Organisms Commons^™

Development Of A Novel Ex Vivo Equine Corneal Model, Todd L. Marlo, Elizabeth A. Giuliano, Ajay Sharma, Rajiv R. Mohan

Pharmacy Faculty Articles and Research

Objective

To develop an ex vivo equine corneal organ culture model. Specifically, to assess the equine cornea's extracellular matrix and cellularity after 7 days using two different culture techniques: either (i) immersion system or (ii) air/liquid interface system, to determine the best ex vivo equine corneal model.

Animals Studied

Fourteen healthy equine corneas of various breeds.

Procedures

Equine corneas with 2 mm of perilimbal sclera were freshly harvested from 7 horses undergoing humane euthanasia. One corneal–scleral ring (CSR) from each horse was randomly placed in the (i) immersion condition organ culture system (IC), with the contralateral CSR being placed in …

Ciliate Codon Translator Program Manual, Quentin D. Altemose

Mathematics Summer Fellows

Understanding the evolutionary history of organisms allows us to better comprehend selective pressures and their effects on larger populations. In our study, we focused on analyzing the DNA of ciliate groups, which are single celled protozoans characterized by the presence of cilia on their outer membrane. We utilized the DNA of the organisms to analyze the changes in population genotype over time. We tested existing evolutionary models (designed to represent natural genetic variation over time in populations) against our data to identify the model with the best fit and likelihood. From the DNA and the evolutionary model with the highest …

The Confounding Effects Of Particle Size And Substrate Bulk Density On Phanerochaete Chrysosporium Pretreatment On Panicum Virgatum, Amanda N. Hickman, Sue E. Nokes, William S. Sympson, Mathew J. Ruwaya, Michael D. Montross, Barbara L. Knutson

Biosystems and Agricultural Engineering Faculty Publications

Phanerochaete chrysosporium treatment is less effective as a biological pretreatment on feedstock with larger particle sizes. We hypothesized that the improved effectiveness of the pretreatment when smaller particle sizes are used may be due to the inherently higher bulk density with smaller particle sizes. The effects of substrate bulk density and particle size on the efficacy of P. chrysosporium pretreatment of switchgrass (Panicum virgatum) was tested experimentally. Phanerochaete chrysosporium was grown on senesced switchgrass (2 different particle sizes) with various bulk densities. In all treatments, the fungal-pretreated samples released more glucose during enzymatic saccharification than the control sample. …

Assessment Of A Mycorrhizal Fungi Application To Treat Stormwater In An Urban Bioswale, Alaina Diane Melville

Dissertations and Theses

This study assessed the effect of an application of mycorrhizal fungi to stormwater filter media on urban bioswale soil and stormwater in an infiltration-based bioswale aged 20 years with established vegetation. The study tested the use of commercially available general purpose biotic soil blend PermaMatrix^® BSP Foundation as a treatment to enhance Earthlite^™ stormwater filter media amelioration of zinc, copper, and phosphorus in an ecologically engineered structure designed to collect and infiltrate urban stormwater runoff before it entered the nearby Willamette River.

These results show that the application of PermaMatrix^® BSP Foundation biotic soil amendment to Earthlite …

Gram-Negative Bacteria And Sepsis, Christine D. Ridge

Nursing Student Class Projects (Formerly MSN)

Today’s medical world encompasses an environment in which gram-negative bacteria that once were defeated with common antibiotics, have now become resistant. Gram-negative bacteria like Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterobacter, and Acinetobacter are pathogens that are an emerging threat causing sepsis due to multidrug-resistance (Pop-Vicas & Opal, 2014, p.189). The multidrug-resistance mechanisms of gram-negative bacteria coupled with a patient population commonly seen in hospital settings, that consist of immunocompromised adults due to advancing age, comorbidities (e.g. AIDS, history of transplants, diabetes, and chemotherapy), and immunotherapies, create an environment for advanced infection or sepsis to take place.

Complications of multidrug-resistant gram-negative bacteria …

Investigating The Origin And Functions Of A Novel Small Rna In Escherichia Coli, Fenil Rashmin Kacharia

Dissertations and Theses

Non-coding small RNAs (sRNAs) regulate various cellular processes in bacteria. They bind to a chaperone protein Hfq for stability and regulate gene expression by base-pairing with target mRNAs. Although the importance of sRNAs in bacteria has been well established, the mode of origination of novel sRNA genes is still elusive, mainly because the rapid rate of evolution of sRNAs obscures their original sources. To overcome this impediment, we identified a recently formed sRNA (EcsR2) in E. coli, and show that it evolved from a degraded bacteriophage gene. Our analyses also revealed that young sRNAs such as EcsR2 are expressed …

Genetic Analysis Reveals A Hierarchy Of Interactions Between Polycystin-Encoding Genes And Genes Controlling Cilia Function During Left-Right Determination, Daniel T. Grimes, Jennifer L. Keynton, Maria T. Buenavista, Xingjian Jin, Saloni H. Patel, Shinohara Kyosuke, Jennifer Vibert, Debbie J. Williams, Hiroshi Hamada, Rohana Hussain, Surya M. Nauli, Dominic P. Norris

Pharmacy Faculty Articles and Research

During mammalian development, left-right (L-R) asymmetry is established by a cilia-driven leftward fluid flow within a midline embryonic cavity called the node. This ‘nodal flow’ is detected by peripherally-located crown cells that each assemble a primary cilium which contain the putative Ca²⁺ channel PKD2. The interaction of flow and crown cell cilia promotes left side-specific expression of Nodal in the lateral plate mesoderm (LPM). Whilst the PKD2-interacting protein PKD1L1 has also been implicated in L-R patterning, the underlying mechanism by which flow is detected and the genetic relationship between Polycystin function and asymmetric gene expression remains unknown. Here, we …

A Pan-Dengue Virus Reverse Transcription-Insulated Isothermal Pcr Assay Intended For Point-Of-Need Diagnosis Of Dengue Virus Infection By Use Of The Pockit Nucleic Acid Analyzer, Yun Young Go, R. P. V. Jayanthe Rajapakse, Senanayake A. M. Kularatne, Pei-Yu Alison Lee, Keun Bon Ku, Sangwoo Nam, Pin-Hsing Chou, Yun-Long Tsai, Yu-Lun Liu, Hsiao-Fen Grace Chang, Hwa-Tang Thomas Wang, Udeni B. R. Balasuriya

Maxwell H. Gluck Equine Research Center Faculty Publications

Dengue virus (DENV) infection is considered a major public health problem in developing tropical countries where the virus is endemic and continues to cause major disease outbreaks every year. Here, we describe the development of a novel, inexpensive, and user-friendly diagnostic assay based on a reverse transcription-insulated isothermal PCR (RT-iiPCR) method for the detection of all four serotypes of DENV in clinical samples. The diagnostic performance of the newly established pan-DENV RT-iiPCR assay targeting a conserved 3′ untranslated region of the viral genome was evaluated. The limit of detection with a 95% confidence was estimated to be 10 copies of …

Assessment Of Daf-19 Related Behavioral Defects, Loraina A. Stinson

Lawrence University Honors Projects

The daf-19 gene encodes the only RFX transcription factors in C. elegans, producing at least four related protein isoforms, one of which, DAF-19C, is responsible for ciliogenesis. Previous work by Senti and Swoboda (2008) demonstrated that adult worms deficient in all four DAF-19 proteins have extremely aberrant dwelling and roaming behavior on bacterial food. Most intriguingly, the addition of cDNA encoding the DAF-19C isoform restores cilia formation, but does not fully restore wild-type dwelling and roaming behavior. We are suggesting that additional neuron functions are needed to properly execute behaviors and these neuron functions require the activity of other …

Impact Of Emergency Department Sepsis Policy, Lynette Rayman

Evidence-Based Practice Project Reports

Sepsis is a serious concern of key healthcare stakeholders due to high incidence, mortality, and cost. The objectives of this evidence-based project were to 1) identify potential sepsis patients early during the emergency department (ED) triage process and 2) implement Sepsis Order Sets. Kotter’s change model and the Stetler model of evidence-based practice guided this project. An extensive literature search was undertaken to find best practice evidence regarding care of sepsis patients. Recommended care includes a protocolized format utilizing a screening tool and point of care lactate levels for early identification of sepsis, and early treatment with antibiotics and fluid …

Characterization Of Bacterial Pathogens Involved In Aerobic Vaginitis: Prevalence, Strain Characterization And Sequelae, Leslie A. Lafferty

Graduate School of Biomedical Sciences Theses and Dissertations

Aerobic vaginitis (AV) is a more recently defined infection that involves aerobic pathogenic bacteria that replace the normal flora of the vaginal tract. It is commonly mistaken for other vaginal infections, such as bacterial vaginosis (BV), because they share many common symptoms. AV leads to complications during pregnancy, such as premature delivery and amnion infection, and is diagnosed by indications that range from vaginal discharge to inflammation. Because this infection is difficult to diagnose differentially from other vaginal infections, it is important to determine what pathogens are involved in AV so that we may have the ability to detect them. …

Redesigning Gfp Reporter System For Utilization In Clostridium Difficile, Laura E. Fitzgerald

Biological Sciences Undergraduate Honors Theses

Clostridium difficile (C. difficile) is a gram-positive bacterium that comprises part of the healthy human gut microbiome. When it gains sufficient access to peptides, C. difficile flourishes and releases tissue-damaging toxins, which cause inflammation of the colon that can develop into a Clostridium difficile Infection (CDI).¹⁰ The Ivey Laboratory believes that the best tactic in preventing CDIs is stopping peptide ingestion, which theoretically could be accomplished by manipulating the oligopeptide permease (App) system.⁷ In order to verify that altering the App system would successfully impede peptide uptake, first the expression of the app Promoter Region ( …

Stabilization Of Gp120 Outer Domain For Hiv-1-1 Vaccine Immunogen Design, Duoyi Hu

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

The sole envelope glycoprotein spike on the surface of Human Immunodeficiency Virus (HIV-1) is composed of two subunits: gp120 and gp41. The gp120 consists of three domains: the inner domain, outer domain and bridging sheet, to which the viral primary receptor CD4 binds and induces a conformational change in gp120 to expose the co-receptor binding site. Previous studies have found that the outer domain of gp120 is relatively more stable than the inner domain and bridging sheet. When superimposed, the co-crystal structures of CD4-gp120 complex and VRC01-gp120 complex revealed that the CD4-binding site (CD4-BS) antibody VRC01 actually mainly bound to …

A Preliminary Study On The Role Of Enhancer Of Flavonoid Production (Efp) In Flavonoid Biosynthesis, Jia Guo

Honors Scholar Theses

Flavonoids are involved in a variety of biological roles ranging from pathogen protection, pigment intensity, antioxidant effects, and even prevention from cancer or cardiovascular diseases. Because of the diverse and beneficial functions that flavonoids have, the flavonoid biosynthetic pathway has been well studied. Recently, a gene called the Enhancer of Flavonoid Production (EFP) was discovered when mutations in this gene caused the Japanese morning glory flowers to exhibit a pale-colored phenotype. Although EFP is known to increase flavonoid production, the direct mechanism to how EFP enhances enzymes in the flavonoid biosynthetic pathway has yet to be discovered. It …

Programming Heart Disease: Does Poor Maternal Nutrition Alter Expression Of Cardiac Markers Of Proliferation, Hypertrophy, And Fibrosis In Offspring?, Cathy Chun

Honors Scholar Theses

Maternal malnutrition can affect fetal organogenesis, metabolic processes, and factors involved in developmental regulation. Of the many physiological effects poor maternal nutrition can induce in offspring, one of the most important organs affected is the heart. Cardiovascular disease has been associated with poor maternal diet. It also been suggested that hypertension can originate during impaired intrauterine growth and development. Hypertension can trigger hypertensive heart disease and is associated with numerous heart complications. We hypothesized that poor maternal nutrition would alter critical growth factors associated with normal heart development, specifically, insulin-like growth factor (IGF)-1, IGF-2, transforming growth factor (TGF)β, and connective …

Assessment Of The Zoonotic Potential Of A Novel Bovine Influenza Virus, Laura Evelyn Eckard

Theses and Dissertations (ETD)

A novel orthomyxovirus was recently identified from pigs, with subsequent work suggesting the natural reservoir being bovine populations. The virus had genome characteristics most similar to influenza C viruses (ICV) but, due to the extent of sequence divergence, was proposed as a new genus, influenza D virus (IDV). Current literature on IDV has largely focused on the agricultural significance of the virus and provided evidence for the agricultural impact via observation of widespread prevalence and pathology in laboratory infected cattle. However, only one study, which identified 1.3% seroprevalence in a small cohort, has addressed the zoonotic potential of IDV to …

The Roles Of Malt1 In Nf-Κb Activation And Solid Tumor Progression, Deng Pan

Dissertations and Theses (Open Access)

The transcription factor NF-κB plays a central role in many aspects of biological processes and diseases, such as inflammation and cancer. Although it has been suggested thatNF-κB is critical in tumorigenesis and tumor progression, the molecular mechanism by which NF-κB is activated in solid tumor remains largely unknown. In the current work, we focus on growth factor receptor-induced NF-κB activation and tumor progression, including epidermal growth factor receptor (EGFR)-induced NF-κB in lung cancer and heregulin receptor (HER2)-induced NF-κB in breast cancer. We found that Mucosa-associated lymphoma translocation protein 1 (MALT1), also known as paracaspase, is required for EGFR-induced NF-κB activation …

Peptidomimetic Small Molecules Disrupt Type Iv Secretion System Activity In Diverse Bacterial Pathogens, Carrie L. Shaffer, James A.D. Good, Santosh Kumar, K. Syam Krishnan, Jennifer A. Gaddy, John T. Loh, Joseph Chappell, Fredrik Almqvist, Timothy L. Cover, Maria Hadjifrangiskou

Pharmaceutical Sciences Faculty Publications

Bacteria utilize complex type IV secretion systems (T4SSs) to translocate diverse effector proteins or DNA into target cells. Despite the importance of T4SSs in bacterial pathogenesis, the mechanism by which these translocation machineries deliver cargo across the bacterial envelope remains poorly understood, and very few studies have investigated the use of synthetic molecules to disrupt T4SS-mediated transport. Here, we describe two synthetic small molecules (C10 and KSK85) that disrupt T4SS-dependent processes in multiple bacterial pathogens. Helicobacter pylori exploits a pilus appendage associated with the cag T4SS to inject an oncogenic effector protein (CagA) and peptidoglycan into gastric epithelial cells. In …

Geodemographic Features Of Human Blastomycosis In Eastern Wisconsin, Megan E. Huber, Dennis J. Baumgardner, Jessica J. F. Kram, Melissa A. Lemke

Journal of Patient-Centered Research and Reviews

Purpose

Blastomycosis is an endemic fungal infection. In rural northern Wisconsin, blastomycosis cases are associated with certain environmental features including close proximity to waterways. Other studies have associated blastomycosis with particular soil chemicals. However, blastomycosis also occurs in urban and suburban regions. We explored the geodemographic associations of blastomycosis cases in the more urban/suburban landscape of eastern Wisconsin.

Methods

We conducted a retrospective study of 193 laboratory-identified blastomycosis cases in a single eastern Wisconsin health system, 2007–2015. Controls were 250 randomly selected cases of community-diagnosed pneumonia from a similar time period. Geographic features of home addresses were explored using Google …

Antibacterial Derivatives Of Marine Algae: An Overview Of Pharmacological Mechanisms And Applications, Emer Shannon, Nissreen Abu-Ghannam

Articles

The marine environment is home to a taxonomically diverse ecosystem. Organisms such as algae, molluscs, sponges, corals, and tunicates have evolved to survive the high concentrations of infectious and surface-fouling bacteria that are indigenous to ocean waters. Both macroalgae (seaweeds) and microalgae (diatoms) contain pharmacologically active compounds such as phlorotannins, fatty acids, polysaccharides, peptides, and terpenes which combat bacterial invasion. The resistance of pathogenic bacteria to existing antibiotics has become a global epidemic. Marine algae derivatives have shown promise as candidates in novel, antibacterial drug discovery. The efficacy of these compounds, their mechanism of action, applications as antibiotics, disinfectants, and …

Antifungal Activity Of Essential Oils On Aspergillus Parasiticus Isolated From Peanuts, Mina M. Yooussef, Quyen Pham, Premila Achar, Marikunte Yanjarappa Sreenivasa

Faculty Articles

Aspergillus parasiticus is one of the most common fungi which contaminates peanuts by destroying peanut shells before they are harvested and the fungus produces aflatoxins. The aim of this study was to evaluate the antifungal activities of seventeen essential oils on the growth of the aflatoxigenic form of A. parasiticus in contaminated peanuts from commercial outlets in Georgia. The agar dilution method was used to test the antifungal activity of essential oils against this form of A. parasiticus at various concentrations: 500; 1,000; 1,500; 2,000; 2,500 ppm. Among the seventeen essential oils tested, the antifungal effect of cinnamon, lemongrass, clove …

Blastomyces: Why Be Dimorphic?, Dennis J. Baumgardner

Journal of Patient-Centered Research and Reviews

In introducing the infectious disease focus for this edition of the Journal of Patient-Centered Research and Reviews, the author describes the unsolved mysteries surrounding the dimorphic fungus Blastomyces and the related pathogenesis of pulmonary blastomycosis.

Epidemiology Crucial To Cracking Elizabethkingia Crisis, Angela Tonozzi

Journal of Patient-Centered Research and Reviews

The author explains the epidemiological methods, tools and personnel required to pinpoint the source of Wisconsin’s 2016 outbreak of Elizabethkingia infections.

Bacteriophages: The Answer To Antibiotic Resistance?, Allie Casto, Adam Hurwitz, Kunny Kou, Gregory Mansour, Allison Mayzel, Rachel Policke, Alexander Schmidt, Rowan Shartel, Olivia Smith, Augustus Snyder, Allison Woolf

James Madison Undergraduate Research Journal (JMURJ)

Bacteriophages, viruses that infect bacteria, have numerous applications in the medical, agricultural, and research fields, especially as an alternative to antibiotics in the age of antibiotic resistance. Phages are able to lyse, or break apart, bacterial cells with fewer side effects, more specificity, and less likelihood of resistance than antibiotics. The acceptance of phages in medicine and agriculture around the world today is not universal, and the United States Food and Drug Administration (FDA) has been slow to recognize phage therapy as a legitimate treatment. However, the successful use of phages in the past, as well as promising trial results …

Non-Essentiality Of Alr And Muri Genes In Mycobacteria, Philion L. Hoff, Denise Zinniel, Raúl G. Barletta

UCARE: Research Products

Amino acids are the building blocks of life. If DNA is the blueprint, amino acids are the lumber that proteins are built with. Proteins are built with left-handed, L- forms of amino acids. Bacteria have an essential cell wall component that happens to be an exception: peptidoglycan. Bacteria have enzymes called racemases that convert L- amino acid forms into right-handed, D- forms. Amino acids participate in many reactions with keto acids. Transaminases allow conversion between amino acids by transfer of an amino group.

Previous reports claimed there is no D-ala transaminase activity in mycobacteria and thus alr and murI genes …

The Effect Of Nitrate On The Release Of Glucose Into The Hemolymph Of Crayfish, Procambarus Clarkii, Alec R. Flores, Lee Kats, David Green, Gary Bucciarelli

Seaver College Research And Scholarly Achievement Symposium

Pollutants can change the behaviors of invertebrate stream animals. The level of one common pollutant, nitrate (NO3), has been rising in many local rivers and streams throughout the United States due to increases in anthropogenic sources. Nitrate, heavily regulated for its toxic effects to human health, namely the aiding in the development of cancer, also dangerously affects aquatic species by converting oxygen-carrying pigments to forms that are incapable of carrying oxygen. To understand the stress effects of ambient nitrate exposure on P. clarkii, we collected hemolymph samples from red swamp crayfish (Procambarus clarkii) over a 48-hour period after exposure to …

An Analysis Of Bacterial Contamination Of Chicken Eggs And Antimicrobial Resistance, Holly Spitzer

All College Thesis Program, 2016-2019

Chicken eggs are a major component of American diets, with an average yearly consumption of approximately 250 eggs per person (American Humane Society). While highly nutritious, eggs are also one of the leading causes of food poisoning and food borne illness in the United States. Eggs may become contaminated by a number of different types of bacteria during production, including Salmonella, a group of bacteria that, according to the CDC, causes more than 1.2 million cases of food borne illness in the United States every year. In an effort to decrease the frequency of bacterial contamination, many food producers …

Three-Year Survey Of Abundance, Prevalence And Genetic Diversity Of Chlorovirus Populations In A Small Urban Lake, Cristian F. Quispe, Olivia Sonderman, Anya Seng, Brenna Rasmussen, Garrett Weber, Claire Mueller, David Dunigan, James L. Van Etten

James Van Etten Publications

Inland water environments cover about 2.5 percent of our planet and harbor huge numbers of known and still unknown microorganisms. In this report, we examined water samples for the abundance, prevalence, and genetic diversity of a group of infectious viruses (chloroviruses) that infect symbiotic chlorella-like green algae. Samples were collected on a weekly basis for a period of 24 to 36 months from a recreational freshwater lake in Lincoln, Nebraska, and assayed for infectious viruses by plaque assay. The numbers of infectious virus particles were both host- and site-dependent. The consistent fluctuations in numbers of viruses suggest their impact as …

No Nonsense: The Protection Of Wild-Type Mrnas From Nonsense-Mediated Mrna Decay In Saccharomyces Cerevisiae, Krista D. Patefield

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

Gene regulation in eukaryotes is tightly controlled at multiple levels to ensure proper expression and cellular homeostasis. Misregulation of gene expression is a common source of genetic disease. One mechanism by which cells are able to control gene expression is through the synthesis and degradation of the mRNA molecules encoding the genes. The transcription and degradation of mRNA molecules controls the pool mRNAs that are available to the translational machinery. One of the well-studied mRNA decay pathways is the Nonsense-Mediated mRNA Decay pathway (NMD). Originally, NMD was discovered as a posttranscriptional mRNA surveillance mechanism responsible for the deadenylation-independent decapping and …

Localized Jnk Signaling Regulates Organ Size During Development., Helen Rankin Willsey, Xiaoyan Zheng, José Carlos Pastor-Pareja, A Jeremy Willsey, Philip A Beachy, Tian Xu

Anatomy and Regenerative Biology Faculty Publications

A fundamental question of biology is what determines organ size. Despite demonstrations that factors within organs determine their sizes, intrinsic size control mechanisms remain elusive. Here we show that Drosophila wing size is regulated by JNK signaling during development. JNK is active in a stripe along the center of developing wings, and modulating JNK signaling within this stripe changes organ size. This JNK stripe influences proliferation in a non-canonical, Jun-independent manner by inhibiting the Hippo pathway. Localized JNK activity is established by Hedgehog signaling, where Ci elevates dTRAF1 expression. As the dTRAF1 homolog, TRAF4, is amplified in numerous cancers, these …