Microbiology Commons^™

System Design For The Quantification Of Microbial Motility In Extreme Environments, Megan Marie Dubay

Dissertations and Theses

Motility of microorganisms is understudied but provides useful insights into their behavior. Organisms' ability to move autonomously changes how they interact with their environment--finding nutrients, interacting with other organisms, and avoiding unfavorable conditions. Understanding motility features can also be used to identify specific species, such as the identification of Vibrio cholerae in human samples. Motility might also be used as evidence of life existing in even the most extreme environments on Earth, and possibly beyond. Specialized microscopy systems can be required to examine the motility of microorganisms due to the nature of the environments to which the instruments are exposed. …

Phage Resistance Accompanies Reduced Fitness Of Uropathogenic Escherichia Coli In The Urinary Environment, Jacob J Zulk, Justin R Clark, Samantha Ottinger, Mallory B Ballard, Marlyd E Mejia, Vicki Mercado-Evans, Emmaline R Heckmann, Belkys C Sanchez, Barbara W Trautner, Anthony W Maresso, Kathryn A Patras

Faculty, Staff and Students Publications

Urinary tract infection (UTI) is among the most common infections treated worldwide each year and is caused primarily by uropathogenic Escherichia coli (UPEC). Rising rates of antibiotic resistance among uropathogens have spurred a consideration of alternative treatment strategies, such as bacteriophage (phage) therapy; however, phage-bacterial interactions within the urinary environment are poorly defined. Here, we assess the activity of two phages, namely, HP3 and ES17, against clinical UPEC isolates using in vitro and in vivo models of UTI. In both bacteriologic medium and pooled human urine, we identified phage resistance arising within the first 6 to 8 h of coincubation. …

Integrated Relationship Of Nasopharyngeal Airway Host Response And Microbiome Associates With Bronchiolitis Severity, Michimasa Fujiogi, Yoshihiko Raita, Marcos Pérez-Losada, Robert J Freishtat, Juan C Celedón, Jonathan M Mansbach, Pedro A Piedra, Zhaozhong Zhu, Carlos A Camargo, Kohei Hasegawa

Faculty, Staff and Students Publications

Bronchiolitis is a leading cause of infant hospitalizations but its immunopathology remains poorly understood. Here we present data from 244 infants hospitalized with bronchiolitis in a multicenter prospective study, assessing the host response (transcriptome), microbial composition, and microbial function (metatranscriptome) in the nasopharyngeal airway, and associate them with disease severity. We investigate individual associations with disease severity identify host response, microbial taxonomical, and microbial functional modules by network analyses. We also determine the integrated relationship of these modules with severity. Several modules are significantly associated with risks of positive pressure ventilation use, including the host-type I interferon, neutrophil/interleukin-1, T cell …

Redundancy And Developmental Coordination In Myxococcus Xanthus: Insights From The Phenome, Jessica A. Comstock

Dissertations - ALL

Genotype-to-phenotype mapping can typically involve disrupting the function of a gene and observing the impact of mutation on phenotype. While this can be a powerful tool for uncovering gene function, complicating factors such as influences between genes and the environment, epistatic interactions with other genes, and genetic redundancy could all potentially mask the phenotype of a mutation such that functional inferences cannot be made. On the level of the single gene, this may not be particularly informative, but it is possible that studying phenotype in this way at a genome scale might allow for the observation of patterns between genes …

Nla28 Activator Modulates Σ54-Dependent Gene Regulation In Myxococcus Xanthus, Muqing Ma

Dissertations - ALL

The complex life cycle of Myxococcus xanthus makes it a model organism for studying multicellular developmental processes in bacteria. In response to environmental changes, M. xanthus cells collectively and dramatically adjust their morphology, physiological functions, and biosynthesis. Particularly, M. xanthus copes with starvation by producing fruiting bodies filled with dormant and stress-resistant spores. During secondary metabolism, it synthesizes polyketide (PK) and non-ribosomal peptide (NRP) natural products that are crucial sources of antibiotics. Bacteria including M. xanthus, require the alternative σ54 regulatory system to initiate the transcription of necessary genes for settling stress and completing developmental process. This dissertation introduces in …

Listeria Monocytogenes Is A Solvent Tolerant Organism Secreting A Solvent Stable Lipase: Potential Biotechnological Applications, Priyanka Priyanka Dr, Gemma K. Kinsella, Gary T. Henehan Prof, Barry J. Ryan Dr

Articles

Purpose The emerging biobased economy will require robust, adaptable, organisms for the production and processing of biomaterials as well as for bioremediation. Recently, the search for solvent tolerant organisms and solvent tolerant enzymes has intensifed. Resilient organisms secreting solvent stable lipases are of particular interest for biotechnological applications.

Methods Screening of soil samples for lipase-producing organisms was carried out on Rhodamine B plates. The most productive lipase-producing organisms were further screened for their resistance to solvents commonly used in biotechnological applications.

Results In the course of screening, one of the isolated organisms that exhibited extracellular lipaseactivity, was identifed as the …

The Roles Of Gut Microbiome And Plasma Metabolites In The Associations Between Abo Blood Groups And Insulin Homeostasis: The Microbiome And Insulin Longitudinal Evaluation Study (Miles), Ruifang Li-Gao, Kirk Grubbs, Alain G Bertoni, Kristi L Hoffman, Joseph F Petrosino, Gautam Ramesh, Martin Wu, Jerome I Rotter, Yii-Der Ida Chen, Anne M Evans, Richard J Robinson, Laura Sommerville, Dennis Mook-Kanamori, Mark O Goodarzi, Gregory A Michelotti, Patricia A Sheridan

Faculty, Staff and Students Publications

Non-O blood groups are associated with decreased insulin sensitivity and risk of type 2 diabetes. A recent study pinpointed the associations between ABO blood groups and gut microbiome, which may serve as potential mediators for the observed increased disease risks. We aimed to characterize associations between ABO haplotypes and insulin-related traits as well as potential mediating pathways. We assessed insulin homeostasis in African Americans (AAs; n = 109) and non-Hispanic whites (n = 210) from the Microbiome and Insulin Longitudinal Evaluation Study. The ABO haplotype was determined by six SNPs located in the ABO gene. Based on prior knowledge, …

Igg Antibodies To Sars-Cov-2 In Asymptomatic Blood Donors At Two Time Points In Karachi, Muhammad Hasan, Bushra Moiz, Shama Qaiser, Kiran I. Masood, Zara Ghous, Areeba Hussain, Natasha Bahadur Ali, Syed Hani Abidi, Kulsoom Ghias, Erum Khan, Zahra Hasan

Department of Pathology and Laboratory Medicine

Introduction: An estimated 1.5 million cases were reported in Pakistan until 23 March, 2022. However, SARS-CoV-2 PCR testing capacity has been limited and the incidence of COVID-19 infections is unknown. Volunteer healthy blood donors can be a control population for assessment of SARS-CoV-2 exposure in the population. We determined COVID-19 seroprevalence during the second pandemic wave in Karachi in donors without known infections or symptoms in 4 weeks prior to enrollment.
Materials and methods: We enrolled 558 healthy blood donors at the Aga Khan University Hospital between December 2020 and February 2021. ABO blood groups were determined. Serum IgG reactivity …

Behavioural Support And Nicotine Replacement Therapy For Smokeless Tobacco Cessation: Protocol For A Pilot Randomised-Controlled Multi-Country Trial, Faraz Siddiqui, Linda Bauld, Ray Croucher, Cath Jackson, Ian Kellar, Mona Kanaan, Subhash Pokhrel, Rumana Huque, Romaina Iqbal, Javaid Ahmed Khan

Community Health Sciences

Background: Smokeless tobacco (ST) is consumed globally by more than 350 million people, with approximately 85% of all users based in South and Southeast Asia. In this region, ST products are cheap and easily accessible. Evidence-based interventions to people quit ST use are lacking. This study aims to test the feasibility of conducting a future definitive trial of ST cessation, using a culturally adapted behavioural intervention, and/or nicotine replacement therapy (NRT) in three South Asian countries.
Methods: We will conduct a factorial design, randomised-controlled pilot trial in Bangladesh, India and Pakistan. Daily ST users will be recruited from primary health …

Mechanisms Of Carbapenemase-Mediated Resistance Among High-Risk Pseudomonas Aeruginosa Lineages In Peru, Isabella A. Tickler, Juan Carlos Gomez De La Torre, Luis Alvarado, Anne E. Obradovich, Fred C. Tenover

Biology Faculty Publications

Objectives: Pseudomonas aeruginosa is one of the leading causes of healthcare-associated infections globally. High-risk carbapenemase-encoding P. aeruginosa clones are disseminating in many regions. The aim of this study was to learn more about the lineages and mechanisms of resistance of P. aeruginosa circulating in Peru.

Methods: A total of 141 carbapenemase-producing isolates recovered from hospitalized and ambulatory patients in Lima were sequenced and analyzed to infer their lineages through whole-genome sequence typing (wgST) and to identify their antimicrobial resistance genes.

Results: wgST identified nine sequence types (STs); ST111 and ST357 were the most frequently encountered (44.0% and 38.3%, respectively), followed …

Consequences Of Biofilm Architecture On Vibrio Cholerae Ecology And Life History, Benjamin Ray Wucher

Dartmouth College Ph.D Dissertations

The diversity of microbes and the environments they inhabit are staggering. In many of these environments, bacteria have evolved to form sessile surface attached communities called biofilms. These biofilms have wide reaching impacts from importance in global carbon cycling, to persistent catheter infections, to biofouling and wastewater treatment. While many species of microbes form biofilms to survive in their environment, the architectures of these structures vary widely between organisms. Even though a great deal of work has been done to understand bacterial communities and their functions, little work has examined how the spatial aspects of biofilm architecture can affect the …

Microbial Dimension Of Symbiosis And Dysbiosis In Fungus–Gardening Ants, Blake S. Bringhurst

Biology Theses

With symbiotic partners, the means by which a host obtain a symbiont influence the specificity between the host and the symbiont. One such system where symbiont specificity is seen to varying degrees is with higher attine ants. Higher attine ants have symbiotic relationships with the fungal cultivar they grow and the bacterial symbionts in their microbiomes. Among the higher attines, there are two broad groups of fungi. Most ants in the genus Trachymyrmex tend to grow Clade–B fungi, which are a group of undescribed Leucocoprinus species, while leaf–cutting ants in the genera Acromyrmex and Atta tend to grow Clade–A fungi …

Complete Genome Sequences Of Two Temperate Bacillus Subtilis Phages Isolated At Tumamoc Hill Desert Laboratory, Gregory P. Krukonis, Amanda K. Kemp, Katie F. Storrie, Vivian R. Chavira, Hayden W. Lantrip, Victoria D. Perez, Desiree A. Reyes, Julian A. Truax, Rachel Loney, Veronique A. Delesalle

Biology Faculty Publications

Bacteriophages are important in structuring bacterial communities, including desert soils dominated by Bacillus species. Here, we describe two genetically similar temperate phages isolated on a Bacillus subtilis strain from soil in Tucson, Arizona. Their double-stranded DNA (dsDNA) genomes contain 98 and 102 genes, with a set of 4 genes being found in only one phage.

From The Headlines: A Textual Analysis Of Social Polarization And Discord In Times Of Pandemic Across A Century In The United States, Alexa Demarco

Undergraduate Honors Theses

Within the past century, three major pandemics have affected the United States – the Spanish Flu, AIDS, and COVID-19. Each of these pandemics has tested the capabilities of the public health sector and the social resilience of the population. Scientists have studied the viruses and implemented public health measures to limit viral transmission, but the social responses to these preventative measures proved to be difficult to predict and control. The dissonance and polarization between the public health initiatives and the response of the general public in the most recent pandemic was apparent. Was this a pattern in other pandemics? Was …

Intrinsic Cardiac Effects Of Severe Acute Respiratory Syndrome Coronavirus 2 In Coronavirus Disease 2019, Brittany Danielle Brumback

McKelvey School of Engineering Graduate Student Theses & Dissertations

Cardiac arrhythmias, particularly ventricular arrhythmias, can be life-threatening and caused by both congenital genetic mutations and acquired cardiac injury. My thesis work was originally focused on delineating the effects of genetic mutation-driven dysregulation of a protein called Hey2 in Brugada Syndrome, a complex disease characterized by a predisposition to dangerous arrhythmias originating in the right ventricular outflow tract. In response to the pandemic, my thesis work shifted toward understanding the mechanisms of cardiovascular injury in Coronavirus disease 2019 (COVID-19), which is associated with serious cardiovascular complications, including ventricular arrhythmias and sudden cardiac death as well as endothelial dysfunction and coagulopathies. …

Understanding Control Of Metabolite Dynamics And Heterogeneity, Christopher John Hartline

McKelvey School of Engineering Graduate Student Theses & Dissertations

Microbes live in complex and continually changing environments. Rapid shifts in nutrient availability are a common challenge for microbes, and cause changes in intracellular metabolite levels. Microbial response to dynamic environments requires coordination of multiple levels of cellular machinery including gene expression and metabolite concentrations. This coordination is achieved through metabolic control systems, which sense metabolite concentrations and direct cellular activity in response. Several reoccurring control architectures are found throughout diverse metabolic systems, which suggests underlying evolutionary advantages for using these control systems to coordinate metabolism. One common, yet understudied, control architecture is the positive feedback metabolite uptake loop, which …

Comparative Genomics And Virulence Studies Of Streptomyces Soil Rot And Scab Pathogen Species, Natasha Soares

LSU Doctoral Dissertations

Comparative genomic analyses were performed to gain insights into the organization and content of the genome of Streptomyces ipomoeae, the soil rot pathogen that infects sweetpotatoes. Unlike Streptomyces scab pathogens, the thaxtomin phytotoxin gene cluster (txt) in S. ipomoeae does not appear to reside within a genomic island and has diverged from its scab pathogen counterparts. Increased usage of the rare TTA codon, particularly for the txt cluster, suggests greater translational control by the bldA tRNA in S. ipomoeae. Orthologous gene searches and secondary metabolite profiling yielded ortholog groups and metabolite gene clusters that were exclusive …

Formulasi Pembawa Rizobakteri Penambat Nitrogen Dan Pelarut Fosfat, Serta Aplikasinya Di Pembibitan Kelapa Sawit Yang Diberi Komposisi Dan Dosis Amelioran Yang Berbeda, Roby Ibnu Syarifain, Mohammad Raihan Rashaun, Eka Dewi Anggrainy, Tualar Simarmata

Jurnal Kultivasi

Keberhasilan aplikasi pupuk hayati berkaitan dengan viabilitas mikroba dalam pembawa, dan aplikasinya di lapangan. Penelitian ini bertujuan mengetahui viabilitas Bakteri Penambat Nitrogen (BPN) dan Bakteri Pelarut Fosfat (BPF) pada berbagai komposisi karier, konsentrasi molase, dan aplikasinya dengan berbagai dosis serta komposisi amelioran pada pembibitan kelapa sawit. Penelitian dilaksanakan dari bulan Oktober 2019 - Mei 2020 di laboratorium dan kebun percobaan Ciparanje. Tahap pertama menggunakan Rancangan Acak Lengkap dua faktor (komposisi karier dan konsentrasi molase) dengan tiga ulangan. Tahap kedua menggunakan rancangan acak kelompok faktorial dua faktor (komposisi amelioran dan dosis aplikasi) pada pembibitan kelapa sawit sebanyak tiga ulangan. Hasil riset …

Investigating Host Defenses Of North American Salamanders Against The Recently Emerged Chytrid Pathogen, Batrachochytrium Salamandrivorans, Kenzie Pereira

Electronic Theses and Dissertations

A recently emerged chytrid fungal pathogen, Batrachochytrium salamandrivorans (Bsal) threatens salamander biodiversity. Bsal susceptibility varies between and within salamander species, but little is known about the mechanisms underlying these differences. Susceptibility is likely influenced by numerous interacting factors, but my dissertation studied the role of host immune responses.

My first aim investigated between species differences by studying the bioactive properties of salamander skin peptides against Bsal and the related pathogen, B. dendrobatidis (Bd). Skin peptides were collected from five salamander species, used for in vitro assays, and analyzed by RP-HPLC. While skin peptides from one …

Novel Signal Sequences And Fusion Partners For Paratransgenesis In Asaia, Christina Grogan

Electronic Theses and Dissertations

Mosquitoes transmit many pathogens that cause human disease. One such disease, malaria, is caused by parasites in the genus Plasmodium, infecting over 200 million people and killing over 600,000 per year. Current strategies to control vector-transmitted diseases are increasingly undermined by mosquito and pathogen resistance. Research has turned to additional and novel methods of control, such as altering the microbiota of the vectors. In this method, called paratransgenesis, symbiotic bacteria are genetically modified to affect the mosquito’s phenotype by engineering them to deliver antiplasmodial molecules into the midgut to kill parasites. These molecules must be released by the …