Microbiology Commons^™

Dissolved Inorganic Carbon Metabolism In Bacteria, Jana Wieschollek

USF Tampa Graduate Theses and Dissertations

Dissolved inorganic carbon (DIC: CO2, HCO3⁻, CO32⁻) plays a central role in the metabolism of all living organisms. DIC is necessary for steps in essential biosynthetic processes, such as the synthesis of amino acids and nucleobases; in autotrophic bacteria, organic molecules are synthesized entirely from DIC. To ensure a steady supply of CO2 and HCO3 - needed for biosynthesis and/or autotrophy, organisms use bicarbonate transporters to increase the cytoplasmic concentration of this anion, and carbonic anhydrase (CA) to speed the interconversion of CO2 and HCO3 -, both in the cytoplasm and at the cell surface. This dissertation investigates DIC metabolism …

Vaccination Against Onchocerca Volvulus Induces Igg-Mediated Protective Immunity Dependent On Neutrophils And Complement, Nathan M. Ryan, Jessica A. Hess, Mohini Nakhale, Annabel A. Ferguson, William Stump, Sara Belko, Rachel Monane, Robert S. Pugliese, Nikolai Petrovsky, Benjamin L. Makepeace, Sean A. Gray, Darrick Carter, Sara Lustigman, David Abraham

Department of Microbiology and Immunology Faculty Papers

Onchocerciasis remains a significant cause of morbidity and economic loss in sub-Saharan Africa. Despite the existence of effective therapeutics, a prophylactic vaccine targeting the etiologic agent, Onchocerca volvulus, is needed to control ongoing disease and transmission. Mice were vaccinated against O. volvulus with a fusion of the recombinant antigens Ov-103 and Ov-RAL-2 (Ov-FUS-1) with Advax-CpG adjuvant. Immunized mice developed protective immunity with the killing of third-stage larvae (L3) within 36 h of challenge infection. IgG from immunized mice passively transferred protective immunity to naïve mice, indicating that antigen-specific IgG mediated parasite elimination. Neutrophils were the most abundant subset of immune …

Scalable Biosynthesis And Recovery Of Poly-3-Hydroxybutyrate Produced From Cotton-Derived Glucose By Cupriavidus Necator, Ashley M. Clark, Lucia E. Gargano, Gabriella M. Fioravanti, Hannah M. Schapiro, Ron G. Kander

School of Design and Engineering Papers

To combat the growing issue of petroleum plastic waste, alternative bio-based polymers are being developed. Many of these biopolymers are made from bio-derived materials, or are biodegradable, but the most promising polymers fall in both categories. Polyhydroxyalkanoates (PHAs) are one such class of polymers, and poly-3-hydroxybutyrate (P3HB), the most popular PHA, has shown great potential. This study utilized two types of cotton-derived glucose, alongside commercial glucose, as a feedstock for the biosynthesis of P3HB by Cupriavidus necator (also known as Ralstonia eutropha). The fermentation took place in a 2-L bioreactor, showing potential for scale-up. A single-solvent extraction method was …

Evaluation Of Anti-Bacterial Efficacy Of Ginger, Resin Gum, And Nigella Sativa Irrigants Against Enterococcus Faecalis: An In Vitro Study, Iman El Ghazzawy, Leen Imad Hasbini, Reem Chamseddine, Wael Betbout, Roula Abiad

International Arab Journal of Dentistry

Objectives: To evaluate the antibacterial efficacy of Ginger, Resin Gum, and Nigella Sativa, against Enterococcus Faecalis.

Methods: Thirty-eight extracted single-rooted premolars were inoculated with E.faecalis, except the negative control, and incubated for 4 weeks. After instrumentation samples were divided into 4 groups (n=7) according to final irrigation: NaOCl+EDTA (Group A), Nigella sativa (B), Resin Gum (C), Ginger (D), plus 2 control groups (n=5): Saline (E), and Saline without bacterial inoculation (F). Cultures were collected at baseline and after irrigation.

Results: One-way ANOVA showed that in groups A-D a statistically significant reduction of bacterial load was observed at …

The Effects Of Plastic Mulch And Irrigation On Hemp Chemistry And Leaf Endophytes, Allison Rietman, Connor Morozumi, Robert C. Pearce, Natalie Christian

Journal of Agricultural Hemp Research

As an emerging crop, cultivation techniques for industrial hemp (Cannabis sativa L.) are still being developed and optimized. For example, irrigation and plastic mulching are some management practices that have been touted for their benefits in improving crop quality. Both techniques ensure ample water availability, which has often been attributed to improving hemp cannabinoid and terpene composition. In this study, we examined how supplemental irrigation implemented in a plastic mulch system influenced the cannabinoid and terpene profiles of one cultivar of CBD hemp, Lifter. We grew industrial hemp in field with plastic mulch and applied regular irrigation to one group …

Preliminary Microbial Community Analysis Of Non-Native And Native Plants In The Depauw Nature Park Quarry Bottom, Madeleine Cruz, Dana Dudle

Annual Student Research Poster Session

The DePauw Nature Park Quarry Bottom is a former limestone quarry that was mined for decades and then lay dormant. Through the years, it has developed from being uninhabited to being populated by a diversity of organisms at every scale of life. All organisms in the Quarry Bottom must withstand the changing conditions of the quarry, including the proliferation of invasive plants that are well-adapted to stress. In particular, two invasive wetland grasses, Phragmites and Typha have observed competitive interactions, increased spatial distributions, and possible influence on native species. We have studied these species at our scale of life, but …

Role Of Growth Factors In The Pathogenesis Of Systemic-Sclerosis-Associated Fibrosis, Fabian A. Mendoza, Sonsoles Piera-Velazquez, Sergio A. Jimenez

Jefferson Institute of Molecular Medicine Papers and Presentations

Systemic Sclerosis (SSc) is a systemic autoimmune disease of unknown etiology characterized by a severe fibroproliferative vasculopathy and frequently progressive cutaneous and internal organ fibrosis. The small-vessel vasculopathy and the tissue fibrotic alterations are responsible for the most serious clinical and pathological manifestations of the disease and for its high mortality. Despite the high severity and frequent mortality, there are currently no optimal therapeutic approaches for SSc, and its complex pathogenesis has not been fully elucidated. Numerous studies have suggested that growth factors and related regulatory macromolecules released from inflammatory and other cells present in the affected tissues play a …

Exploring The Diversity And Biology Of Unique Giant Broad Host Range Bacteriophages In Natural Environments, Tannaz Mohammadi

Theses and Dissertations

Microbial interactions within the rhizosphere play a crucial role in shaping bacterial community diversity and function. To explore these dynamics, we isolated 21 bacterial strains from soil and plant root samples collected near Rocky Branch Creek on the University of South Carolina campus. Our findings revealed that a significant proportion of these bacteria are lysogenic for CbK-like phages belonging to the Dolichocephalovirinae subfamily. Additionally, we isolated free bacteriophages directly from the same soil samples and found them to be closely related to those harbored within lysogenic bacteria. Surprisingly, despite predictions of a narrow host range, most of these phages, both …

Decorin Evokes A Pro-Lysosomal Pathway In Lymphatic Endothelial Cells, Gabriel J. Pascal, Dipon K. Mondal, Sadie Kim, Christopher Xie, Devanarayanan Siva Sankar, Jörn Dengjel, Renato V. Iozzo

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

The lymphatic system is critical to the body's immune and circulatory system, and lymphangiogenesis, the development of new lymphatic vessels from pre-existing ones, is a significant process capitalized upon by cancer during tumorigenesis. Decorin is a small leucine-rich proteoglycan which we have previously shown to be anti-tumorigenic and a suppressor of lymphangiogenesis. We have also shown that decorin exercises its anticancer properties through its ability to evoke autophagy. Through a comprehensive and unbiased proteomic analysis, we explored the implications of decorin exposure on protein expression within mouse lymphatic endothelial cells. We discovered that decorin enriches several protein pathways, notably proteasomal …

Characteristics And Potential Indigenous Bacteria Isolated From Shallot Farming In Brebes Regency As Diazinon Pesticide Remediation Agents, Wahyu Purbalisa, Dian Hendrayanti, Wahida Annisa Yusuf

Makara Journal of Science

Diazinon is an organophosphate pesticide that is widely used by shallot farmers in Brebes Regency. Due to its toxicity, diazinon residue in agricultural lands as well as plants’ cultivation is harmful to humans and the environment. Using indigenous soil bacteria as a remediation agent is an alternative solution to overcome diazinon contamination. Firstly, this study aimed to characterize isolates from diazinon-contaminated shallot farming. The second objective was to test the diazinon tolerance of the isolates in various diazinon concentrations. Isolation was carried out using nutrient agar (NA) media containing diazinon concentrations of 5, 25, 50, and 100 ppm. The characterization …

Detection Method For Escherichia Coli Using Real-Time Polymerase Chain Reaction Targeting The Yhav Gene, Muktiningsih Nurjayadi, Anisa Fitriyanti, Royna Rahma Musie, Gusti Angieta Putri, Puan Aqila Azizah, Helzi Angelina, Grace Grace, Ananda Indah Putri Sihombing, Agus Setiawan, Jefferson Lynford Declan, Gladys Indira Putri, Dandy Akbar Juliansyah, Siti Fatimah, Ayu Berkahingrum, Irma Ratna Kartika, Fera Kurniadewi, Vira Saamia, Shyi-Tien Chen, Bassam Aboemolak, Hesham Ali El Enshasy

Makara Journal of Science

Escherichia coli is a foodborne pathogenic bacterium that can cause diarrhea, while yhaV is a virulence-associated gene linked to the toxin–antitoxin system in E. coli. This study was aimed at evaluating the confirmation, specificity, and sensitivity of a yhaV gene primer using real-time polymerase chain reaction. The yhaV-targeting PCR successfully amplified a DNA fragment with an amplicon length of 207 bp (base pairs) under an annealing temperature optimized to a range of 54 °C to 62 °C via gradient PCR. The PCR using the primer pair produced a consistent Ct (cycle threshold) of 14.14 ± 0.05 and showed …

Effect Of Red And Blue Light On Lipid, Protein, Carbohydrate, And Pigment Contents Of Navicula Sp., Sofyan Maulana, Aulia Setyo Nurul Hida, Ismia Wulandari, Siti Mudrikah, Dedy Kurnianto, Khusnul Qonita Maghfiroh, Ria Amelia, Tia Erfianti, Renata Adaranyssa Egistha Putri, Irika Devi Anggraini, Septhian Marno, Eko Agus Agus Suyono

Makara Journal of Science

Light quality critically modulates the physiology of diatoms, influencing photosynthetic efficiency and metabolite synthesis. This study examines how monochromatic red (620–750 nm) or blue (450–495 nm) light affects the biochemical profiles and pigment production in Navicula sp. versus white light (control). Cultures were grown in sterile f/2 medium, and biomass was tracked via OD₆₈₀. Biochemical analyses included lipids (Bligh and Dyer method), carbohydrates (phenol-sulfuric acid assay), proteins (Bradford assay), and pigments (spectrophotometric quantification). The growth dynamics were modeled using logistic and Gompertz equations. No significant differences in OD-based growth rates, carbohydrates, proteins, or lipids content were observed with …

Clinical Applications Of Probiotics: A Comprehensive Review Of Benefits And Challenges, Riyam Wissam Hassan

Maaen Journal for Medical Sciences

Probiotics are beneficial microorganisms that help balance microbes in intestines and promote growth beneficial bacteria, they vary between bacteria, yeasts, and fungi and they are helpful to human health when taken in adequate and suitable amounts. In addition to maintaining intestinal health and help with digestion and absorption, also inhibiting development and preventing spread of harmful microorganisms. It exists in different forms, in the intestines and in the foods, products fermented, and in the pharmaceutical supplements. Because human health depends largely on the interaction between humans and these microorganisms known as probiotics, it has found that these organisms have vital …

Metagenomic Characterization Of Gut Microbiota In Children With Autism Spectrum Disorder: Microbial Signatures And Modulation By Anti-Inflammatory Diet And Probiotics, Marysol Valencia-Buitrago, Rodrigo Dias Oliveira-Carvalho, Valbert Cardoso, Jessica Triviño-Valencia, Luisa Matilde Salamanca-Duque, Vanessa Martínez-Díaz, Jovanny Zabaleta, Narmer Fernando Galeano-Vanegas, Carlos Andrés Naranjo-Galvis

School of Medicine Faculty Publications

Background: Autism Spectrum Disorder (ASD) is increasingly associated with alterations in gut microbiota, intestinal permeability, and immune dysregulation. However, integrative studies exploring these mechanisms in Latin American populations are lacking. Objective: To characterize gut microbiota profiles in Colombian children with ASD and evaluate the effects of two microbiota-targeted interventions, an anti-inflammatory diet and a probiotic formulation, on microbial diversity and taxonomic composition. Methods: In a two-phase study, shotgun metagenomic sequencing was performed on fecal samples from 23 children with ASD and 7 typically developing (TD) controls. In the second phase, 17 children with ASD were randomized to receive a 12-week …

Probiotic Biogeography In The Neonatal Intestine, Sierra Hansen

All ETDs from UAB

Neonatal infection remains a leading cause of both neonatal morbidity and mortality worldwide, particularly in preterm infants. Probiotic bacteria have been demonstrated to protect against the development of neonatal intestinal dysbiosis, however, formulations and efficacy vary substantially, highlighting a critical gap in the current understanding of the mechanisms governing probiotic efficacy in this population. This gap is exacerbated by regulatory standards which favor economic expansion over scientific rigor. Furthermore, current studies on probiotic efficacy largely rely on indirect or relative readouts of intestinal bacterial burden. Herein, we directly quantify the probiotic effects of Ligilactobacillus murinus V10 and Escherichia coli Nissle …

Lineage-Associated Zinc Metalloprotease B And Its Impact On Cardiac Damage Elicited During Invasive Pneumococcal Disease, Jennifer Nichelle Luck

All ETDs from UAB

During invasive disease, certain strains of Streptococcus pneumoniae (Spn) can invade the myocardium, damaging cardiomyocytes and predisposing patients to life-threatening cardiac complications. To identify genetic loci involved in pneumococcal cardio-virulence, we performed a bacterial genome-wide association study using 825 genomes corresponding to 17 distinct Spn lineages associated with varying rates of cardiac complications during hospitalization for pneumonia. This led to the identification of an allele of zmpB, the gene encoding Zinc metalloprotease B (ZmpB). Infection of mice with a ZmpB deficient mutant, i.e., TIGR4ΔzmpB, found that ZmpB was required to form foci of infection in the heart, i.e., cardiac microlesions. …

Structural Basis For Promoter Recognition By Pseudomonas Phage Dev Virion Associated Rna Polymerase, Brittney Bird

All ETDs from UAB

Bacteriophage DEV, a member of the Schitoviridae family, encodes a large virion-associated RNA polymerase (vRNAP) and shows significant potential for use in phage therapy. However, many aspects of DEV’s biology remain poorly understood, especially how it regulates transcription once inside the host. Recent work in our lab suggests that gene product 71 (gp71) functions as a DNA-dependent vRNAP. Analogous to the vRNAP of coliphage N4, gp71 likely initiates transcription by recognizing single-stranded DNA templates that contain early gene hairpin promoters. Based on this, my working hypothesis is that specific interactions between gp71 and the DEV early promoters PE1 and PE5 …

Characterizing The Role Of Pneumococcal Surface Protein A And Humoral Immunity To Biofilm Antigens During Streptococcus Pneumoniae Colonization, Jessica Lane

All ETDs from UAB

Streptococcus pneumoniae (Spn), or “the pneumococcus”, is a Gram-positive bacterium that colonizes the upper respiratory tract as a pathobiont. Spn is a deadly human pathogen, and one of the leading etiological agents of community-acquired pneumonia (CAP). One virulence factor of Spn is pneumococcal surface protein A (PspA), a choline-binding protein (CBP) at the surface of the bacteria that interacts with the host environment. Here, we demonstrated a novel role for PspA involving adhesion to dying host nasal epithelial cells via a multimeric complex with host lactoferrin (LF) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). We found that the PspA-GAPDH complex aggregated the bacteria …

Influenza A Virus Increases Susceptibility To Streptococcus Pneumoniae By Damaging The Airway Epithelium, Erin Yepsen Earnhardt

All ETDs from UAB

Influenza A Virus (IAV) is commonly complicated by secondary bacterial infections with Streptococcus pneumoniae (Spn), leading to increased morbidity and mortality. Recent work from our lab demonstrates that an IAV-induced loss of cystic fibrosis transmembrane conductance regulator (CFTR) in the airway disrupts the rheostatic properties of the airway surface liquid (ASL). In cystic fibrosis, caused by mutations in the CFTR gene, there is an increase in the bacterial burden of the airway. However, the underlying mechanisms and damage caused by IAV-induced CFTR dysfunction in the airway remains unknown. Using a primary differentiated human bronchial airway epithelial cell culture (HBEC) system, …

The Role Of The Glycerol Metabolism Regulator Glpr On Pseudomonas Aeruginosa’S Physiology, Nicholas Jordan Evans

All ETDs from UAB

Chronic infections with Pseudomonas aeruginosa are a leading cause of morbidity and mortality in people with cystic fibrosis. P. aeruginosa persists in the CF lung through adaptations, including altering the expression of metabolic genes to acquire nutrients that are abundant in the CF airway. Glycerol in the airway is imported and metabolized by proteins encoded in the glp regulon, which is regulated in part by GlpR. The loss of GlpR was previously shown to increase biofilm development in a P. aeruginosa CF isolate compared to a wound isolate. In the first half of this work, we investigated the influence that …