Organisms Commons^™

The Physiological Significance Of Nitric Oxide Synthase In Staphylococci, Ryan M. Singh

Theses & Dissertations

Staphylococci, particularly Staphylococcus epidermidis, are common causes of implant-associated infections that may result in notable morbidity and mortality. One of the ways the innate immune system attempts to combat these invading pathogens is via the respiratory burst, in which free radical species such as nitric oxide (NO^•), toxic to bacterial respiration, are released in large quantities. Despite the toxicity of NO^•, some bacteria, including staphylococci, encode an endogenous bacterial nitric oxide synthase (bNOS), whose physiological role has been unclear until now. In this dissertation, we demonstrate that S. epidermidis is able to overcome the toxicity …

Rosarugosides A And D From Osa Rugosa Flower Buds: Their Potential Anti-Skin-Aging Effects Intnf-Α-Induced Human Dermal Fibroblasts, Kang Sub Kim, So-Ri Son, Yea Jung Choi, Yejin Kim, Si-Young Ahn, Dae Sik Jang, Sullim Lee

Faculty, Staff and Student Publications

This present study investigated the anti-skin-aging properties of Rosa rugosa. Initially, phenolic compounds were isolated from a hot water extract of Rosa rugosa's flower buds. Through repeated chromatography (column chromatography, MPLC, and prep HPLC), we identified nine phenolic compounds (1-9), including a previously undescribed depside, rosarugoside D (1). The chemical structure of 1 was elucidated via NMR, HR-MS, UV, and hydrolysis. Next, in order to identify bioactive compounds that are effective against TNF-α-induced NHDF cells, we measured intracellular ROS production in samples treated with each of the isolated compounds (1- …

Utilizing Biomimicry To Design Sustainable Architecture, Virginia Hammond

Architecture Undergraduate Honors Theses

Nature has an integral relationship with architecture and serves as a sustainable role model and inspiration for designers. The process of biomimicry in architecture has the potential to produce more sustainable design solutions and foster a connection between humans and nature. Existing biomimetic design projects have varying strengths and weaknesses as examples of the process. Utilizing guidelines and references from key leaders in biomimetic design consultancy (Biomimicry 3.8), selected case studies are assessed for their ability to demonstrate the benefits of this design strategy. Using these evaluations, the case studies are diagrammed and critiqued to determine how new projects could …

Analysis Of Antibiotic Sensitivity Patterns In Pasteurellaceae Family Isolates: A Microbial And Molecular Investigation, Jillian Barron

Honors Scholar Theses

Bacteria in the Pasteurellaceae family are known to cause disease in both human and animal species. Like all species of bacteria, the pathogens in the Pasteurellaceae family evolve and acquire antimicrobial-resistant traits. Antimicrobial resistance of bacteria is a significant public health concern, as treatment of resistant pathogens becomes more difficult, if not impossible, with current medical capabilities. In this project, phenotypic and genotypic analyses were performed on Pasteurellaceae family isolates sourced from the Connecticut Veterinary Medical Diagnostic Laboratory. Phenotypic antibiotic sensitivity patterns of each isolate were assessed against a panel of antibiotics through a Kirby-Bauer disk diffusion test. Disk diffusion …

A Meta-Analysis For Laboratory Diagnostics For Coccidioidomycosis, Mary C. Cowen

Biological Sciences Undergraduate Honors Theses

Coccidioidomycosis, commonly referred to as Valley Fever, is a fungal infection found in arid regions of the southwestern United States and Mexico. Infection occurs through inhalation of airborne spores from Coccidioides species, Coccidioides immitis and/or Coccidioides posadasii, and proceeds in both pulmonary and disseminated fashions. Approximately 60% of patients with coccidioidomycosis remain asymptomatic, while 40% will experience symptoms. Within the literature, there are no papers that summarize sensitivity and specificity values between different tests; therefore, this paper presents sensitivity and specificity results across different tests and companies (Meridian, IMMY, and MiraVista).

Perinatal Buprenorphine Effects On Offspring Growth, Opioid Withdrawal, And Brain Morphology In Rats, Parker Barnes

Electronic Theses and Dissertations

Opioid use disorder (OUD) impacts 5.6 million people in the US. Buprenorphine (BUP) is a commonly prescribed opioid medication used to treat OUD, including in pregnant women. However, opioid use during pregnancy is associated with poorer infant outcomes including reduced fetal growth, neurodevelopmental deficits, and neonatal opioid withdrawal syndrome (NOWS). Recent clinical data suggests that providing mothers with a lower dose of BUP may result in fewer negative outcomes in infants. Here, a preclinical rodent model of low-dose perinatal BUP exposure was used to study offspring health outcomes in the neonate, juvenile, and adolescent offspring. Dams were given clinically relevant …

Effect Of Source Of Trace Minerals On Nutrient Digestibility And Rumen Fermentation Of Dairy Cows, Cesar Velasquez Rios

All Theses

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Evaluating The Importance Of Biosecurity In Swine Operations, Lindsey Lemley, Lilly Rogers, Austin Calhoun

ATU Scholars Symposium

Swine health is critical to maintaining a profitable and productive swine operation. Biosecurity and sanitation are important practices that help maintain herd health. This study aimed to discover how biosecurity protocols and management practices differ between swine operations of different sizes. With diseases such as Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), Brucellosis, and Porcine Circovirus type 2 (PCV2) being common in the swine industry, a strong biosecurity protocol protects swine farmers from financial losses associated with disease outbreaks. In 2004 alone, the estimated financial loss to PRRSV was over $761 million. Data concerning biosecurity and sanitation was collected from …

Screening Environmental Soil Samples For Antibiotic Production, Paige Mattick

SACAD: Scholarly Activities

Antibiotic resistance is a detrimental worldwide challenge, producing bacterial infections that are progressively more difficult to treat and cure. To attempt to help alleviate this issue, we screened soil samples for the presence of antibiotic-producing microorganisms. Soil samples were collected and diluted to 1:100 and 1:1000 ratios of soil and distilled water. These soil mixtures were then streaked onto tryptic soy agar (TSA) plates and incubated at 30℃ until colonies developed. These colonies were then selected and plated on a lawn of Serratia marcescens, which was utilized as the target organism.

Serratia marcescens was selected due to its known resistance …

An Ecological Analysis Of The Elevational Gradient Effect On Mushroom Community Diversity Near Andasibe, Madagascar, Zoe Garver

Independent Study Project (ISP) Collection

The effect of elevational gradients on biodiversity has been widely studied in the field of ecology (Rahbek, 1995). The evidence supports a trend for highest biodiversity at mid latitudes and decreasing biodiversity as elevation increases (Rahbek, 1997; Grytnes, 2003; Hariharan and Buckley, 2022). This effect has primarily been explained by variation of temperatures and resource availability at different elevations. However, the effect that elevation plays on fungal communities is relatively underrepresented in the literature (Dahlberg, 2001). This study analyzes changes in mushroom diversity across an elevational gradient in Mitsinjo Reserve and Analamazaotra National Park found in Madagascar. Using the Braun-Blanquet …

Mushroom Composition Across An Elevational Gradient During The 2024 Wet Season In Mazumbai Forest Reserve, Tanzania, Christopher Brady

Independent Study Project (ISP) Collection

Mushrooms are key bioindicators that contribute greatly to ecological health, and their diversity is indicative of a healthy ecosystem. However, even with the vital role they play in ecological health, there are few studies which measure the diversity of mushrooms in Mazumbai Forest Reserve (MFR), Tanzania, Africa, and none which focus on diversity along the elevational gradient within the reserve (1300-1900m). This study measures the diversity and equitability of mushrooms growing in six elevational zones within MFR during the rainy season of 2024. A species checklist of mushrooms growing in MFR during the 2024 rainy season was created, tracking the …

Single-Cell Analysis Of Age-Related Changes In Leukocytes Of Diabetic Mouse Hindpaws, James M Nichols, Hoang Vu Pham, Eric F Lee, Rajasekaran Mahalingam, Andrew J Shepherd

Faculty, Staff and Student Publications

Complications associated with Type 1 and Type 2 diabetes, such as diabetic peripheral neuropathy and diabetic foot ulcers, are a growing health-care concern. In addition, this concern increases as diabetic patients age due to their increased susceptibility to complications. To address this growing problem, it is important to understand fluctuations in physiology which lead to pathological changes associated with the metabolic disturbances of diabetes. Our study explores dysregulation of immune cell populations in the hindpaws of healthy and diabetic mice at 12 and 21 weeks of age using single-cell RNA sequencing to provide insight into immune disruptions occurring in the …

The Influence Of Incubation Temperature On Offspring Traits Varies Across Northern And Southern Populations Of The American Alligator (Alligator Mississippiensis), Christopher R Smaga, Samantha L Bock, Josiah M Johnson, Thomas Rainwater, Randeep Singh, Vincent Deem, Andrew Letter, Arnold Brunell, Benjamin B Parrott

Faculty, Staff and Student Publications

Maternal provisioning and the developmental environment are fundamental determinants of offspring traits, particularly in oviparous species. However, the extent to which embryonic responses to these factors differ across populations to drive phenotypic variation is not well understood. Here, we examine the contributions of maternal provisioning and incubation temperature to hatchling morphological and metabolic traits across four populations of the American alligator (Alligator mississippiensis), encompassing a large portion of the species' latitudinal range. Our results show that whereas the influence of egg mass is generally consistent across populations, responses to incubation temperature show population-level variation in several traits, including …

Tail-Tape-Fused Virion And Non-Virion Rna Polymerases Of A Thermophilic Virus With An Extremely Long Tail, Anastasiia Chaban, Leonid Minakhin, Ekaterina Goldobina, Brain Bae, Yue Hao, Sergei Borukhov, Leena Putzeys, Maarten Boon, Florian Kabinger, Rob Lavigne, Kira S Makarova, Eugene V Koonin, Satish K Nair, Shunsuke Tagami, Konstantin Severinov, Maria L Sokolova

Rowan-Virtua School of Osteopathic Medicine Departmental Research

Thermus thermophilus bacteriophage P23-45 encodes a giant 5,002-residue tail tape measure protein (TMP) that defines the length of its extraordinarily long tail. Here, we show that the N-terminal portion of P23-45 TMP is an unusual RNA polymerase (RNAP) homologous to cellular RNAPs. The TMP-fused virion RNAP transcribes pre-early phage genes, including a gene that encodes another, non-virion RNAP, that transcribes early and some middle phage genes. We report the crystal structures of both P23-45 RNAPs. The non-virion RNAP has a crab-claw-like architecture. By contrast, the virion RNAP adopts a unique flat structure without a clamp. Structure and sequence comparisons of …

Managing Stress: A Study Of Stress Response Mechanisms In Mycobacteria, Augusto C. Hunt Serracin

Biology Dissertations - Archive

Mycobacteria encompass many pathogenic species known to cause severe disease in humans. A well-known example is Mycobacterium tuberculosis (Mtb), the causative agent of the lung disease tuberculosis, which kills millions of humans worldwide yearly. Pathogenic mycobacteria like Mtb are challenging to treat because of their innate ability to adapt to environmental stress. Their unique cell physiology and conserved stress responses allow them to combat biological insults, regulate growth, and regulate genes involved in stress; all these responses increase tolerance to antibiotics. The current therapies to treat mycobacterial infections are lengthy and, at times, unsuccessful, partly due to antibiotic tolerance. A …

Spatial Analysis Of Socioeconomic Factors At Found Locations Of Orphaned Mammals In Champaign County, Illinois, Usa, Colleen Elzinga, Stephanie Heniff, William Sander, William Marshall Brown, Csaba Varga, Samantha Sander

Human–Wildlife Interactions

Young mammals make up a significant portion of animals brought into wildlife rehabilitation centers. Unfortunately, some of these presumed orphaned individuals are inappropriately removed from their native habitat. As such, there is a need for educational community outreach centered on the proper identification of orphaned wildlife that benefit from human intervention, while maximizing limited resources of rehabilitation facilities. This study evaluated found locations of common mammalian orphans presenting from Champaign County to the University of Illinois Wildlife Medical Clinic, Illinois, USA, between 2015 and 2020. The found locations of the orphans (99 Virginia opossums [Didelphis virginiana], 80 common …

Diel Vertical Migration Rates Of The Dinoflagellate Species Margalefidinium Polykrikoides In A Lower Chesapeake Bay Tributary, S. Clayton, Jacqueline B. Chrabot, Michael Echevarria, Leah Gibala-Smith, Kathryn Mogatas, Peter Bernhardt, Margaret R. Mulholland

OES Faculty Publications

Margalefidinium polykrikoides is a mixotrophic dinoflagellate harmful algal bloom (HAB) species that blooms annually in the lower Chesapeake Bay. M. polykrikoides undertakes a diel vertical migration (DVM) which may give it a competitive advantage over purely phototrophic organisms who cannot access deeper nutrient pools and allow it to form large toxic blooms. Laboratory-based estimates of M. polykrikoides’ DVM rates suggest that it is one of the fastest known dinoflagellate swimmers and understanding this behavior is likely important for modeling and predicting M. polykrikoides blooms. However, to date, no field-derived estimates of M. polykrikoides’ DVM rates have been made in the …

Exploration Of Potential Broad-Spectrum Antiviral Targets In The Enterovirus Replication Element: Identification Of Six Distinct 5' Cloverleaves, Morgan G. Daniels, Meagan E. Werner, Rockwell T. Li, Steven M. Pascal

Chemistry & Biochemistry Faculty Publications

Enterovirus genomic replication initiates at a predicted RNA cloverleaf (5′CL) at the 5′ end of the RNA genome. The 5′CL contains one stem (SA) and three stem-loops (SLB, SLC, SLD). Here, we present an analysis of 5′CL conservation and divergence for 209 human health-related serotypes from the enterovirus genus, including enterovirus and rhinovirus species. Phylogenetic analysis indicates six distinct 5′CL serotypes that only partially correlate with the species definition. Additional findings include that 5′CL sequence conservation is higher between the EV species than between the RV species, the 5′CL of EVA and EVB are nearly identical, and RVC has the …

Contributions Of The Replication Initiator Protein Dnaa To Physiology And Virulence Of The Lyme Disease Spirochete, Andrew Krusenstjerna

Theses and Dissertations--Microbiology, Immunology, and Molecular Genetics

Borrelia burgdorferi, the etiological agent of Lyme disease, is the most prevalent vector-borne disease in the United States. The spirochetal population is naturally maintained by consistently cycling between Ixodid ticks and small vertebrates. To survive within these diverse niches, B. burgdorferi has evolved a unique physiology and regulatory network to sense and respond to environmental fluxes. Replication is a hallmark of the Lyme spirochete’s enzootic life cycle, specifically at the nymphal tick-to-vertebrate interface. The mechanisms and regulatory schema for the basic cellular processes in B. burgdorferi, or indeed any member of the phylum spirochaetota, are largely unknown. The central hypothesis …

Genetic And Biochemical Analysis Of Novel Borrelia Burgdorferi Genes Bb0244 And Bb0246, Christian J. Ruiz-Rodriguez

Honors Undergraduate Theses

As the cause of the most common vector-borne disease in the US, Borrelia burgdorferi continues to affect an estimated hundreds of thousands of patients each year. The spirochete boasts one of the most complex genomes in comparison to all other prokaryotes as it is fragmented across up to 21 different replicons. Moreover, the functions of a majority of the encoded genes remain unknown. Gene of unknown function, bb0244, along with putative co-transcribed genes bb0245, and bb0246 are hypothesized to be involved in the vital functions of cell division and cell wall biogenesis. B. burgdorferi lacking bb0244 demonstrate a significant growth …

Harnessing Antagonistic Pleiotropy: Tolc-Dependent Coliphages Can Drive Reduced Antibiotic Resistance In E. Coli, Cooper Mckenna

CMC Senior Theses

The rise of multidrug-resistant (MDR) bacterial pathogens has been a growing concern in healthcare around the world, and bacteriophage (phage) therapy is a promising method to combat MDR infections. One defense mechanism of E. coli against antibiotics is the TolC-AcrAB efflux pump. At the same time, some phages use TolC as a surface receptor to infect the cell. This puts TolC at a crossroads in which it is beneficial to the bacteria to protect against antibiotics but harmful by allowing phage infection, creating the potential for evolutionary trade-offs. Previous research has identified only three TolC-dependent phages and shown phage-resistant E. …

Gut Dysbiosis Correlates With Covid-19 Severity, Ednita Escobar

CMC Senior Theses

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) impacts not only respiratory but also gut and oral microbiomes, influencing the manifestations of COVID-19. Each person’s unique microbiome consists of microorganisms such as bacteria, fungi, and viruses, some of which are symbiotic and others potentially harmful. Alterations in the gut microbiome, specifically, can affect the severity and symptoms of COVID-19. A review of studies indicate a pattern of gut dysbiosis in COVID-19 patients characterized by a decrease in beneficial microbiota and/or an increase in opportunistic pathogens. This gut imbalance correlates with disease severity, suggesting that the gut microbiome plays a significant role …

Tim/Tam Receptors: A Potential Biomarker For Predicting Sensitivity To Zika Virus-Induced Oncolysis In Non-Small Cell Lung Cancers, Shankari Somasekar

Honors Undergraduate Theses

Non-small cell lung cancers (NSCLC) constitute 80-85% of lung cancers and are the leading cause of cancer-related deaths globally. The most common cause is prolonged smoking. Current treatment options for NSCLC include surgery, radiation, chemotherapy, targeted drug therapy, and immunotherapy. Although these medications are effective in the short term, patients often face issues of drug resistance and debilitating side effects with prolonged use. Currently, the use of Zika virus (ZIKV) is being researched as a possible alternative treatment for cancer, which minimizes side effects and the risk of drug resistance. TIM/TAM proteins are identified as the putative ZIKV receptors on …

Invasion Of Superbugs: Cockroach-Driven Outbreak Of Multidrug-Resistant Enterobacter In An Icu, Jennifer Hanrahan, Nicholas Schouten, Steven H. Fyffe, Annette Jencson, Stephanie Stroever

Department of Medicine Faculty Publications

Objective: To describe factors in an outbreak of multidrug-resistant Enterobacter cloacae (MRE) in an intensive care unit (ICU) over a 20-month period including the likely contribution of cockroaches to the outbreak.

Design: This is a retrospective descriptive study.

Setting: ICU in an urban hospital.

Patients: All patients admitted to the ICU during the 20-month outbreak period were included in the study.

Interventions: Infection prevention interventions included contact isolation, hand hygiene, dedicated patient equipment, environmental cultures, and pest control.

Results: 25 patients were identified as being colonized or infected with MRE. Relatedness of the outbreak strain and strains found in cockroaches …

Reducing Food Scarcity: The Benefits Of Urban Farming, S.A. Claudell, Emilio Mejia

Journal of Nonprofit Innovation

Urban farming can enhance the lives of communities and help reduce food scarcity. This paper presents a conceptual prototype of an efficient urban farming community that can be scaled for a single apartment building or an entire community across all global geoeconomics regions, including densely populated cities and rural, developing towns and communities. When deployed in coordination with smart crop choices, local farm support, and efficient transportation then the result isn’t just sustainability, but also increasing fresh produce accessibility, optimizing nutritional value, eliminating the use of ‘forever chemicals’, reducing transportation costs, and fostering global environmental benefits.

Imagine Doris, who is …

Plants As Vectors For Environmental Prion Transmission, Christina M Carlson, Samuel Thomas, Matthew W Keating, Paulina Soto, Nicole M Gibbs, Haeyoon Chang, Jamie K Wiepz, Annabel G Austin, Jay R Schneider, Rodrigo Morales, Christopher J Johnson, Joel A Pedersen

Faculty, Staff and Student Publications

Prions cause fatal neurodegenerative diseases and exhibit remarkable durability, which engenders a wide array of potential exposure scenarios. In chronic wasting disease of deer, elk, moose, and reindeer and in scrapie of sheep and goats, prions are transmitted via environmental routes and the ability of plants to accumulate and subsequently transmit prions has been hypothesized, but not previously demonstrated. Here, we establish the ability of several crop and other plant species to take up prions via their roots and translocate them to above-ground tissues from various growth media including soils. We demonstrate that plants can accumulate prions in above-ground tissues …

Comparison Of Molecular Methods For Absolute Quantification Of Low-Abundant Bacterial Communities In Milk, Carmina Chavez, Janet E. Williams, Michelle K. Mcguire, Mark A. Mcguire

Undergraduate Research Symposium Posters

Milk was historically thought to be generally sterile. However, use of culture-dependent and culture-independent methods has provided strong evidence that milk has a microbiome (Figure 1). Culture-independent methods (e.g., high-throughput sequencing) have demonstrated the diversity of microbes in milk but provide relative abundance data. Culture-dependent methods have indicated microbial communities in milk are of low abundance, but it is challenging to measure absolute quantities accurately. Real-time quantitative polymerase chain reaction (RT-qPCR) has been used to quantify bacterial taxa in milk, However, concentrations often fall below the detection limit (Figure 2 & 3). Digital droplet PCR (ddPCR) allows detection of low-abundant …

The Developmental Process For Adenoviral Vectored Canine Influenza Vaccines, Nicholas Jeanjaquet

School of Biological Sciences: Dissertations, Theses, and Student Research

Canine Influenza Virus (CIV) is a recently emerged branch of Influenza A virus that is highly infectious in dogs. The first strain was isolated in 2003, and it has quickly become endemic in areas with dense dog populations, most notably in Asia. The proximity of dogs to humans, along with their potential to serve as mixing vessels for reassortment, raises concern for possible zoonotic transmission and a potential human pandemic. Available vaccines are not frequently updated and struggle to prevent the spread of currently circulating strains. This highlights the need for a new and more effective vaccine. We outline the …

How Megadrought Causes Extensive Mortality In A Deep-Rooted Shrub Species Normally Resistant To Drought-Induced Dieback: The Role Of A Biotic Mortality Agent, Natalie M. Aguirre, Marissa E. Ochoa, Helen I. Holmlund, Gabriella N. Palmeri, Emily R. Lancaster, Gina S. Gilderman, Shaquetta R. Taylor, Kaitlyn E. Sauer, Adriana J. Borges, Avery N.D. Lamb, Sarah B. Jacques, Frank W. Ewers, Stephen D. Davis

School of Medicine Faculty Publications

Southern California experienced unprecedented megadrought between 2012 and 2018. During this time, Malosma laurina, a chaparral species normally resilient to single-year intense drought, developed extensive mortality exceeding 60% throughout low-elevation coastal populations of the Santa Monica Mountains. We assessed the physiological mechanisms by which the advent of megadrought predisposed M. laurina to extensive shoot dieback and whole-plant death. We found that hydraulic conductance of stem xylem (Ks, native) was reduced seven to 11-fold in dieback adult and resprout branches, respectively. Staining of stem xylem vessels revealed that dieback plants experienced 68% solid-blockage, explaining the reduction in water transport. Following Koch's …

Urobiome Screening For Antimicrobial Peptides Against Uropathogenic Escherichia Coli, Jennifer Jones

ORBioM (Open Research BioSciences Meeting)

BACKGROUND: Urinary tract infections (UTIs) are one of the most common bacterial infections worldwide. As global incidences of UTIs caused by multidrug resistant bacteria continue to increase, so too does the demand for novel antimicrobial therapies.

Due to its relatively understudied nature, the urinary microbiome represents a niche with an untapped source of potentially novel antimicrobials (e.g., bacteriocins). Improvements to bacterial culturing and sequencing techniques have highlighted these potential alternative treatments and control strategies to target antibiotic resistant uropathogenic E. coli (UPEC).

METHODS: Expanded quantitative urine culture (EQUC) was used to culture bacterial isolates from mid-stream urine samples. Urinary isolates …