Microbiology Commons^™

Orientia Tsutsugamushi Secretes Two Ankyrin Repeat-Containing Effectors Via A Type 1 Secretion System To Inhibit Host Nf-Κb Function, Sean M. Evans

Theses and Dissertations

Scrub typhus is a potentially fatal infection that threatens one billion persons in the Asia-Pacific region and is caused by the obligate intracellular bacterium, Orientia tsutsugamushi. How this organism facilitates its intracellular survival and pathogenesis is poorly understood. Intracellular bacterial pathogens utilize the Type 1 (T1SS) or Type 4 secretion system (T4SS) to translocate ankyrin repeat-containing proteins (Anks) into the host cell to modulate host cell processes. The O. tsutsugamushi genome encodes one of the largest known bacterial Ank libraries as well as Type 1 and Type 4 secretion systems (T1SS and T4SS), which are expressed during infection. In …

Development Of A High Throughput (Ht) Raman Spectroscopy Method For Rapid Screening Of Liquid Blood Plasma From Prostate Cancer Patients, Dinesh Medipally, Adrian Maguire, Jane Bryant, John Armstrong, Mary Dunne, Marie Finn, Fiona Lyng, Aidan Meade

Articles

Extensive research has been undertaken on the examination of tissue biopsies using vibrational spectroscopic techniques. However, fewer studies have focused on less invasive and commonly acquired blood samples. Recent studies have shown the ability of Raman and Fourier transform infrared (FTIR) spectroscopy to discriminate between non-cancer controls and cancer cases using blood serum or plasma. Even though many studies have proposed Raman spectroscopy as a potential diagnostic tool in various cancers, the Raman spectroscopic technique has not been introduced as a routine clinical technology. This is due to multiple drawbacks with the application of the technique, including sample preparation, the …

Actionable Patient Safety Solution (Apss) #3b: Antimicrobial Stewardship: The Role Of A Pharmacy And The Microbiology Lab In Patient Safety, Jerika Lam, Jason Yamaki, Ron Jordan, Celine Peters, Steven Barker, Michael Ramsay, Ariana Longley, Joe Kiani

Pharmacy Faculty Articles and Research

This report presents a plan of action for introducing an Antimicrobial Stewardship Plan (ASP) to combat the inappopriate use of antimicrobial drugs, which are a significant cause of patient morbidity and mortality.

The Microbiome Of Neotropical Ticks Parasitizing On Passerine Migratory Birds, Khemraj Budachetri, Jaclyn Williams, Nabanita Mukherjee, Michael Sellers, Shahid Karim

Faculty Publications

Seasonal migration of passerine birds between temperate North America and tropical Central and South America is an ecological phenomenon. Migration of birds has been associated with the introduction of ectoparasites like ticks or tick-borne pathogens across the avian migration routes. In this study, the microbial diversity was determined in the ticks and bird DNA samples using 454 pyrosequencing of bacterial 16S rRNA gene. Tick DNA samples showed the dominance of genera Lactococcus, Francisella, Raoultella, Wolbachiaand Rickettsia across all the ticks, but birds DNA did not share common microbial diversity with ticks. Furthermore, “Candidatus Rickettsia amblyommii” …

Studying Microflora Of Semi-Hard Cheese, And Sporulation Within Contact Surface Biofilms, Dalia Khan

Electronic Theses and Dissertations

The first study was conducted on commercial Italian semi-hard cheese samples that were analyzed microbiologically to understand the effect of fast and slow rate of cooling on cheese microflora during ripening process at different temperatures. A cheese plant noticed an active growth of non-starter lactic acid bacteria, especially the heterofermentative bacteria, in ripened cheese blocks, which weren’t fully cooled. For that, three cheese sample sets, each having 8 samples, were received from the cheese plant for microbiological analysis. The first set included a group of fast cooled cheese samples to 38°F, and the other group was slow cooled to 50°F. …

Effects Of Root Isoflavonoids And Hairy Root Transformation On The Soybean Rhizosphere Bacterial Community Structure, Laura White

Electronic Theses and Dissertations

Rhizodeposits play a key role in shaping rhizosphere microbial communities. In soybean, isoflavonoids are a key rhizodeposit component that aid in plant defense and enable symbiotic associations with rhizobia. However, it is uncertain if and how they influence rhizosphere microbial communities. Isoflavonoid biosynthesis was silenced via RNA interference of isoflavone synthase in soybean hairy root composite plants. Successive sonication was implemented to isolate soil fractions from 3 different rhizosphere zones at 1 and 3 weeks post planting. PCR amplicons from 16S rRNA gene variable regions V1- V3 and V3-V5 from these soil fractions were analyzed via denaturing gradient gel electrophoresis …

Senecavirus A: Epidemiology, Pathogenesis And Infection Dynamics, Lok Raj Joshi

Electronic Theses and Dissertations

Senecavirus A (SVA) is a positive sense single-stranded virus that belongs to the genus Senecavirus within the family Picornaviridae. Senecavirus has been present in US swine population since 1988. However, there have been only a few reports of SVA associated with disease in last two decades. In late 2014 early 2015, a sudden increase in the number of cases of Senecavirus A associated with vesicular disease was observed in Brazil, the US and China. Affected pigs presented vesicles on snout, coronary band, and dewclaw. Additionaly, increased neonatal mortality has been reported in the field. Many aspects of SVA epidemiology, …

The Synthetic Biology Of N2-Fixing Cyanobacteria For Photosynthetic Terpenoid Production, Charles T. Halfmann

Electronic Theses and Dissertations

In the last few decades, concerns over global climate change, energy security, and environmental pollution have been rising. To overcome these challenges, the concept of “-n^th generation” biofuels has emerged as a strategy to convert solar radiation into fuels and bulk industrial chemicals for societal use, while decreasing our consumption of nonrenewable energy sources. Nitrogen-fixing cyanobacteria hold a distinct advantage in biofuel production over plants, given their ability to convert sunlight, air (CO₂ and N₂), and mineralized water to energy-dense carbon molecules, as well as fix atmospheric nitrogen gas into ammonia for metabolism. Engineered cyanobacteria with …

Characterizing Regulatory Factors Of The Sumoylation System, David Quintanar

Open Access Theses & Dissertations

The effects that influenzaâ??s seasonal epidemics have on human health and the global economy have been clearly noted; while they are indeed very impressive, the impact of influenza pandemics arguably surpass other known infectious agents. Influenza A virus attaches to, enters, and infect cells by releasing its segmented genome which localize to the nucleus then use the hostâ??s cellular machinery to replicate and create viral progeny. The virus is able to hijack transcriptional components as well as to interact with other known and unknown host proteins which ultimately allows for a balance between cell viability and viral propagation. One known …

Defining The Roles Of The Lipoic Acid Ligases In Promoting Staphylococcus Aureus Metabolic Homeostasis And Virulence, Irina Laczkovich

Master's Theses

Staphylococcus aureus is a major human pathogen known to cause disease in a wide range of tissues. In order to thrive in such diverse environments, S. aureus uses multiple adaptive traits such as trace metal/nutrient acquisition, shifts in metabolic activity, and expression of detoxification systems, all of which allow the bacterium to proliferate and survive in nutritionally deficient and inhospitable environments.

One essential metabolite used by S. aureus is lipoic acid, a cofactor of enzyme complexes used in aerobic metabolism, fatty acid biosynthesis, glycine detoxification, and maintenance of redox homeostasis. Prior studies in the lab used a genetic approach to …

Profiling Resistance To P450-Activated Food Carcinogens Using Toxicogenomic Approaches In Budding Yeast, Nicholas Stjohn

Legacy Theses & Dissertations (2009 - 2024)

The human response to environmental carcinogens, some of which require metabolic activation, is highly variable. Factors such as environment, lifestyle, and genetics all influence the rates of exposure to and ultimate bioactivation of these compounds. Genetic factors include mutations to cell-cycle regulation, cell proliferation, and DNA repair genes; however, epidemiological studies may lack significance due to inadequate patient numbers. We used budding yeast as a model organism to determine genetic susceptibility to food-associated carcinogens, including aflatoxin (AFB1) and heterocyclic aromatic amines (HAAs). Budding yeast does not contain P450s that activate these compounds, so expression vectors were induced that contain human …

Novel Approaches To Mitigating Bacterial Biofilm Formation And Intercellular Communication, Stephen Kasper

Legacy Theses & Dissertations (2009 - 2024)

Long thought of as solitary single-cell organisms, it is now widely accepted that bacteria can act and cooperate as social organisms. Phenomena such as biofilm formation and quorum sensing (QS) are two intimately intertwined cooperative behaviors that significantly contribute to the pathogenesis of many bacteria. Biofilms are surface associated communities of bacteria encased in a secreted extracellular matrix, which provides several advantages over an individualized lifestyle, such as increased protection from antimicrobial agents as well as enhanced opportunity for the exchange of genetic material. Bacterial QS is a system of population-based communication through the production, sensing, and response to chemical …

Structural And Functional Characterization Of An Unusual Camp Responsive Transcription Factor, Cmr, In Tb Complex Mycobacteria, Sridevi Ranganathan

Legacy Theses & Dissertations (2009 - 2024)

Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis in humans, is an intracellular pathogen that infects millions of people every year. Mtb can survive inside the host for extended periods of time by sensing and adapting to the host environmental stressors. Transcriptional gene regulation plays a critical role in this adaptation. This dissertation focuses on understanding the structural and functional aspects of one such transcriptional regulatory unit, Cmr (Rv1675c), in Mtb.

Investigating The Role Of Epitranscriptomics In Viral Immunity, Kaycie S. Lawson

Legacy Theses & Dissertations (2009 - 2024)

The characterization of host-virus relationships is essential for understanding the process of viral replication and driving the development of effective viral targeting strategies. In this work, I tested the hypothesis that ribonucleic acid (RNA) post-transcriptional modifications (PTMs) may play a significant role in defining host-virus interactions. The model system consisted of a yeast strain capable of harboring the endogenous L-A virus, which allowed me to evaluate the possible involvement of PTMs in the process of cellular immunity to virus-borne toxicity. A mass spectrometry-based platform was utilized to compare the global PTM profile of wild-type yeast with those of the same …

A Tale Of Two Regulators : Characterization Of The Novel Transcription Factor Abmr And The Small Non-Coding Rna Mcr11 In Mycobacterium Tuberculosis, Roxanne Candice Girardin

Legacy Theses & Dissertations (2009 - 2024)

Genes of unknown function make up nearly one third of Mtb’s genome (Cole,

Characterization Of A New Chlorovirus Type With Permissive And Non-Permissive Features On Phylogenetically Related Algal Strains, Cristian F. Quispe, Ahmed Esmael, Olivia Sonderman, Michelle Mcquinn, Irina Agarkova, Mohammed Battah, Garry A. Duncan, David D. Dunigan, Timothy P. L. Smith, Cristina Decastro, Immacolata Speciale, Fangrui Ma, James L. Van Etten

Nebraska Center for Virology: Faculty Publications

A previous report indicated that prototype chlorovirus PBCV-1 replicated in two Chlorella variabilis algal strains, NC64A and Syngen 2-3, that are ex-endosymbionts isolated from the protozoan Paramecium bursaria. Surprisingly, plaque-forming viruses on Syngen 2-3 lawns were often higher than on NC64A lawns from indigenous water samples. These differences led to the discovery of viruses that exclusively replicate in Syngen 2-3 cells, named Only Syngen (OSy) viruses. OSy-NE5, the prototype virus for the proposed new species, had a linear dsDNA genome of 327 kb with 44-nucleotide-long, incompletely base-paired, covalently closed hairpin ends. Each hairpin structure was followed by an identical …

การยับยั้งการเจริญและการผลิตอะฟลาทอกซินของ Aspergillus Flavus ในไซเลจข้าวโพดโดยใช้ยีสต์และแล็กติกแอซิดแบคทีเรียปฏิปักษ์, ทรรศภรณ์ รุ่งชัยวัฒนกุล

Chulalongkorn University Theses and Dissertations (Chula ETD)

วัตถุประสงค์ของงานวิจัยนี้เพื่อศึกษาความสามารถของยีสต์และแล็กติกแอซิดแบคทีเรียปฏิปักษ์ในการยับยั้งการเจริญและการผลิตอะฟลาทอกซินรวมของ Aspergillus flavus บนจานอาหารเลี้ยงเชื้อและในไซเลจข้าวโพด และเพื่อหาปริมาณความเข้มข้นและอัตราส่วนของแล็กติกแอซิดแบคทีเรียและยีสต์ผสมที่ให้ผลการยับยั้งสูงสุดในไซเลจข้าวโพด โดยเริ่มจากการทดสอบประสิทธิภาพของยีสต์ (Wickerhamomyces anomalus MSCU 0652 และ Kluyveromyces marxianus MSCU 0655) และแล็กติกแอซิดแบคทีเรีย (Lactobacillus casei AN2 และ Lactobacillus paracasei AN3) ในการยับยั้งการเจริญและการผลิตอะฟลาทอกซินของ A. flavus บนอาหารเลี้ยงเชื้อ พบว่า จุลินทรีย์ปฏิปักษ์ที่ใช้ทดสอบทั้งหมดให้ผลการยับยั้งการเจริญของราค่อนข้างต่ำ (10-20 เปอร์เซ็นต์) อย่างไรก็ตาม ยีสต์ผสมระหว่าง W. anomalus MSCU 0652 และ K. marxianus MSCU 0655 และ L. paracasei AN3 แบบเดี่ยวมีประสิทธิภาพในการลดการผลิตอะฟลาทอกซินรวมสูงสุด (43.25 และ 35.64 เปอร์เซ็นต์ ตามลำดับ) ดังนั้น จึงนำยีสต์ผสมและ L. paracasei AN3 มาทดสอบความสามารถในการยับยั้งการเจริญและการผลิตอะฟลาทอกซินรวมของ A. flavus ในไซเลจข้าวโพดปลอดเชื้อและไซเลจข้าวโพดร่วมกับจุลินทรีย์ประจำถิ่น พบว่า การใช้ L. paracasei AN3 ร่วมกับยีสต์ผสมระหว่าง W. anomalus MSCU 0652 และ K. marxianus MSCU 0655 สามารถยับยั้งการเจริญและลดปริมาณอะฟลาทอกซินรวมของราได้ดีทั้งในไซเลจข้าวโพดปลอดเชื้อและไซเลจข้าวโพดที่หมักร่วมกับจุลินทรีย์ประจำถิ่น จากนั้น เมื่อทดสอบความเข้มข้นและอัตราส่วนของ L. paracasei AN3 ร่วมกับยีสต์ผสมระหว่าง W. anomalus MSCU 0652 และ K. marxianus MSCU 0655 ที่เหมาะสม พบว่า การเติม L. paracasei AN3 ที่ความเข้มข้นมากกว่ายีสต์ผสม (10⁸:10⁶) …

Biochemical, Structural, And Drug Design Studies Of Norovirus And Zika Virus Proteases, Ben Kuiper

Wayne State University Dissertations

Noroviruses, which are the leading cause of acute gastroenteritis, cause an estimated 677 million infections and 213,000 deaths each year worldwide. Noroviruses are classified into seven genogroups (GI-GVII); GI, GII, and GIV have been shown to be infectious in humans. However, GII noroviruses cause the majority of outbreaks (89%). No pharmacologic treatment or vaccine currently exists to treat or prevent norovirus infections.

Recently, the development of a norovirus replicon system, a murine model of norovirus infection, and the development of a biochemical protease assay have allowed for the design and development of norovirus inhibitors. However, the replicon and biochemical assay …

Investigation Into Roseburia Intesinalis For Optimal Growth And Survivability Conditions For Potential Probiotic Use, Lisa Rana Felczak

Wayne State University Theses

Obesity and diabetes is an epidemic of increasing concern. Certain novel bacteria have been found to be an aid in reversing some of the mechanisms associated. This study focused on investigating the optimal stability conditions for R.intestinalis that can associate with an increase in growth. First, environmental conditions were tested to find the optimal conditions associated with each. Once growth conditions were found, generation time was calculated and various prebiotics were used to investigate a potential for additional growth. Next, common antibiotics were tested to see if the R.intestinalis could still show growth when exposed. Large batches of R.intestinalis were …

Human Cytomegalovirus Cytoplasmic Virion Assembly Complex: Structure In Vivo And Role Of Pul103 In Its Biogenesis, Ma Christina Raye Lim

Wayne State University Theses

Human Cytomegalovirus (HCMV) is a linear, double stranded DNA virus that causes severe disease in the immunocompromised, and is one of the common cause of congenital disease. Antivirals that are currently available for treatment target the DNA replication of the virus cycle, and are highly toxic. Finding new drug targets, such as proteins responsible for virion assembly and egress, would help to alleviate the disease burden.

HCMV remodels the host cell to form a structure called the cytoplasmic virion assembly complex (cVAC), a site of virion maturation and egress. The first objective of this work is to study the structure …

The Potential Stimulation Of C. Minuta Growth By Various Prebiotics, And Its Sensitivity To Various Antibiotics, Maria Elena Hakim

Wayne State University Theses

Gut microbiota play a crucial role in maintaining intestinal health and integrity; a feature that is both heritable, as well as affected by the environment and lifestyle. Probiotics are supplements containing live microorganisms that act in a similar manner to gut microflora, and maintain a balance in the latter. C. minuta is a novel bacterium in the gut that was found to be associated with reduction in body weight and adiposity. The aim of this study was to determine the possible effects of different prebiotics on C. minuta growth, and the survival of C. minuta in response to different antibiotics. …

The Neonatal Anti-Viral Response Fails To Control Measles Virus Spread In Neurons Despite Interferon-Gamma Expression And A Th1-Like Cytokine Profile, Priya Ganesan

Electronic Theses and Dissertations

Neonates are highly susceptible to infections in the central nervous system (CNS) and have a greater risk of viral infections and encephalopathies. Neurotropic viral infections can lead to blindness, hearing loss and neurological deficiencies such as cognitive impairment, epilepsy, and even death in the neonatal and pediatric populations. Viral infections also are hypothesized to indirectly contribute to neurodegenerative and neuropsychiatric diseases such as Schizophrenia and Parkinson’s disease later in life due to early neuronal damage or stress. Many diverse viruses are capable of invading the neonatal CNS including Borna Disease Virus, Coxsackievirus (CV), Herpes simplex viruses (HSV), and measles virus. …

Antifungal Genome Mining And Genetics In Filamentous Actinomycete Bacteria Isolated From Local Soils, Jacob Alex, Kevin Lou, Bilal Makhdoom

Undergraduate Research Symposium Posters

Actinomycetes are gram positive, filamentous bacteria that produce useful antibiotics, antitumor agents, and agricultural products. A series of enrichments were undertaken to isolate actinomycetes from local soils, varying enrichment media, antibacterials, and soil treatments (including heat and CaCO3). Isolates were characterized by 16S rDNA sequencing, phenotypic and morphological observations, and antibiotic production. The genetic tractability of select isolates was analyzed using a panel of integrating vectors derived from ɸC31, ɸBT1, and OzzyJ phage using intergeneric conjugation. Further, a semi-degenerate multiplex PCR assay to detect ɸBT1 genomic integrants was designed and tested for the first time. Finally, PCR screens were used …

Fractionation And Characterization Of Lignin Streams From Genetically Engineered Switchgrass, Enshi Liu

Theses and Dissertations--Biosystems and Agricultural Engineering

Development of biomass feedstocks with desirable traits for cost-effective conversion is one of the main focus areas in biofuels research. As suggested by techno-economic analyses, the success of a lignocellulose-based biorefinery largely relies on the utilization of lignin to generate value-added products, i.e. fuels and chemicals. The fate of lignin and its structural/compositional changes during pretreatment have received increasing attention; however, the effect of genetic modification on the fractionation, depolymerization and catalytic upgrading of lignin from genetically engineered plants is not well understood. This study aims to fractionate and characterize the lignin streams from a wild-type and two genetically engineered …

Role Of Intracellular Growth During The Gastrointestinal Stage Of Listeria Monocytogenes Infection, Grant Steven Jones

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

Listeria monocytogenes is a facultative intracellular bacterium that causes foodborne disease in humans. L. monocytogenes invade the gut mucosa and then disseminate, causing systemic infections associated with high mortality rates in immunocompromised individuals. It is unknown how L. monocytogenes traffic to the mesenteric lymph nodes, which represent an important bottleneck for systemic spread. In addition, little is known about the gastrointestinal stage of infection due to the general resistance of mice to oral infection with L. monocytogenes. Our laboratory developed a novel foodborne mouse model of listeriosis utilizing a murinized strain of L. monocytogenes to investigate the gastrointestinal stage …

Evolution Of Equine Arteritis Virus During Persistent Infection In The Reproductive Tract Of The Stallion And The Male Donkey, Bora Nam

Theses and Dissertations--Veterinary Science

Equine arteritis virus (EAV) establishes persistent infection in the stallion reproductive tract, and the carrier stallion continues to shed virus in semen for weeks to years or lifelong. The objective of this study was to elucidate the intra-host evolution of EAV during persistent infection in stallions. Seven EAV seronegative stallions were experimentally infected with EAV KY84 strain and followed for 726 days post-infection, and sequential clinical samples including semen were collected for virus isolation and next-generation sequencing (NGS). In addition, archived sequential semen samples from two stallions that were naturally infected with EAV KY84 for a long-period (up to 10 …

Designing A Luminescence Assay To Measure In Vitro Binding Of The Fibronectin Attachment Protein (Fap) Of Mycobacterium Avium Subspecies Paratuberculosis To Fibronectin, Sirri Ngwa

All Graduate Theses, Dissertations, and Other Capstone Projects

The attachment and penetration of epithelial cells by Mycobacterium avium subsp. paratuberculosis (MAP) requires a bacterial fibronectin (FN) attachment protein FAP-P, which facilitates binding of FN by MAP. The region of FAP-P that interacts with FN is known, however, the region of FN that is bound by FAP-P is to be determined. Identification of the region of FN to which FAP-P binds would enable the synthesis of a competing peptide that could prevent FN binding by MAP. The first step toward locating this binding site is the design of a reliable FN binding assay. The purpose of this investigation was …

Humboldt Journal Of Microbiology: Volume 19, Number 1- May 2017, Press Humboldt

Humboldt Journal of Microbiology

No abstract provided.

A First Look At The Microbial Community Of Rabidosa Rabida, A Wolf Spider In Searcy, Arkansas, Patricia Rivera, Ryan Stork, Amber Hug

Journal of the Arkansas Academy of Science

Many diverse animal models have been used to explore the interactions between host organisms and their microbiota. Increased understanding of microbe-host interactions could lead to improved healthcare and drug development. Spiders have venom, digestive fluid, and body fluid components that have been suggested to possess antimicrobial properties that could lead to new and interesting host-microbe interactions. While studies have been published on interactions between bacteria affecting the immune function and behavior of spiders, the spider microbiome has not been established to date. Excreta and body swabs were collected from Rabidosa rabida, a wolf spider typically found on tall grass …

Identification And Analysis Of Bacterial Genomic Metabolic Signatures, Nathaniel Bowerman, Nathan L. Tintle, Matthew Dejongh, Aaron A. Best

Faculty Work Comprehensive List

With continued rapid growth in the number and quality of fully sequenced and accurately annotated bacterial genomes, we have unprecedented opportunities to understand metabolic diversity. We selected 101 diverse and representative completely sequenced bacteria and implemented a manual curation effort to identify 846 unique metabolic variants present in these bacteria. The presence or absence of these variants act as a metabolic signature for each of the bacteria, which can then be used to understand similarities and differences between and across bacterial groups. We propose a novel and robust method of summarizing metabolic diversity using metabolic signatures and use this method …