Microbiology Commons^™

Thrombospondin-1 Expression And Modulation Of Wnt And Hippo Signaling Pathways During The Early Phase Of Trypanosoma Cruzi Infection Of Heart Endothelial Cells, Ashutosh Arun, Kayla J. Rayford, Ayorinde Cooley, Tanu Rana, Girish Rachakonda, Fernando Villalta, Siddharth Pratap, Maria F. Lima, Nader Sheibani, Pius N. Nde

Publications and Research

The protozoan parasite, Trypanosoma cruzi, causes severe morbidity and mortality in afflicted individuals. Approximately 30% of T. cruzi infected individuals present with cardiac pathology. The invasive forms of the parasite are carried in the vascular system to infect other cells of the body. During transportation, the molecular mechanisms by which the parasite signals and interact with host endothelial cells (EC) especially heart endothelium is currently unknown. The parasite increases host thrombospondin-1 (TSP1) expression and activates the Wnt/β-catenin and hippo signaling pathways during the early phase of infection. The links between TSP1 and activation of the signaling pathways and …

Clinical Performance Of The Xpert® Ct/Ng Test For Detection Of Chlamydia Trachomatis And Neisseria Gonorrhoeae: A Multicenter Evaluation In Chinese Urban Hospitals, Fred C. Tenover, Yan Han, Mei-Qin Shi, Qing-Ping Jiang, Wen-Jing Le, Xiao-Lin Qin, Han-Zhen Xiong, He-Ping Zheng, Yi-Wei Tang, Yue-Ping Yin

Biology Faculty Publications

Background: We aimed to evaluate the clinical performance of the GeneXpert® (Xpert) CT/NG assay for the detection of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) using urine and cervical swabs collected from patients in China.

Methods: This study was conducted from September 2016 to September 2018 in three Chinese urban hospitals. The results from the Xpert CT/NG test were compared to those from the Roche cobas® 4800 CT/NG test. Discordant results were confirmed by DNA sequence analysis.

Results: In this study, 619 first void urine (FVU) specimens and 1,042 cervical swab specimens were included in the final dataset. There were …

Design Of A Synthetic Temperature-Activated Epigenetic Biocontainment System, Owen Rivers Page

Theses and Dissertations

The need for an internal control to govern engineered strain survival is becoming apparent when considering the biosafety and ethics within biotechnological research. Using understudied regulatory elements known as RNA thermometers (RNATs) that can modulate protein translation based on temperature changes and a Type II restriction modification system, we posit the creation of a synthetic temperature-activated epigenetic biocontainment system, termed the ‘sentinel switch’. We have mined a wide variety of bacteria from Yersinia pestis to Synechocystis sp. looking for novel RNATs. A complementary synthetic biology approach based on library generation and screening of chimeric RNATs (ChRNATs) was also conducted. RNATs …

Phage Hunters: The Discovery Of Two Novel Bacteriophages That Infect Gordonia Rubripertincta, Sarah Ballarin, Neel Balusa, Melissa Bell, Samia Caballero, Joshua Chan, Maria Farez, Ashley J. Guillen-Tapia, Nashrah Pierre-Louis, Victoria Polishuk, Bhavya Soni, Julie Torruellas Garcia, Katie E. Crump

Sea-Phages

Antibiotic resistance is a global healthcare concern because it poses a threat to effectively treating bacterial infections and the need for alternative therapeutics are urgently required. Phage therapy, which uses viruses to treat bacterial infections, is a promising alternative to conventional antibiotics. Phages have also been widely used in the food industry to prevent microbial growth on certain foods and are currently being explored as a method for bioremediation of oil spills and wastewater treatment. Although phages are ubiquitous in nature, many have yet to be discovered. Through the SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) program …

The Use Of Probiotic Applications In Early Life Stages To Mitigate Batrachochytrium Dendrobatidis Infections In Rana Luteiventris (Columbia Spotted Frogs), Autumn N. Holley

2022 Symposium

Chytridiomycosis, an amphibian skin disease caused by a chytrid fungal pathogen, Batrachochytrium dendrobatidis (Bd), has been linked to global amphibian declines. Some amphibian populations are resistant to severe infection due to symbiotic antifungal skin bacteria, but attempts to develop probiotics from these bacteria have been inconsistently successful because bacteria fail to persist on the skin. Studies have largely been conducted on adult and juvenile amphibians, despite amphibians having fewer known mechanisms for microbiome regulation prior to metamorphosis. We hypothesize that probiotics will persist longer and thus be more effective against pathogen infection if they are applied at an early life …

Interrelationships Of Systemic Changes In Hepatic Encephalopathy, Els Reuvekamp

Biology and Microbiology Graduate Students Plan B Research Projects

Hepatic encephalopathy is a temporary decline in mental function that is often associated with liver disease and/or portal-systemic disease. Hepatic encephalopathy (HE) symptoms can range from minor cognitive declines to coma and are known to result from excess ammonia accumulations in the blood stream subsequent to liver failure. While HE is known to result from hepatobiliary disorder, many of the physiological process underlying its development and progression remain to be elucidated. Recent studies have identified neurological, metabolic, and microbiome changes implicated in the disease state of HE. In this review, the roles of traditional pharmaceutical interventions and newly developing understandings …

Non-Invasive Biomarkers For The Diagnosis Of Endometriosis And Polycystic Ovary Syndrome, Chandana Kamaraj

Biology and Microbiology Graduate Students Plan B Research Projects

Benign gynecological disorders can affect a high percentage of women of reproductive age, ages 15-44 years. These conditions can affect the lifestyle of the individual and can be associated with infertility. The gold standard to identify and diagnose endometriosis requires invasive surgical procedures, while the Rotterdam Criteria is used to identify and diagnose polycystic ovary syndrome. The purpose of this paper is to discuss, describe, and characterize potential non-invasive biomarkers that are present in various pathological stages of both endometriosis and polycystic ovary syndrome. These biomarkers include CA125, Serum galectin-9, hsa-miRNA-154-5p, miRNA-93, miRNA-320 and ET-1, miRNA-222, miRNA-146a, and miR-30c used …

The Isolation And Characterization Of Bacteriophage Hasitha, Gillian Brown

Mahurin Honors College Capstone Experience/Thesis Projects

Microbacteriophage Hasitha is a virus that infects Microbacterium foliorum, a bacterium associated with grasses that was first discovered in Germany. Hasitha was isolated from an enriched compost sample and is of particular interest due to its unusual growth pattern. Most bacteriophages require actively growing host cells to produce new phage progeny. However, Hasitha can infect and kill stationary (non-replicating) bacterial cells. We discovered this unusual characteristic through a fortuitous observation of infected lawns that were allowed to incubate in the lab workspace for approximately one month. During this time, a noticeable “halo” grew around the initial site of infection …

Decolorization Of Synthetic Textile Dyes By Fungal Endophytes Isolated From The Leaves Of Philippine Mangrove (Avicennia Marina), Steve P. Obanan, Resureccion B. Sadaba, Pamela Alva-Gatchalian, Annabelle V. Cadiz, Evelyn M. Basilio, Dennis B. Bela-Ong

Biology Faculty Publications

Textile dyes in wastewater can be harmful pollutants when released into the environment without treatment. Biodegradation of textile dye effluents by different microbes, including fungi, has become popular as an alternative to physicochemical methods. The mangrove Avicennia marina is known to harbor endophytic fungi which have the potential to carry out dye degradation. Therefore, this study assessed the ability to decolorize synthetic dyes of endophytic fungi isolated from the leaves of A. marina. Of the nine fungal endophytes, Aspergillus niger, Syncephalastrum racemosum and Penicillium citrinum exhibited the highest mycelial growths in solid media, while all endophytes adsorbed Congo red. Through …

Isolating Bacteriophage For Potential Treatment Of Chronic Multi-Drug Resistant Escherichia Coli Infections, Leila Oswalt

Honors Projects

The misuse and overuse of antibiotics has led to the intense rise in antibiotic resistance. As society transitions into the post antibiotic era, there will be a great need for new therapeutic strategies to address multiple drug resistant bacterial infections. One such method, called bacteriophage therapy, allows for specific targeting of certain pathogenic bacteria through the use of viruses that attack bacteria; termed “bacteriophage” or simply “phage”. Urinary tract infections are among the most common pathological human infections that rely heavily on the use of antibiotics, the major cause of which is the bacterium Escherichia coli. During the Spring 2021-Spring …

The Quest To Identify A New Virus Disease Of Sunflower From Nebraska, Robert M. Harveson, Maher Al Rwahnih, California Department Of Food And Agriculture, Alex Karasev, Tom J. Gulya, Jeff Bradshaw

Panhandle Research and Extension Center

Between 2010 and 2018, sunflower plants exhibiting virus-like symptoms, including stunting, mottling, and chlorotic ringspots on leaves, were observed from commercial fields and research plots from four sites within three distinct counties of western Nebraska (Box Butte, Kimball, and Scotts Bluff). Near identical symptoms from field samples were reproduced on seedlings mechanically in the greenhouse on multiple occasions, confirming the presence of a sap-transmissible virus from each site. Symptomatic greenhouse-inoculated plants from the 2010 and 2011 Box Butte samples tested negative for sunflower mosaic virus (SuMV), sunflower chlorotic mottle virus (SuCMoV), and all potyviruses in general by ELISA and RT-PCR. …

Examining Behavioral Defenses Of The Fungus-Growing Ant Trachymyrmex Septentrionalis Against Trichoderma-Derived Metabolites, Darren Lee

Holster Scholar Projects

Fungus-growing ants defend their fungal mutualist against pathogens through a number of chemical and behavioral mechanisms. Work by Dr. Jonathan Klassen’s lab has found that Trachymyrmex septentrionalis ants maintain their fungal symbionts’ health through physical removal (“weeding”) upon infection with pathogenic fungi in the genus Trichoderma. Ants also exhibited weeding behavior when the fungus was inoculated with peptaibols, a class of secondary metabolites produced by Trichoderma, suggesting that these molecules act as chemical cues that induce ant weeding. However, the mechanisms by which weeding behaviors are communicated between the ants and their fungal symbiont are unknown. Behavioral experiments demonstrated that …

Clostridioides Difficile Motility In Defined Culture Media And Its Response To Nutrients, Mary Ishak

Honors Undergraduate Theses

In recent years, Clostridiodes difficile has caused a sharp increase in hospital-acquired infections. Patients on multiple courses of antibiotics experience a general clearing of normal gut microbiota, leading to dysbiosis and an opportunity for C. difficile to colonize the colon. Understanding which nutrients produce optimal respiratory metabolism in C. difficile will help to determine the reasoning behind whether the microbe invests its energy into various cellular processes, such as motility. Different C. difficile strains were first cultured in BHIS broth (brain-heart infusion, supplemented) and CDMM broth (C. difficile minimal media) before being used to inoculate soft agar wells. The …

Novel Microbe-Resistant Clay Dressing For Healing Burn Wounds, Kasey L. Rigby

Honors Undergraduate Theses

Every year, about 550,000 patients receive medical attention for minor and major burns in the United States.¹ In 2020, it was estimated that 11 million people worldwide suffered from burn injuries, with 150,000 of those burns being fatal.² Burns are among the most painful and debilitating recalcitrant wounds that can often turn terminal when infection occurs. The different grades for burns that we aim to treat are first, second, and third degrees.² Each burn type is susceptible to secondary infection that can be life threatening, and as a result, are extensively treated with antimicrobial agents.2 At present, …

Whole Exome Sequencing Identifies A Novel Mutation In Aspm And Ultra-Rare Mutation In Cdk5rap2 Causing Primary Microcephaly In Consanguineous Pakistani Families, Ehtisham Ul Haq Makhdoom, Haseeb Anwar, Shahid Mahmood Baig, Ghulam Hussain

Department of Biological & Biomedical Sciences

Background & objectives: Primary Microcephaly (MCPH) is a rare neurogenetic disease, manifesting congenitally reduced head circumference and non-progressive intellectual disability (ID). To date, twenty-eight genes with biallelic mutations have been reported for this disorder. The study aimed for molecular genetic characterization of Pakistani families segregating MCPH.
Methods: We studied two unrelated consanguineous families (family A and B) presenting >2 patients with diagnostic symptoms of MCPH, born to asymptomatic parents. We employed whole-exome sequencing (WES) of probands to find putative causal mutations. The candidate variants were further confirmed and analyzed for co-segregation by Sanger sequencing of all available members of each …

Phip Variants Associated With Chung–Jansen Syndrome Disrupt Replication Fork Stability And Genome Integrity, Neysha Tirado-Class, Caitlin Hathaway, Wendy K. Chung, Huzefa Dungrawala

Molecular Biosciences Faculty Publications

Chung–Jansen syndrome (CJS) is a rare, autosomal dominant disorder characterized by developmental delay, intellectual disability/cognitive impairment, behavioral challenges, obesity, and dysmorphic features. CJS is associated with heterozygous variants in PHIP (Pleckstrin-Homology Interacting Protein), a gene that encodes one of several substrate receptors for Cullin4-RING (CRL4) E3 ubiquitin ligase complex. Full-length PHIP, also called DCAF14, was recently identified to function as a replication stress response protein. Herein, we report the identification of two PHIP missense variants identified by exome sequencing in unrelated individuals with CJS. The variants p.D488V and p.E963G occur in different functional elements of DCAF14-WD40 repeat domain and pleckstrin …

Sequence Properties Of An Intramolecular Interaction That Inhibits P53 Dna Binding, Emily Gregory, Gary W. Daughdrill

Molecular Biosciences Faculty Publications

An intramolecular interaction between the p53 transactivation and DNA binding domains inhibits DNA binding. To study this autoinhibition, we used a fragment of p53, referred to as ND WT, containing the N-terminal transactivation domains (TAD1 and TAD2), a proline rich region (PRR), and the DNA binding domain (DBD). We mutated acidic, nonpolar, and aromatic amino acids in TAD2 to disrupt the interaction with DBD and measured the effects on DNA binding affinity at different ionic strengths using fluorescence anisotropy. We observed a large increase in DNA binding affinity for the mutants consistent with reduced autoinhibition. The ΔΔG between DBD and …

Magnaporthe Oryzae Telomeric Retrotransposon (Moter) Relics Further Highlight Telomere Dynamics In A Rapidly Evolving Fungal Pathogen, Jane Ellen Dostart

Online Theses and Dissertations

The telomeres of M. oryzae can experience unique rearrangements within a single generation. These rearrangements are frequently attributed to the presence of two retrotransposons (MoTeR 1 and MoTeR 2) that are endemic to the telomeres. These rearrangements can leave footprints within the interior of the genome that document previous telomere breakage events. The purpose of this study was to examine MoTeR relics within 10 genomes of strains of M. oryzae to document telomere instability among strain lineages, as well as to uncover MoTeR relic distribution, shared evolutionary history, and associated genome rearrangements. A series of local BLASTn and grep searches …

Isolation And Characterization Of Novel B. Subtilis Bacteriophages, Johnson Phung, Rebecca Adams

Science University Research Symposium (SURS)

Bacteriophages are viruses that infect bacteria cells. Bacteria, being the most abundant form of life on the planet, have an estimated ten to a hundred different types of bacteriophages that infect each species. Bacteriophages are everywhere on Earth, but the number of phages that have been identified is only a fraction of what are thought to exist. This project focuses on isolating and identifying phages that infect the bacterium Bacillus subtilis. B subtilis is a decomposition microbe commonly found in the soil. Our first goal was to determine whether the 3 samples of Bacillus subtilis phages that were previously …

An Optimal Lysis Time Maximizes Bacteriophage Fitness In Quasi-Continuous Culture, Sherin Kannoly, Abhyudai Singh, John J. Dennehy

Publications and Research

Optimality models have a checkered history in evolutionary biology. While optimality models have been successful in providing valuable insight into the evolution of a wide variety of biological traits, a common objection is that optimality models are overly simplistic and ignore organismal genetics. We revisit evolutionary optimization in the context of a major bacteriophage life history trait, lysis time. Lysis time refers to the period spanning phage infection of a host cell and its lysis, whereupon phage progenies are released. Lysis time, therefore, directly determines phage fecundity assuming progeny assembly does not exhaust host resources prior to lysis. Noting that …

Adenoviral-Vectored Centralized Consensus Hemagglutinin Vaccine Provides Broad Protection Against H2 Influenza A Virus, Erika M. Petro-Turnquist, Brianna L. Bullard, Matthew J. Pekarek, Eric A. Weaver

Nebraska Center for Virology: Faculty Publications

Several influenza pandemics have occurred in the past century, one of which emerged in 1957 from a zoonotic transmission of H2N2 from an avian reservoir into humans. This pandemic caused 2–4 million deaths and circulated until 1968. Since the disappearance of H2N2 from human populations, there has been waning immunity against H2, and this subtype is not currently incorporated into seasonal vaccines. However, H2 influenza remains a pandemic threat due to consistent circulation in avian reservoirs. Here, we describe a method of pandemic preparedness by creating an adenoviral-vectored centralized consensus vaccine design against human H2 influenza. We also assessed the …

The Application Of The Skin Virome For Human Identification, Ema H. Graham, Jennifer Clarke, Samodha Fernando, Joshua Herr, Michael Adamowicz

Nebraska Center for Virology: Faculty Publications

The use of skin virome offers a unique approach for human identification purposes in instances where a viable and statistically relevant human DNA profile is unavailable. The skin virome may act as an alternative DNA profile and/or an additional form of probative genetic material. To date, no study has attempted to investigate the human virome over a time series across various physical locations of the body to identify its diagnostic potential as a tool for human identification. For this study, we set out to evaluate the stability, diversity, and individualization of the human skin virome. An additional goal was to …

Computational Strain Analysis In Microbiome Datasets With Application To Skin Disease, Minerva Fatimae Ventolero

Electronic Theses and Dissertations, 2020-2023

Identifying bacterial strains is important not only for human health research but also for various environmental and industrial applications. The plethora of available shotgun metagenomic datasets provide an unprecedented opportunity to discover novel bacterial strains in different environmental niches. In this thesis, we evaluated the existing novel-strain-based tools and showed that their performance is still suboptimal. Due to the difficulty in distinguishing strains of similar abundance by available tools, the SMS (strains in multiple samples) tool was developed to de novo identify bacterial strains in multiple shotgun metagenomic samples. We showed that SMS distinguishes strains of similar abundance well and …

Elucidation Of Novel And Established Campylobacter Species With Clinical And Agricultural Significance Through Phenotypic, Genotypic, And Taxonomic Investigation, Caoimhe Lynch

Theses

Campylobacter spp. are well-established human, veterinary and economic pathogens, with a broad host range spanning from terrestrial and marine mammalian, avian and reptilian hosts. The scope of the study includes novel and notorious species within the genus, with reference to zoonotic agents Campylobacter jejuni and Campylobacter coli - the leading cause of human bacterial gastroenteritis in the EU and Ireland, Campylobacter fetus that represents the most common campylobacter causing bacteraemia and two novel species isolated from pigs not described in the literature previously. C. jejuni and C. coli isolates (n = 350) recovered from broiler caecal and neck skin samples, …

Investigating The Development Of Alcohol Tolerance By The Opportunistic Pathogen Staphylococcus Aureus, Vaughn Perveiler

West Chester University Master’s Theses

With the ongoing COVID-19 pandemic, the use of alcohol-based antiseptics by the general public has greatly increased. While this form of antimicrobial is effective in stopping the spread of both bacterial and viral infections, little research has been conducted in the development of alcohol tolerance by microorganisms or its mechanisms. In this study, experimental evolution was conducted on four separate strains of Staphylococcus aureus to determine if tolerance can develop towards moderate to high concentrations of ethanol. Once ethanol tolerance was established in the evolved populations, whole genome sequencing was performed to identify the potential mutations responsible for the observed …

Evaluation Of Oasl And Herc5’S Role In The Non-Lytic Clearance Of Influenza A Virus From Club Cells, Steve Crisafulli

West Chester University Master’s Theses

Influenza A virus (IAV) is a highly infectious pathogen responsible for causing severe respiratory illness and death in humans and animals worldwide. Due to highly effective strategies to negate host antiviral defenses, IAV leads to the death of nearly all infected cells. Furthermore, IAV induces high levels of genome-damaging oxidative stress within infected cells and suppresses the cellular mismatch repair (MMR) mechanism, thereby inhibiting expression of key antiviral genes, which further contributes to cell death. However, recent studies have demonstrated that a subset of respiratory epithelial cells, called club cells, are able to non-lytically clear IAV and continue to survive …

Effect Of Metal-Containing Nanoparticles On Bacterial Biofilms And On The Microbiome Of Girardia Tigrina, Azar Saikali

West Chester University Master’s Theses

Anthropogenically-produced nanoparticles are a form of nanotechnology being used in industries including food and textiles. Humans and livestock are frequently exposed to metal-containing nanoparticles (MCNPs), that have been washed into streams and rivers, have been deliberately used in food packaging as antimicrobials, preservatives or for supplementation. The animal microbiome, which consists of a diverse community of microorganisms, provides a number of benefits to the host in terms of nutrition availability, immune support, and can influence behavior. Biofilms of diverse microbes may cause detrimental effects, for instance by causing dental diseases in humans. However, the scientific community has not reached consensus …

Degradation And Nitrogen Cycling In The Context Of Biodiversity-Ecosystem Function Relationships In The Inquiline Bacterial Community Of Darlingtonia Californica, Megan Teigen

Cal Poly Humboldt theses and projects

Biodiversity-ecosystem function (BEF) research aims to explain how species and their environments interact with each other. Microbial communities engage in vital biogeochemical pathways in a variety of natural ecosystems, and yet there are large knowledge gaps about the specific metabolic pathways in which they are involved. Degradation specifically contributes to nitrogen cycling globally through the breakdown of large organic nitrogen compounds into small inorganic nitrogen that is necessary for the survival of many other organisms. In this study, I focused on the degradative function of the inquiline microbial communities found within the carnivorous pitcher plant, Darlingtonia californica. Darlingtonia grows in …

Evidence For Metabolic Diversity In Meso-Neoproterozoic Stromatolites (Vazante Group, Brazil), Flavia Callefo, Fresia Ricardi-Branco, Mirian Mírian Liza Alves Forancelli Pacheco, Alexandre Ribeiro Cardoso, Nora Noffke, Verônica De Carvalho Teixeira, Itamar Tomio Neckel, Lara Maldanis, Emma Bullock, Dina Bower, Adalene Moreira Silva, Dario Ferreira Sanchez, Fabio Rodrigues, Douglas Galante

OES Faculty Publications

Deciphering the evolution of ecological interactions among the metabolic types during the early diversification of life on Earth is crucial for our understanding of the ancient biosphere. The stromatolites from the genus Conophyton cylindricus represent a datum for the Proterozoic (Meso to Neoproterozoic) on Earth. Their typical conical shape has been considered a result of a competition between microorganisms for space, light and nutrients. Well-preserved records of this genus from the "Paleontological Site of Cabeludo ", Vazante Group, São Francisco Craton (Southern Brazil) present in situ fossilized biofilms, containing preserved carbonaceous matter. Petrographic and geochemical analyses revealed an alternation between …

Defining The Realized Niche Of The Two Major Clades Of Trichodesmium: A Study On The West Florida Shelf, Kristina A. Confesor, Corday R. Selden, Kimberly E. Powell, Laura A. Donahue, Travis Mellett, Salvatore Caprara, Angela N. Knapp, Kristen N. Buck, P. Dreux Chappell

OES Faculty Publications

The cyanobacterium Trichodesmium plays an essential role supporting ocean productivity by relieving nitrogen limitation via dinitrogen (N-2) fixation. The two common Trichodesmium clades, T. erythraeum and T. thiebautii, are both observed in waters along the West Florida Shelf (WFS). We hypothesized that these taxa occupy distinct realized niches, where T. thiebautii is the more oceanic clade. Samples for DNA and water chemistry analyses were collected on three separate WFS expeditions (2015, 2018, and 2019) spanning multiple seasons; abundances of the single copy housekeeping gene rnpB from both clades were enumerated via quantitative PCR. We conducted a suite of statistical …