Microbiology Commons^™

Novel Antivirals Unveiled Against Acute And Persistent Coxsackievirus B3 Infection Via Rapid Screening, Maria Del Mar Villanueva Guzman

Master's Theses

Enteroviruses cause 10 to 15 million infections annually in the United States, and Coxsackievirus B3 is one of the most commonly reported. Coxsackieviruses may become persistent, characterized as a viral infection that is not cleared from host cells and that generates a continuous infection. Patients who develop persistent CVB3 infection may not respond to the same antivirals as an acute infection, which may be detrimental. Therefore, there is a need for broad-range antiviral drugs to combat acute and persistent CVB3 infection, as there is no well-accepted treatment available. We developed a model system to study persistent CVB3 using a pancreatic …

Disambiguation Of Aerococcus Urinae Species Diversity, Brian Ian Choi

Dissertations

Aerococcus urinae is an uncommon inhabitant of the human urogenital tract. The Gram-positive bacterium has been implicated in a wide range of urinary tract diseases that, if left untreated or undiagnosed, can progress to severe disease such as infective endocarditis. Comparative analysis of 115 A. urinae isolates from infection episodes of urinary tract infection, bacteremia, infective endocarditis, urgency urinary incontinence, stress urinary incontinence, interstitial cystitis / painful bladder syndrome, and asymptomatic individuals reveal substantial diversity with respect to predicted virulence factors, metabolism, and observed biofilm behavior. Through whole genome sequencing analysis, these strains can be reorganized into six new taxonomic …

Characterization Of The Glyoxal Response In Pseudomonas Aeruginosa, Christopher James Corcoran

Dissertations

The toxic dialdehyde glyoxal is found in all domains of life and results as a by-product from a variety of metabolic activities such as DNA oxidation, lipid peroxidation, and autoxidation of sugars such as glucose. If allowed to accumulate, the reactive aldehyde groups of glyoxal have the ability to react with a plethora of molecules including, DNA, lipids, and protein side chains. Most notably, glyoxal can react with arginine, lysine, and cysteine residues, forming irreversible covalent modifications known as advanced glycation end products (AGEs). These glyoxal-derived AGEs can impair protein function, leading to cellular toxicity and eventual cell death. Due …

Investigating The Antimicrobial Potential Of Bovine Lactoferrin Against The Neonatal Pathogen, Staphylococcus Capitis, Anna Desmond, Lesley Cotter, Des Field, Fiona O'Halloran

Department of Biological Sciences Publications

Lactoferrin is an antimicrobial glycoprotein that demonstrates a broad-spectrum of activity against a wide variety of clinical pathogens. This study investigated the potential of bovine lactoferrin (bLf) against multidrug resistant Staphylococcus capitis (S. capitis) strains. Growth curve analysis and time-kill curves demonstrated that at 750 µg ml−1 lactoferrin significantly inhibited (50.6%, P < 0.05) the growth of most isolates tested (90%), and this effect was based on a bacteriostatic mechanism. At the same concentration, bLf also significantly inhibited (30%, P < 0.05) biofilm formation in 40% of strains tested. Combinations of bLf with selected antibiotics were assessed for enhanced antimicrobial activity using growth curves. BLf combined with β-lactam antibiotics reduced the growth of S. capitis strains, however, the effects were not significant. BLf displays antimicrobial effects against multidrug resistant S. capitis isolates, but with strain-specific effects.

Effects Of Vitis Vinifera L. Seed Extract On Short-Term Memory Of Amyloid-Beta-Mediated Neurodegeneration In Transgenic Caenorhabditis Elegans, Elise Patrick

Theses

Alzheimer's disease (AD) is a neurodegenerative condition that is a common cause of dementia and a growing concern worldwide with no effective treatment or cure. Two pathological AD hallmarks include buildup of amyloid beta (Aβ) plaques and neurofibrillary tangles in the brain. Recent attention has turned to exploring natural products and compounds for AD symptom relief and treatment. Vitis vinifera grape seed extract (GSE) contains many beneficial substances. GSE has been tested in several animal models and has shown to improve memory and is even being examined in an AD treatment human clinical trial. In this study, the aim was …

Study Of Atypical Alarmone Synthesis In Clostridioides Difficile, Declan Nathaniel Butler

Chemistry & Biochemistry Theses & Dissertations

Clostridioides difficile is a Gram-positive anaerobic bacterium that causes infections in humans that costs healthcare systems billions per year. C. difficile infection has high rates of recurrence due to multiple antibiotic resistance. When bacteria are in stressful environments, they produce hyperphosphorylated guanosine ribonucleotide signaling molecules called alarmones. The accumulation of alarmones activates the stringent response (SR), in which bacterial cells induce transcription of stress survival genes to delay growth and replication. The C. difficile SR is regulated by enzymatic activity of a bifunctional synthetase/hydrolase, RelA/SpoT homolog (RSH), and a monofunctional small alarmone synthetase (RelQ). Additionally, the SR is potentially regulated …

Effects Of Spatial And Temporal Variability On Bacterial Diversity And Community Composition In Roof-Harvested Rainwater Across Central Virginia, Jade Riddle

Longwood Senior Thesis Proposal

No abstract provided.

Characterization And Evaluation Of Bacteriophages Φpa-C And Φpa-Tc Infecting Pseudomonas Aeruginosa, Joanne Harrison

Master's Theses

Pseudomonas aeruginosa are prevalent opportunistic bacterial pathogens that cause nosocomial infections in at-risk individuals. The rise of multidrug-resistant P. aeruginosa poses an immense threat to hospitals. Additionally, P. aeruginosa are common food spoilage organisms that contribute to food waste. Alternative effective treatment methods are needed to improve public health and reduce food waste. Recent studies have shown that bacteriophages, viruses that only kill host-specific bacteria, are promising alternatives. This study characterizes two lytic P. aeruginosa phages, ΦPa-C and ΦPa-Tc, and evaluates their efficacy against P. aeruginosa in two model food systems. The morphology, genome, structural proteins, host range, growth kinetics, …

Manipulations Of The Caenorhabditis Elegans Microbiome Reveal Influences Of Detrimental Members On Host Life History Traits, Ashley Elizabeth Foltz

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Microbiomes are a fundamental part of eukaryotic organisms and play a role in both host health and fitness. Although microbiomes are often associated with health and positive effects on the host, certain microbiome compositions are also associated with disease. We used Caenorhabditis elegans and its experimental microbiome, CeMbio to explore the interactions that individual microbiome members have with other microbes, with the host, and how the entire microbiome community interacts with the host. We found that individual CeMbio members have varying effects on host health and fitness compared to the whole community. This suggested that there is synergy occurring in …

Elucidation Of Potential Antimicrobial Properties Of Chalcones, Caleb Howell

Theses

The rise of antibiotic-resistant bacteria is a growing concern for the medical and biological community. Increased use of antibiotics has led to increased development of bacterial tolerances. This phenomenon, driven by the principles of evolution, has been exacerbated by the improper antibiotic use of these antibiotics. Often, individuals stop taking antibiotics once symptoms subside, mistakenly believing the infection is cured. This practice allows bacteria or fungi to develop resistance.

These antibiotics have been developed from secondary metabolites. While we have many effective antibiotics we are facing new threats. Chalcones are being looked at for their potential in addressing this issue. …

Isolation Of Naegleria Lustrarea N. Sp. (Excavata, Discoba, Heterolobosea) From The Feces Of Ambystoma Annulatum (Ringed Salamander) In Northwest Arkansas, Brian M. Becker, Idan Banson, James M. Walker, Anant Deshwal, Matthew W. Brown, Jeffrey D. Silberman

Biological Sciences Faculty Publications and Presentations

The salamander, Ambystoma annulatum, is considered a “species of special concern” in the state of Arkansas, USA, due to its limited geographic range, specialized habitat requirements and low population size. Although metazoan parasites have been documented in this salamander species, neither its native protists nor microbiome have yet been evaluated. This is likely due to the elusive nature and under-sampling of the animal. Here, we initiate the cataloguing of microbial associates with the identification of a new heterlobosean species, Naegleria lustrarea n. sp. (Excavata, Discoba, Heterolobosea), isolated from feces of an adult A. annulatum.

Exome Sequencing Identifies Novel Genes Underlying Primary Congenital Glaucoma In The National Birth Defects Prevention Study, Elizabeth E Blue, Kristin J Moore, Kari E North, Tania A Desrosiers, Suzan L Carmichael, Janson J White, Jessica X Chong, Michael J Bamshad, Mary M Jenkins, Lynn M Almli, Lawrence C Brody, Sharon F Freedman, Jennita Reefhuis, Paul A Romitti, Gary M Shaw, Martha Werler, Denise M Kay, Marilyn L Browne, Marcia L Feldkamp, Richard H Finnell, Wendy N Nembhard, Faith Pangilinan, Andrew F Olshan, National Institutes Of Health Intramural Sequencing Center, University Of Washington Center For Mendelian Genomics, National Birth Defects Prevention Study

Faculty, Staff and Students Publications

Background: Primary congenital glaucoma (PCG) affects approximately 1 in 10,000 live born infants in the United States (U.S.). PCG has a autosomal recessive inheritance pattern, and variable expressivity and reduced penetrance have been reported. Likely causal variants in the most commonly mutated gene, CYP1B1, are less prevalent in the U.S., suggesting that alternative genes may contribute to the condition. This study utilized exome sequencing to investigate the genetic architecture of PCG in the U.S. and to identify novel genes and variants.

Methods: We studied 37 family trios where infants had PCG and were part of the National Birth Defects Prevention …

Author Reply To Letter By Topkan Et Al Regarding Delays In Starting Postoperative Radiotherapy, Kelsey A Duckett, Byung Joo Lee, Bhisham S Chera, Sidharth V Puram, Vlad C Sandulache, Russel Kahmke, Shaun A Nguyen, Brian Nussenbaum, Anthony J Alberg, Chanita Hughes Halbert, Katherine R Sterba, Evan M Graboyes

Faculty, Staff and Students Publications

No abstract provided.

Characterization And Evaluation Of Bacteriophages Φpa-C And Φpa-Tc Infecting Pseudomonas Aeruginosa, Joanne Harrison

Master's Theses

Pseudomonas aeruginosa are prevalent opportunistic bacterial pathogens that cause nosocomial infections in at-risk individuals. The rise of multidrug-resistant P. aeruginosa poses an immense threat to hospitals. Additionally, P. aeruginosa are common food spoilage organisms that contribute to food waste. Alternative effective treatment methods are needed to improve public health and reduce food waste. Recent studies have shown that bacteriophages, viruses that only kill host-specific bacteria, are promising alternatives. This study characterizes two lytic P. aeruginosa phages, ΦPa-C and ΦPa-Tc, and evaluates their efficacy against P. aeruginosa in two model food systems. The morphology, genome, structural proteins, host range, growth kinetics, …

Characterizing The Quorum Sensing (Qs) System In The Model Eukaryote Chlamydomonas Reinhardtii, Kirstin Donnette Cutshaw

Theses and Dissertations

Group behaviors in microorganisms are often regulated by low-molecular weight molecules that enable them to sense population density, a signaling system known as quorum sensing (QS). QS in prokaryotes has provided insight into the role ‘social’ behaviors play in the bacterial world and refined our models of virulence, bacterial motility, and more. While less common, similar behaviors are observed in certain fungi, primarily yeasts, in which QS controls cell morphology, biofilm production, and other phenotypes. We have recently pursued the potential for QS to be more broadly distributed among unicellular eukaryotes, which could significantly alter our understanding of social behaviors …

Uses Of Herbal Extracts In Endodontology: A Literature Review, Reem Chamseddine, Roula S. Abiad

BAU Journal - Science and Technology

The use of natural herbal extracts in the field of dentistry, and specifically in endodontology had gained a high popularity in the past few years. The main objective of endodontic treatment is to prevent and eliminate the infection from the root canal, seize the invasion of microorganisms to periradicular tissues and preserve the natural dentition. Studies had shown that some herbs are better alternatives to traditional chemical irrigants or medicaments used in root canal treatment, based on their potential antimicrobial effect, smear layer removal capabilities, tissue dissolution effect, antioxidant, anti-inflammatory and regenerative properties. Aim: The purpose of this literature review …

Optimizing The Expression Of Polyethylene Terephtalate Hydrolase-Encoding Synthetic Gene In Escherichia Coli Arctic Express (De3), Jocelyn Nataniel, Maria Ulfah, Dini Achnafani, Niknik Nurhayati, Gabriela Christy Sabbathini, Sri Rezeki Wulandari, Abinawanto Abinawanto, Is Helianti

Makara Journal of Science

The waste of polyethylene terephthalate (PET) plastic waste in Indonesia is a pressing concern due to its slow degradation and potential environmental damage. One promising solution is to utilize polyethylene terephthalate hydrolase from Ideonella sakaiensis (IsPETase), an enzyme that specifically degrades PET. However, inducing the expression of IsPETase synthetic gene in Escherichia coli BL21 (DE3) has been challenging because much of it remains insoluble. This study aimed to express IsPETase in E. coli Arctic Express (DE3) and optimize the conditions to enhance its production. First, pET22b(+)pelB-IsPETase was inserted into E. coli Arctic Express (DE3). The …

Dietary Saturated Fatty Acids Modulate Host Innate Immunity, Amy Lorraine Seufert

Dissertations and Theses

Nutrition, cellular metabolism, and inflammatory regulation of the immune system are interconnected, and advancing our understanding of this will greatly improve treatment of metabolic and inflammatory disease. Specifically, dietary saturated fats are becoming increasingly appreciated for their ability to modify innate immune cell function in mammals following absorption into the blood and lymphatic circulation systems. The work herein focuses on the capacity for lipids in the diet to modulate innate immune memory. My thesis first broadly outlines fundamental background, including: the evolution of human nutrition, the discovery of innate immune memory, and key topics that reoccur throughout the text surrounding …

Metagenomic Analysis Of Antarctic Microbial Communities, David Michael Robinson

Biology ETDs

The research presented in this dissertation focuses on microbial roles in biogeochemical cycling in Antarctic aquatic environments. The major objective of my research was to examine the impact of biotic and abiotic pressures on nutrient cycling in microbially dominated systems. I used three perennially ice covered lakes in the McMurdo Dry Valleys (MDVs) along with subglacial lakes Whillans and Mercer as natural case studies. The MDVs are located in Victoria Land, East Antarctica and have been studied since 1993 as part of the McMurdo Long Term Ecological Research Project. Viruses in the MDVs were shown to be seasonally abundant and …

Group B Streptococcus Intestinal Barrier Disruption And The Protective Role Of Butyrate, Kristen Dominguez

USF Tampa Graduate Theses and Dissertations

Group B Streptococcus (Streptococcus agalactiae; GBS) is a leading cause of neonatal sepsis worldwide. Intrapartum antibiotics in GBS-colonized mothers significantly reduced the incidence of early-onset sepsis occurring in the first week of life; however, there are currently no prophylactic interventions for late-onset sepsis, occurring within the first 3 months of life. GBS is a pathobiont that primarily colonizes the gastrointestinal tract and can cross the intestinal barrier via both the paracellular and transcellular routes, causing invasive disease. Neonatal susceptibility to GBS intestinal translocation is mediated by inadequate epithelial barrier function and microbiome immaturity; however, the mechanisms by which GBS exploits …

Beneficial Plant-Microbe Interactions And Stress Tolerance In Maize, Saroj Burlakoti, Ananta R. Devkota, Shital Poudyal, Amita Kaundal

Plants, Soils, and Climate Faculty Publications

Beneficial microbes are crucial for improving crop adaptation and growth under various stresses. They enhance nutrient uptake, improve plant immune responses, and help plants tolerate stresses like drought, salinity, and heat. The yield potential of any crop is significantly influenced by its associated microbiomes and their potential to improve growth under different stressful environments. Therefore, it is crucial and exciting to understand the mechanisms of plant-microbe interactions. Maize (Zea mays L.) is one of the primary staple foods worldwide, in addition to wheat and rice. Maize is also an industrial crop globally, contributing 83% of its production for …

Degradation Of Chlorpyrifos Residue On Tropical Inceptisol Soil With Indigenous Bacteria Treatment, Asep Kurnia, Hidayatuz Zu`Amah, Baiq Nunung Sulastri, Ria Fauriah Makmur

Makara Journal of Science

The use of soil microbes is one of the most effective methods for degrading pesticide residue in soil. Microbes can accelerate the degradation of persistent pollutants including chlorpyrifos in soil. This research aims to find soil bacteria with the greatest potential to degrade chlorpyrifos residue in tropical inceptisol soil and determine its degradation index (DI). The soil used in this experiment was collected from agricultural fields in the districts of Demak, Central Java Province, Indonesia. The experiment was performed using factorial randomize complete block design composed of two factors and four replications. The first factors were made up of two …

Analyzing Efficiency Of A Lentiviral Shrna Knockdown System In Human Enteroids Using Western Blot And Flow Cytometry, Adam P Wilson, Karni S Moshal, Addison P Franca, Sasirekha Ramani, Randle Gallucci, Hala Chaaban, Kathryn Y Burge

Faculty, Staff and Students Publications

Enteroids are in vitro models to study gastrointestinal pathologies and test personalized therapeutics; however, the inherent complexity of enteroids often renders standard gene editing approaches ineffective. Here, we introduce a refined lentiviral transfection protocol, ensuring sufficient lentiviral engagement with enteroids while considering spatiotemporal growth variability throughout the extracellular matrix. Additionally, we highlight a selection process for transduced cells, introduce a protocol to accurately measure transduction efficiency, and explore methodologies to gauge effects of gene knockdown on biological processes.

Comparing The Genomes Of Multidrug And Vancomycin-Resistant Enterococcus Faecium From A Florida Wastewater Treatment Plant, Eleanor Brodrick

USF Tampa Graduate Theses and Dissertations

Vancomycin-resistant Enterococcus (VRE) are a serious health threat, causing 50,000 infections and 5,000 deaths each year in the United States (CDC, 2019). Multidrug-resistant VRE are becoming more prevalent, and treatment options for infections caused by these organisms are limited (Arias et al., 2010; CDC, 2019). Multidrug resistant VRE have been previously isolated from wastewater in Brazil, Canada, and Portugal (Araújo et al., 2010; de_Farias et al., 2022; Sanderson et al., 2019). Thirteen vancomycin-resistant Enterococcus faecium isolated from three stages of a Florida wastewater treatment plant were fully resistant to the following antibiotics: vancomycin, ampicillin, ciprofloxacin, erythromycin, tetracycline, and nitrofurantoin, and …

Prochlorococcus Death By A Ubiquitous Zooplankton Filter Feeder, Avery Harman

University Honors Theses

Prochlorococcus is a globally abundant cyanobacterium that can help reveal the ecology of microorganisms in the ocean. Specifically, mortality by zooplankton such as appendicularians is globally important and Prochlorococcus can help reveal some of the choices made around feeding for this ubiquitous filter feeder. Two ecotypes of Prochlorococcus were introduced to appendicularians to determine if appendicularian feed selectively between these ecotypes. Further, a single ecotype of Prochlorococcus was fed to appendicularians over a variety of life stages to determine if retention rate changed with appendicularian life stage. My results reveal that there is no significant selection between the two Prochlorococcus …

Heavy Metals Implications To Sediment Microbiome And Coral Response To Arsenic Dosing, Dimitrios G. Giarikos, Amy Hirons, Jose V. Lopez, Abigail Renegar, Jason Gershman

SECLER Data

No abstract provided.

Fleq And Gac/Rsm-Mediated Regulation Of Biofilm Formation And Swarming Motility In Pseudomonas Fluorescens, Alexander Benito Pastora

Dartmouth College Ph.D Dissertations

Pseudomonas fluorescens is a gram-negative Gammaproteobacterium that survives and persists in diverse environments. This survivability is dependent on the bacterium’s ability to form a biofilm. Within Pseudomonas fluorescens, biofilm formation is a complex and dynamic process involving multiple protein- and polysaccharide-based components which each individually serve a specific purpose. Of these components, the repeats-in-toxin (RTX) adhesins LapA and MapA are critical for biofilm formation. Specifically, LapA is important for initial establishment of a biofilm and MapA is important in forming a fully mature biofilm. Deployment of the RTX adhesins during biofilm formation is a highly coordinated process involving multiple …

Protein Nanoparticles As Vaccine Platforms For Human And Zoonotic Viruses, Kush Kumar Pandey, Bikash R. Sahoo, Asit K. Pattnaik

Nebraska Center for Virology: Faculty Publications

Vaccines are one of the most effective medical interventions, playing a pivotal role in treating infectious diseases. Although traditional vaccines comprise killed, inactivated, or liveattenuated pathogens that have resulted in protective immune responses, the negative consequences of their administration have been well appreciated. Modern vaccines have evolved to contain purified antigenic subunits, epitopes, or antigen-encoding mRNAs, rendering them relatively safe. However, reduced humoral and cellular responses pose major challenges to these subunit vaccines. Protein nanoparticle (PNP)-based vaccines have garnered substantial interest in recent years for their ability to present a repetitive array of antigens for improving immunogenicity and enhancing protective …

Establishment Of Bacteroides In The Gut And Its Role In The Cystic Fibrosis Gut-Lung Axis, Rebecca A. Valls

Dartmouth College Ph.D Dissertations

In the quest to understand the complex interplay between the gut microbiota and cystic fibrosis (CF), a disease characterized by chronic upper respiratory complications and an exacerbated proinflammatory response, our lab engaged in a collaborative study with Dartmouth-Hitchcock Medical Center (DHMC) to characterize the gut microbiota of pediatric CF patients. Initial analyses established a connection between gut microbial composition and respiratory health, particularly highlighting a scarcity of Bacteroides species compared to healthy controls. In following investigations, we utilized random forest models to understand how stool microbiota may influence clinical outcomes of these pediatric CF patients, including: age, upper respiratory infections, …

Hell's Tails: Localizing The Tail Proteins Of The Hyperthermophile-Infecting Virus Ssv1, Jane Arterberry

University Honors Theses

The tail of Saccharolobus spindle-shaped virus 1 (SSV1) has long been thought to be composed solely of viral protein 4 (VP4), but recent SSV1 structural studies have implicated the presence of additional structural proteins C166 and B78 in SSV1's unique tail. The exact locations of these proteins have not been confirmed. Structural proteins VP4 (C-terminus) and B78 are hypothesized to contribute to an adapter region bridging the viral capsid to the tail, whereas C166 is thought to comprise the majority of an internal extended structure, respectively. SSV1 structural proteins lack cysteine residues providing targets to determine their locations in the …