Microbiology Commons^™

The Application Of Microbial Source Tracking To Aid In Site Prioritization For Remediation In Lower Michigan, John J. Hart

Masters Theses

Non-point source fecal pollution is a threat to both the environment and public health. Climate change, aging infrastructure, and intensified agricultural practices are predicted to accentuate this issue. In Michigan, due to the high instance of aging infrastructure and intensified agriculture, non-point source fecal pollution has caused many waterbodies to exceed the state standards posing a risk to recreational activities and source water. Due to this threat, there is an increased effort to identify and remediate these sources. My study focused on improving the identification of non-point source fecal pollution through a combination of culture-based and molecular fecal indicator bacteria …

Development, Optimization, And In Vitro/In Vivo Evaluation Of Azelaic Acid Transethosomal Gel For Antidermatophyte Activity, Ali Nasr, Noha Badawi, Yasmine Tartor, Nader Sobhy, Ali Nasr

Pharmacy

Treatment of dermatophytosis is quite challenging. This work aims to investigate the antidermatophyte action of Azelaic acid (AzA) and evaluate its efficacy upon entrapment into transethosomes (TEs) and incorporation into a gel to enhance its application. Optimization of formulation variables of TEs was carried out after preparation using the thin film hydration technique. The antidermatophyte activity of AzA-TEs was first evaluated in vitro. In addition, two guinea pig infection models with Trichophyton (T.) mentagrophytes and Microsporum (M.) canis were established for the in vivo assessment. The optimized formula showed a mean particle size of 219.8 ± 4.7 nm and a …

The Sars-Cov-2 Utr’S Intrudes Host Rbp’S And Modulates Cellular Splicing, Anjali Singh, Kush Kumar Pandey, Shubham Kumar Agrawal, Rupesh K. Srivastava, Sankar Bhattacharyya, Bhupendra Verma

Nebraska Center for Virology: Faculty Publications

SARS-CoV-2 is a novel coronavirus that causes a potentially fatal respiratory disease known as coronavirus disease (COVID-19) and is responsible for the ongoing pandemic with increasing mortality. Understanding the host-virus interaction involved in SARS-CoV-2 pathophysiology will enhance our understanding of the mechanistic basis of COVID-19 infection. The characterization of post-transcriptional gene regulatory networks, particularly pre-mRNA splicing, and the identification and characterization of host proteins interacting with the 5' and 3'UTRs of SARS-CoV-2 will improve our understanding of posttranscriptional gene regulation during SARS-CoV-2 pathogenesis. Here, we demonstrate that either SARS-CoV-2 infection or exogenous overexpression of the 5' and 3’UTRs of the …

Reactive Chlorine Species Reversibly Inhibit Dnab Protein Splicing In Mycobacteria, Daniel Wahl

Scholars Week

Intervening proteins, or inteins, are mobile genetic elements translated within host polypeptides and removed at the protein level by splicing. In protein splicing, a selfmediated reaction removes the intein, leaving only a peptide bond in place. While protein splicing can proceed in the absence of external co-factors, several natural examples of conditional protein splicing (CPS) have emerged. In CPS, the rate and accuracy of splicing is highly-dependent on environmental conditions. As activity of the intein-containing host protein is compromised prior to splicing, and inteins are highly abundant in the microbial world, CPS represents an emerging form of …

Role Of Microorganisms In Communication Between Soil And Plants, Domenico Prisa

Karbala International Journal of Modern Science

Microbial population in the rhizosphere establishes a number of important interactions with plants, whose study is crucial in perspective of sustainable agricultural production. Studies on various plant crops have revealed that, despite the complex microbial biodiversity of the soil, the bacterial microbiome is characterised by multiple functionalities. A better understanding of the molecular mechanisms, underlying the interactions between plants and the microbiome, could enable better development of plants, related to the beneficial action of microorganisms. Therefore, this review aims to describe the characteristics of the rhizosphere microbiome with the interactions that occur between soil and roots, as well as the …

The Effects Of Specialized Pro-Resolving Mediator Lipoxin A4 On Pseudomonas Aeruginosa Biofilms And Interactions With Monocytes, Julianne M. Thornton

Graduate School of Biomedical Sciences Theses and Dissertations

Pseudomonas aeruginosa (P. aeruginosa) is an opportunistic pathogen known as a major cause of hospital-acquired secondary infections, commonly causing chronic respiratory infections in immunocompromised individuals, especially those with cystic fibrosis, and often found in wound infections. P. aeruginosa uses the quorum sensing pathway to readily form protective biofilms, which reduce the efficacy of antibiotics and access by host immune cells to eradicate the pathogen. Specialized pro-resolving mediators (SPMs) are lipids endogenously produced by the host immune response to infection to aid in infection resolution. One SPM, Lipoxin A4 (LxA4), has been shown to be a robust quorum sensing inhibitor.

The …

Investigating The Antibacterial And Immunomodulatory Properties Of Lactobacillus Acidophilus Postbiotics, Rachael M. Wilson

Graduate School of Biomedical Sciences Theses and Dissertations

Probiotics are nonpathogenic microorganisms that have been extensively studied for their ability to prevent various infectious, gastrointestinal, and autoimmune diseases. The mechanisms underlying these probiotic effects have not been elucidated. However, we and other researchers have evidence suggesting that probiotic bacteria secrete metabolites that are antimicrobial and anti-inflammatory. As such, we developed a methodology to collect the secreted metabolites from a probiotic bacterium, Lactobacillus acidophilus, and tested this cell free filtrate (CFF) both in vitro and in vivo. Using this CFF, we have demonstrated that L. acidophilus secretes a molecule(s) that has specific bactericidal activity against the opportunistic pathogen, Pseudomonas …

Microbial Community Interactions Between Honey Bee Symbionts, Jillian P. Lewis

2023 Midwest Ecology & Evolution Conference

Bombella apis is a bacterial honey bee symbiont that benefits larvae by supplementing their nutrition and protecting them from pathogenic fungi. B. apis co-occurs with another bee-associated bacterium, Apilactobacillus kunkeei, in certain hive niches: nectar, larvae, honey stomachs of nurse bees, the queen gut, and royal jelly. Because bacterial species existing in the same ecological niche are apt to form microbial communities that interact, these interactions may modulate B. apis’ positive impact on the honey bee larvae. We hypothesize that due to its faster growth, A. kunkeei outcompetes B. apis for shared resources in nutrient rich conditions such …

Variation In Synthetic Floral Microbiome Composition Is Largely Ignored By Foraging Bumblebees, Nevin P. Cullen

2023 Midwest Ecology & Evolution Conference

Most flowers are occupied by diverse communities of microbes, which can alter floral attractiveness to key pollinators and floral fitness by interacting with floral traits. Different species of flower often acquire unique communities of microbes. Consequently, pollinators are frequently forced to choose between two flowers with distinct floral microbiomes while foraging. However, it is currently unknown whether pollinators have an inherent preference for flowers containing one floral microbiome over another, and whether microbial preference is modified by variation in floral traits. We investigated this knowledge gap using distinct bacteria and yeasts cultured from a nickel-hyperaccumulating plant and its non-accumulating relative. …

An Optimal Patch Use Model For Nitrogen Foraging In Arbuscular Mycorrhizal Fungi, Xin Lin

2023 Midwest Ecology & Evolution Conference

Optimal Foraging Theory has been widely used to study animal foraging behaviors, but has seldom been applied to symbiotic microbes like arbuscular mycorrhizal (AM) fungi. To date we know little about how AM fungi make decisions to forage in different nutrient patches. To help address this gap we here apply Optimal Foraging Theory to understand how AM fungi forage for nitrogen. We focus on nitrogen because AM fungi need more nitrogen than their plant hosts and soil nitrogen availability can shift the relationship between AM fungi and their hosts from mutualism to parasitism. We present a stochastic dynamic programming model …

Elevated Co2 Drives Community And Network Structural Change Within Foliar Microbiomes Of Soybean, Connor Morozumi

2023 Midwest Ecology & Evolution Conference

Microbiomes within plants can play large roles in determining responses to stress or perturbation, increasingly common in a rapidly changing world. For example, foliar endophytes are known to increase stress tolerance to drought and decrease herbivory among many other effects. How these microbes are likely to respond to global change themselves is poorly understood. Global changes, such as increased atmospheric CO₂, which can influence host plant physiological processes, have the potential to directly and indirectly alter microbiome community structure. Here, we assessed community and network structure of bacterial and fungal phyllosphere microbiomes within soybean (Glycine max). …

Initial Steps In Testing The Stress Gradient Hypothesis For Selenium Exposure In Soil Bacteria, Kristian J. Harris

2023 Midwest Ecology & Evolution Conference

The Stress Gradient Hypothesis (SGH) states that interspecific interactions should shift from competitive to facilitative interactions as environmental stress increases. Selenium (Se) is a naturally occurring metalloid that acts as an environmental pollutant and as an essential micronutrient. Due to its metallic properties, Se acts as an oxidative stress and can be toxic to plants and animals. Given this, Se in soil systems acts as an abiotic stress that influences species composition and species interactions. Within soils, bacteria and fungi have evolved to tolerate Se via detoxification and Se processing for respiration and studies show that metal detoxification traits like …

Metagenomic And Meta-Transcriptomic Analysis Reveal The Colonization And Expression Profile Of Probiotic Strains In Humans And Animals, Yunjuan Peng, Routing Chen, Zhihao Zhang, Rui Jin, Ting Xe, Xinting Liu, Jianmin Chai, Samantha Howe, Jiangchao Zhao, Ying Li, Feilong Deng

Animal Science Faculty Publications and Presentations

In humans and animals, probiotics are widely accepted as crucial for host health and growth. The investigation of the probiotic colonization and expression of probiotics in the host is beneficial for proper usage of probiotics and isolation of indigenous probiotics. In this study, we analyzed commonly used probiotic strains in the intestines/rumen of humans and animals by analyzing metagenomic and paired meta-transcriptomic data from the gut or rumen microbiome of humans (n = 13), pigs (n = 6), chickens (n = 6), cattle (n = 14), sheep (n = 10), and mice (n = …

Acute Necrotizing Encephalopathy In An Infant: A Case Report, Elisamia Ngowi, Zeenat Juneja, Jacqueline Gabone, Maria Bulimba, Mohamedraza Ebrahim, Yaser Abdallah

Paediatrics and Child Health, East Africa

Background: Acute necrotizing encephalopathy is a rare, severe neurological condition, characterized by symmetrical necrotic brain lesions affecting the thalamus, cerebral white matter, brain stem, and cerebellum. Diagnosis relies on characteristic clinical and radiological features.

Methodology: We describe a 10-month-old female infant presenting with multiple seizures following a brief febrile upper respiratory illness.

Findings: MRI of the brain showed bilateral symmetrical abnormal signal intensities involving both thalami and caudate nucleus, consistent with ANE. Management of ANE is symptom-related but high-dose steroids and IVIG have been used.

Conclusion: This case highlights the importance of recognizing ANE beyond its …

Life Line Spring 2023, Otterbein Biology And Earth Science Department

Life Line - The Biology Department Newsletter

In this Issue:

Feathered Friends Living on Campus; The Hidden Mussels of the Olentangy River; Early Assurance Program Students Graduate from HCOM; Students Present at American Society for Microbiology Microbe 2022 Meeting; Environmental Science Upgrades Its Remote Monitoring Capabilities; Speed!; UK Students Visit Local Attractions; That's a Lottl Axolotls.

Resources For Preparing And Using Antibiograms In Hospital Settings, Fred Tenover, Dana Tawa, Stephanie Mitchell, Isabella A. Tickler, John Stelling, Janet Hindler, Debra A. Goff, Dan Diekema

Training Materials on Antimicrobial Resistance

This is a guide to resources that are available to assist laboratories with the preparation and dissemination of their antimicrobial susceptibility testing data in a format known as an "antibiogram" as an aid to antimicrobial stewardship activities in their hospital. There are three color-coded pathways in the slide deck: Pathway A for laboratories with no experience with antibiograms; Pathway B for laboratories with some experience that want to improve and expand the use of their antibiograms; and Pathway C for experienced laboratories that want to share their data with external surveillance systems.

Modulatory Roles Of Human Adenovirus Type 3 In Extracellular Vesicle Development, Trafficking, And Inhibition, Ayodeji Oludare Ipinmoroti

Dissertations

Respiratory human adenovirus (HAdV) has been closely linked with acute respiratory infections such as pharyngitis and coryza (common cold). While some HAdV serotypes antagonize the immune system leading to meningitis, gastroenteritis, and acute hemorrhagic cystitis among other conditions, HAdV type 3 (HAdV3) predominantly infects the upper respiratory tract. Studies have shown that the release of small, membrane-derived extracellular vesicles (EVs), termed exosomes, may offer a mechanism by which certain viruses, enter cells via receptor-independent entry. EVs play a major role in both cellular homeostasis and intercellular communication under both healthy and pathological conditions. Firstly, in this study, we demonstrated that …

Human Microbiome Transfer In The Built Environment Differs Based On Occupants, Objects, And Buildings, Andrew J. Hoisington, Christopher E. Stamper, Katherine L. Bates, Maggie A. Stanislawski, Michael C. Flux, Teodor T. Postolache, Christopher A. Lowry, Lisa A. Brenner

Faculty Publications

Compared to microbiomes on other skin sites, the bacterial microbiome of the human hand has been found to have greater variability across time. To increase understanding regarding the longitudinal transfer of the hand microbiome to objects in the built environment, and vice versa, 22 participants provided skin microbiome samples from their dominant hands, as well as from frequently and infrequently touched objects in their office environments. Additional longitudinal samples from home environments were obtained from a subset of 11 participants. We observed stability of the microbiomes of both the hand and built environments within the office and home settings; however, …

Up-03 Identifying The Determinants Of Pediatric Vaccine Uptake During The Covid-19 Pandemic, Colleen Phan, Brandon Mercardo, Justin Travis Ph.D., Ginny Webb Ph.D.

SC Upstate Research Symposium

COVID-19 has caused over a million deaths in the United States. Preventative measures such as masks, social distancing, and vaccination have been implemented to fight against the disease. Unfortunately, a large subset of Americans opposed these efforts.

SC DHEC reports that as of January 2023, only 53.9 % of eligible South Carolinians have been fully vaccinated against COVID-19. Previous studies have shown vaccine hesitancy is influenced largely by personal concerns about vaccine development, peer vaccination status, and general skepticism of immunization.

Hesitancy towards pediatric vaccination is particularly concerning because unvaccinated children can act as vessels to exponentially accelerate COVID-19 transmission. …

Small Molecule Compounds, Active Ingredients Of Tcm, As Novel Therapeutics For Eosinophilic Esophagitis, Anish Maskey

NYMC Student Theses and Dissertations

Eosinophilic Esophagitis (EoE), a chronic inflammatory condition of the esophagus, characterized by esophageal dysfunction and eosinophilic inflammation. Current treatments for EoE include dietary elimination and swallowed steroids. Recently, Dupixent was approved for the treatment of EoE, but it has side effects such as eye inflammation and eczema. Traditional Chinese Medicine (TCM) practice has been used to improve GI symptoms in EoE patients. Two key active ingredients of a TCM formula, 7,4’-Dihydroxyflavone (DHF) and Berberine (BBR), have shown remarkable results in treating EoE.

To understand the role of two active ingredients in EoE, different experimental models were used. First, a computational …

Effects Of Vacuum Packaging And Chilling Storage On The Microbiological Changes Of The Superheated Steam Dried Sardines, Prissillah Antelm, Ibrahim Juma, Leonard M.P. Rweyemamu, Lillian Daniel Kaale

Tanzania Journal of Science

Fish are important sources of protein and micronutrients for combating malnutrition. Since fish are highly perishable, methods for processing and preserving them should be the main focus to increase their shelf life and maintain their quality. The present study assessed the effectiveness of the superheated steam dryer (SSD) in processing sardines, and examined the effects of packaging and storage conditions on their microbiological quality. Sardines collected from the Mafia Island were dried in SSD, air-packed and stored at room temperature (AR), air-packed and stored at chilling temperature (AC), vacuum-packed and stored at room temperature (VR), and vacuum-packed and stored at …

Ethanol Extracts From Selected Tanzanian Medicinal Plants Selectively Inhibit Plasmodium Falciparum Growth In Vitro, Robert Christopher, Amina Msonga, Heinrich C. Hoppe, Fabrice F. Boyom

Tanzania Journal of Science

This study aimed to assess the in vitro antiplasmodial and cytotoxic activities of ethanol extracts from the root barks, leaves and stem barks of seven medicinal plant species growing in Tanzania. The antiplasmodial activities of extracts against chloroquine-sensitive (3D7) and multidrug-resistant (Dd2) strains of Plasmodium falciparum were determined using a SYBR green I-based fluorescence assay, while the cytotoxicity of active extracts was determined against the human HepG2 cell line using a resazurin-based assay. Out of twenty-one extracts screened, two of them, namely, DFRE from Dracaena fragrans root bark (IC50Pf3D7 = 2.4 mg/mL) and EHSE from Erythrina haerdii stem bark (IC50Pf3D7 …

Renovating A Double Fence With Or Without Notifying The Next Door And Across The Street Neighbors: Why The Biogenic Cytoplasmic Membrane Of Gram-Negative Bacteria Display Asymmetry?

Faculty, Staff and Student Publications

The complex two-membrane organization of the envelope of Gram-negative bacteria imposes an unique biosynthetic and topological constraints that can affect translocation of lipids and proteins synthesized on the cytoplasm facing leaflet of the cytoplasmic (inner) membrane (IM), across the IM and between the IM and outer membrane (OM). Balanced growth of two membranes and continuous loss of phospholipids in the periplasmic leaflet of the IM as metabolic precursors for envelope components and for translocation to the OM requires a constant supply of phospholipids in the IM cytosolic leaflet. At present we have no explanation as to why the biogenic E. …

Protocol To Identify The Core Gene Supported By An Essential Gene In E. Coli Bacteria Using A Genome-Wide Suppressor Screen, Isao Masuda, Ya-Ming Hou

Department of Biochemistry and Molecular Biology Faculty Papers

We describe here a genome-wide screening approach to identify the most critical core reaction among a network of many that are supported by an essential gene to establish cell viability. We describe steps for maintenance plasmid construction, knockout cell construction, and phenotype validation. We then detail isolation of suppressors, whole-genome sequencing analysis, and reconstruction of CRISPR mutants. We focus on E. coli trmD, which encodes an essential methyl transferase that synthesizes m1G37 on the 3'-side of the tRNA anticodon. For complete details on the use and execution of this protocol, please refer to Masuda et al. (2022).

Surveillance And Stewardship: Where Infection Prevention And Antimicrobial Stewardship Intersect, Fred C. Tenover, Debra A. Goff

Biology Faculty Publications

Colonization with multidrug-resistant organisms (MDROs) is a risk factor for subsequent infection. Surveillance for MDROs, including methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, extended-spectrum beta-lactamase-producing Enterobacterales, and carbapenemase-producing organisms, is commonly conducted in hospitals to prevent spread of MDROs, in part to reduce the potential for additional infections. Although colonization is a risk factor for infection, data on colonization with various MDROs are often not considered when selecting anti-infective therapy. There are conflicting data on the strength of the positive and negative predictive values of the colonization test results to guide therapeutic strategies. Defining therapeutic strategies for patients with complicated or …

Damped Oscillating Phosphoryl Transfer Reaction In The Cyanobacterial Circadian Clock, Hye In Jang, Pyonghwa Kim, Yongick Kim

Chemistry Faculty Research

Most organisms have circadian clocks to ensure the metabolic cycle to resonate with the rhythmic environmental changes without “damping,” or losing robustness. Cyanobacteria is the oldest and simplest form of life that is known to harbor this biological intricacy. Its KaiABC-based central oscillator proteins can be reconstituted inside a test tube, and the post-translational modification cycle occurs with 24 h periodicity. KaiC’s two major phosphorylation sites, Ser-431 and Thr-432, become phosphorylated and dephosphorylated by interacting with KaiA and KaiB, respectively. Here, we mutate Thr-432 into Ser to find the oscillatory phosphoryl transfer reaction damps. Previously, this mutant KaiC was reported …

Enrichment Media Selection And Co-Culture Potential Among Exoelectrogen Bacteria Vary With Ecological Factors, Nur Syafira Khoirunnisa, Syaiful Anwar, Untung Sudadi, Dwi Andreas Santosa

Makara Journal of Science

Staphylococcus saprophyticus ICBB 9554 and Citrobacter freundii ICBB 9763 are exoelectrogen bacteria applied as microbial fuel cells (MFC). We selected enrichment media for both these exoelectrogen bacteria, characterized their synergistic traits, and evaluated the growth conditions under different ecological factors. In this study, different enrichment media, such as those containing sugar, molasses, and palm sugar (2, 4, and 6% w/v) were tested for S. saprophyticus ICBB 9554. Meanwhile, technical sodium acetate (NaAc), commercial vinegar 25%, and cider vinegar (5, 10, and 15 mM acetate concentration) were tested for C. freundii ICBB 9763. Both the exoelectrogen bacteria were tested for the …

Rna Virus-Mediated Changes In Organismal Oxygen Consumption Rate In Young And Old Drosophila Melanogaster Males, Eli Hagedorn, Dean Bunnell, Beate Henschel, Daniel Smith Jr, Stephanie Dickinson, Andrew Brown, Maria De Luca, Ashley Turner, Stanislava Chtarbanova

Research, Publications & Creative Work

Aging is accompanied by increased susceptibility to infections including with viral pathogens resulting in higher morbidity and mortality among the elderly. Significant changes in host metabolism can take place following virus infection. Efficient immune responses are energetically costly, and viruses divert host molecular resources to promote their own replication. Virus-induced metabolic reprogramming could impact infection outcomes, however, how this is affected by aging and impacts organismal survival remains poorly understood. RNA virus infection of Drosophila melanogaster with Flock House virus (FHV) is an effective model to study antiviral responses with age, where older flies die faster than younger flies due …

Thymic Stromal Lymphopoietin Participates In The Host Response To Intra-Amniotic Inflammation Leading To Preterm Labor And Birth, Tomi Kanninen, Li Tao, Roberto Romero, Yi Xu, Marcia Arenas-Hernandez, Jose Galaz, Zhenjie Liu, Derek Miller, Dustyn Levenson, Jonathan M. Greenberg, Jonathan Panzer, Justin Padron, Kevin Theis, Nardhy Gomez-Lopez Phd

Medical Student Research Symposium

Objective: To determine if bacteria (Ureaplasma parvum and Sneathia spp.) associated with intra-amniotic infection can trigger the induction of cytokine Thymic stromal lymphopoietin (TSLP) in human amnion epithelial cells (hAECs) in vitro.

Material or subjects: Amniotic fluid and chorioamniotic membrane (CAM) were collected from women with sPTL who delivered at term (n=30) or preterm without intra-amniotic inflammation (n=34), with sterile intra-amniotic inflammation (SIAI, n=27), or with intra-amniotic infection (IAI, n=17). Amnion epithelial cells (AECs), Ureaplasma parvum, and Sneathia spp. were also utilized.

Methods: The expression of TSLP, TSLPR, and IL-7Rα was evaluated in amniotic fluid or CAM by …

Accelerating Biosafety Capacity Building To Ensure National Biosecurity, Peipei Liu, Jiafu Jiang, Hao Lu, Peilei Cong, Lilin Zhao, Gexia Qiao, Dongsheng Zhou, Guizhen Wu

Bulletin of Chinese Academy of Sciences (Chinese Version)

Biosafety is an essential part of the national security system, which is related to people's lives and health, the country's longterm stability, and sustainable development, which is the bottom line that must be guaranteed. The international biosafety situation is grim and complex, while domestic biosafety faces challenges. Therefore, biosafety capacity building has become an international hot spot, among which scientific and technological innovation, talent training, and infrastructure platform construction are the top priorities. Although China has achieved strategic results in the rapid identification of pathogens, research, and development of specific vaccines and medicine in fighting against COVID-19 by relying on …