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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 ...


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 ...


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 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 2018 Carroll College

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 2018 Carroll College

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, Benedict Lenhart 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, Chen Tian, Yuxin Chen, Yong Liu, Shixia Wang, Yang Li, Guiyang Wang, Juan Xia, Xiang-An Zhao, Rui Huang, Shan Lu, Chao Wu 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 ...


The Bi-Directional Relationship Between Gut Microbiota And Autoimmunity, Trevor O. Kirby 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 ...


Emergence Of New Metabolic Pathways In Escherichia Coli, Michael Kristofich 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 ...


Molecular Classification And Uv Tolerance Of Pigmented Antarctic Extremophiles, Aaron M. Perry 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, Rajesh Singh, Michael S. Guzman, Arpita Bose 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, 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 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, Audrey C. Bergeron 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 ...


Quorum Sensing Signals Produced By Heterotrophic Bacteria In Black Band Disease (Bbd) Of Corals And Their Potential Role In Bbd Pathogenesis, Chinmayee D. Bhedi 2017 Florida International University

Quorum Sensing Signals Produced By Heterotrophic Bacteria In Black Band Disease (Bbd) Of Corals And Their Potential Role In Bbd Pathogenesis, Chinmayee D. Bhedi

FIU Electronic Theses and Dissertations

Black band disease (BBD) of corals is a temperature dependent, highly virulent, polymicrobial disease affecting reef-building corals globally. The microbial consortium of BBD is primarily comprised of functional physiological groups that include photosynthetic cyanobacteria, sulfate reducers, sulfide oxidizers and a vast repertoire of heterotrophic bacteria. Quorum sensing (QS), the cell-density dependent communication phenomenon in bacteria, is known to induce expression of genes for a variety of virulence factors in diseases worldwide. Microbes capable of QS release signals such as acyl homoserine lactones (AHLs) and autoinducer-2 (AI-2), which coordinate microbial interaction. The focus of the present study was to investigate the ...


Protein-Protein Interactions Of Bacterial Topoisomerase I, Srikanth Banda 2017 Florida International University

Protein-Protein Interactions Of Bacterial Topoisomerase I, Srikanth Banda

FIU Electronic Theses and Dissertations

Protein-protein interactions (PPIs) are essential features of cellular processes including DNA replication, transcription, translation, recombination, and repair. In my study, the protein interactions of bacterial DNA topoisomerase I, an essential enzyme, were investigated. The topoisomerase I in bacteria relaxes excess negative supercoiling on DNA and maintains genomic stability. Investigating the PPI network of DNA topoisomerase I can further our understanding of the various functional roles of this enzyme. My study is focused on topoisomerase I of Escherichia coli and Mycobacterium smegmatis. Firstly, we have explored the biochemical mechanisms for an interaction between RNA Polymerase, and topoisomerase I in E. coli ...


Intestinal Organoids Model Human Responses To Infection By Commensal And Shiga Toxin Producing Escherichia Coli, Sayali S. Karve, Suman Pradhan, Doyle V. Ward, Alison A. Weiss 2017 University of Cincinnati

Intestinal Organoids Model Human Responses To Infection By Commensal And Shiga Toxin Producing Escherichia Coli, Sayali S. Karve, Suman Pradhan, Doyle V. Ward, Alison A. Weiss

Open Access Articles

Infection with Shiga toxin (Stx) producing Escherichia coli O157:H7 can cause the potentially fatal complication hemolytic uremic syndrome, and currently only supportive therapy is available. Lack of suitable animal models has hindered study of this disease. Induced human intestinal organoids (iHIOs), generated by in vitro differentiation of pluripotent stem cells, represent differentiated human intestinal tissue. We show that iHIOs with addition of human neutrophils can model E. coli intestinal infection and innate cellular responses. Commensal and O157:H7 introduced into the iHIO lumen replicated rapidly achieving high numbers. Commensal E. coli did not cause damage, and were completely contained ...


Development Of A Core Clostridium Thermocellum Kinetic Metabolic Model Consistent With Multiple Genetic Perturbations, Satyakam Dash, Ali Khodayari, Jilai Zhou, Evert K. Holwerda, Daniel Olson, Lee Lynd, Costas Maranas 2017 The Pennsylvania State University

Development Of A Core Clostridium Thermocellum Kinetic Metabolic Model Consistent With Multiple Genetic Perturbations, Satyakam Dash, Ali Khodayari, Jilai Zhou, Evert K. Holwerda, Daniel Olson, Lee Lynd, Costas Maranas

Open Dartmouth: Faculty Open Access Articles

Clostridium thermocellum is a Gram-positive anaerobe with the ability to hydrolyze and metabolize cellulose into biofuels such as ethanol, making it an attractive candidate for consolidated bioprocessing (CBP). At present, metabolic engineering in C. thermocellum is hindered due to the incomplete description of its metabolic repertoire and regulation within a predictive metabolic model. Genome-scale metabolic (GSM) models augmented with kinetic models of metabolism have been shown to be effective at recapitulating perturbed metabolic phenotypes.

In this effort, we first update a second-generation genome-scale metabolic model (iCth446) for C. thermocellum by correcting cofactor dependencies, restoring elemental and charge balances, and ...


Scanning Labyrinthulomycete Genomes For Yeast Transcription Factor Binding Site Motifs, Jackie L. Collier, Joshua Rest 2017 SUNY Stony Brook

Scanning Labyrinthulomycete Genomes For Yeast Transcription Factor Binding Site Motifs, Jackie L. Collier, Joshua Rest

Interdisciplinary Research Data

To develop broadly useful methods for the genetic manipulation of Labyrinthulomycetes (a diverse group of ubiquitous osmoheterotrophic marine protists), it is essential to understand the similarities and differences in regulation of gene expression among them. Toward this end we have used FIMO from the MEME suite (http://meme-suite.org/doc/fimo.html) to identify potential transcription factor binding sites in each of the three available genome sequences: Aplanochytrium kerguelense PBS07, Schizochytrium aggregatum ATCC 28209, and Aurantiochytrium limacinum ATCC MYA-1381


Proteomic Approach For Extracting Cytoplasmic Proteins From Streptococcus Sanguinis Using Mass Spectrometry, Fadi Elrami, Kristina Nelson, Ping Xu 2017 Virginia Commonwealth University

Proteomic Approach For Extracting Cytoplasmic Proteins From Streptococcus Sanguinis Using Mass Spectrometry, Fadi Elrami, Kristina Nelson, Ping Xu

Philips Institute for Oral Health Research Publications

Streptococcus sanguinis is a commensal and early colonizer of oral cavity as well as an opportunistic pathogen of infectious endocarditis. Extracting the soluble proteome of this bacterium provides deep insights about the physiological dynamic changes under different growth and stress conditions, thus defining “proteomic signatures” as targets for therapeutic intervention. In this protocol, we describe an experimentally verified approach to extract maximal cytoplasmic proteins from Streptococcus sanguinis SK36 strain. A combination of procedures was adopted that broke the thick cell wall barrier and minimized denaturation of the intracellular proteome, using optimized buffers and a sonication step. Extracted proteome was quantitated ...


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