Organisms Commons^™

Comprehensive Resolution And Classification Of The Epstein Barr Virus Transcriptome, Truong D. Nguyen, Jia Wang, Meggie T. Lam, Harris Mcferrin, Tina M. O’Grady, Claire Roberts, Nicholas Van Otterloo, Trang T. Nguyen, Melody Baddoo, Dorota Wyczechowska, Maria Morales, Yan Dong, Erik K. Flemington

School of Graduate Studies Faculty Publications

Virus genomes harbor compacted repertoires of genes and regulatory elements. Through long-read sequencing, we provide a comprehensive Epstein Barr virus (EBV) transcriptome analysis, identifying 1453 transcript isoforms and resolving the major isoform of all but one lytic reading frame. Further, we categorize each transcript according to their dependence on viral DNA replication. We show that the late gene viral preinitiation complex, vPIC also activates early promoters/genes, we identify active alternate promoters with distinct dependencies on viral DNA replication, we discover biphasic promoters with embedded features of both early and late promoters. Genetic and chromatin interaction studies identify an enhancer function …

Distinct Echinocandin Responses Of Candida Albicans And Candida Auris Cell Walls Revealed By Solid-State Nmr, Malitha C. Dickwella Widanage, Kalpana Singh, Jizhou Li, Jayasubba Reddy Yarava, Faith J. Scott, Yifan Xu, Neil A.R. Gow, Frederic Mentink-Vigier, Ping Wang, Frederic Lamoth, Tuo Wang

School of Graduate Studies Faculty Publications

Invasive candidiasis affects 1.6 million people annually, with high mortality among immunocompromised and hospitalized patients. Echinocandins are frontline antifungals, but rising resistance limits their efficacy. Here, we show that Candida albicans and multidrug-resistant Candida auris share a conserved cell wall architecture yet differ markedly in their adaptive responses to echinocandins. Solid-state NMR reveals that both species possess a rigid inner layer of tightly associated chitin microfibrils and β−1,3-glucans, supported by a flexible matrix of β−1,6-glucans and additional β−1,3-glucans. Outer mannan fibrils rely on α−1,2-linked sidechains to maintain contact with the inner wall. In both species, caspofungin rigidifies β−1,6-glucans and mannan …

Polymorphic Α-Glucans As Structural Scaffolds In Cryptococcus Cell Walls For Chitin, Capsule, And Melanin: Insights From 13c And 1h Solid-State Nmr, Ankur Ankur, Jayasubba Reddy Yarava, Isha Gautam, Faith J. Scott, Frederic Mentink-Vigier, Christine Chrissian, Li Xie, Dibakar Roy, Ruth E. Stark, Tamara L. Doering, Ping Wang, Tuo Wang

School of Graduate Studies Faculty Publications

Cryptococcus species are major fungal pathogens responsible for life-threatening infections in approximately a million individuals globally each year, with alarmingly high mortality rates. These fungi are distinguished by a distinctive cell wall architecture further reinforced by two virulence-associated layers, melanin and capsule, rendering them insensitive to antifungal agents targeting the cell wall, such as echinocandins. The molecular interplay between these three biomolecular layers remains poorly understood. Here we employ solid-state NMR spectroscopy to examine intact cells of both wild-type and capsule-deficient strains of C. neoformans, along with melanized cells. High-resolution 13C and 1H data revealed five distinct structural forms of …

Use Of High-Throughput Phenomics With And Without Fungicide As A Wheat Breeding Tool, Gerardo Ivan Rivera Collazo

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Wheat (Triticum aestivum) is an important food staple for many countries around the world and current consumption and production data demonstrate a production deficit. Breeders are challenged to help close this gap in production by selecting better cultivars with improved yields. Several methods aim to accelerate the breeding process to reduce the time required for releasing an elite variety. One of the main breeding bottlenecks is the lack of fast and reliable phenotypic data acquisition that could dissect physiological and morphological plant data. High-throughput remote sensing could have the potential to reduce this bottleneck by streamlining data acquisition, …

Chemical And Physical Characterization Of Verbenaceae Essential Oils Using Modern Analytical Methods And Chemometrics, Aleksandra N. Hilliard

Master's Theses

Essential oils have been used for generations to treat various health issues, including mitigating insomnia, reducing stress, inflammation, and preserving foods, to mention a few. Essential oils have complex chemistry, which defines the essence of the host plant. Recently, increased commercial uses of essential oils have prompted attention at the governmental level to monitor the chemical, physical, or biological activity of essential oils. This study is an attempt to add new information for consumers to the understanding of the composition of essential oils.

Modern analytical techniques including FTIR-ATR, GC-MS, LC-MS-MS, multivariate analysis statistics, and physio-chemical techniques (electrochemistry, DPPH, TRC, and …

Abdominal Tuberculosis In Children, Melike Emiroglu, Gulsum Alkan, Meltem Kiymaz, Sadiye Kubra Tuter Oz, Hatice Turk Dagi, Mehmet Öztürk, Zeliha Esin Çelik

Journal of Pediatric Infectious Diseases

Objective: To provide an insight into the presentation, diagnosis and management of gastrointestinal tuberculosis in children.

Methods: We reviewed the medical records of children who were diagnosed with gastrointestinal tuberculosis, between October 2013 and October 2023. The analysis was performed using descriptive statistics.

Results: During the study period, 11 of 76 tuberculosis pediatric patients (14.5%) were diagnosed with gastrointestinal tuberculosis. Six of 11 patients (54.5%) were female. The median age of the patients was 60 months (51-205 months). Eight of 11 patients had intra-abdominal lymph node involvement, 3 of 11 patients had intestinal tuberculosis and 2 of 11 patients had …

Evaluation Of Pediatric Patients Diagnosed With Measles: A Retrospective Study In Istanbul, Zehra Yazi, Nahide Haykir Zehi̇r, Merve Akçay, Ufuk Yükselmiş, Ceren Çetin, Ayşe Karaaslan, Yasemin Akin

Journal of Pediatric Infectious Diseases

Objective: Measles, predominantly impacting the pediatric population, manifests symptoms encompassing fever, rash, rhinorrhea, cough, conjunctivitis, accompanied by infrequent yet plausible life-threatening complications.

Methods: This retrospective study conducted between January 2022 and July 2023 at a 1105-bed tertiary hospital in Istanbul, Türkiye, was focused on children diagnosed with measles and aged(PCR) were defined as definite measles cases.

Results: A total of 78 pediatric patients were diagnosed with measles, of whom 40 were evaluated as definite (51.3%) cases. Among the definite cases, 29 (72.5%) and 11 (27.5%) were girls and boys, respectively. Their median age was 78 (42–158) months. It was observed …

The Multifunctional Ascorbate Peroxidase Moapx1 Secreted By Magnaporthe Oryzae Mediates The Suppression Of Rice Immunity, Muxing Liu, Ziqian Guo, Jiexiong Hu, Yuke Chen, Fang Chen, Weizhong Chen, Wenya Wang, Boyang Ye, Zhixiang Yang, Gang Li, Xinyu Liu, Haifeng Zhang, Ping Wang, Zhengguang Zhang

School of Graduate Studies Faculty Publications

Fungi secrete effector proteins, including extracellular redox enzymes, to inhibit host immunity. Redox enzymes have been hypothesized to inhibit host reactive oxygen species (ROS); however, how they suppress host immunity remains unknown. We characterized an extracellular ascorbate peroxidase (MoApx1) that is secreted into rice chloroplasts by the rice blast fungus Magnaporthe oryzae. MoApx1 displays multifunctional capabilities that significantly contribute to fungal virulence. Firstly, MoApx1 neutralizes host-derived H2O2 within the chloroplast through its peroxidase activity, thereby inhibiting chloroplast ROS (cROS)-mediated defense responses. Secondly, MoApx1 targets the photosystem I subunit OsPsaD, disrupting photosynthetic electron transport to further suppress cROS production. Most importantly, …

Overcoming Vaccine-Associated Enhanced Respiratory Disease In Swine Flu With Lipid Nanoparticle-Dna Technology, The Nguyen

School of Veterinary and Biomedical Sciences: Dissertations, Theses, and Student Research

The two primary challenges in developing vaccines against swine influenza A virus (IAV-S) are the continuous viral evolution and vaccine-associated enhanced respiratory disease (VAERD). Current vaccine strategies share a common limitation: the significant time required for licensing updated vaccines. Moreover, the strain selection for vaccine updates depends entirely on predictions, raising the risk that chosen strains may not match circulating viruses. Such mismatches not only reduce vaccine efficacy but also risk exacerbating disease severity through VAERD. Here, in this thesis, we developed and evaluated a novel DNA-based vaccine platform designed to address the need for rapid updates in response to …

Field Journal: The Excluded Middle, Carrie E. Kouts

Masters Theses

What does it look like to engage with organisms and landscapes at the periphery of anthropocentric value structures? How does one break the internalized myth that the “built” environment is excluded from the natural world? When does a hyper-mobile and hyper-commodified society confront the exponential crisis of animal death? Within this series of journal entries, field notes, collection observations, weird prose, and sensory musings, one will find questions on the nature of being human and the complex narratives of care we encounter in a world shared with more-than-humans. Each handwritten vignette and photograph from daily life weaves a non-linear and …

Addressing Socioeconomic Disparities In The Treatment Of Antimicrobial-Resistant Infections: The Role Of Pharmacists In Mitigating Barriers, Arin Wade, Danielle Egbujor, Anna Spalvieri, Owen Fox, Marisa Petrunich, Joshua Honaker, Samantha Mccord, Kasie Landin

Pharmacy and Wellness Review

Antimicrobial resistance is an escalating global threat driven by inappropriate antibiotic use and shaped by socioeconomic disparities. Social determinants of health, including limited healthcare access, poverty, low health literacy, and environmental conditions, contribute to higher rates of resistant infections and poorer treatment outcomes in underserved populations. Barriers such as pharmacy deserts, self-medication, and inadequate stewardship infrastructure amplify these risks. Pharmacists, as accessible and highly trained healthcare professionals, play a critical role in combating antimicrobial resistance by optimizing antibiotic use, delivering culturally competent education, and leading antimicrobial stewardship programs across settings. Community and clinical pharmacists are especially well positioned to bridge …

A Retrospective Study Of Pulmonary Function Tests In Bronchiectasis: An Infectious Disease Of The Respiratory System, Vinod Mutkule, Mahesh Shinde, Vidya Bapmare, Sangramsingh Dixit, Atharva Sharma, Kshitij Sarwey, Yogeshwari Patil, Sanket Jethlia, Aayushi Dwivedi, Disha Pardeshi, Anmol Rai, Kunal Shah, Vidhi Kalwar

The University of Louisville Journal of Respiratory Infections

Introduction: Bronchiectasis, currently being recognized worldwide, is an abnormal dilatation of the bronchi and bronchioles brought on by recurrent cycles of inflammation and airway infection. Impaired pulmonary function has a predictive significance in bronchiectasis. When treating patients with suspected or confirmed respiratory diseases, pulmonary function tests (PFT) are useful examinations. Very few studies have been done on PFTs in bronchiectasis. The main aim of this study is to study PFTs in bronchiectasis.

Method: This is a retrospective observational study done on 50 patients over two years at the tertiary care center. The previous records of patients were collected from the …

Exploring The Landscape Of Animal Advocacy In Egypt: Insights Into Stray, Wildlife, And Farmed Animal Rights, Yara Moussa, Wasseem Emam

General - Animal Protection

This article examines the landscape of animal advocacy in Egypt, a nascent and growing field in one of Africa’s largest economies and most densely populated countries. It focuses on three types of animal advocacy: 1) stray animal welfare, 2) wildlife conservation, and 3) farmed animal welfare. The paper critically analyses current practices and trends in each of these areas, highlighting the main challenges and opportunities facing the growth of the movement. Our research draws on insights from interviews with active animal welfare organizations, situating their practical experiences, daily operational struggles, as well as instances of success, within Egypt’s wider socio-economic …

A Modified Sir Model Used To Investigate The Relationship Between Congenital And Adult Syphilis, Kaleesta R. Waysman

Honors Thesis

A complex SIR model integrating the relationship between adult and congenital syphilis was developed. The goal of the project was to determine the specific population(s) or control strategies that should be enforced, altered, or removed to decrease the number of children experiencing clinical sequelae due to congenital syphilis. Early clinical sequelae include hydrops fetalis, preterm birth, central nervous system infection, hepatosplenomegaly, hyperbilirubinemia, cholestasis, hemolytic anemia, snuffles, osteochondritis, and lesions or rashes in the palms and soles. Late clinical sequelae include interstitial keratitis, hearing loss, Hutchinson teeth, saber shins, Clutton joints, mulberry molars, and saddle nose. After implementing real-world data into …

A Fatal Triad: Concurrent Pulmonary Infections With Candida, Mucorales, And Aspergillus In An Immunocompromised Patient With Underlying Vasculitis And Diabetes, Paridhi Ghai, Kavitha Gopalratnam

Posters

We present a case of disseminated fungal disease involving simultaneous infections with Candida, Mucorales, and Aspergillus.

Justification For The Biological Foundation Of Methane On Mars: Methanogens’ Capacity To Metabolize On Montmorillonite Clay And Basalt, Ashley Ezeldin

Biological Sciences Undergraduate Honors Theses

The possibility of extraterrestrial life, particularly on Mars, remains a compelling question in astrobiology. Mars' harsh atmospheric conditions, dominated by carbon dioxide and extreme cold, prevent the survival of aerobic species. However, it still leaves the possibility of methanogens, an anaerobic species that can survive in extreme conditions, to inhabit this planet. Due to the discovery of methane on Mars, it is possible that methanogens may live and grow in the subsurface of this planet.

For this experiment, basalt and montmorillonite clay were chosen as substrates because they are believed to be found in the composition of Mars's subsurface. Methane, …

Personalizing Intermittent Fasting: The Role Of Microbiome Diversity And Fiber Intake In Shaping Health Outcomes, Jana Gjini, Robin Moore, Venkateswar Venkataraman

Rowan-Virtua Research Day

BACKGROUND: Intermittent fasting (IF) has been linked to improved metabolic health, reduced inflammation, and increased longevity in animal models. These effects are thought to be mediated through changes in the gut microbiome. Murine studies consistently show that IF enhances microbial diversity and promotes beneficial species like Lactobacillus and Bifidobacterium, improving metabolic profiles and gut barrier function. However, human studies reveal inconsistent results, suggesting that individual-level factors such as baseline microbiome composition and fiber intake may influence response to IF.

HYPOTHESIS: Baseline gut microbiome diversity and habitual dietary fiber intake modulate the metabolic and inflammatory benefits of intermittent fasting in humans. …

Exploring The Role Of Lysine Acetylation During Biofilm Formation In Bacillus Subtilis, Jennifer Nguyen, Briana Ericka Reid, Valerie Carabetta

Rowan-Virtua Research Day

Biofilms are structured communities of bacterial cells encased in a self-produced extracellular matrix, composed of polysaccharides, extracellular DNA, and proteins. Bacteria in a biofilm pose significant challenges in healthcare due to their resistance to disinfectants and tolerance to antibiotics. In some species, histone-like proteins were found to be important structural components of the biofilm. Nε-Lysine acetylation is a widespread post-translational modification (PTM) in bacteria, which can alter a protein’s function. The histone-like protein HBsu in Bacillus subtilis is acetylated at seven sites in vivo. We hypothesized that the acetylation state of HBsu may alter biofilm structure or the genetic programming, …

Acetylcholine Release In The Dorsal Lateral Straitum During Social Approach Task, Taylor Good, Oyku Dinckol, Noah Wenger, Jake Caselli, Munir Gunes Kutlu

Rowan-Virtua Research Day

Nicotine Decreases ACh Release in the DS leading to a Serenic Effect during Social Approach Task

Acetylcholine (ACh) regulates attention, learning, and stress responses (Benarroch E. E., 2012). The dorsal striatum (DS), essential for stimulus-response learning, is also linked to anxiety and compulsivity (Casado-Sainz et al., 2021). We used behavioral pharmacology and in vivo fiber photometry to study ACh responses during social approach tasks in the dorsal striatum. Male and female C57BL/6J mice underwent stereotaxic surgeries to inject a fluorescent ACh sensor (ACh.Sn.Fr) and implant fiber optic cannulas in the DS. Using in vivo fiber photometry, we tracked ACh release …

Implications Of Type Iv Pilus Retraction For Dna Uptake By Acinetobacter Baumannii, Yafan Yu

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Horizontal gene transfer (HGT) via natural competence allows bacteria to incorporate extracellular DNA (eDNA) into their genomes, facilitating genetic diversity and adaptation. In Acinetobacter species, natural competence depends on DNA binding and uptake mediated by type IV pili (T4P). T4P are dynamic extracellular filaments composed primarily of the major pilin subunit PilA, along with a few minor subunits. T4P drive a range of cellular functions including twitching motility, biofilm formation, and DNA uptake, with some functions dependent on pilus retraction and others not. However, how Acinetobacter T4P bind DNA and how T4P/eDNA interactions impact biofilm formation remain unclear. Here, I …