Microbiology Commons^™

The Role Of Conserved Poly(A) Sequences In The 3'Utr Of Zika Virus Gene Expression, Kristen Kaytes

Legacy Theses & Dissertations (2009 - 2024)

Following its discovery in 1947, Zika virus garnered little attention in the global stage until 2015, when a rapidly spreading epidemic brought the virus, and its devastating clinical manifestations to light. Zika virus pathologies include Congenital Zika Syndrome, a known causative of microcephaly, as well as spontaneous miscarriages and the development of Guillain Barré syndrome. Despite recent advances in research, the molecular biology of Zika virus is largely unknown.

Retrotransposon-Mediated Transduction Of An Environmental Cue To Regulate Centrosome Fate, Shawn Patrick Murphy

Legacy Theses & Dissertations (2009 - 2024)

In 1969, the enrichment of mobile element repeat sequences led Britton and Davidson to propose the hypothesis that gene expression in higher eukaryotes is regulated through the exaptation of mobile elements. In this work, I have explored the hypothesis that mobile elements can also be harnessed by the host to regulate asymmetric cell division, thereby determining cell fate. Retrotransposons are ubiquitous eukaryotic mobile elements that transpose through an RNA intermediate. They are often active in cell types that divide asymmetrically to yield daughter cells with different fates, such as embryonic stem cells, germline stem cells, neuronal stem cells and the …

The Phosphodiesterase, Rv0805, Is An Unheralded Component Of Tb Complex Mycobacterial Physiology In And Beyond Camp Homeostasis, James R. Mcdowell

Legacy Theses & Dissertations (2009 - 2024)

Phosphodiesterases (PDEs) are integral components of 3’,5’-cyclic adenosine monophosphate (cAMP) signaling pathways by degrading cAMP to modulate the concentration, duration, and localization of the cAMP signal which maintains the specificity of cAMP pathways. The human pathogen, Mycobacterium tuberculosis (Mtb) has a unique cAMP network architecture with at least 15 adenylyl cyclases (ACs) that generate cAMP, but only one characterized PDE, Rv0805, which is found exclusively in pathogenic mycobacteria. Rv0805 can influence Mtb cAMP levels but the absence of Rv0805 orthologs in non-pathogenic mycobacteria and apparent separation of Rv0805 from cAMP directed roles led to numerous questions surrounding PDE function in …

Rna Modifications As A Novel Mediator Of Viral Infection, Rachel Netzband

Legacy Theses & Dissertations (2009 - 2024)

Viral epitranscriptomics is a novel field of RNA biology. Chemical groups are appended to RNA nucleotides under different conditions in cells, and I examine these changes using a mass spectrometry-based approach. Various changes are found to occur in post-transcriptional modifications (PTMs) during viral infection. The field primarily studies a small number of PTMS, such as m6A, while I explore a variety of novel modifications and their impact on viral infection. Hepatitis C virus (HCV) infection induces a variety of modification changes, including the novel presence of dimethylcytosine (m5Cm/m44C). One Writer enzyme for this modification is determined to likely be METTL15, …

Describing The Gut Microbiome Of Amblema Plicata, Lauren Lawson

Electronic Theses and Dissertations

Freshwater mussels are important for nutrient cycling and ecosystem health, as they filter feed on their surrounding water column. This form of feeding makes these bivalves especially sensitive to conditions in their environment. Gut microbial communities (microbiomes) have been recognized as important to both host organism and ecosystem health; however, how microbiomes are organized and influenced is still unclear. In this study, the gut microbiomes of 58 individuals of the freshwater mussel Amblema plicata were compared across two river basins, five rivers, and nine sites in the southeastern USA. Planctomycetes, Firmicutes, and Cyanobacteria were the most common phyla within all …

The Probiotic Effect Of Clostridium Cochlearium Is Associated With Significant Change In Short-Chain Fatty Acid Metabolism And Gut Microbiota, Qing Ai

Wayne State University Dissertations

The prevalence of obesity is rising steadily across the world, which increases the risk of many metabolic diseases and life-threatening illnesses. A specific strain, Clostridium cochlearium (C. cochlearium), reported as a butyrate producer, could have potential probiotic effects against obesity. The objective of this study was to evaluate the effects of dietary supplementation of C. cochlearium on a high-fat diet-induced obese (DIO) mouse model. The 16S rRNA sequencing of mice gut microbiome was performed at the end of the experimental period to identify the changes in gut microbial composition, investigate possible functional genes, and elucidate potential mechanisms. Thirty-six C57BL/6 6-8 …

Narratives On The Academic Resilience Of Former Homeless Students, Alia Aboulhosn

Walden Dissertations and Doctoral Studies

The number of homeless students in U.S public schools continues to rise. Although many homeless students drop out due to challenges they face, lacking is research on how some homeless students overcome challenges and graduate high school, referred to as academically resilient. The purpose of this qualitative narrative study was to gain a deeper understanding of the experiences that promoted former students who were homeless during their senior year of high school to graduate despite adversity, using Resiliency Theory as the theoretical framework. Semi-structured interviews with five participants provided insight into the broader sociopolitical and personal contexts in their stories, …

College Of Natural Sciences 2021 Year-End Publication, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Page 2 Welcome, Table of Contents
Page 3 Our Departments: Highlights From 2021
Page 4 Overview of the College
Page 5 Overview of Bold & Blue
Pages 6, 7 Announcing the First Endowed Professorship in the College of Natural Sciences
Page 8 Spooky Science, Astronomy Outreach, SDSU Chemistry Research Features on Journal Cover
Page 9 Students Win Business Plan Competition With Aims to Improve Shelf Life of Produce, Summer Researchers
Page 10 NIH Grant Helps Unravel Rare Inflammatory Genetic Disorders, International Excellence in South Dakota
Page 11 The Next Frontier of Science Education: Virtual Reality, SDSU Researchers Uncover how Cancer …

Polycystic Kidney Disease: An Examination And Review Of Disease Type, Presentation, Treatment, And Prognosis, Zoey Mann

Biology and Microbiology Graduate Students Plan B Research Projects

Polycystic Kidney Disease (PKD) is a ciliopathy that primarily presents as renal cysts. Inherited as either a dominant (ADPKD) or recessive (ARPKD) mutation, PKD is one of the most commonly inherited kidney diseases. ADPKD is caused by the inheritance of a mutation in either PKD1 or PKD2, which code for the polycystin-1 and -2 proteins, respectively. The less severe form of PKD, ADPKD is typically adult-onset, with the possibility of extremely late-stage presentation. In addition to renal cysts, hepatic and pancreatic cysts are common, as well as other non-cystic symptoms including headache and hypertension. ARPKD is caused by the inheritance …

Guillain-Barre Syndrome: A Review Of Current Diagnostic Tools, Treatments, And Research, Kaitlyn Hespen

Biology and Microbiology Graduate Students Plan B Research Projects

Guillain-Barre Syndrome is a rare post-infection inflammatory disorder. It is caused by the cross-reactivity of antibodies produced from a recent infection which then attack the gangliosides of the peripheral nervous system. Guillain-Barre syndrome includes multiple subtypes which are categorized based on both disease course and symptoms, which include length of progression phase, pain, and cranial nerve involvement. This paper will serve as a review of diagnostic tools and treatment options used for Guillain-Barre syndrome patients. It will also discuss recent research on these topics as well as studies on viral outbreaks which may be linked to Guillain-Barre syndrome. These will …

Current And Future Perspectives In The Treatment Of Fracture Nonunions, Zebadiah Nelson

Biology and Microbiology Graduate Students Plan B Research Projects

Fracture nonunions comprise one of the serious clinical complications in orthopedics. Fracture nonunions result when the time to union is greater than 6 to 9 months. It is estimated that approximately 5% to 10% of all fractures progress to fracture nonunion due to a host of complicating patient variables and risk factors. New scoring systems have emerged which help in directing the treatment strategies. Fracture nonunion management should be directed toward maintaining the diamond concept which introduces osteogenic cells lines, an osteoconductive scaffold for those cells to grow, as well as the necessary growth factors, and a stable mechanical microenvironment. …

Association Between Colorectal Cancer Prevalence And Patients Age, Race And Sex, Arsiema Fisuh

Biology and Microbiology Graduate Students Plan B Research Projects

Colorectal cancer is one of the top leading causes of cancer deaths affecting people of different ages, sex and races disproportionately. The American Cancer society researchers have studied that lack of physical activities, smoking, consumption of red meat, and heavy alcohol use to be high risk factors for developing colorectal cancer in addition to genetic inheritances. Previous research studies have shown that disparities in cancer screening, socioeconomic status and others impacts on colorectal cancer prevalence and death. The objective of this project is to review the existing literature to better understand the disparities in colorectal cancer prevalence and deaths in …

The Importance Of Care Coordination Of Patients With Multimorbidity: An Evaluation Of The Patient-Centered Medical Home Model, Mary Boksa

Biology and Microbiology Graduate Students Plan B Research Projects

The rise in multimorbidity among various patient populations has made fragmentation of care an increasingly common issue due to the need for specialized care of each chronic condition and complexity of treatment plans. Implementation of care coordination intervention models has been identified as an essential component in combating this fragmented nature of our current health care system. This is done by providing an organized model of care and improving communication between all parties involved in care and treatment plans. This literature review will begin with a brief discussion on the importance of care coordination and components needed for implementation and …

The Relationship Between Land Use Change And Disease Prevalence, Allison Bjornstad

Biology and Microbiology Graduate Students Plan B Research Projects

Zoonotic disease outbreaks are becoming more novel and are increasing in frequency. This increase can be partially attributed to land use changes including deforestation, urbanization, and cultivation. Land use change alters disease prevalence by causing an increase in contact rates between disease hosts and humans. Land use changes also alter species compositions in the area to contain more competent disease hosts. Each pathogen can react to these changes in different ways. The specific reactions that each pathogen has to land use changes should be further researched so proper mitigation steps can be taken. Once the effects of land use change …

Expression Of Programmed Cell Death 1 (Pd-1) In Human Monocytic Cell Line Thp-1 And Its Regulatory Mechanism, Kittitach Sri-Ngern-Ngam

Chulalongkorn University Theses and Dissertations (Chula ETD)

Cancer is the leading cause of death worldwide. Immune system defends the host against foreign antigens, not only pathogens or their products, but also cancer cells via coordinated complex responses. The immune response against cancer; however, often poorly control the cancer growth because tumors can effectively escape the immune defense mechanisms by various immune evasion strategies. Programmed cell death 1 (PD-1) is a co-inhibitory immune checkpoint receptor expressed on various immune cells, especially in activated T cells. Engagement of PD-1 with its ligand, PD-L1 or PD-L2, leads to the negative regulation of T cell functions, resulting in impaired antitumor immunity. …

Application Of Genetic Techniques To Investigate Chlamydia Trachomatis Type Iii Secretion Effector Biology, Gabrielle Keb

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

Chlamydia trachomatis is the causative agent of the most reported bacterial sexually transmitted disease in the United States. The establishment of an intracellular niche within mucosal epithelium is sufficient to drive immunopathology and disease sequela. As obligate intracellular bacteria, Chlamydia spp. have evolved numerous mechanisms for establishing an intracellular growth environment. The type III secretion system (T3SS) delivers effector proteins to the host cytosol and is essential for C. trachomatis invasion and development. The effectors TmeA, TmeB, and TarP, are all secreted during C. trachomatis invasion. TarP and TmeA have been associated with manipulation of actin networks and are …

Characterizing The Physiology And Genetics Of Contact Dependent Growth Inhibiton Systems In Burkholderia Species, Alice Elizabeth Oates

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

Contact-dependent growth inhibition (CDI) systems mediate interbacterial competition. The genes encoding these systems are widespread among Gram-negative bacteria, including Burkholderia pathogens. CDI systems of Burkholderia species are composed of two-partner secretion pathway proteins and function to deliver the toxic C-terminus of a polymorphic surface-exposed exoprotein BcpA (Burkholderia CDI protein A) to the cytoplasm of neighboring recipient bacteria upon cell-cell contact. Specific outer and inner membrane proteins facilitate BcpA translocation both out of the donor bacterium and into the recipient cell cytoplasm. Most Burkholderia species-specific CDI translocation factors in recipient cells are unknown. BcpA intoxication functions as a mechanism by …

The Roles Of The Actin Network And Co-Opted Host Factors In Tbsv Replication, Melissa Gabriela Molho Medina

Theses and Dissertations--Plant Pathology

Positive-stranded (+) RNA viruses are the largest family of viruses that infect plants, causing important economic losses in different crops. Tomato bushy stunt virus (TBSV), a small positive-stranded RNA virus, has emerged as a model virus to study virus-host interactions. TBSV encodes for only five proteins, therefore, to infect the host cell TBSV co-opts selected host components and subverts specific molecular pathways.

Firstly, I performed a proteomic screening using Arabidopsis proteins. I found that TBSV viral replication proteins interact with 88 host proteins, including the ubiquitin-conjugating enzyme 2 (Ubc2), fructose 1,6 biphosphate aldolase (Fba1), and several members of the Hps70 …

Auxin-Based Herbicide Program And Rhizobia Application For Weed Control And Nodulation Potential In Auxin Tolerant Soybean, Joy Amajioyi

Electronic Theses and Dissertations

Foliar-applied Bradyrhizobia to V4 soybean has been reported to increase yield up to 5%. However, a stand-alone product application may not be practical. Applying with other treatments such as post-emergence herbicide application may be economical but herbicide and/or additives may be deleterious to rhizobial growth. A laboratory study investigated the impact of herbicides (glyphosate and dicamba), additives (an oil to improve absorption and spreading; and AMS used to overcome hard water impacts on glyphosate), and herbicide + additives on bacterial growth. Optical density (OD) measurements at the wavelength of 650 nm assessed solution turbidity, a surrogate measure of bacterial growth. …

Community Opioid Overdose Prevention And Naloxone Distribution Programs: An Evidence-To-Practice Review, Madison M. Hauge, Kathryn C. Downs, Zachary K. Winkelmann

Clinical Practice in Athletic Training

According to the Centers for Disease Control and Prevention, 100 people die of drug overdose in the United States every day. This frighteningly high mortality rate has created the need for community-based opioid overdose prevention programs (OOPPs). Currently, there are more than 188 community-run programs operating in the United States. These programs teach individuals how to distribute naloxone and respond properly to a drug overdose situation. This guiding systematic review depicts the current literature available on OOPPs and their effectiveness. The authors performed an article search to discover the most relevant and recent articles, which were graded using a quality …

Mite Diet Sequences Obtained By High Throughput Sequencing Of Gut Contents Of Freshly Collected Water Mites, Adrian Amelio Vasquez, Obadeh Mohiddin, Zeyu Li, Brittany L. Bonnici, Katherine Gurdziel, Jeffrey L. Ram

Physiology Faculty Research Publications

Cytochrome oxidase subunit I (COI) barcode sequences in this file were obtained from gut DNA extracted from 54 freshly collected water mites, comprising 21 Lebertia quinquemaculosa , 30 Lebertia davidcooki , 1 Limnesia , and 2 Arrenurus specimens. Methods and other details about these sequences are described in a paper by the same authors in a submitted publication (2021: URL to be given here when published). Data on collection locations, primers (mLep and LCOI), amino acid translations, etc. are included in corresponding sequences uploaded to GenBank. The right column below contains additional notes on naming the taxa of the sequences …

Roles Of Non-Frankia Bacteria In Root Nodule Formation And Function In Alnus Sp., Kelsey Christine Mercurio

Honors Theses and Capstones

Plant roots are home to a wide variety of beneficial microbes; understanding and optimizing plant-microbe interactions may be critical to enhance global food security in a sustainable, equitable way. With the help of their nitrogen-fixing bacterial partner, Frankia, actinorhizal plants form symbiotic root nodules and play important roles in agroforestry and land reclamation. However, Frankia does not live alone in nodules, and the other microbial residents may contribute to nodule formation and function. We collected root nodules from alder trees (Alnus sp.) in 2018 and 2019, then isolated DNA and individual bacterial strains to characterize the nodule microbial …

A Survey Of Opportunistic Fungi In The Portsmouth, Nh Region, Chloe E. Richard

Honors Theses and Capstones

Opportunistic mycoses are caused by ubiquitous fungi that we encounter daily. This study identified the most common opportunistic fungi in a local area during the current winter season. A survey of fungi was conducted in the Portsmouth, New Hampshire region by taking environmental samples from both indoor and outdoor locations. The samples were then cultured and identified using colony morphology, microscopic characteristics, and biochemical testing. Despite the cold weather, the results showed that fungal species are still prevalent outdoors, with the most variation in single samples coming from areas with exposed soil and decaying vegetation, while less fungal presence was …

Determining The Effects Of Imidacloprid On Non-Target Soil Organisms In Hemlock Stands, Braley Burke

Graduate Theses, Dissertations, and Problem Reports (ETD)

The hemlock woolly adelgid (HWA), Adelges tsugae Annand (Hemiptera: Adelgidae), is an invasive insect that is causing mortality of eastern hemlock trees, Tsuga canadensis, and Carolina hemlock trees, Tsuga caroliniana, across the eastern United States. To protect these ecologically important tree species, a neonicotinoid insecticide, imidacloprid, is commonly used. Imidacloprid is an effective treatment and can remain effective against HWA for four to six years but long-term (≥ one year after application) non-target effects of imidacloprid on forest ecosystems are not well-studied. This study examined terrestrial non-target effects of imidacloprid in hemlock stands with different treatment histories to …

Ecological And Anthropogenic Influences On A Sentinel Species' Gut Microbiome, Carson E. Black

All Master's Theses

Central and South American primates face augmented challenges due to increased rates of forest fragmentation. Among these challenges are implications on the nonhuman primate gut microbiome. Wild Argentine black and gold howler monkeys (Alouatta caraya) are listed as “least concern” with a population that is decreasing. Despite their propensity to occupy habitats with varying degrees of degradation and disturbance, they are not immune from the stressors that forest fragmentation places on them. Their increased exposure to humans and livestock leaves them vulnerable to cross-species transmission of emerging infectious diseases and pathogens. Therefore, their role as sentinels of ecosystems, …

Rotavirus A Genome Segments Show Distinct Segregation And Codon Usage Patterns, Irene Hoxie, John J. Dennehy

Publications and Research

Reassortment of the Rotavirus A (RVA) 11-segment dsRNA genome may generate new genome constellations that allow RVA to expand its host range or evade immune responses. Reassortment may also produce phylogenetic incongruities and weakly linked evolutionary histories across the 11 segments, obscuring reassortment-specific epistasis and changes in substitution rates. To determine the co-segregation patterns of RVA segments, we generated time-scaled phylogenetic trees for each of the 11 segments of 789 complete RVA genomes isolated from mammalian hosts and compared the segments’ geodesic distances. We found that segments 4 (VP4) and 9 (VP7) occupied significantly different tree spaces from each other …

Effectiveness Of Take-Home Naloxone Programs In Athletic Training: An Evidence-To-Practice Review, Michael J. Palm, Amanda N. Flanscha, Zachary K. Winkelmann

Clinical Practice in Athletic Training

The number of opioid overdoses (ODs) has risen in recent years and has become more complex due to the co-involvement of both prescription and illicit opioid drug use. Provisional programs for take-home naloxone (a medication designed to rapidly reverse opiate OD symptoms) kits have been distributed to combat this potentially fatal epidemic. Although there is strong evidence to support the efficacy of naloxone in the reversal of opiate OD, there is limited evidence to support the efficacy of take-home naloxone (THN) kits. The purpose of this evidence-to-practice review was to summarize a systematic review on the efficacy of THN programs. …

Free-Living Diazotrophs And The Nitrogen Cycle In Natural Grassland Revealed By Culture Dependent And Independent Approaches, Amrit Koirala

Electronic Theses and Dissertations

Biological nitrogen fixation contributes to half of the global supply of nitrogen to the biosphere. It is carried out by a diverse group of prokaryotes called diazotrophs via the nitrogenase enzyme. Nitrogen fixation research is focused on the narrow group of symbiotic diazotrophs, and the vast majority of free-living diazotrophs which contribute significantly to fixed nitrogen are yet to be explored. The goal of this research was to access phylogeny of diazotrophs considering the most up-to-date genomic information and apply that knowledge to understand the diversity of free-living diazotrophs in a natural grassland ecosystem, both by culture dependent and independent …

Comparison Of The Effects Of Land Use / Land Cover On Water Quality And The Intertidal Marine Macroalgae Communities At The Fluvial Outflows Of The Dingle Peninsula, Cassandra Lew

Theses

The Milltown, Feohanagh, and Owenmore river basins located on the Dingle Peninsula in Ireland were studied to see how variation in land use and land cover (LU/LC) affected water quality and the macroalgal communities at each river’s respective fluvial outflow. Abundance and composition of macroalgae in river and coastal water bodies have been designated as an indicator of water quality according to the Water Framework Directive 2000. The results of this study found that the Feohanagh’s macroalgal community had the highest species richness for most months while the Milltown had the highest Shannon Diversity Index. The Owenmore’s community was consistently …

Il-10 And Tgf-Beta Increase Connexin-43 Expression And Membrane Potential Of Hl-1 Cardiomyocytes Coupled With Raw 264.7 Macrophages, Cora B. Cox

Browse all Theses and Dissertations

Cardiomyocytes and macrophages have been found to interact via connexin-43 hemichannels. The role of connexin-43, however, is not fully understood. This study shows that these interactions aid in increasing the membrane potential of cardiomyocytes allowing contraction of the cells. HL-1 cardiomyocytes and RAW 264.7 macrophages in coculture increased expression of connexin-43 compared to cardiomyocytes alone. Co-cultures also increased the fluorescence of Di-8-ANEPPS potentiometric dye indicating an increase in cardiomyocyte membrane potential. Treatment with IL-10 and TGF-beta further increased connexin-43 expression and membrane potential. Treatment with SOCS3 inhibited the effects of TGF-beta and IL-10 while having no effect on its own. …