Biology Commons^™

Ecological Researcher, Alex Demmers

Celebration of Learning

This is my field research I complete during the summer of 2018.

Snake Fungal Disease In Lake Eerie Water Snakes And Its Affect On Attitude And Behavior During Treatment, Kelcie Fredrickson

Celebration of Learning

Snake fungal disease (SFD) is caused by the fungus Ophidiomyces ophiodiicola. Infection occurs when the outer skin is breached, and the organism enters the epidermis. The epidermis becomes necrotic and produces a yellow/brown crust. When the crust breaks off, ulcerations/lesions are formed along the snake’s body, head and tail. It has been found that SFD can be treated with a terbinafine nebulization treatment. Ellen Haynes, a PhD student, created a study in which 26 Lake Eerie water snakes are separated into treatment and control groups to determine the effectiveness of the nebulization treatment. Through daily observations, this research aimed …

Effects Of Single And Integrated Water, Sanitation, Handwashing, And Nutrition Interventions On Child Soil-Transmitted Helminth And Giardia Infections: A Cluster-Randomized Controlled Trial In Rural Kenya, Amy J. Pickering, Sammy M. Njenga, Lauren Steinbaum, Jenna Swarthout, Audrie Lin, Benjamin F. Arnold, Christine P. Stewart, Holly N. Dentz, Maryanne Mureithi, Benard Chieng, Marlene Wolfe, Ryan Mahoney, Jimmy Kihara, Kendra Byrd, Gouthami Rao, Theodora Meerkerk, Priscah Cheruiyot, Marina Papaiakovou, Nils Pilotte, Steven A. Williams, John M. Colford Jr., Clair Null

Biological Sciences: Faculty Publications

Helminth and protozoan infections affect more than 1 billion children globally. Improving water quality, sanitation, handwashing, and nutrition could be more sustainable control strategies for parasite infections than mass drug administration, while providing other quality of life benefits.

The Developmental And Behavioral Effects Of Δ9-Tetrahydrocannabinol On A Spastic Mutant, Victoria Mendiola

Master of Science in Integrative Biology Theses

Hyperekplexia is a neurological disorder affecting infants and can be characterized by excessive startle reactions in response to unexpected stimuli. This disease can be modeled in zebrafish in the bandoneon (beo) mutant, where the glrbbmutation results in glycine receptor (GLYR) loss of function glycine receptors and ultimately, improper inhibitory signaling. Though hyperekplexia is a glycinergic-based signaling disorder, disease symptoms are often alleviated with GABA-agonistic benzodiazepines. Exogenous cannabinoids also modulate GABAergic signaling, and THC, one of the natural compounds that prompted the discovery of the endocannabinoid system mimics the effects of endogenous cannabinoids at endocannabinoid and non-cannabinoid sites in the …

Development Of Real-Time Polymerase Chain Reaction (Q-Pcr) Assays For The Detection And Identification Of Drug-Resistance Genes In Carbapenem-Resistant Enterobacteriaceae (Cre), Richard A. Robison, Ph.D.

Journal of Undergraduate Research

I. The Specific aims for the project were as follows:

1. Develop q-PCR assays for the various carbapenem-resistance genes, such as KPC, IMP, VIM, and NDM-1, and then multiplex them into single assays that can be used to quickly characterize an isolate.

A Race Against Time: Deciphering Evolution And Describing New Species Of Threatened Tropical Stick Insects (Phasmatodea), Michael F. Whiting

Journal of Undergraduate Research

Funding was received in 2016 to support mentored research into the phylogeny and evolution of stick insects. Specific goals include providing students with scientific design experience, field-based research experience, collections-based experience, molecular lab experience, bioinformatics experience, and experience in presentation at national meetings and publication in peer reviewed journals. One particular focus was to describe new stick insect species, but it became clear very quickly that the phylogeny portion of this work was essential before any new species could be described, so we concentrated our efforts on stick insect phylogeny. The following is a brief summary of accomplishments.

Byu Undergraduates Solving The Genetic Causes Of Alzheimer’S Disease, John Kauwe

Journal of Undergraduate Research

Successful enrollment in and completion of graduate programs requires a constellation of skills. Students must be prepared to plan and execute experiments, present their findings both verbally and in manuscript form and interact effectively with senior scientists in the field of their choice. In this MEG I will mentor three undergraduate students (Sheradyn Hamilton, Kristen Cockriel, and Moroni Chalita) as they develop skills in study design, data analysis, manuscript preparation, presentation and networking while identifying genetic factors that protect individuals from Alzheimer’s disease.

T Cell Immunotherapy Of Infection Disease And Cancer, Scott Weber

Journal of Undergraduate Research

This project was focused on improving the immune response to infectious disease and cancer. We have engineered T cell receptors with 1000-fold increase in affinity and will characterize their value as diagnostics and therapeutics. In addition, we examined changes in T cell function due to the co-receptor CD5. We also examined how T cell responses to infection are dependent upon metabolic and epigenetic regulation.

Sex-Specific Personalities In The Purple Marsh Crab, Jillian Sterman, Jessica Barton, Panagiota Delmedico, Samantha Sweeney

DePaul Discoveries

Animals are considered to possess personalities when individuals differ in behavior, and these differences are consistent between situations. Several studies have identified personalities in diverse groups but less is known about personality variation between the sexes. In this study, we examined variation in two key personality traits (boldness, activity) in female and male purple marsh crabs (Sesarma reticulatum) using a semi-field approach. Specifically, we measured boldness and activity on two consecutive days using the same behavioral assays during each time point. Consistency (personality) was determined using Kendall’s coefficient of concordance based on Spearman correlation coefficients for each behavior. …

Behavioral Responses To Gold Nanoparticle Exposure And H2o2-Induced Oxidative Stress In Caenorhabditis Elegans, Rachel Pride, Ashley Wagner

DePaul Discoveries

Gold nanoparticles (AuNPs) have been utilized in many biomedical disciplines, most notably cancer therapy and drug delivery. Recent research suggests that with specific peptide manipulation, AuNPs can deliver drugs across the blood-brain barrier (BBB), allowing for treatment of neurodegeneration and other neurological afflictions. Neurodegeneration has been shown to be caused by oxidative stress. The present experiment aimed to assess the effects of AuNPs on C. elegans behavior that had undergone H₂O₂-induced oxidative stress. It was predicted that worms exposed to both H₂O₂ and AuNPs would have higher survival, mechanosensation, and thrashing rates than …

Effects Of Reduced Ph On Health Biomarkers Of The Seagrass Cymodocea Nodosa, Regan A. Mcenaney

DePaul Discoveries

Ocean acidification is a growing problem that may affect many marine organisms in the future. Within 100 years the pH of the ocean is predicted to decrease to 7.8, from the current ocean pH of around 8.1. Using phenolic acid levels as a stress indicator as well as respiration and chlorophyll content as a measure of health, the effect of lowering pH was tested on the seagrass, Cymodocea nodosa, in a controlled environment. Plant samples, water, and soil were taken from the Bay of Cádiz, Spain, and placed in aquaria in a temperature-controlled room. One control group was left …

On The Composistion Of Cymodocea Nodosa Root Exudate Under Artificial Blue, Green And Natural Light Conditions, Armand Martin, Ben Manriquez, Christian Pompa, Aaron Saper, Kyle A. Grice, Jason Bystriansky

DePaul Discoveries

Seagrasses are identified as a sentinel species: a good indicator of overall marine ecosystem health and function. At the rhizome, they are known to interact with marine bacteria by exchanging energy in the form of glucose and free amino acids secreted through root exudate in exchange for microbe-fixated nitrogen that can be utilized for plant growth. To analyze potential outcomes of possible future changes in light availability, an experiment was designed to collect and analyze the root exudate of Cymodocea nodosa under three light conditions (standard fluorescent light, blue LED, and green LED light). After 72 hours of treatment, the …

Increasing The Accuracy Of Molecular Biomarkers Via Evidence-Based Algorithm Selection, Stephen R. Piccolo

Journal of Undergraduate Research

In making medical decisions, physicians need observable criteria that they can use to make accurate diagnoses, determine optimal treatments, and estimate a patient’s prognosis. The promise of precision medicine is that molecular-level observations can more accurately predict such information than traditional observations. I worked with undergraduate students at Brigham Young University to develop ways to improve the accuracy of such predictions by optimizing computer algorithms to handle the complexity of large, molecular data sets.

Guided Evolution To Expand The Host Range In Phages, Jamison Walker, Sandra Hope

Journal of Undergraduate Research

My project proposal included the use of Darwin’s theory of evolution by natural selection to determine if genetic mutations will arise in Bacteriophages that would allow them to infect related strains in a species of bacteria. Bacteriophages naturally have a target host range that they can infect. Within species of bacteria, the phage has tail receptors that allow it to infect specific strains. The other strains of the bacteria will be unaffected by the phage. In phage therapy, multiple phages with varied host ranges are chosen to combat this problem. Some phages are more effective than others in killing a …

Determining The Role Of Cd5 In Regulatory T Cell Function, Charles Teames, Scott Weber

Journal of Undergraduate Research

Regulatory T cells (Tregs) inhibit the immune response and play a key role in preventing autoimmunity. Unfortunately, Tregs also often prevent an effective immunological response against cancer. CD5 is a T cell surface protein known to regulate the threshold for T cell activation. CD5 is known to influence Treg development, but it is unclear exactly how CD5 impacts the function of Tregs.

Past studies have indicated that mice lacking CD5, known as CD5 knockouts, produce more Tregs than wild type mice (1). It is thought that Tregs from these CD5 knockouts may be more effective in preventing T cells from …

Chemokine Receptor Ccbp2-V41a And Its Role In Inflammation And Alzheimer’S Disease, Allen Weinert, Scott Weber

Journal of Undergraduate Research

The leading cause of dementia in elderly patients is Alzheimer’s disease (AD), a degenerating and fatal neurodegenerative condition. AD is a proteopathic disease caused by extensive accumulation of amyloid beta plaques and neurofibrillary tangles. A recent genomewide association study analyzing 59 AD-associated cerebrospinal fluid (CSF) samples statistically associated chemokine receptor mutant CCBP2-V41A with increased CSF protein levels of the proinflammatory chemokine CCL2. CCBP2 is a known binding partner of CCL2. We hypothesized that CCBP2-V41A receptor alters CSF levels of CCL2 and that raised CCL2 levels alters immune cell function, resulting in amyloid beta deposition in the brain (Figure 1).

Combating Obesity Through Gut Microbiome Targeted Bacteriophage Therapy, Gongze Zhao, Dr. Laura Bridgewater

Journal of Undergraduate Research

The human gut consists of approximately 1.5 kg of bacteria, and 50% of the biomass in our fecal matter is bacterial cells (Nicholson, 2005). Diet is a major factor in shaping the composition of the gut microbiota, (Zhang, 2010) which in turn influences the body by producing metabolites that enter the circulation through different pathways. In 2013, by using Koch’s postulates, scientists were able to demonstrate that the gram-negative opportunistic pathogen E. cloacae B29 can cause obesity and chronic inflammation in its host (Fei & Zhao, 2013). Bacteriophage (phage) are viruses that infect bacteria. Phages bind to their bacterial host …

Herbivory And Inbreeding Affect Growth, Reproduction, And Resistance In The Rhizomatous Offshoots Of Solanum Carolinense (Solanaceae), Chad T. Nihranz, Rebecca L. Kolstrom, Rupesh R. Kariyat, Mark C. Mescher, Consuelo M. De Moraes, Andrew G. Stephenson

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Resource sharing within clonal plant networks can occur via the translocation of water, nutrients, and photoassimilates through rhizomes and stolons. Similar mechanisms may mediate the sharing of information (e.g., about herbivory or other environmental stressors) among ramets via molecular or biochemical signals. The storage of such information in belowground structures could facilitate the transmission of appropriate phenotypic responses across growing seasons in perennial species. However, few previous studies have explored the potential transfer of ecologically relevant information within such networks. This study addresses the effects of foliar herbivory and belowground overwintering on the growth and flowering, physical defenses, and herbivore …

Linking Nutrient Stoichiometry To Zika Virus Transmission In A Mosquito, Andrew S. Paige, Shawna K. Bellamy, Barry W. Alto, Catherine L. Dean, Donald A. Yee

Faculty Publications

Food quality and quantity serve as the basis for cycling of key chemical elements in trophic interactions; yet the role of nutrient stoichiometry in shaping host–pathogen interactions is under appreciated. Most of the emergent mosquito-borne viruses affecting human health are transmitted by mosquitoes that inhabit container systems during their immature stages, where allochthonous input of detritus serves as the basal nutrients. Quantity and type of detritus (animal and plant) were manipulated in microcosms containing newly hatched Aedes aegypti mosquito larvae. Adult mosquitoes derived from these microcosms were allowed to ingest Zika virus-infected blood and then tested for disseminated infection, transmission, …

Tk1 As A Biomarker Of Chemosensitivity And Metastatic Potential In Breast Tumors, Eric Olsen, Kim O'Neill

Journal of Undergraduate Research

Breast cancer is the most common form of cancer in women, accounting for 23% of total cancer cases and 14% of cancer deaths. Breast carcinoma is not a simple disease. It is comprised of many different biological forms with distinct phenotypes and prognoses. Hormone receptor expression, such as ER, PR, and HER2, along with more universal clinical manifestations like pathological stage, grade, and lymph node invasion are often used for patient prognosis. The heterogeneous nature of breast tumors makes prognosis and response to therapies difficult to determine, and further research is needed to classify breast tumors and their response to …

Damselfies Of Vanuatu, Madison Lallatin, Seth Bybee

Journal of Undergraduate Research

Vanuatu is a string of active volcanic islands in Micronesia near Fiji and Australia. The islands undergo regular submersion and emersion from the ocean, and the most recent emergence was 2 million years ago (Hamilton et al. 2010). As a result, all organisms on the islands of Vanuatu have migrated there, likely from other islands, within the past 2 million years. Fiji is one likely candidate for contributing species, being geographically close to Vanuatu and exhibiting similar species. Fourteen of us went to Vanuatu for 6 weeks on a study abroad led by Dr. Seth Bybee to collect and observe …

Quantifying Predictive Value Of Biological Data Types In Machine Learning Models Of Cancer Outcome, Samantha Jensen, Stephen Piccolo

Journal of Undergraduate Research

Precision medicine is a growing movement toward utilizing molecular diagnostics to guide medical decisions. It is particularly useful when applied to cancer treatment, as knowing details about cancer stage, genetic pathology, and tumor type can inform life-saving decisions. Increasingly, physicians may use genetic, proteomic, epigenetic, and expression data to determine treatment strategy and even choose specific chemotherapy drugs1.

Using Remote Video Systems To Measure Effectiveness Of Small Scale Mpas In Saipipi, Samoa, Calvin Quigley, Dr. Richard Gill

Journal of Undergraduate Research

Coral reefs represent an invaluable natural, providing $30 billion dollars of fishing and recreational profits worldwide, and housing nearly a quarter of the oceans species [1, 2]. However, threats such as climate change, ocean acidification, coastal development and overharvesting have destroyed more than a fifth of the worlds coral reefs in recent decades[3]. One of the most common management plans that has been implemented to help protect and restore coral reefs is the establishment of marine protected areas (MPAs)[4]. MPAs have been proven to be effective in helping restore fish populations and coral cover, however the majority of MPAs are …

Effectiveness Of Hospital Disinfectants Against Clostridium Spores, Bejamin Ogilvie, Richard Robinson

Journal of Undergraduate Research

Clostridium is a genus of anaerobic spore-forming bacteria notable for causing human infections. C. difficile has an especially high impact, affecting roughly 453,000 individuals in the U.S. in 2011 (1). C. tetani and C. perfringens infections occur much less frequently, although they remain clinically important. Disinfecting objects contaminated with Clostridium is challenging, as Clostridium spores are resistant to extreme temperature, desiccation, and most chemicals (2, 3). Clostridium is also frequently found within soil, making it a likely contaminant on almost any piece of medical equipment (3).

Currently, the U.S. EPA only requires sporicidal disinfectant efficacy tests against C. sporogenes, a …

Could Tk1 Suppress The Immune System And Promote Tumor Development?, Joshua Keller, Roman Kovtun, Kim O'Neill

Journal of Undergraduate Research

Cancer is a widespread disease that affects millions of people worldwide and in many cases is difficult to treat. In order to find new and better treatment, it is important to understand how this disease progresses. Thymidine Kinase 1 (TK1) is a recognized biomarker that is upregulated in cancer cells compared to healthy tissue. Although this protein is normally found inside the cells (cytosol), it becomes upregulated on the surface of malignant cells. Moreover, recent research shows that TK1 expression is further upregulated in breast cancer tissues that undergo a transition from stationary (epithelial) cells to more mobile (mesenchymal) cells. …

Cd5 Deficient Mice Exhibit Altered Cognitive Function In Behavioral Studies, Tyler Cox, Dr. Scott Weber

Journal of Undergraduate Research

The immune system plays a role in protecting and maintaining the central nervous system (CNS). 1Dysfunctions within the immune system can affect the CNS and it is associated with diseases such as Multiple Sclerosis, Alzheimer’s and Parkinson’s disease. Having an imbalanced activation of immune cells within CNS results in cognitive impairments. CD5 is a protein on the surface of T cells and certain B cells that inhibits cellular activation and prevents immune cells from reacting too strongly to antigens and causing autoimmunity to our own tissues. Modulating CD5 and the immune system could affect the CNS and cognitive function. Observations …

Characterization Of Mutant Chemokine (C-C) Motif Receptor-Like 2 (Ccrl2) And Its Role In Inflammation And Alzheimer’S Disease, Meganne Ferrel, Dr. John S. K. Kauwe

Journal of Undergraduate Research

Alzheimer’s Disease (AD) is identified as a proteopathic disease that results from an extensive accumulation of amyloid plaques and neurofibrillary tangles in the brain. Several researchers have discovered that cerebrospinal fluid (CSF) contains biomarkers for AD such as Amyloid-beta and tau. Neuritic plaques in AD are surrounded by activated microglia and astrocytes which can initiate complement and inflammation in the presence of amyloid-beta. Macrophage inflammatory protein chemokine (C-C motif) ligand 4 (CCL4) is a biomarker found in CSF. A high level of expression is associated with risk of developing AD. CCL4 is expressed in a subpopulation of reactive astrocytes and …

Histone Post-Translational Modifications And Nucleosome Positioning: A New Layer In The Histone Code Hypothesis?, Andrew Earl, Dr. Steven Johnson

Journal of Undergraduate Research

Nucleosomes are the fundamental unit of chromatin organization. They consist of an octamer of histone proteins (two of each H2A, H2B, H3, and H4) wrapped around by 147 base pairs of DNA. Their positioning and occupancy around important genetic elements such as enhancers and promoters are some of the most important means of epigenetic regulation: changes in expression of genes that reflect a change in something other than DNA sequence. For example, highly-expressed genes are generally associated with low nucleosome occupancy, whereas inactive genes are associated with high nucleosome occupancy. It has also been shown that the positioning of nucleosomes …

Discovery And Characterization Of Bacteriophage Luckybarnes, Savannah L. Underwood, Amanda Foto, Amanda F. Ray, Alexander E. Nelms, Keyshawn L. Kennedy, Shelby G. Hartley, Logan M. Ryals, Chandan Gurung, William A. D'Angelo, Welkin H. Pope, Dmitri V. Mavrodi

Faculty Publications

Here, we report the genome sequence of LuckyBarnes, a newly isolated singleton siphovirus that infects Brevibacterium iodinum ATCC 15728 and has a 50,774-bp genome with 67 predicted genes.

Functional Characterization Of The Ovarian Tumor Domain Deubiquitinating Enzyme 6b, Jasmin M. D'Andrea

USF Tampa Graduate Theses and Dissertations

The posttranslational modification ubiquitination is major regulatory mechanism used throughout cell signaling pathways such as cell cycle regulation and the DNA damage response. As such, the E3 ligases and their deubiquitinating enzyme counterparts, which conjugate and deconjugate ubiquitin to and from protein substrates respectively, must be tightly regulated to prevent aberrant cellular behaviors that could lead to diseases such as cancer.

Of the five families of deubiquitinating enzymes, the Ovarian Tumor Domain (OTU) family is fairly unique and under-studied; many of its family members hold a linkage specificity to certain ubiquitin chains and a number of them have been implicated …