Biology Commons^™

The Influences Of Green Infrastructure On Levels Of Somatic And Male-Specific Coliphages At Shadyside Park, Oula Salih

Student Papers and Reports

Microbial contamination is still considered one of the major causes of diminished function and quality of urban rivers and streams in Michigan. Floodplains, a type of green infrastructure used to reduce flooding after large amounts of rainfall, were reported to have variable effects of reducing levels of stormwater runoff within these bodies of water ( Hubbart et al., 2011 ). Viral indicators of fecal contamination in bodies of water include male-specific and somatic coliphages. Water samples from Plaster Creek were collected before and after the floodplain in order to identify the levels of somatic and male-specific coliphages during dry and …

Identifying Essential Viral Genes Through Genomic Engineering, Amber Carroll

Mahurin Honors College Capstone Experience/Thesis Projects

Bacteria developed resistance to penicillin a mere four years after the groundbreaking antibiotic was first mass produced (Casadevall, 2010). Since then, the development of antibiotic-resistant bacteria has steadily risen, causing millions of difficult to treat infections annually. The challenge is to identify ways to combat these menacing microbes. Bacteriophages are viruses that infect bacteria and can potentially be used to eliminate deadly antibiotic-resistant bacteria. The number of sequenced bacteriophage genomes has increased tremendously over the past 10 years, but little is known about the function of most bacteriophage genes. The purpose of this study was to expand our understanding of …

Crispr-Cas9 Editing Of Nitrate Transporter Gene, Um03849, In Ustilago Maydis, Luke A. Schroeder, Sunita Khanal, Michael H. Perlin

Undergraduate Arts and Research Showcase

Ustilago maydis, the basidiomycete smut-fungus, can infect and cause tumors in corn plants. For this, mating between compatible haploid cells is important. The mating and subsequent dimorphic transition in U. maydis require starvation for nutrients such as nitrogen, in addition to pheromone-receptor interactions between compatible partners. In this research, the CRISPR-Cas9 gene-editing technique was used to create INDEL mutations (sequence insertion or deletion) in the nitrate transporter gene, um03849, in U. maydis. The gene was edited in mating compatible haploid strains 1/2 and 2/9. The phenotypes were characterized for the um03849 mutants as to growth ability, mating …

The Effects Of Nutrient Availability On Pseudomonas Aeruginosa Mono And Co-Culture Biofilms, Julie T. Nguyen, Deborah R. Yoder-Himes Ph.D., Rhiannon Cecil

Undergraduate Arts and Research Showcase

Cystic Fibrosis (CF) is a genetic disorder characterized by faulty ion channels and result in thick mucus accumulation, especially in lungs. Mucus buildup provides ideal conditions for bacterial infections. Pseudomonas aeruginosa (PA) is the second most prevalent bacterium isolated from people with CF and has a high clinical importance. Most CF pathogens form biofilms which make treatment of infections difficult. Biofilms are clusters of cells attached to a surface enclosed in a structured matrix. These structures are a means to provide shelter for bacteria from the environment, especially antibiotics and the immune system. PA alone can form these biofilms, but …

Biogeography Of American Northwest Hot Spring A/B′-Lineage Synechococcus Populations, Eric D. Becraft, Jason M. Wood, Frederick M. Cohan, David M. Ward

Biology

Previous analyses have shown how diversity among unicellular cyanobacteria inhabiting island-like hot springs is structured relative to physical separation and physiochemical differences among springs, especially at local to regional scales. However, these studies have been limited by the low resolution provided by the molecular markers surveyed. We analyzed large datasets obtained by high-throughput sequencing of a segment of the photosynthesis gene psaA from samples collected in hot springs from geothermal basins in Yellowstone National Park, Montana, and Oregon, all known from previous studies to contain populations of A/B′-lineage Synechococcus. The fraction of identical sequences was greater among springs separated by …

Hiding In Plain Sight: The Globally Distributed Bacterial Candidate Phylum Pauc34f, Michael L. Chen, Eric D. Becraft, Maria Pachladaki, Julia M. Brown, Jessica K. Jarett, Josep M. Gasol, Nikolai V. Ravin, Duane P. Moser, Takuro Nunoura, Gerhard J. Herndl, Tanja Woyke, Ramunas Stepanauskas

Biology

Bacterial candidate phylum PAUC34f was originally discovered in marine sponges and is widely considered to be composed of sponge symbionts. Here, we report 21 single amplified genomes (SAGs) of PAUC34f from a variety of environments, including the dark ocean, lake sediments, and a terrestrial aquifer. The diverse origins of the SAGs and the results of metagenome fragment recruitment suggest that some PAUC34f lineages represent relatively abundant, free-living cells in environments other than sponge microbiomes, including the deep ocean. Both phylogenetic and biogeographic patterns, as well as genome content analyses suggest that PAUC34f associations with hosts evolved independently multiple times, while …

Analysis Of Bacterial Dna And Water Quality: Surface Water Sampling At Gardner-Webb University, Celsea Reeder

Undergraduate Honors Theses

Part 1 of this experiment was to explore the bacterial types within the surface water on the campus of Gardner-Webb University, located in Boiling Springs, NC. Two water samples were collected from four locations on campus, including the boiling spring, Lake Hollifield, and an adjacent creek. Using the Zymo Research “Quick-DNA^™ Fungal/Bacterial Miniprep Kit,” the bacterial DNA within these samples was isolated and sent to Psomagen, Inc. for analysis. The resulting DNA sequences were analyzed through BLAST, and subsequently interpreted. For the second part of this experiment, one surface water sample was taken from the boiling spring, and another …

Massard Prairie Restoration And Soil Microbiome Succession, Jeffrey M. Shaver, Emily S. Bellis, Chizuko Iwaki, Jake Qualls, Jay Randolph, Jeremiah Smith

Journal of the Arkansas Academy of Science

We have initially sequenced soil microbial DNA from 4 restored and 4 virgin tallgrass prairie soil samples from Ben Geren Park and Massard Prairie (Fort Smith, AR), respectively. As expected, the soil microbiomes are distinct, with several lineages of nitrogen-fixing bacteria more common in virgin tall grass prairie. However, we predict that as restoration of tallgrass prairie in Ben Geren Park progresses, the soil microbiome of restored prairie will more closely mirror those of the virgin prairie.

A Natural Antimicrobial From Bacillus Subtilis As A Biosanitizer For Resilient Membrane Biofilms, Pratishtha Verma

Electronic Theses and Dissertations

The microbial attachment and colonization on separation membranes lead to biofilm formation. Some selective isolates within the biofilm constitutive microflora acquire resistance and emerge predominant over prolonged use of the membrane. Thus, proving the cleaning and sanitization protocols to be ineffective in adequately removing resilient biofilms. This subsequently leads to selecting microbial resistance within the constitutive microflora to almost all antimicrobial treatments and hence, creates a need to develop novel alternative strategies to control biofilm formation on membrane surfaces. The first research project under this study was designed to understand the microbial interactions and emergence of predominance within biofilm constitutive …

Interaction Of Streptomyces Closely Associated With Bacillus In Nitrogen-Limiting Conditions, Aminya Baniya

Electronic Theses and Dissertations

Biological Nitrogen Fixation is the process of conversion of atmospheric dinitrogen into ammonia which is performed by symbiotic as well as free-living diazotrophic bacteria. A previous project to isolate free-living nitrogen fixing bacteria from a natural prairie yielded Streptomyces which grew on nitrogen free medium. Genome sequencing of three isolates revealed the presence of a second 16S rRNA gene sequence aligning with Bacillus, however repeated streaking only yielded Streptomyces colonies. The aim of this research was to characterize the interaction of three Streptomyces isolates that grow under nitrogen-free conditions, and appeared to be associated with Bacillus. The separation of Bacillus …

Investigating Links Between Soil Microbial Structure And Function In Three Major Plant Communities Across Temporal Scales Of Arctic Alaska, Kaj Lynoe

Electronic Theses and Dissertations

Arctic microbial systems continue to get attention today as our understanding regarding their structure and function in a changing system is paramount to C feedbacks with warming and changes in precipitation. Plant communities and microbial community processes across the Arctic landscape are central to understanding tundra ecosystem processes because environmental conditions and plant community structure drive microbial cycling of soil organic matter. Here, we want to understand how soil microbial respiration, mineralization, biomass, and community composition are linked to three Alaskan tundra plant communities, namely Shrub, Tussock, and Sedge tundra and the seasonal variability in this system. A total of …

Characterization Of The Putative Polysaccharide Synthase Cpsa And Its Effects On The Virulence Of The Human Pathogen Aspergillus Fumigatus, Binita Nepal

Graduate Research Theses & Dissertations

The fungus Aspergillus fumigatus is a ubiquitous opportunistic human pathogen capable of causing a life-threatening disease called invasive aspergillosis, or IA, with an associated 40–90% mortality rate in immunocompromised patients. Of the approximately 250 species known in the genus Aspergillus, A. fumigatus is responsible for up to 90% of IA infections. This study focuses on examining the role of the putative polysaccharide synthase cpsA gene in A. fumigatus virulence. Additionally, we evaluated its role in cellular processes that influence invasion and colonization of host tissue. Importantly, our results support that cpsA is indispensable for virulence in A. fumigatus infection of …

Utilizing Rhizospheric And Bacterial Endophytes For Use As Potential Bio-Fertilizers For Sustainable Agricultural Production, Vincent Peta

Electronic Theses and Dissertations

Brassica carinata crop production offers an exciting alternative approach to the energy crisis when looking at novel ways to power our motor vehicles. Bacterial endophytes, while residing in host-plant tissues, offer a wide array of plant growth promotion benefits such as nitrogen fixation to impart nitrogen (N) nutrition, phosphate (P) solubilization to make soil-bound phosphate more mobile in soil for plant uptake, can suppress pathogenic microbes such as fungus and produce plant growth hormones to offset stress incurred by the plant. Previous literature has shown that there is large interest in studying endophytes from economically important crops such as wheat, …

Crispr/Cas9 Whole Genome Screens Reveal Novel Regulators Of Endocytic Processes In Macrophages, Jared Wollman

Electronic Theses and Dissertations

Macrophages maintain tissue homeostasis by identifying and eliminating threats within their tissue microenvironment. Pattern recognition receptors allow macrophages to recognize and internalize specific ligands while macropinocytosis allows the internalization of all extracellular solutes from their environment. Without pattern recognition receptors, pathogens may grow unchecked if they cannot be detected, and without macropinocytosis, macrophages struggle to detect and move around their environment. This thesis presents the results of CRISPR/Cas9 whole-genome screens used to identify the regulators of both endocytosis (Chapter 2) and macropinocytosis (Chapter 3). In Chapter 2, we report genes regulating dextran uptake in primary murine macrophages and reveal Mrc1-mediated …

Development Of Small Molecule Antibiotics Against A Conserved Rna Gene Regulatory Element In Gram-Positive Bacteria, Ville Yrjö Petteri Väre

Legacy Theses & Dissertations (2009 - 2024)

Bacterial infections and the rise of antibiotic resistance, especially multidrug resistant strains, have generated a clear need for discovery of novel therapeutics. Most antibiotics in use today are derivatives of previous antibiotics to which resistance mechanisms already exist, and traditionally they have a single target: either a protein or rRNA. Gram-positive bacteria regulate the expression of several essential genes or operons using a mechanism called the T-box. The T-box is a structurally conserved riboswitch-like gene regulator in the 5’-untranslated region (UTR) of numerous essential genes of Gram-positive bacteria. T-boxes are stabilized by cognate, unacylated tRNA ligands, allowing the formation of …

Regulation Of Gene Expression Through Ribosome-Associated Proteins, Clare Margaret Miller

Legacy Theses & Dissertations (2009 - 2024)

Translation is a crucial mechanism for generating proteins to carry out cellular processes and for ensuring proper cell functions. Ribosomes are at the center of translation and are complex pieces of machinery. They consist of at least 80 core eukaryotic ribosomal proteins, which are conserved from prokaryotes, and four ribosomal RNAs (rRNAs): 18S, 28S, 5,8A 5S. In addition, numerous translation factors aid the ribosome in protein production. While ribosomes are typically described by these core features, they are known to exist in a heterogenous pool with variations in protein composition, modifications of rRNA, and an assortment of non-ribosomal proteins that …

Hedgehog Signaling Inhibators And Their Importance For Cancer Treatment, Haileselassie Tefera

Biology and Microbiology Graduate Students Plan B Research Projects

The Hedgehog (Hh) signaling pathway plays a crucial role during embryonic development as well as tissue maintenances in adults. Deregulated Hh signaling has been implicated in different diseases and conditions including cancer. Previously, the mechanisms of Hh signaling pathway and its role in cancer formation have been studied and has led to the development of therapeutic drugs. Among those agents, vismodegib and sonidegib are FDA approved drugs to treat basal cell carcinoma and other cancers. Up to date, several hedgehogs (Hh) signaling inhibitors and drugs have been made and evaluating for cancer treatment. In this review, I will discuss the …

The Oral Microbiome And Its Effects On Human Systemic Diseases, Hee Chang Shin

Biology and Microbiology Graduate Students Plan B Research Projects

In the past decade, scientists and healthcare professionals have gained interest in the microbiome and its function as part of the human body. The two most diverse microbiome environments are found in the gut and the oral cavity. While the gut microbiome has been investigated more deeply and continues to be a great interest, the oral microbiome is in comparison a more recent subject with fewer reports on the topic. The purpose of this review paper is to highlight the main human systemic diseases associated with the oral microbiome and to discuss how our understanding of the oral microbiome’s effect …

Freestanding Emergency Departments: A Possible Solution To Rural Hospital Closure, Emily Steadman

Biology and Microbiology Graduate Students Plan B Research Projects

Freestanding emergency departments have become more and more common over the years and have started to pop up in many states across the country. A freestanding emergency department is a facility that provides healthcare in the form of emergency services separate from those at a hospital. FEDs can be seen as independent structures that are distinct from hospital-based emergency rooms and urgent facilities. Just as freestanding emergency departments have spread across the country in a bit of a frenzy, another prevalent issue has been sweeping the country, the closure of rural hospitals. Over the last decade rural hospitals have struggled …

Parkinson’S Disease: Current Treatment Options, Luke Kovaleski

Biology and Microbiology Graduate Students Plan B Research Projects

Parkinson’s Disease is a neurodegenerative disease that is caused by a lack of dopamine. This lack of dopamine has many effects on a person’s body who has Parkinson’s Disease including loss of motor control, slowed movement (bradykinesia), changes in speech, impaired posture and balance, and muscle rigidity. The object of this paper is to explore some of the many different options for treatment of symptoms of Parkinson’s Disease that are currently available. There is not one over-arching treatment that can alleviate the symptoms that are caused by Parkinson’s Disease. However, if multiple treatments are used together, a patient who is …

Role Of Adiponectin In Neuroinflammation & Neuroprotection, Nathan Stadem

Biology and Microbiology Graduate Students Plan B Research Projects

Microglial cells play a significant role in defense of the brain. However, in certain disease states, their response can lead to inflammation that can be detrimental to the survival of brain cells and have harmful effects on a person’s brain activity. Currently, the treatment options for microglial induced neuroinflammation are relatively limited. Adiponectin has recently appeared as a potential moderator of neuroinflammation as well as a promoter of neuroprotection. Adiponectin is a naturally occurring cytokine that has been shown to play a role in a multitude of processes throughout the body including potential as a microglial induced neuroinflammation. Adiponectin’s role …

Hiv Vaccine Development: The Importance Of Gp120 Variable Loop 3 For The Survival Of The Human Immunodeficiency Virus And The Potency Of The Neutralizing Antibody To Bind To The Variable Loop 3, Riham Hussien

Biology and Microbiology Graduate Students Plan B Research Projects

The tendency for the Human Immunodeficiency Virus (HIV) to proliferate and mutate it’s trimeric envelop (Env), is one of the reasons why it’s a challenge for an antibody-based vaccine to be developed. Glycoprotein 160 (gp160,) which consists of glycoprotein 120 (gp120) and glycoprotein 41 (gp41), is the main focus for a research vaccine design. Gp120 consists of an outer membrane, inner membrane and bridging sheet. The protein is trimeric, and non-covalently binds to gp41. The outer domain is where the neutralizing antibody bind, such as 2G12, immunoglobulin G1b12, and anti-V3 antibodies. V3 stands for the Variable loop 3, gp120 has …

Intermittent Fasting (If) Promotes Longevity Through Alterations Of The Mammalian Target Of Rapamycin (Mtor) And The Epigenome, Tayt Boeckholt

Biology and Microbiology Graduate Students Plan B Research Projects

Many studies with a range of subjects from Nematodes to Homo sapiens have found intermittent fasting (IF) to significantly improve the cardiometabolic health of individuals, but how IF promotes longevity through epigenetic modulations remains a sparse understanding throughout the literature. The process of aging may be characterized by a loss of cellular identity sprouted from a disrupted epigenome rich with information for a cell, while also losing the ability to recycle ineffective cellular components. The nutrient-sensing kinase Mammalian Target of Rapamycin (mTOR) is disrupted during bouts of fasting which allows for the recycling of cellular components through increased autophagy. Furthermore, …

A Social Review Of The Opioid Epidemic: The History, Pathophysiology, And Effects On Rural America, Holly J. Goehring

Biology and Microbiology Graduate Students Plan B Research Projects

One of the more pressing issues in modern day health care is the nationwide heath care crisis known as the opioid epidemic. The beginning of this literature review will focus on the history of opioid use and early prescription rates, as well as the summary and definitions of the drugs involved in the current opioid epidemic. The review then shifts to the pathophysiology of addiction involving the activation of opioid receptors and opioid use disorder. The main focus of this literature review is the societal impacts of the opioid epidemic, making special reference to the economic burden and effects on …

Antidepressant Effects On Rem Sleep, Mitchel Adams

Biology and Microbiology Graduate Students Plan B Research Projects

Individuals who deal with depression are typically prescribed antidepressants in order to alleviate the depressive symptoms that they may be having. Polysomnographic sleep research has revealed that depression is associated with altered sleep architecture and distorted REM sleep quality.² Specifically, increased REM sleep duration and density have proved to be markers that predict recurrence and relapse for depressed individuals. REM sleep serves to stimulate regions of the brain that are important with learning and memory consolidation. However, an increased duration of REM sleep in depressed individuals proves to be unfavorable. Antidepressants drugs aim to weaken sleep quality, which is …

Impact Of Chytrid Fungus Pathogen On The Skin Microbiome Of Frogs In Northern Idaho And Turnbull National Wildlife Refuge, Washington, Philip M. Campos

EWU Masters Thesis Collection

Amphibians worldwide are under threat from the infectious disease chytridiomycosis, which is caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd). Bd is associated with the population declines of an estimated 501 species, 90 of which are presumed or confirmed extinct, making this the greatest documented loss of biodiversity attributed to a disease. Researching the amphibian skin microbiome may provide solutions to conservation of amphibians. Two main relationships have been observed between Bd and the microbiome: 1) bacteria producing antifungal metabolites can inhibit Bd and improve survival against the disease and 2) infection by Bd is believed to affect the composition …

Helicobacter Pylori Gene Regulation By Virulence Region Located Srnas, Veronica Janette Albrecht

EWU Masters Thesis Collection

Approximately 50% of the human population is infected with Helicobacter pylori, which can lead to gastrointestinal diseases such as ulcers and gastric adenocarcinoma. Helicobacter pylori strains are genetically variable, and some contain a DNA region called the cytotoxin associated gene pathogenicity island (cagPAI) that encodes virulence factors. Gastrointestinal disease associated with H. pylori are more likely to occur in infections with cagPAI positive strains. Helicobacter pylori has few known transcriptional regulators, but still must regulate expression to survive a constantly changing environment. A mechanism to facilitate this regulation was revealed in a transcriptome analysis conducted by Sharma et al. (2010) …

Evaluation Of The Symbiotic Relation Between Endophyte And Poplar Trees Exposed To Landfill Leachate, Catalina Vega Hurtado

Masters Theses

“The contamination of soil and groundwater from leachate leakage from landfill has turned, nowadays, into a global public issue. One of the main concerns about this pollutant is the potential threat to human and ecosystem health. The current research studied endophyte bacteria in association with poplar trees (Populus sp.), as a method of bioremediation of landfill leachates. The objective of the project was to identify treatment strategies that may improve plant performance (survival rates, plant fitness, and degradation efficacy) with the purpose of being implemented in phytoremediation plots, aimed to intercept and treat landfill leachate, before the contamination of watershed. …

Essential Concepts And Learning Outcomes For Cell And Molecular Biology, Laura L. Newcomb Phd, Mike Chao Phd, Dan Nickerson Phd, Paul Orwin Phd, Jeremy Dodsworth Phd, David Rhoads Phd

Q2S Enhancing Pedagogy

In the new, transformed Biology BS program for conversion from quarter to semester, multiple faculty will teach varied courses under the “Cell and Molecular” requirement for our program. Our old program required multiple core courses, leading to bottlenecks as students could not get seats in needed classes. We have designed our new program to provide students with options under core categories, providing students more flexibility which should improve time to graduation. Students must take at least ONE of the courses, although students who chose to focus on Cell and Molecular Biology should be able to learn new material in ALL …

Characterisation Of Carbapenem-Resistant Gram-Negative Organisms From Clinical Specimens In Yola, Nigeria, Shuwaram A. Shettima, Isabella A. Tickler, Caitlin M. Dela Cruz, Fred C. Tenover

Biology Faculty Publications

Objectives: This study aimed to identify carbapenem-resistant Gram-negative bacteria from clinical specimens of patients in Yola, Nigeria.

Methods: Routine clinical specimens were screened for the presence of carbapenem-resistant Gramnegative bacteria using chromogenic agar plates. Susceptibility of all presumptive isolates to carbapenems was tested by MIC and disk diffusion methods. Real-time PCR was used to test for the presence of carbapenemase genes.

Results: Screening of 1741 clinical specimens yielded 119 (6.8%) presumptive carbapenem-resistant Gram-negative bacteria. Antimicrobial susceptibility testing confirmed carbapenem resistance in 105 of these isolates. New Delhi metallo-β-lactamase (blaNDM) gene was detected in 26 isolates and Verona integron-encoded metallo-β-lactamase (bla …