Microbiology Commons^™

Molecular Diversity Of Foliar Fungal Endophytes In Relation To Defense Strategies And Disease In Whitebark Pine, Lorinda Bullington

Graduate Student Theses, Dissertations, & Professional Papers

An invasive fungal pathogen, Cronartium ribicola (the causative agent of white pine blister rust) infects and kills whitebark pine (Pinus albicaulis) throughout the western US. Blister rust has decreased whitebark pine populations by over 90% in some areas. Whitebark pine, a keystone species, has been proposed for listing under the Endangered Species Act in the U.S., and the loss of this conifer is predicted to have severe impacts on forest composition and function in high elevations. Hundreds of asymptomatic fungal species live inside whitebark pine tissue, and recent studies suggest that these fungi can influence the frequency and …

Eukaryotic Microbes, Principally Fungi And Labyrinthulomycetes, Dominate Biomass On Bathypelagic Marine Snow, Alexander B. Bochdansky, Melissa A. Clouse, Gerhard J. Herndl

OES Faculty Publications

In the bathypelagic realm of the ocean, the role of marine snow as a carbon and energy source for the deep-sea biota and as a potential hotspot of microbial diversity and activity has not received adequate attention. Here, we collected bathypelagic marine snow by gentle gravity filtration of sea water onto μm filters from similar to 1000 to 3900 m to investigate the relative distribution of eukaryotic microbes. Compared with sediment traps that select for fast-sinking particles, this method collects particles unbiased by settling velocity. While prokaryotes numerically exceeded eukaryotes on marine snow, eukaryotic microbes belonging to two very distant …

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 …