals. 16S rRNA genes sequence analysis is one of the most popular and commonly used methods in the analysis of microbiotas associated with hosts. In this dissertation, the microbiotas of chickens (broilers, breeders, and layers) and turkeys were evaluated by 16S rRNA gene sequencing. Characterization of the culturable subpopulations of Lactobacillus in the chicken gut can serve as a valuable resource for probiotic development. In Chapter 2, Lactobacillus subpopulations recovered on MRS from chicken gut were defined comprehensively for the first time using 16S rRNA gene profiling ...


A Novel Phox/Cd38/Mcoln1/Tfeb Axis Important For Macrophage Activation During Bacterial Phagocytosis, Mehran Najibi, Joseph A. Moreau, Havisha H. Honwad, Javier E. Irazoqui 2019 University of Massachusetts Medical School

A Novel Phox/Cd38/Mcoln1/Tfeb Axis Important For Macrophage Activation During Bacterial Phagocytosis, Mehran Najibi, Joseph A. Moreau, Havisha H. Honwad, Javier E. Irazoqui

University of Massachusetts Medical School Faculty Publications

Macrophages are a key and heterogenous class of phagocytic cells of the innate immune system, which act as sentinels in peripheral tissues and are mobilized during infection. Macrophage activation in the presence of bacterial cells and molecules entails specific and complex programs of gene expression. How such triggers elicit the gene expression programs is incompletely understood. We previously discovered that transcription factor TFEB is a key contributor to macrophage activation during bacterial phagocytosis. However, the mechanism linking phagocytosis of bacterial cells to TFEB activation remained unknown. In this article, we describe a previously unknown pathway that links phagocytosis with the ...


How A Cell Knows Where To Divide: Oscillation Of Mind In Vivo, Colby Ferreira 2019 University of Rhode Island

How A Cell Knows Where To Divide: Oscillation Of Mind In Vivo, Colby Ferreira

Senior Honors Projects

Over two-million people in the United States are infected by antibiotic resistant bacteria each year. Of this number 23,000 die from these infections and other complications. Due to this, novel antibiotic targets are constantly being investigated. One process in prokaryotes that holds promise is cellular division. Bacterial cells grow and reproduce using a series of proteins known as the cell division machinery. This machinery enables the division of the parental cell into two identical daughter cells. The cell division machinery is similar between bacterial taxa, making it an ideal target for new classes of antibiotics. Therefore, understanding the molecular ...


Consistency Is Futile!: Selecting Phycoremediators For Consortia, Tori Spencer 2019 Lincoln University, Jefferson City Missouri

Consistency Is Futile!: Selecting Phycoremediators For Consortia, Tori Spencer

BIO 410 Spring 2019 Research Papers

Bioremediation is the process by which organisms remove and transform toxic compounds in a contaminated source. This is a waste management technique currently used to clean up man-made contamination. Many organisms act as natural remediators; in the case of algae, they are called phycoremediators who perform phycoremediaton. The term algae encompasses a variety of taxonomic groups and their diversity is still being realized; there are over 44,000 named species of the 72,000 species that we have identified. Some estimates calculate that there are over 200,000 diatom species alone. This diversity continues to be difficult to organize, which ...


Properties Of A Genetically Unique Mycobacteriophage, Amanda K. Staples 2019 Western Kentucky University

Properties Of A Genetically Unique Mycobacteriophage, Amanda K. Staples

Masters Theses & Specialist Projects

Bacteriophage MooMoo is a temperate phage that was isolated and propagated on Mycobacterium smegmatis (M. smeg). It typically produces turbid plaques, however spontaneous clear plaque mutants can be readily isolated. Both turbid (MooMoo-T) and clear plaque (MooMoo-C) formers can establish stable lysogens, but the parental turbid plaque forming phage has a higher lysogenic frequency. The phage repressor protein typically plays the central role in regulating the lysis/lysogeny decision. Therefore, we expected that the mutation responsible for the clear plaque phenotype would be located in the repressor gene. Remarkably, whole genome sequencing detected a single base pair mutation in the ...


Serum Amyloid P Component Binds Fungal Surface Amyloid And Decreases Human Macrophage Phagocytosis And Secretion Of Inflammatory Cytokines, Nicole E. Behrens, Peter N. Lipke, Darrell Pilling, Richard H. Gomer, Stephen A. Klotz 2019 University of Arizona

Serum Amyloid P Component Binds Fungal Surface Amyloid And Decreases Human Macrophage Phagocytosis And Secretion Of Inflammatory Cytokines, Nicole E. Behrens, Peter N. Lipke, Darrell Pilling, Richard H. Gomer, Stephen A. Klotz

Publications and Research

In patients with invasive fungal diseases, there is often little cellular inflammatory response. We tested the idea that binding of the human constitutive plasma protein serum amyloid P component (SAP) (also called PTX2) to Candida albicans dampens the innate immune response to this fungus. Many pathogenic fungi have cell surface amyloid-like structures important for adhesion and biofilm formation. Human SAP bound to fungi that expressed functional cell surface amyloid, but SAP had minimal binding to fungi with reduced expression of cell surface amyloid. In the absence of SAP, phagocytosis of fungi by human macrophages was potentiated by expression of amyloid ...


Effectiveness Of Windrow Composting Methodology In Killing A Thermo-Tolerant Species Of Salmonella During Mortality Composting, Spencer Gabriel Myers 2019 California Polytechnic State University, San Luis Obispo

Effectiveness Of Windrow Composting Methodology In Killing A Thermo-Tolerant Species Of Salmonella During Mortality Composting, Spencer Gabriel Myers

Master's Theses and Project Reports

In a large agricultural operation, such as the one at Cal Poly San Luis Obispo, disposal of deceased animals is an immense issue. The cost of transporting and rendering every dead animal is inhibitory to the general function of the agricultural operations and their thin budget. Therefore, we propose that composting mortalities could be an economical alternative. Composting is a recognized method for taking animal waste products along with carbon waste and turning it into a pathogen-free, nutrient-rich topsoil. Carcass composting is in fact performed in other countries and states to varying degrees of success. However, the California EPA limits ...


Shrimp Production Environment And The Gut Microbiome: Effects Of Aquaculture Practices And Selective Breeding On The Gut Microbiome Of Pacific Whiteleg Shrimp, Litopenaeus Vannamei, Angela Landsman 2019 South Dakota State University

Shrimp Production Environment And The Gut Microbiome: Effects Of Aquaculture Practices And Selective Breeding On The Gut Microbiome Of Pacific Whiteleg Shrimp, Litopenaeus Vannamei, Angela Landsman

Electronic Theses and Dissertations

Knowledge of the functional role of the gut microbiome in animal health and nutrition may provide solutions to shrimp aquaculture challenges, such as improving disease resistance and optimizing growth particularly with low cost feeds. Successful manipulation of bacteria found in the gut requires a deeper understanding of shrimp microbial communities and how their compositional structure is influenced by environmental conditions, and inherent host factors such as genetics. The initial research investigated the intestinal bacterial communities of the Pacific whiteleg shrimp (Litopenaeus vannamei) reared in pond systems compared to indoor aquaculture facilities as an exploration of the effects of aquaculture practices ...


Metabolic Engineering For Biocatalyst Robustness To Organic Inhibitors, Liam Royce, Laura R. Jarboe 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 ...


Stress Response Mechanisms Of Listeria Monocytogenes, Oindrila Paul 2018 The University of Southern Mississippi

Stress Response Mechanisms Of Listeria Monocytogenes, Oindrila Paul

Dissertations

Listeria monocytogenes is a Gram-positive, facultative intracellular food-borne pathogen that causes the disease listeriosis. In order to establish an infection, L. monocytogenes must survive multiple stressors encountered within the gastrointestinal tract, including alterations in pH, bile, salt, and oxygen availability. This dissertation focused on understanding the stress response of L. monocytogenes to bile. Bile acts as a bactericidal agent by disrupting the membrane integrity and causing instability to macromolecules like DNA. Thus, a bacterium must be able to maintain its membrane architecture, composition and integrity.

Often times, bacteria will modulate their fatty acid composition in the membrane to cope with ...


Investigating The Single Cell Heterogeneity And Physiological Impact Of Mistranslation, Christopher Evans 2018 The University of Texas M D Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences

Investigating The Single Cell Heterogeneity And Physiological Impact Of Mistranslation, Christopher Evans

UT GSBS Dissertations and Theses (Open Access)

Bacterial populations grow clonal populations; however, individual cells have a variety of phenotypes. The physiological heterogeneity observed in populations has been attributed to variations in the processes of gene expression. For example, promoter expression has been shown to be heterogeneous within a population and contribute to increased stress tolerance in a subpopulation of cells. In comparison to transcription, the influence of translation on single cells is unclear. In this study, my collaborators and I have developed a dual-fluorescence reporter that allows us to measure the mistranslation rate in single cells in vivo. Using this reporter, we found that mistranslation rates ...


Assembly And Display Of Surface Proteins In Actinomyces Oris, Sara Siegel 2018 The University of Texas M D Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences

Assembly And Display Of Surface Proteins In Actinomyces Oris, Sara Siegel

UT GSBS Dissertations and Theses (Open Access)

Bacteria are an integral part of human health and disease. In the human host, dental plaques form as a result of up to 700 individual bacterial species colonizing oral surfaces and forming a multispecies biofilm. These biofilms are the cause of prevalent human diseases such as dental caries, gingivitis, and periodontitis. The microbes present in the oral biofilm are highly spatially and temporally structured and require a primary colonizing species to adhere to host tissue. As an important primary colonizer of the oral biofilm, the actinobacterium Actinomyces oris utilizes cell wall anchored proteins and glycoconjugates to initiate adherence to host ...


Insights Into The Reactivation, Regulation And Essentiality Of Oxidative Protein Folding Pathways In Actinobacteria, Belkys Sanchez 2018 The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences

Insights Into The Reactivation, Regulation And Essentiality Of Oxidative Protein Folding Pathways In Actinobacteria, Belkys Sanchez

UT GSBS Dissertations and Theses (Open Access)

Accurate disulfide bond formation is important for proper folding, stability and function of exported proteins. The process of disulfide bond formation, termed oxidative protein folding, is catalyzed by thiol-disulfide oxidoreductase enzymes. Oxidative protein folding pathways influence processes essential for bacterial physiology and pathogenicity. In the Gram-positive actinobacterial pathogens Actinomyces oris and Corynebacterium diphtheriae oxidative protein folding is catalyzed by the primary thiol-disulfide oxidoreductase MdbA. MdbA is required for assembly of adhesive pilus, which mediate receptor-dependent bacterial interactions, or coaggregation, in A. oris. In the first part of this dissertation, I identify components of the electron transport chain (ETC) required for ...


Methanogens, Plausible Extraterrestrial Life Forms On Mars, And Their Tolerance To Increasing Concentrations Of Illite Clay, Chandler Kern 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, Cody Bullock 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 ...


Hydrogen Stress And Syntrophy Of Hyperthermophilic Heterotrophs And Methanogens, Begum Topcuoglu 2018 University of Massachusetts Amherst

Hydrogen Stress And Syntrophy Of Hyperthermophilic Heterotrophs And Methanogens, Begum Topcuoglu

Doctoral Dissertations

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 ...


A Broad Spectrum Racemase In Pseudomonas Putida Kt2440 Plays A Key Role In Amino Acid Catabolism, Atanas D. Radkov, Luke A. Moe 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 ...


Identification Of A Tola Protein Binding Site For Bacterial Toxins, Monica Ferrante 2018 Bowling Green State University

Identification Of A Tola Protein Binding Site For Bacterial Toxins, Monica Ferrante

Honors Projects

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 ...


Inefficient Metabolism Of The Human Milk Oligosaccharides Lacto-N-Tetraose And Lacto-N-Neotetraose Shifts Bifidobacterium Longum Subsp. Infantis Physiology, Ezgi Ozcan, David Sela 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 ...


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