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. …

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. …

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 …

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 …

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 …

Identification And Characterization Of Genetic Elements That Regulate A C-Di-Gmp Mediated Multicellular Trait In Pseudomonas Fluorescens, Collin Kessler

Electronic Theses and Dissertations

Microbial communities contain densely packed cells where competition for space and resources are fierce. These communities are generally referred to as biofilms and provide advantages to individual cells against immunological and antimicrobial intervention, dehydration, and predation. High intracellular pools of cyclic diguanylate monophosphate (c-di-GMP) cause cells to aggregate during biofilm formation through the production of diverse extracellular polymers. Genes that encode c-di-GMP catalytic enzymes are commonly mutated during chronic infections where opportunists display enhanced resistance to phagocytosis and antibiotics. Our lab uses an emergent multicellular trait in the model organism Pseudomonas fluorescens Pf0-1 to study the emergence of c-di-GMP mutations …

Neural Stem Cells: Age-Dependent Outcomes During Viral Infections In The Central Nervous System, Manisha N. Chandwani

Electronic Theses and Dissertations

Viral infections in the central nervous system (CNS) are associated with neurodevelopmental and neurobehavioral deficits. The outcomes of viral infections can be driven by damage and death of neurons. Neural stem cells (NSCs) play key roles in neurodevelopment, repair, and physiological brain function. During a viral infection, NSC activity can disturbed by direct infection of NSCs by the virus or by anti-viral immune response. Here, we aimed to assess whether the anti-viral immune response can impact NSC activity during an immunocompetent response in the adult brain. We utilized a transgenic mouse model of Measles virus infection where only the CNS …

Investigating The Role Of Sphingosine Kinases During Alphavirus Infection, Opeoluwa Oyewole

Theses & Dissertations

Several alphaviruses, critical human pathogens, have re-emerged in recent years. Alphaviruses are found on all continents and infect both invertebrates and vertebrates, including some aquatic animals. They are classified as arboviruses because hematophagous arthropods transmit them. Based on the symptoms they cause, alphaviruses are classified as either arthritogenic or encephalitic.

Rising global travel has led to outbreaks of infections in new regions, increasing the geographical ranges of alphaviruses and causing new infections in susceptible hosts. Currently, there are no approved prophylactic or therapeutic measures to prevent or treat alphavirus infections; prevention measures have focused on vector control. These measures are …

Uji Kemampuan Bakteri Diazotrof Asal Perakaran Bawang Merah Dalam Mendukung Pertumbuhan Dan Hasil Tanaman Bawang Merah, Ananda Rahmalia Yuniarti, Eny Rokhminarsih, Purwanto

Jurnal Kultivasi

Budidaya tanaman bawang merah saat ini dihadapkan pada masalah stagnasi produksi akibat aplikasi pupuk kimia secara berlebihan sehngga efisiensi pemupukan rendah. Teknologi ramah lingkungan dan efisien pupuk dengan aplikasi bioteknologi melalui aplikasi bakteri berguna seperti bakteri penambat nitrogen. Penelitian bertujuan untuk (1) mengetahui respons pertumbuhan dan hasil tanaman bawang merah terhadap bakteri diazotrof, (2) menetapkan isolat bakteri diazotrof yang paling baik untuk pertumbuhan dan hasil tanaman bawang merah. Percobaan dilaksanakan pada bulan Januari 2021 sampai April 2021. Percobaan dilaksanakan di Rumah Kassa serta Laboratorium Agronomi dan Hortikultura Fakultas Pertanian, Universitas Jenderal Soedirman. Rancangan percobaan yang digunakan yaitu Rancangan Acak Kelompok …

Effects Of Mass Death On Community Structure And Ecosystem Function, Abby Kimpton Jones

Theses and Dissertations

Death and decomposition are natural processes that are generally well-understood. However, large events of death, such as mass mortality events (MMEs) are increasing in frequency and their impacts on the ecosystem are largely unknown. These events may have both bottom-up effects from increased nutrient input as well as top-down effects from loss of an ecological functional group by the affected population. Different functional MMEs may result in different top-down effects, creating cascading effects. In Chapter 1, I test the hypothesis that scavenger and herbivore simulated MMEs generate novel bottom-up and top-down effects. Results indicate that MMEs have a significant effect …

Qualitative Proteomic And Genomic Analysis Of Klebsiella Pneumoniae Bacteriophage Kaomega, Emilee Carr

Undergraduate Honors Theses

Klebsiella pneumoniae is a Gram-negative Enterobacteriaceae that is a common nosocomial pathogen causing pneumonia, infections in the bloodstream, wound infections, and meningitis. It has developed natural resistance to multiple antibiotics, most notably carbapenems which are often seen as the last line of defense against multi-drug resistant pathogens. Bacteriophages are being investigated as a promising alternative treatment to antibiotics in fighting these resistant pathogens. KaOmega, a Klebsiella pneumoniae bacteriophage, was isolated, sequenced, and annotated to characterize and understand its potential for use in a phage therapy. Characterization included Phyre2 analysis to predict putative protein functions based on structural homology, burst size …

The Sars-Cov-2 Differential Genomic Adaptation In Response To Varying Uvindex Reveals Potential Genomic Resources For Better Covid-19 Diagnosis And Prevention, Naveed Iqbal, Muhammad Rafiq, Masooma Ali, Sanaullah Tareen, Maqsood Ahmad, Faheem Nawaz, Sumair Khan, Rida Riaz, Ting Yang, Ambrin Fatima

Department of Biological & Biomedical Sciences

Coronavirus disease 2019 (COVID-19) has been a pandemic disease reported in almost every country and causes life-threatening, severe respiratory symptoms. Recent studies showed that various environmental selection pressures challenge the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infectivity and, in response, the virus engenders new mutations, leading to the emergence of more virulent strains of WHO concern. Advance prediction of the forthcoming virulent SARS-CoV-2 strains in response to the principal environmental selection pressures like temperature and solar UV radiation is indispensable to overcome COVID-19. To discover the UV-solar radiation-driven genomic adaption of SARS-CoV-2, a curated dataset of 2,500 full-grade genomes from …

Genome Sequence Of Sn1, A Bacteriophage That Infects Sphaerotilus Natans And Pseudomonas Aeruginosa, K.M. Damitha Gunathilake, Denise M. Tremblay, Pier-Luc Plante, Ellen Jensen, Kenneth Nickerson, Sylvain Moineau

Kenneth Nickerson Papers

Phage SN1 infects Sphaerotilus natans and Pseudomonas aeruginosa strains. Its genome consists of 61,858 bp (64.3% GC) and 89 genes, including 32 with predicted functions. SN1 genome is very similar to Pseudomonas phage M6, which contains hypermodified thymidines. Genome analyses revealed similar base-modifying genes as those found in M6.

Phage SN1 was isolated in 1979 from activated sludge samples obtained from a wastewater treatment plant (Lincoln, Nebraska, USA) using S. natans ATCC 13338 as the host (1, 2). An early study showed that the siphophage SN1 has unusual bases in its genome as confirmed by cellulose thin-layer chromatography (1). Its …

Perception Of Illness And Its Association With Willingness To Adhere To Treatment In Chronic Hepatitis C Patients With New Diagnosis Of Nonalcoholic Fatty Liver Disease, Carmel Kruse

The Eleanor Mann School of Nursing DNP Capstone Projects

Chronic liver disease is becoming the most common cause of mortality, morbidity, and utilization of healthcare services globally. Both nonalcoholic fatty liver disease (NAFLD) and chronic hepatitis C (CHC) are frequent causes of chronic liver disease. Recently, there have been significant findings on the relationship between NAFLD and CHC; patients with CHC have a higher incidence of NAFLD. The introduction of direct-acting antivirals has cured more CHC patients than ever before. Unfortunately, the current interventions for NAFLD requiring behavioral change remain ineffective. Patient’s ability to follow advice depends largely on their health beliefs; therefore, understanding their illness perception is an …

Functional Characterization Of Mycobacterium Smegmatis Phage Moomoo Gene Products: Identification Of Toxic Genes, Whitney Heard

Masters Theses & Specialist Projects

Mycobacteriophages are a group of phages that infect members of the genus Mycobacteria. Previous studies have conducted extensive comparisons of the mycobacteriophage genomes and amino acid sequences to establish different phage families. MooMoo is a singleton mycobacteriophage that has been characterized due to its lack of appreciable homology to other phages. Some of its unique properties include its structure and the isolation of a mutant that causes clear plaque phenotypes. The experiments described in this thesis identified three MooMoo phage (gp87, gp90, and gp91) encoded proteins that are toxic to the bacterial host, Mycobacterium smegmatis.Through the use of a …

Reproductive Ecology And Microbial Communities From Wood Duck Nest Boxes In Georgia And Florida, Jake Shurba

All Theses

Wood ducks (Aix sponsa) are an important game species throughout the Atlantic Flyway that was nearly extirpated by the early 20^th century due to overhunting and the loss of habitat. Wood ducks are secondary cavity-nesters that utilize artificial nest boxes and natural cavities. It is reported that the use of nest boxes is likely what led to re-establishment of the species in North America. Where boxes are numerous, overuse of boxes by multiple hens throughout a nesting season can occur and result in a buildup of bacteria, parasites and other potentially detrimental pathogens that can impact egg …