Microbiology Commons^™

Effect Of Hydrogen Peroxide On Algae And Microcystin In Control And Lake Waters, Tatiana Castillo Hernandez

Biological and Agricultural Engineering Undergraduate Honors Theses

Cyanobacteria are photo-autotrophic organisms with a worldwide distribution, which can result in Harmful Algal Blooms (HABs) producing toxins. One of the most common strains of cyanobacteria is Microcystis, which produces the most abundant cyanotoxin, microcystin. In this study, we analyzed the effect of H₂O₂ on algae and microcystin using both lake and reagent grade water. The first objective was to determine the effect of H₂O₂ on algae and cyanobacteria in lake water that was nutrient enriched. The second objective was to detect the effect of H₂O₂ at oxidizing microcystin in …

Gut Bacteria Are Essential For Normal Cuticle Development In Herbivorous Turtle Ants, Christophe Duplais, Vincent Sarou-Kanian, Dominique Massiot, Alia Hassan, John T. Wertz

University Faculty Publications and Creative Works

Across the evolutionary history of insects, the shift from nitrogen-rich carnivore/omnivore diets to nitrogen-poor herbivorous diets was made possible through symbiosis with microbes. The herbivorous turtle ants Cephalotes possess a conserved gut microbiome which enriches the nutrient composition by recycling nitrogen-rich metabolic waste to increase the production of amino acids. This enrichment is assumed to benefit the host, but we do not know to what extent. To gain insights into nitrogen assimilation in the ant cuticle we use gut bacterial manipulation, 15N isotopic enrichment, isotope-ratio mass spectrometry, and 15N nuclear magnetic resonance spectroscopy to demonstrate that gut bacteria contribute to …

Bicuspid Aortic Valve In Pregnancy Complicated By Aortic Valve Vegetation, Aortic Root Abscess, And Aortic Insufficiency, Shan He, Christopher A Huynh, Yi Deng, Sandeep Markan, Anvinh Nguyen

Faculty, Staff and Students Publications

A 39-year-old patient presented to our Labor and Delivery unit with fever and nausea in the context of recent bacteriuria. She was found to be in sepsis due to an incidental bicuspid aortic valve (BAV) complicated by aortic valvular vegetations, severe aortic insufficiency, and aortic root abscess, requiring an emergent cesarean section. Three days after delivery, the patient successfully underwent a mechanical aortic valve replacement and root reconstruction. In this case report, medical, surgical, and anesthetic management of parturient patients with BAV are discussed. The management of this congenital valvulopathy and vasculopathy is complicated by the extensive hemodynamic and cardiovascular …

Relative Success Of Native Plants In Curb Cut Rain Gardens, Ana Singh, Rachel Warners, Jonathan Walt, Patrick Jonker, David P. Warners

Faculty and Professional Research

No abstract provided.

Three-Dimensional Graph Matching To Identify Secondary Structure Correspondence Of Medium-Resolution Cryo-Em Density Maps, Bahareh Behkamal, Mahmoud Naghibzadeh, Mohammad Reza Saberi, Zeinab Amiri Tehranizadeh, Andrea Pagnani, Kamal Al Nasr

Computer Science Faculty Research

Cryo-electron microscopy (cryo-EM) is a structural technique that has played a significant role in protein structure determination in recent years. Compared to the traditional methods of X-ray crystallography and NMR spectroscopy, cryo-EM is capable of producing images of much larger protein complexes. However, cryo-EM reconstructions are limited to medium-resolution (~4–10 Å) for some cases. At this resolution range, a cryo-EM density map can hardly be used to directly determine the structure of proteins at atomic level resolutions, or even at their amino acid residue backbones. At such a resolution, only the position and orientation of secondary structure elements (SSEs) such …

Study Of The D-Dimer, C-Reactive Protein, And Autoantibodies Markers Among Hbv Infected Patients In Babylon Province, Iraq, Ahmed Abdul-Abbas Bayram, Hussein O.M. Al-Dahmoshi, Noor S.K. Al-Khafaji, Raheem Tuama Obayes Al Mammori, Ali Husain Shilib Al-Shimmery, Morteza Saki

BioMedicine

Background: Hepatitis B can be defined as one of the dangerous diseases caused by the hepatitis B virus (HBV), which infects the liver and causes liver failure, cirrhosis, and death.

Aims: This study aimed to evaluate the D-dimer, C-reactive protein (CRP), and autoantibodies markers among HBV- infected patients in Babylon province, Iraq, compared to a healthy control group.

Methods: In this cross-sectional study, all patients referred to GIT and liver centers in Merjan Medical City, Babylon, Iraq from January 2016 to January 2018 were screened for HBV infection by quantitative real-time polymerase chain reaction (qPCR). Antinuclear antibody (ANA), dsDNA, D-dimer, …

Image-Based Microbiome Profiling Differentiates Gut Microbial Metabolic States, Sarwesh Rauniyar

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Quantification Of Soil Microbial Biomass In The Mcmurdo Dry Valleys, Antarctica, Emily Ruth Reynebeau

Biology ETDs

Quantifying microbial biomass is important for understanding microbial contribution to nutrient cycling and population flux. Widely accepted biomass estimation methods are sufficient for well-studied and high biomass systems, though are often not sensitive enough for systems with extremely low biomass. The McMurdo Dry Valleys of Antarctica are characterized as an extremely harsh environment with severe restrictions on life, with perhaps some of the lowest biomass in the world. We measured prokaryote biomass across Taylor and Wright Valleys using four estimation metrics to determine the most appropriate method for this ecosystem. The chloroform fumigation method was not sensitive enough for the …

Lyme Arthritis: A Primer For Primary Care, Ganesh Arun, Farhan Ali, Sowmya Srinivas, Justin Nistico, Pranav Nair

Advances in Clinical Medical Research and Healthcare Delivery

Lyme disease is caused by a bacteria belonging to the Borreliaceae family. Wooded forests and terrains are affected, including those in the Northeastern United States. Teenage ticks are most commonly discovered on humans as those ticks need to satisfy their nutritional requirements for growth. They bite warm, moist areas of the body and take 24 to 48 hours to transmit the Borrelia Burgdorferi infection. Lyme disease manifests as a multisystem disorder in humans, and is known for its dermatological, neurological and rheumatological findings. For the primary care provider, Lyme disease should be on the differential in multisystem diseases. Our case …

Multifaceted Approach To Understanding Acinetobacter Baumannii Biofilm Formation And Drug Resistance, Jessie L. Allen

USF Tampa Graduate Theses and Dissertations

Acinetobacter baumannii is a multi-drug resistant nosocomial pathogen known for causing wound related- and respiratory-infections. It is currently on the WHO’s list of critical pathogens due to its broadly drug resistant nature and the constant appearance of pan-resistant isolates. A majority of the infections caused by this organism are biofilm associated, however there is limited existing knowledge regarding the mechanisms used to engage in this multicellular lifestyle. As such, we set out to explore the factors influencing this behavior using an 10,000+ isolate transposon mutant library of A. baumannii strain AB5075. Of the strains tested, 6.45% demonstrated some level of …

Responses Of Wetland Soil Microbial Communities To Different Types Of Anthropogenic Stress, Grace Ann Cagle

LSU Doctoral Dissertations

Microorganisms are the major drivers of biogeochemical transformations of carbon and nitrogen in wetlands. These processes are crucial for ecological sustainability and are heavily impacted by human activities. How anthropogenic stress affects the microbial drivers of carbon storage and nutrient cycling in wetlands is not well understood. I investigated the response of wetland soil microbial communities to three different types of anthropogenic stress using DNA sequencing. First, I studied the effect of warming on microbial carbon processing in a peatland underlaid by permafrost by comparing the abundances of specific genes between sites subjected to five years of warming and controls. …

Unraveling The Role Of Novel G5 Peptidase Family Proteins In Virulence And Cell Envelope Biogenesis Of Staphylococcus Aureus, Stephanie M. Marroquin

USF Tampa Graduate Theses and Dissertations

Virulence factors and the bacterial cell envelope are two important components in S. aureus pathogenesis and survival. More importantly, understanding the regulation of these cellular processes is crucial to further understanding and combating this successful pathogen. To date, numerous factors have been identified as playing a role in the regulation of Agr activity in S. aureus, including transcription factors, antisense RNAs, and host elements. Herein we investigate the product of SAUSA300_1984 (termed MroQ), a transmembrane G5 peptidase family protein, as a novel effector of this system. Using a USA300 mroQ mutant we observed a drastic reduction in proteolysis, hemolysis, and …

Type Vi Secretion System Mutations Reduced Competitive Fitness Of Classical Vibrio Cholerae Biotype, Benjamin Kostiuk, Francis J. Santoriello, Laura Diaz-Satizabal, Fabiana Bisaro, Kyung-Jo Lee, Anna N. Dhody, Daniele Provenzano, Daniel Unterweger, Stefan Pukatzki

Publications and Research

The gram-negative bacterium Vibrio cholerae is the causative agent of the diarrhoeal disease cholera and is responsible for seven recorded pandemics. Several factors are postulated to have led to the decline of 6th pandemic classical strains and the rise of El Tor biotype V. cholerae, establishing the current 7th pandemic. We investigated the ability of classical V. cholerae of the 2nd and 6th pandemics to engage their type six secretion system (T6SS) in microbial competition against non-pandemic and 7th pandemic strains. We report that classical V. cholerae underwent sequential mutations in T6SS genetic determinants that initially exposed 2nd pandemic strains …

Risk Based Simulations Of Sporeformers Population Throughout The Dairy Production And Processing Chain: Evaluating On-Farm Interventions In Nebraska Dairy Farms, Rhaisa A. Crespo Ramírez

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Sporeformer bacteria are ubiquitous in the farm environment. These bacteria produce enzymes that negatively affect the quality of dairy products representing a problem for the dairy industry. Two major issues associated with high levels of sporeformers in raw milk are shelf-life reduction of fluid milk and market limitations for milk powder. Specific attention has been given to the contamination of milk powders with sporeformers due to their ability to survive pasteurization and milk powder processing conditions. Hence, the control of sporeformers is crucial to benefit the whole dairy industry. Researchers have suggested that certain management practices could decrease sporeformers in …

The Temperature-Dependent Conformational Ensemble Of Sars-Cov-2 Main Protease (Mpro), Ali Ebrahim, Blake T. Riley, Desigan Kumaran, Babak Andi, Martin R. Fuchs, Sean Mcsweeney, Daniel A. Keedy

Publications and Research

The COVID-19 pandemic, instigated by the SARS-CoV-2 coronavirus, continues to plague the globe. The SARS-CoV-2 main protease, or M^pro, is a promising target for development of novel antiviral therapeutics. Previous X-ray crystal structures of M^pro were obtained at cryogenic temperature or room temperature only. Here we report a series of high-resolution crystal structures of unliganded M^pro across multiple temperatures from cryogenic to physiological, and another at high humidity. We interrogate these datasets with parsimonious multiconformer models, multi-copy ensemble models, and isomorphous difference density maps. Our analysis reveals a temperature-dependent conformational landscape for M^pro, including …

Complete Genome Sequence Of The Pantoea Phage Ah07, Gregory P. Krukonis, Sam J. Roth, Veronique A. Delesalle

Biology Faculty Publications

Bacteriophages of the phyllosphere have not been extensively described, despite their role in bacterial communities on this plant organ. Here, we describe a temperate Pantoea phage, AH07, that was isolated from the leaves of horse chestnut trees. The 37,859-bp linear double-stranded DNA genome contains 58 putative genes, including an integration cassette.

Complete Genome Sequences Of Four Phages Of The Horse Chestnut Phyllosphere, Gregory P. Krukonis, Sam J. Roth, Veronique A. Delesalle

Biology Faculty Publications

Bacteriophages play important roles in determining bacterial communities, including plant microbiota. Here, we describe four lytic phages, three Siphoviridae and one Podoviridae, isolated from four different bacterial species found on the leaves of horse chestnut trees. Their double-stranded DNA (dsDNA) genomes range from 39,095 to 46,062 bp and contain 51 to 70 genes.

Genome Sequences Of Erwinia Phyllophages Ah04 And Ah06, Gregory P. Krukonis, Sam J. Roth, Veronique A. Delesalle

Biology Faculty Publications

Although crucial in shaping bacterial communities, few bacteriophages of the phyllosphere have been described. We provide genome data for two Myoviridae phages, AH04 and AH06, isolated on Erwinia billingiae strains. AH04 shares limited genetic similarity with previously described phages, while AH06 shares over 75% similarity with various Erwinia phages.

Monoclonal Antibodies Protect Aged Rhesus Macaques From Sars-Cov-2-Induced Immune Activation And Neuroinflammation, Anil Verma, Chase E. Hawes, Yashavanth Shaan Lakshmanappa, Jamin W. Roh, Brian A. Schmidt, Joseph Dutra, William Louie, Hongwei Liu, Zhong Min Ma, Jennifer K. Watanabe, Jodie L. Usachenko, Ramya Immareddy, Rebecca L. Sammak, Rachel Pollard, J. Rachel Reader, Katherine J. Olstad, Lark L. Coffey, Pamela A. Kozlowski, Dennis J. Hartigan-O'Connor, Michel Nussenzweig

School of Graduate Studies Faculty Publications

Anti-viral monoclonal antibody (mAb) treatments may provide immediate but short-term immunity from coronavirus disease 2019 (COVID-19) in high-risk populations, such as people with diabetes and the elderly; however, data on their efficacy in these populations are limited. We demonstrate that prophylactic mAb treatment blocks viral replication in both the upper and lower respiratory tracts in aged, type 2 diabetic rhesus macaques. mAb infusion dramatically curtails severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-mediated stimulation of interferon-induced chemokines and T cell activation, significantly reducing development of interstitial pneumonia. Furthermore, mAb infusion significantly dampens the greater than 3-fold increase in SARS-CoV-2-induced effector CD4 …

Assessment Of Bacteriological Quality Of Drinking Water In Some Primary And Secondary Schools In Mukalla City-Hadhramout/Yemen, Eidha Ali Bin Hameed, Khaled Saleh Bin Alshikh Bubkr

Hadhramout University Journal of Natural & Applied Sciences

Assessment of faecal contamination and detection enumeration of coliforms and other microorganisms in water is one of the measurements to determine the hygienic quality of water. This study aimed to assess the drinking water in some primary and secondary schools in Mukalla city-Hadhramout/Yemen to estimate the bacterial contamination of drinking water and its safety to the public. The water samples were studied for bacteriological analysis in which was inoculated into culture media using two methods, the presumptive test for the most probable number (MPN) and confirmatory test for bacterial identification. Also, some physiochemical properties of water such as temperature, total …

Contact Normalization And The Role Of Maackia Amurensis Seed Lectin As A Novel Chemotherapeutic And Antiviral Agent, Stephanie A. Sheehan

Graduate School of Biomedical Sciences Theses and Dissertations

Cells communicate with each other to coordinate tissue function and homeostasis. Diseases including cancer, arthritis, and acute respiratory disease syndrome (ARDS) require a breakdown in this intercellular communication. For example, cancer progression is suppressed by junctional communication between nontransformed and transformed cells. This process is called contact normalization. Junctional communication must be disrupted to enable transformed cells to grow into malignancies. However, the junctions and mechanisms by which nontransformed cells normalize cell behavior have not been clearly defined. My project aimed to identify junctions and elucidate mechanisms underlying contact normalization. We discovered that cadherins, specifically N-cadherin, form junctions that enable …

College Of Natural Sciences Scholarship Brunch Program, November 6th 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

This is the program for the first annual College of Natural Sciences Scholarship Brunch, held on November 6th, 2021 at McCrory Gardens.

College Of Natural Sciences Newsletter, November 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2, Issue 11

Page 1 Dean's Message
Page 2 Awards & Recognition
Page 3 Media Coverage of CNS
Page 4 2021 Day of Scholars
Page 5 Astronomy Outreach
Page 6 SDSU Faculty & Students Host American Society for Microbiology Annual Conference
Page 7 Scholarship Brunch
Page 8 Open PRAIRIE Data, SI Final Exam Review Sessions
Page 9 Aamlid Family Anatomy Lab Photos

Spotted Salamander Egg Masses Exhibit A Unique Internal Microbiome In Relation To Their Environment, Elizabeth Leonard

Senior Honors Theses

Microbial studies have led to various ecological and medicinal discoveries. Amphibian eggs, like those of Ambystoma maculatum, exhibit natural resistance to bacterial invasion that may be microbiome related. The purpose of this research was to sequence the external and internal microbiome of A. maculatum egg masses and compare with the environmental microbiome. It was hypothesized that the external and internal microbiome would bear more similarity to each other than the water. A significant difference was observed between the microbiome of the inside surface of the egg mass and the water but not the outside surface of the egg and …

Dietary Fiber Utilization In The Gut: The Role Of Human Gut Microbes In The Degradation And Consumption Of Xylose-Based Carbohydrates, Elizabeth Drey

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Xylans are a family of xylose-based polysaccharides naturally present in fruits, vegetables, and cereal grains. Resistant to digestion by host enzymes, xylans reach the large intestine intact, where they are utilized by members of the gut microbiome. They are initially hydrolyzed by primary degraders that utilize extracellular xylanases to cleave xylan into smaller oligomers. These xylooligosaccharides (XOS) can then either be further hydrolyzed by primary degraders or can cross-feed secondary consumers, including Bifidobacterium. While several Bifidobacterium species have metabolic systems for XOS, studies have shown these species grow poorly on longer XOS and xylan substrates. In this thesis, …

Microbial Dark Matter: Culturing The Uncultured In Search Of Novel Chemotaxonomy, Sarah J. Kennedy

USF Tampa Graduate Theses and Dissertations

Although <1% of environmental isolates can be cultured, insights into the culturable fraction refine future techniques to unlock the cryptic biodiversity. This cryptic biodiversity is omnipresent within culture-independent surveys of environmental bacterial populations. Subsequently, these elusive organisms are termed “microbial dark matter” due to the intrigue surrounding their potential taxonomic and biosynthetic impacts. To this end of investigating bacterial-specific dark matter, we employed high-throughput culturing techniques to examine Gulf of Mexico sediments and sponges for chemotaxonomically important bacteria. Through stepwise implementation of permissive and selective recovery techniques, we succeeded in recovering over 150 unique bacterial isolates. We observed several isolates that pose as chemotaxonomically interesting, including several strains that belong to critical bioremediation taxa. In addition to these biotechnological-amenable isolates, we have also succeeded in culturing taxa historically attributed with antibacterial discoveries. One such isolate was a previously sponge-associated organism belonging to the rarely cultured Verrucosispora genus. Through extensive comparative genomics, we identified it as a novel species and subsequently named it Verrucosispora sioxanthis sp. nov. with the published genome serving as a resource for continued microbial dark matter investigations. Following continued passaging of the organism, we observed improved growth, biomass, and liquid growth dispersal within each increasingly sub-passaged generation of the isolate. As such, the laboratory attenuation, or domestication, of the organism warranted in-depth whole genomic analyses to generate insight into the increased laboratory sustainability. Through phenotypically-guided bioinformatics, we determined that the domestication was mediated through genome-wide selective pseudo- or non-pseudogenization of genes. As the previously sponge-associated organism evolved with the selection pressures of the static laboratory, we demonstrate that isolate effectively underwent genomic atrophy to resolve into a largely stable, sustainable laboratory-domesticated strain. Collectively, our chemotaxonomic discovery pipeline expands on the culturable bacterial biodiversity and ultimately provides a previously uncultured model organism for initial forays into resolving the microbial dark matter knowledge gap.

Microbiota From Specific Pathogen-Free Mice Reduces Campylobacter Jejuni Chicken Colonization, Ayidh Almansour, Ying Fu, Tahrir Jatli Alenezi, Mohit Bansal, Bilal Alrubaye, Hong Wang, Xiaolun Sun

Poultry Science Faculty Publications and Presentations

Campylobacter jejuni, a prevalent foodborne bacterial pathogen, is mainly transmitted from poultry with few effective prevention approaches. In this study, we aimed to investigate the role of microbiota on C. jejuni chicken colonization. Microbiota from specific pathogen-free (SPF) mouse stools were collected as SPF-Aerobe and SPF-Anaerobe. Birds were colonized with SPF-Aerobe or SPF-Anaerobe at day 0 and infected with C. jejuni AR101 at day 12. Notably, C. jejuni AR101 colonized at 5.3 and 5.6 log(10) C. jejuni CFU/g chicken cecal digesta at days 21 and 28, respectively, while both SPF-Aerobe and SPF-Anaerobe microbiota reduced pathogen colonization. Notably, SPF-Aerobe and SPF-Anaerobe …

Investigation Of An Alternative Protocol For The Production Of Sars-Cov-2 Antigenic Proteins, Nichole Ninaltowski

USF Tampa Graduate Theses and Dissertations

With the COVID-19 pandemic showing no signs of slowing down, large-scale antigenic protein production is still needed for surveillance using serologic assays. From screening to vaccines to biotherapeutics, being able to produce the proteins for these assays is essential; however, the current gold standard method for producing SARS-CoV-2 spike proteins is prohibitively expensive for most research groups.

Alternative methods of transfecting mammalian cells to produce recombinant proteins that are relatively inexpensive have been used for years. Unlike the expensive, commercially available lipid-based methods, other established methods such as polyethyleneimine (PEI), are considerably easier, and cheaper to meet the needs of …

A Functional Characterization Of The Omega (Ω) Subunit Of Rna Polymerase In Staphylococcus Aureus, Shrushti B. Patil

USF Tampa Graduate Theses and Dissertations

In bacteria, RNA polymerase (RNAP) is a well-characterized and highly conserved multi-subunit enzyme complex responsible for transcription of DNA into RNA. The ω subunit (rpoZ/RpoZ), one of the smaller accessory subunits of RNAP, is often overlooked and under-studied, however, particularly in Gram-positive species. We have previously shown that deleting ω impacts the integrity of RNA polymerase in S. aureus, especially the β' subunit, and alters preference of the core enzyme for sigma factors, skewing heavily towards σB instead of the housekeeping σ factor. Consequently, this causes deregulation of myriad transcriptional processes, strongly rewiring gene expression circuits, and ultimately impairing the …

Prevalence And Multidrug Resistance Pattern Of E. Coli Among Urinary Tract Infection Patients In Tertiary Care Hospital Of Multan, Hubza Ruatt Khan, Mehvish Javeed, Asghar Javed, Nisma Farooq

Journal of Bioresource Management

Urinary Tract Infection is alarming problem worldwide due to the intensity of antimicrobial resistance. Escherichia coli is the most predominant organism in UTI. This study was planned to evaluate demographic parameters, the prevalence of E. coli, and antimicrobial resistance patterns among E. coli isolates from UTI patients in Nishtar Hospital of Multan from January to June 2018. A total of 350 mid-stream urine samples were collected from different patients having age group from 25 to 60 years and processed by standard laboratory procedures. Out of 350 samples, 100 samples were observed as critical bacteremia. Escherichia coli and Klebsiella …