Microbiology Commons^™

Symbiotic Ucyn-A Strains Co-Occurred With El Niño, Relaxed Upwelling, And Varied Eukaryotes Over 10 Years Off Southern California, Colette Fletcher-Hoppe, Yi-Chun Yeh, Yubin Raut, J. L. Weissman, Jed A. Fuhrman

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Biological nitrogen fixation, the conversion of N₂ gas into a bioavailable form, is vital to sustaining marine primary production. Studies have shifted beyond traditionally studied tropical diazotrophs. Candidatus Atelocyanobacterium thalassa (or UCYN-A) has emerged as a focal point due to its streamlined metabolism, intimate partnership with a haptophyte host, and broad distribution. Here, we explore the environmental parameters that govern UCYN-A’s presence at the San Pedro Ocean Time-series (SPOT), its host specificity, and statistically significant interactions with non-host eukaryotes from 2008-2018. 16S and 18S rRNA gene sequences were amplified by “universal primers” from monthly samples and resolved into Amplicon …

Wildfires Disturb The Natural Skin Microbiota Of Terrestrial Salamanders, Lubna Mulla, Obed Hernandez-Gomez

Natural Sciences and Mathematics | Faculty Scholarship

Environmental change can disturb natural associations between wildlife and microbial symbionts, in many cases to the detriment of host health. We used a North American terrestrial salamander system to assess how the skin microbiota of amphibians responds to wildfires. In northern California's redwood/oak forests, we assessed how recent wildfires affected the skin microbiota of three different salamander species (Taricha sp., Batrachoseps attenuatus, and Ensatina eschscholtzii) over two different sampling seasons in 2018 and 2021. We found species-specific responses to wildfire disturbance on the alpha diversity of the skin microbiota of terrestrial salamanders, although burning in general altered the composition of …

Complete Genome Sequences Of 37 Bacteria From The Human Vaginal Tract, Christopher Whidbey, Alyssa N Konopaski, Robel Teshome, Sejal Dhaliwal, M Quinn Peters, Marlyd E Mejia, Mallory B Ballard, Kathryn A Patras

Faculty, Staff and Students Publications

Microorganisms colonizing the human vaginal mucosa are associated with healthy states, as well as conditions such as bacterial vaginosis and infection-associated preterm birth. Here, we report complete genome sequences of 37 bacterial isolates from the human vaginal tract.

Ebi2, Rodney Till, Dr. Brian Poole

Journal of Undergraduate Research

My project this year was a great learning experience and helped me to better understand the complexity of lab work, as well as, the tools used in troubleshooting problems; including collaboration with lab researchers and professors. I learned about flow cytometry and how to analyze migration data. I also learned how to do transfections with HEK cells and how to separate B cells from a fresh sample of blood. I was thankful that I could spend time doing lab work because it’s the best teaching environment I know of in academia. I came across genuine problems and studied topics with …

Examination Of The Role Of The Lana Protein In Persistence Of Kaposi’S Sarcoma-Associated Herpesvirus Infections, Marshall Sheide, Dr. Bradford Berges

Journal of Undergraduate Research

Kaposi’s sarcoma herpes virus (KSHV) is one of seven known cancer causing viruses which have the capacity to persist in the host for many years. This particular virus can undergo a long latent infection which ensures that the virus can hide by not expressing its genes. Last year, we proposed an experiment that would show the importance of a particular gene in the viral genome, LANA, in establishing a latent infection. The experiment required us to create stocks of a mutant virus that did not have the LANA gene inside (bac36deltaLANA) and then infect humanized mice with it. After infection, …

Search For Mitochondrial Dna Mutation In A Family With Myopathies And Lactic Acidosis, Mary Rennick, Dr. Brent Nielsen

Journal of Undergraduate Research

This research focused on the search for the probable mitochondrial DNA (mtDNA) mutation in one family affected with fibromyalgia and lactic acidosis. The hypothesis was that there is mixture of normal and mutated mtDNA, called heteroplasmy. I first obtained the four patients’ consent to participate in the study. The four patients were between the age of 19 and 25 years-­‐two males and two females. They donated urine samples to be used for DNA analysis. I isolated DNA using a Qiagen DNA extraction kit and obtained concentration measurements of 8-­‐ 10 nanograms per microliter using the nanodrop spectrophotometer in the RIC …

Antibody Production And Diversification In Humanized Mice, Stanton Nielsen, Dr. Brad Berges

Journal of Undergraduate Research

Many scientists are skeptical of using humanized mice to study the human adaptive immune response. The reasoning behind this skepticism stems from discrepancies in various studies seen previously. A study conducted by Traggiai et al. showed that humanized mice elicited a human adaptive immune response when challenged with the tetanus toxin (Traggiai). In addition, good antibody responses have been shown in humanized mice when challenged with Dengue virus (Kuruvilla). However, others have found only rare antibody responses to HIV when humanized mice were challenged (Baenziger). As mentioned earlier, a study conducted by Becker et al. showed the production of human …

Vitamin D3 As An Adjuvant To Produce Localized Immunity, Kaitlyn Vance, Dr. Eric Wilson

Journal of Undergraduate Research

The aim of our research was to help elucidate the degree of specificity employed by antibody secreting cells (lymphocytes) through a study of the role of CCR10 in the differential homing of these cells to mucosal issues. We used vitamin D3, known to upregulate expression of CCR10 on activated lymphocytes, as an adjuvant in our vaccines and tracked cell homing to mucosal tissues that express the CCR10 ligand CCL28 by detecting antigen specific antibody accumulation. Since mucosal tissues are ideal locations for vaccinations, the long-term aim was to develop a method for targeting antigen specific lymphocytes, and thus robust immune …

History Of Childhood Physical Abuse Is Associated With Gut Microbiota Diversity Among Adult Psychiatric Inpatients, Jessica C Rohr, Katelynn A Bourassa, Dominique S Thompson, J Christopher Fowler, B Christopher Frueh, Benjamin L Weinstein, Joseph Petrosino, Alok Madan

Faculty, Staff and Students Publications

BACKGROUND: Traumatic life events are associated with the development of psychiatric and chronic medical illnesses. This exploratory study examined the relationship between traumatic life events and the gut microbiota among adult psychiatric inpatients.

METHODS: 105 adult psychiatric inpatients provided clinical data and a single fecal sample shortly after admission. A modified version of the Stressful Life Events Screening Questionnaire was used to quantify history of traumatic life events. 16S rRNA gene sequencing was used to analyze the gut microbial community.

RESULTS: Gut microbiota diversity was not associated with overall trauma score or any of the three trauma factor scores. Upon …

Characterizing Proteins That Interact With Pas Kinase, Jordan Mackay, Dr. Julianne Grose

Journal of Undergraduate Research

Characterizing the interacting protein partners of Per-Arnt-Sim (PAS) kinase has proven to be a formidable task. Since the beginning of 2012, I have been working hard with graduate student Desi DeMille on confirming the putative interactors uncovered by genetic screening done the previous year. This endeavor has yielded both successes and failures.

How ‘Bout Them Apples?: A Study On Antioxidants, Kylie Measom, Dr. Kim O'Neill

Journal of Undergraduate Research

They say “an apple a day keeps the doctor away.” Apples are laden with antioxidants which have been shown to prevent against cancer and other illnesses.¹ Antioxidants are molecules that prevent cancer by collecting excess free radicals in the body. Free radicals are highly reactive molecules. They may interfere with DNA and other biomolecules leading to DNA damage and mutations. Antioxidants prevent this by scavenging for free radicals before they can interact with other important biomolecules.² Apples, particularly the skins, have high phenolic content. Phenols are antioxidants that protect against oxidative damage caused by free radicals.³ Different …

Ebi2 Knockdown And Effects On B-Cell Migration, Jordan Mabey, Dr. Brian Poole

Journal of Undergraduate Research

B cells are specialized cells which participate in the normal immune response to an infection. As B cells encounter antigens in the body, they become activated and travel to what is known as a B cell follicle within a lymph node. At the outer follicle B cells combine with T cells and move to the inner follicle to become specialized immunity participating cells. Normally upon reaching the outer follicle, the B cell up-regulates Epstein-Barr virus induced molecule-2 (EBI2) which causes it to pause until the cell can complex with the proper T cell. Once this connection between the two cells …

Assessing The Effects Of The Irf5 Exon 1b On Translation, Jared Lambert, Dr. Brian Poole

Journal of Undergraduate Research

With our lab’s previous finding revealing a hairpin folding structure in exon 1B (IRF5 risk allele), not found in the other first exons, this project was focused towards more fully understanding the role of IRF5 exon 1B’s hairpin structure and its effect on the translation of downstream proteins. The data acquired through this project will provide much needed information regarding the mechanism through which the risk allele of IRF5 affects the development of Systemic Lupus Erythmatosus (SLE).

Determining The Role Of Kaposi’S Sarcoma-Associated Herpesvirus Lana Protein In The Development Of Persistent Infection, Jamie Gardiner, Dr. Brad Berges

Journal of Undergraduate Research

Kaposi’s Sarcoma-associated Herpesvirus (KSHV) is a human cancer virus that causes Kaposis’ sarcoma, the most common cancer found in AIDS patients. Our lab is working to develop humanized mice as a novel animal model to study KSHV infection and related diseases, since there has previously been no animal model established. The purpose of my project was to determine the role of the viral protein LANA (latencyassociated nuclear antigen) in establishing a latent KSHV infection in humanized mice. My project included two major aims:

Understanding The Molecular Targets Of Antimicrobial Chemokines, Brittany Kartchner, Dr. Eric Wilson

Journal of Undergraduate Research

For this project, I hypothesized that the amino acid composition of the C terminus of chemokine proteins allows some chemokines to bind to different sites on the bacterial cell wall and that the chemokines with a strong positive charge (CCL25 and CCL28) will bind to the same target, while CCL27, which has no positively charged C terminus region, will have a different binding site. In order to study the binding properties of each chemokine, I began by performing binding assays. In these assays, approximately 105 colony-forming units of exponentially growing bacteria were incubated on ice with the appropriate chemokine. This …

Identifying Proteins That Interact With Human Pas Kinase, Tacie Hall, Dr. Julianne Grose

Journal of Undergraduate Research

When PAS kinase is knocked out in mice placed on high-fat diets, these mice show such symptoms as decreased weight gain, hypermetabolic phenotype, decreased liver triglyceride accumulation, and retained insulin sensitivity when compared with their wild type littermates.¹ These symptoms are highly associated with chronic diseases commonly seen in humans today, such as diabetes, obesity, and heart disease. PAS kinase is a highly conserved protein from yeast to man which allows for the use of yeast as model organism to help discover the molecular mechanisms behind PAS kinase function. Since little is known about how PAS kinase functions, it …

Accumulation Of Attached Chemokines On Gram-Negative Bacterial Membranes, Peter Janzen, Dr. Eric Wilson

Journal of Undergraduate Research

The purpose of this project was to see if a genetic alteration to gram-negative bacteria would affect the phenotypic ability to resist the attachment of chemokines. In other words, we were trying to see if we could change the structure of a bacterium by altering the DNA. As a result of that alteration, would our immune systems fight the infection more easily with a chemokines response.

Casting For A Putative Dna Binding Sequence For Nbmp2, Brian Earley, Dr. Laura Bridgewater

Journal of Undergraduate Research

Bmp2 is a secretory mammalian protein that plays important roles in bone development and adult pathology. Recently, a nuclear variant (nBmp2) was discovered with an unknown function for this typically secretory protein in the nucleus (Felin et al., 2010). The purpose of this project is to find an in vitro DNA binding sequence for nBmp2. This discovery would lead to further research for how nBmp2 could affect transcription in vivo. However, since the conception of this CASTing project 16 months ago, I have faced challenges in plasmid construction, cell culture, and concessions with a fused nBmp2:GFP plasmid. While the plasmid …

Ex Vivo Infection And Re‐Isolation Of Human Herpesvirus 6, Stephanie Carlson, Dr. Bradford Berges

Journal of Undergraduate Research

Science rarely cooperates as anticipated, but that can often lead to unexpected insight and solution. I ran into that this semester with a certain aspect of our project. We are continuing to collect data for the American Society for Virology in late July and a future publication. We will need more replicates for a publication, but we have optimized our approach and protocol.

Genomic And Proteomic Analysis Of An Erwinia Amylovora Phage, Alicia Brighton, Dr. Julianne Grose

Journal of Undergraduate Research

Fireblight is a disease, caused by the bacteria Erwinia amylovora, that can infect some fruit trees, including apple and pear trees. When an infection occurs, the effects can be devastating—any infected part of the tree must be removed and destroyed, sometimes resulting in loss of the entire tree. Furthermore, in the warm and moist conditions typical of springtime, the spread of fireblight can be nearly impossible to control with current management methods.¹

The Heat Shock Response, Heat Tolerance, And Drosophila Melanogaster Nora Virus, Blase Rokusek

Biology Theses, Dissertations, and Student Creative Activity

The heat shock response (HSR) is highly conserved across the animal kingdom and is characterized by the activation of heat shock factors (HSF) and the subsequent induction of inducible heat shock proteins (HSP). The HSR and associated HSPs have been implicated in a variety of disease states. In this project, we explored two aspects of this response. First., we expanded the scope of the Drosophila melanogaster heat tolerance phenotype by involving an automated measure of activity. We discovered that heat hardening reduces motility during subsequent heat stress, and we provide evidence that the level of relative early motility can predict …

Viral Dna Accumulation Regulates Replication Efficiency Of Chlorovirus Osy-Ne5 In Two Closely Related Chlorella Variabilis Strains, Ahmed Esmael, Irina V. Agarkova, David D. Dunigan, You Zhou, James L. Van Etten

Nebraska Center for Virology: Faculty Publications

Many chloroviruses replicate in Chlorella variabilis algal strains that are ex-endosymbionts isolated from the protozoan Paramecium bursaria, including the NC64A and Syngen 2-3 strains. We noticed that indigenous water samples produced a higher number of plaque-forming viruses on C. variabilis Syngen 2-3 lawns than on C. variabilis NC64A lawns. These observed differences led to the discovery of viruses that replicate exclusively in Syngen 2-3 cells, named Only Syngen (OSy) viruses. Here, we demonstrate that OSy viruses initiate infection in the restricted host NC64A by synthesizing some early virus gene products and that approximately 20% of the cells produce a …

Improving Microbiome Research Through Enhanced Reporting And Modeling The Effects Of Antibiotic Usage, Chloe A. Mirzayi

Dissertations and Theses

I consider two key areas in the growing field of human microbiome research: improving the quality of study reporting and the impact of antibiotics on participants in human gut microbiome research studies. In the first chapter, a team of evaluators used the Strengthening the Organization and Reporting of Microbiome Studies (STORMS) checklist to assess recently published microbiome literature. I found moderate agreement and reliability between evaluators, identified several items in STORMS that could be improved, and confirmed that the STORMS checklist can serve as a tool for assessing the reporting quality of published microbiome study. The next chapter considers pre-exposure …

Screening And Genomic Characterization Of Multi-Drug Resistant (Mdr) Bacteria From Hospital Wastewater, Showq Abdelaziz Abdelaziz

Theses

Antimicrobial resistance poses an imminent global threat to public health, with multidrug-resistant (MDR) bacteria being particularly worrisome due to their resistance to multiple antibiotics. Hospital wastewater has been identified as a potential source of MDR bacteria and antibiotic-resistant genes (ARGs). This study aimed to investigate MDR bacteria's prevalence, diversity, and genomic potential in hospital wastewater samples collected from three different hospitals in the UAE. Samples were processed for culturing antibiotic-resistant bacteria using different HiCrome™ chromogenic media to screen for ESBL-producing, Vancomycin, Carbapenem, colistin, and Methicillin-resistant bacteria. The isolates were characterized using VITEk2 antibiotic profiling and identified using 16S rRNA sequencing …

Characterization Of Immunomodulatory Properties Of Manuka Honey: Potential Mitigation Against Colon Cancer, Razan Jamil Masad

Dissertations

The focus on using alternative natural products for cancer prevention and treatment has been increasing over the past decade. Among these natural products, Manuka honey (MH) has been extensively investigated for its antimicrobial, wound healing, and anticancer effects. The current study aimed to characterize the immunomodulatory capacity of MH using both in vitro and in vivo approaches and investigate its potential to modulate anti-tumor immune responses in a preclinical model of colorectal cancer. We demonstrate that MH can directly act on macrophages to induce gene expression of several inflammatory cytokines and chemokines and the production of TNF-a, a major proinflammatory …

Reproduction, Early Development, And Larval Rearing Of The Climbing Perch Anabas Testudineus (Teleostei: Anabantidae) In Captivity, Frolan A. Aya, Reylan C. Gutierrez, Luis Maria B. Garcia

The Philippine Agricultural Scientist

Induced spawning, early development, and larval rearing of the climbing perch Anabas testudineus were examined under captive conditions. Five female climbing perch [125.33 ± 3.27 mm SL; 70.67 ± 5.59 g BW] were paired with apparently mature males (108.50 ± 3.97 mm SL; 39.27 ± 4.70 g BW) and induced to spawn with 5,000 IU human chorionic gonadotropin (hCG) + 0.5 mL Ovaprim kg BW^-1. All hCG + Ovaprim-injected fish spawned 9 – 11 h after hormone administration but saline-injected fish (control group) failed to spawn. Mean egg production per female, fertilization and hatching rates, and larval production …

Commentary: Myocardial Relaxation Matters, Paige E Brlecic, Todd K Rosengart

Faculty, Staff and Students Publications

No abstract provided.

Gpr43 Stimulation On Tcrαβ+ Intraepithelial Colonic Lymphocytes Inhibits The Recruitment Of Encephalitogenic T-Cells Into The Central Nervous System And Attenuates The Development Of Autoimmunity, Carolina Prado, Alexandra Espinoza, J Eduardo Martínez-Hernández, Joseph Petrosino, Erick Riquelme, Alberto J M Martin, Rodrigo Pacheco

Faculty, Staff and Students Publications

INTRODUCTION: Gut microbiota plays a critical role in the regulation of immune homeostasis. Accordingly, several autoimmune disorders have been associated with dysbiosis in the gut microbiota. Notably, the dysbiosis associated with central nervous system (CNS) autoimmunity involves a substantial reduction of bacteria belonging to Clostridia clusters IV and XIVa, which constitute major producers of short-chain fatty acids (SCFAs). Here we addressed the role of the surface receptor-mediated effects of SCFAs on mucosal T-cells in the development of CNS autoimmunity.

METHODS: To induce CNS autoimmunity, we used the mouse model of experimental autoimmune encephalomyelitis (EAE) induced by immunization with the myelin …

Functional Response To A Microbial Synbiotic In The Gastrointestinal System Of Children: A Randomized Clinical Trial, Braden T Tierney, James Versalovic, Alessio Fasano, Joseph F Petrosino, Bruno P Chumpitazi, Emeran A Mayer, Jared Boetes, Gerard Smits, Shanthi G Parkar, Noah Voreades, Ece Kartal, Gabriel A Al-Ghalith, Marco Pane, Peter A Bron, Gregor Reid, Raja Dhir, Christopher E Mason

Faculty, Staff and Students Publications

BACKGROUND: Oral microbial therapy has been studied as an intervention for a range of gastrointestinal disorders. Though research suggests that microbial exposure may affect the gastrointestinal system, motility, and host immunity in a pediatric population, data have been inconsistent, with most prior studies being in neither a randomized nor placebo-controlled setting. The aim of this randomized, placebo-controlled study was to evaluate the efficacy of a synbiotic on increasing weekly bowel movements (WBMs) in constipated children.

METHODS: Sixty-four children (3-17 years of age) were randomized to receive a synbiotic (n = 33) comprising mixed-chain length oligosaccharides and nine microbial strains, or …

Investigating The Mammillary Bodies As An Early Target Of Alzheimer's Disease, Cole Martinson

University Honors Theses

Alzheimer's disease (AD) is the most common form of dementia. With minimal treatment options and no cure, developing a deeper understanding of the pathology of the disease is crucial. For nearly four decades, the accumulation of beta-amyloid (Aβ) plaques has been correlated with the disease and its progression. Previous studies mapping this accumulation show that the mammillary bodies (MB) are an early target of the disease. Glutamatergic neurons are of key interest due to their prevalence in the central nervous system, specifically the MB. To understand the effects of AD on the glutamatergic system, we used vesicular glutamate transporter 2 …