Microbiology Commons^™

Investigating The Role Of Cysteine In Biofilm Formation By Vibrio Fischeri, Priyanka Abhishek Singh

Master's Theses

Biofilms are an important area of medical research because bacterial biofilms can form on implants such as catheters and are highly resistant to antibiotics and other antimicrobials. The symbiosis between Vibrio fischeri-Euprymna scolopes, is good model to study biofilm. V. fischeri has 18 gene polysaccharide locus, syp, that is required for biofilm formation and colonization. A recent mutant study suggested the possibility that cysteine biosynthetic genes were involved in biofilm formation by V. fischeri, including cysH, cysJ, cysK, and cysN. My results supported a role for cysK and, to a lesser extent, cysH in biofilm formation. Finally, I have data …

An Analysis Of Microbial Involvement In Biospeleogenesis Within Lechuguilla Cave System, Garrett Sonntag

Williams Honors College, Honors Research Projects

Caves are geologic systems, shaped by inorganic chemical processes (speleogenesis). Nonetheless, there is increasing evidence that biological processes also play a role in the origin and development of caves (biospeleogenesis). In order to examine the role that microorganisms may play in secondary passage enlargement we collected samples from Lechuguilla Cave, a deep cave system that is largely shielded from human impact. Samples were collected from areas where rock corrosion was obvious. In order to determine if microorganisms were involved with the observed corrosion, we used scanning electron microscopy (SEM) to identify apparent microbial pitting of the rock surface. To establish …

Characterization Of Oral Microbiota In Xerostomic Versus Non-Xerostomic Volunteers And In Daily Samples Following Standard Oral Hygiene Practices, Chelsea Myers

Wayne State University Theses

A thesis presented on the characterization of oral microbiota in xerostomic versus non-xerostomic volunteers and in daily samples following standard oral hygiene practices. Xerostomia is a difficult and burdensome disease that can be very difficult to diagnose. Understanding the oral microbiota between these diseased and healthy (non-xerostomic) can give us great insight on new treatments and/or prevention. Goals of the study included determining whether there substantial differences in oral microbial populations between the two groups, and whether varying nightly oral hygiene practices had an impact on next-morning oral microbiota titers or composition. Microbial loads were determined by qPCR using broad-spectrum …

Investigation Of Post-Translational Modifications In Staphylococcus Aureus, Christina Nadia Krute

USF Tampa Graduate Theses and Dissertations

The work presented herein details post-translational modifications (PTMs) in Staphylococcus aureus that are involved in mediating the stress response and normal cellular processes. The first PTM that was investigated is regulated intramembrane proteolysis (RIP) for the activation of the ECF sigma factor σS. We achieved this by analyzing the role of the site-1 protease, which we termed “putative regulator of sigmaS” (PrsS), as it is predicted to be the first enzyme in the RIP cascade, leading to the activation of σS. It was determined that the putative site-1 protease, prsS, mimics transcriptional profiles of sigS; with expression low in all …

Self-Cleaning Applications Of Tio2 By Photo-Induced Hydrophilicity And Photocatalysis, Swagata Banerjee, Dionysios Dionysiou, Suresh Pillai

Articles

Self-cleaning materials have gained considerable attention for both their unique properties and practical applications in energy and environmental areas. Recent examples of many TiO2-derived materials have been illustrated to understand the fundamental principles of self-cleaning hydrophilic and hydrophobic surfaces. Various models including those proposed by Wenzel, Cassie-Baxter and Miwa-Hashimoto are discussed to explain the mechanism of self-cleaning. Examples of semiconductor surfaces exhibiting the simultaneous occurrence of superhydrophilic and superhydrophobic domains on the same surface are illustrated, which can have various advanced applications in microfluidics, printing, photovoltaic, biomedical devices, anti-bacterial surfaces and water purification.

Several strategies to improve the efficiency of …

Whole-Genome Sequencing Of Kaposi’S Sarcoma-Associated Herpesvirus From Zambian Kaposi’S Sarcoma Biopsy Specimens Reveals Unique Viral Diversity, Landon Olp, Adrien Jeanniard, Clemence Marimo, Charles Wood

Nebraska Center for Virology: Faculty Publications

Kaposi’s sarcoma-associated herpesvirus (KSHV) is the etiological agent for Kaposi’s sarcoma (KS). Both KSHV and KS are endemic in sub-Saharan Africa where approximately 84% of global KS cases occur. Nevertheless, whole-genome sequencing of KSHV has only been completed using isolates from Western countries—where KS is not endemic. The lack of whole-genome KSHV sequence data from the most clinically important geographical region, sub-Saharan Africa, represents an important gap since it remains unclear whether genomic diversity has a role on KSHV pathogenesis. We hypothesized that distinct KSHV genotypes might be present in sub-Saharan Africa compared to Western countries. Using a KSHV-targeted enrichment …

Escherichia Coli Surface Display Of Single-Chain Antibody Vrc01 Against Hiv-1 Infection, Lin-Xu Wang, Michael Mellon, Dane Bowder, Meghan Quinn, Danielle Shea, Charles Wood, Shi-Hua Xiang

Nebraska Center for Virology: Faculty Publications

Human immunodeficiency virus type 1 (HIV-1) transmission and infection occur mainly via the mucosal surfaces. The commensal bacteria residing in these surfaces can potentially be employed as a vehicle for delivering inhibitors to prevent HIV-1 infection. In this study, we have employed a bacteria-based strategy to display a broadly neutralizing antibody VRC01, which could potentially be used to prevent HIV-1 infection. The VRC01 antibody mimics CD4-binding to gp120 and has broadly neutralization activities against HIV-1. We have designed a construct that can express the fusion peptide of the scFv-VRC01 antibody together with the autotransporter β-barrel domain of IgAP gene from …

The Hippo/Yap Pathway Interacts With Egfr Signaling And Hpv Oncoproteins To Regulate Cervical Cancer Progression, Chunbo He, Dagan Mao, Guohua Hua, Xiangmin Lv, Xingcheng Chen, Peter C. Angeletti, Jixin Dong, Steven W. Remmenga, Kerry J. Rodabaugh, Jin Zhou, Paul F. Lambert, Peixin Yang, John S. Davis, Cheng Wang

Nebraska Center for Virology: Faculty Publications

The Hippo signaling pathway controls organ size and tumorigenesis

through a kinase cascade that inactivates Yes-associated

protein (YAP). Here, we show that YAP plays a central role in

controlling the progression of cervical cancer. Our results suggest

that YAP expression is associated with a poor prognosis for cervical

cancer. TGF-α and amphiregulin (AREG), via EGFR, inhibit the Hippo

signaling pathway and activate YAP to induce cervical cancer cell

proliferation and migration. Activated YAP allows for up-regulation

of TGF-α, AREG, and EGFR, forming a positive signaling loop to

drive cervical cancer cell proliferation. HPV E6 protein, a major

etiological molecule of …

Activation And Degradation Of Open Reading Frame 45 By The Replication And Transcription Activator Of Kaposi's Sarcoma-Associated Herpesvirus, Ying Wang, Kai Yu, Xiuzhi Pei, Tiancheng Zhang, Yuying Guo, Charles Wood, Jinzhong Wang

Nebraska Center for Virology: Faculty Publications

The open reading frame 45 (ORF45) of the Kaposi's sarcoma-associated herpesvirus (KSHV) is an immediate-early phosphorylated tegument protein critical for viral escape from host immune surveillance. Its expression is upregulated by the viral replication and transcription activator (RTA), a key protein that controls the switch from latency to lytic replication. We report here that ORF45 expression was not only upregulated by RTA, but ORF45 could also be degraded by RTA in a proteasome-dependent manner. The ORF45 was activated by RTA via activation of the ORF45 promoter, and the promoter region from nt 69 271 to nt 69 026 was involved. …

Single-Dose Cpg Immunization Protects Against A Heterosubtypic Challenge And Generates Antigen-Specific Memory T Cells, Alexander J. Vogel, Deborah M. Brown

Nebraska Center for Virology: Faculty Publications

Despite extensive research, influenza A virus (IAV) remains a major cause of morbidity, mortality, and healthcare expenditure. Emerging pandemics from highly pathogenic IAV strains, such as H5N1 and pandemic H1N1, highlight the need for universal, crossprotective vaccines. Current vaccine formulations generate strain-specific neutralizing antibodies primarily against the outer coat proteins, hemagglutinin and neuraminidase. In contrast to these highly mutable proteins, internal proteins of IAV are more conserved and are a favorable target for developing vaccines that induce strong T cell responses in addition to humoral immunity. Here, we found that intranasal administration with a single dose of CpG and inactivated …

Long-Acting Parenteral Combination Antiretroviral Loaded Nano-Drug Delivery System To Treat Chronic Hiv-1 Infection: A Humanized Mouse Model Study, Subhra Mandal, Guobin Kang, Pavan Kumar Prathipati, Wenjin Fan, Qingsheng Li, Christopher J. Destache

Nebraska Center for Virology: Faculty Publications

Human immunodeficiency virus (HIV) patients are often diagnosed in the chronic stage of HIV/AIDS. Combination antiretroviral therapy (cART) has improved quality of life for HIV-infected patients. Present study describes a novel long-acting parenteral formulation of combination antiretroviral (cARV) loaded nano-drugs for treating chronic HIV-1 (cHIV) in a humanized-BLT (hu-BLT) mice model. The cARV (elvitegravir + tenofovir alafenamide + emtricitabine; EVG + TAF + FTC) drugs (mimicking marketed Genvoy® one-pill for HIV-treatment) were encapsulated in poly (lactic-co-glycolic acid) nanoparticles (NPs). To establish cHIV, hu-BLT mice were intravaginally challenged with HIV-1 and maintained for 15 weeks. Plasma viral load (pVL) was monitored …

Characterization Of Cd8+ T Cell Differentiation Following Sivδnef Vaccination By Transcription Factor Expression Profiling, James M. Billingsley, Premeela A. Rajakumar, Michelle A. Connole, Nadine C. Salisch, Sama Adnan, Yury V. Kuzmichev, Henoch S. Hong, R. Keith Reeves, Hyung-Joo Kang, Wenjun Li, Qingsheng Li, Ashley T. Haase, R. Paul Johnson

Nebraska Center for Virology: Faculty Publications

The onset of protective immunity against pathogenic SIV challenge in SIVΔnef-vaccinated macaques is delayed for 15-20 weeks, a process that is related to qualitative changes in CD8⁺ T cell responses induced by SIVΔnef. As a novel approach to characterize cell differentiation following vaccination, we used multi-target qPCR to measure transcription factor expression in naïve and memory subsets of CD8+⁺ T cells, and in SIV-specific CD8⁺ T cells obtained from SIVΔnef-vaccinated or wild type SIVmac239-infected macaques. Unsupervised clustering of expression profiles organized naïve and memory CD8⁺ T cells into groups concordant with cell surface phenotype. Transcription factor …

Identification And Comparative Analysis Of Subolesin/Akirin Ortholog From Ornithodoros Turicata Ticks, Hameeda Sultana, Unnati Patel, Daniel E. Sonenshine, Girish Neelakanta

Biological Sciences Faculty Publications

Background: Subolesin is an evolutionary conserved molecule in diverse arthropod species that play an important role in the regulation of genes involved in immune responses, blood digestion, reproduction and development. In this study, we have identified a subolesin ortholog from soft ticks Ornithodoros turicata, the vector of the relapsing fever spirochete in the United States.

Methods: Uninfected fed or unfed O. turicata ticks were used throughout this study. The subolesin mRNA was amplified by reverse transcription polymerase chain reaction (RT-PCR) and sequenced. Quantitative-real time PCR (QRT-PCR) was performed to evaluate subolesin mRNA levels at different O. turicata developmental stages …

Correlation Analysis Of Climatic Variables, Migration And Dengue Cases In Southeast Florida, Brunilda Lugo

Walden Dissertations and Doctoral Studies

Dengue fever is a debilitating, viral, mosquito-borne disease occurring in tropical and subtropical areas in the world. The majority of dengue cases in the United States were acquired in endemic areas by travelers or immigrants. However, in recent years, autochthonous (locally acquired) dengue cases have been diagnosed in Florida. The purpose of this study was to find an association between potential risk factors and the expansion of dengue fever in the United States. Guided by the eco-bio-social framework, which offers a broad assessment of risk factors for the illness, a retrospective design was used with archival data to correlate changes …

The Effect Of O Antigen Loss On The Protein Composition And Inflammatory Response Elicited By Klebsiella Pneumoniae, Bethaney Cahill

UNF Graduate Theses and Dissertations

Klebsiella pneumoniae is a Gram-negative pathogen associated with numerous infections. Like all Gram-negative bacteria, K. pneumoniae naturally release outer membrane vesicles (OMVs) during all stages of cellular growth. OMVs are composed of the outer membrane components such as lipopolysaccharide (LPS) and outer membrane proteins and contain cytosolic and periplasmic proteins in the lumen. K. pneumoniae is often found to lack an O antigen. The absence of the O antigen has been reported to alter the protein content of the membrane which may further alter the immune response elicited by K. pneumoniae. Therefore the purpose of this study was to …

Characterization Of A Biosynthetic Pathway Yielding Anticancer Natural Products From A Marine Bacterium, Elle D. James

UNF Graduate Theses and Dissertations

Natural products are bioactive secondary metabolites produced by living organisms and are prevalently utilized as pharmaceutical drugs. Marine adapted organisms are a promising source of new natural products possessing unique chemical structures and biological activities. By studying the biosynthetic pathways employed by living organisms to produce natural products, insights into new strategies to generate molecules to combat disease and overcome drug resistance may be gained. This thesis study aimed to uncover the biosynthetic pathway employed by a marine actinomycete, Nocardiopsis sp. CMB-M0232, to catalyze the assembly of the nocardioazines. These molecules are a group of 2,5-diketopiperazine natural products that feature …

Quantitative Study Of Clostridium Difficile Incidence Related To Influenza And Antimicrobial Use, Eileen M. Yaeger

Walden Dissertations and Doctoral Studies

In the United States, influenza causes approximately 36,000 deaths and over 200,000 hospitalizations each year with elderly most often affected. Clostridium difficile infection (CDI) is another major health care challenge and pressing public health issue associated with 14,000 deaths and over 335,000 hospitalizations annually. The use of antibiotics has been implicated in the development of CDI. This study's purpose was to test the relationship of seasonal influenza incidence and antiviral/antibiotic use in CDI development among hospitalized patients. Grounded in the epidemiologic wheel model of man-environment interactions, this retrospective observational study described and analyzed data from a proprietary, laboratory, and pharmacy-based …

Signaling Between Two Sensor Kinases Controls Biofilms And Host Colonization In A Bacterial Symbiont, Allison N. Norsworthy

Dissertations

Organisms within all domains of life must acclimate to fluctuating environments to survive. To do this, cells utilize sensory circuits, which function to connect environmental stimuli to an intracellular response. One common sensory pathway utilized by bacteria is two-component signaling (TCS), composed of an environmental sensor (the sensor kinase, SK) and a cognate, intracellular effector (the response regulator, RR). The marine bacterium Vibrio fischeri uses an elaborate TCS phosphorelay containing a hybrid SK, RscS, and two RRs, SypE and SypG, to colonize its natural squid host, Euprymna scolopes. This TCS pathway regulates V. fischeri's ability to form a biofilm, or …

The Role Of Dksa In The Stringent Response In The Lyme Disease Spirochete Borrelia Burgdorferi, Britney Cheff

Graduate Student Theses, Dissertations, & Professional Papers

Borrelia burgdorferi, the bacterium that causes Lyme disease, is maintained in nature through an enzootic cycle that includes a tick vector and a vertebrate host. The bacterium is acquired by an Ixodes tick from an infected vertebrate. The bacterium alters its gene expression to adapt to different environments of the tick and vertebrate. Between tick feedings, B. burgdorferi must contend with nutrient stress. The stringent response is a physiological mechanism when bacteria switch from “thriving” to “surviving” mode in response to limited nutrient resources; it is mediated by an increase in the nucleotide alarmone guanosine penta- or tetraphosphate, abbreviated …

Application Of Supervised Machine Learning Algorithms For Rapid Identification Of Mrsa Pfge Strain Types, Michael L. Bernauer

Biomedical Informatics Seminar Series (BioMISS)

Introduction: Pulsed-field gel electrophoresis (PFGE) is a molecular typing method used in epidemiologic surveillance of MRSA. PFGE relies on electrophoretic migration of restricted DNA fragments, resulting in characteristic fingerprints which can be used to classify organisms. Current methods of analysis, such as Gel Compar II and BioNumerics rely on unsupervised hierarchical clustering algorithms to group organisms based on pairwise similarity. These methods are labor intensive, often requiring a significant amount of user intervention and oversight. This study presents an automated approach to PFGE typing to reduce the amount of user involvement and time required for analysis.

Methods: A total of …

ประสิทธิภาพของกลุ่มแบคทีเรียจากดินตะกอนบริเวณอ่าวไทยในการย่อยสลายเชิงชีวภาพของพอลิไซคลิกแอโรแมติกไฮโดรคาร์บอนแบบผสม, พลอยชนก จันทร์เอี่ยม

Chulalongkorn University Theses and Dissertations (Chula ETD)

อ่าวไทยเป็นจัดเป็นแหล่งทรัพยากรที่มีความอุดมสมบูรณ์และมีความสำคัญในด้านการคมนาคมทางน้ำ การขุดเจาะน้ำมัน การทำประมง รวมไปถึงเป็นแหล่งท่องเที่ยวที่สำคัญ ทำให้มีโอกาสเกิดการปนเปื้อนและการตกค้างของ PAHs ในดินตะกอน งานวิจัยนี้จึงมีเป้าหมายเพื่อทดสอบประสิทธิภาพกลุ่มแบคทีเรียที่คัดแยกจากตัวอย่างดินตะกอนอ่าวไทยในการย่อยสลาย PAHs ผสม โดยเริ่มจากตรวจนับจำนวนแบคทีเรียโดยวิธี MPN พบจำนวนแบคทีเรียทั้งหมดและแบคทีเรียย่อยสลาย PAHs ใน 22 ตัวอย่าง พบว่ามีค่าอยู่ในช่วง 1.77x108 - 8.30x109 และ 3.00 x104 ถึง 1.10x107 MPN/กรัมดินเปียก ตามลำดับ เมื่อรวมตัวอย่างดินตะกอนตามลักษณะทางกายภาพของพื้นที่และดินตะกอน ได้เป็น 7 ตัวอย่าง (G1-G7) และเพิ่มจำนวนแบคทีเรียย่อยสลาย PAHs ผสมด้วยวิธีเอนริชเมนท์ พบว่ากลุ่มแบคทีเรีย G7 มีประสิทธิภาพในการย่อยสลาย PAHs ผสมได้สูงที่สุด โดยย่อยสลาย PAHs ผสม 4 ชนิด ได้แก่ ฟีแนนทรีน แอนทราซีน ฟลูออแรนทีน และไพรีน ความเข้มข้นชนิดละ 50 มิลลิกรัม/ลิตรได้ 82, 92, 62 และ 50% ตามลำดับ ใน 14 วัน นอกจากนี้ในการย่อยสลาย PAHs 5 ชนิด กลุ่มแบคทีเรีย G7 ยังสามารถย่อยสลายเบนโซ[เอ]ไพรีนซึ่งมีความเป็นพิษสูง ได้ถึง 38% จากความเข้มข้นเริ่มต้น 10 มิลลิกรัม/ลิตร ในขณะที่ยังคงรักษาประสิทธิภาพในการย่อยสลาย PAHs ผสม 4 ชนิดเดิมไว้ได้ อีกทั้งมีประสิทธิภาพในการย่อยสลาย PAHs ผสม 7 ชนิด ได้แก่ อะซีแนพธีน อะซีแนพธิลีน ฟลูออรีน ฟีแนนทรีน แอนทราซีน ฟลูออแรนทีน และไพรีน ซึ่งเพิ่ม PAHs ชนิดมวลโมเลกุลต่ำที่ความเข้มข้นสุดท้ายชนิดละ 30 มิลลิกรัม/ลิตรได้ นอกจากนี้ กลุ่มแบคทีเรีย …

Characterization Of The Nodamura Virus Rna Dependent Rna Polymerase And Formation Of Rna Replication Complexes In Mammalian Cells, Vincent Ulysses Gant

Open Access Theses & Dissertations

Positive-strand RNA viruses amplify their genomes in membrane-bound structures associated with intracellular membranes and organelles called replication complexes (RCs). Here, we begin to elucidate mechanisms of Nodamura virus (NoV; family Nodaviridae) RC assembly. The literature reports that NoV-infected muscle tissue exhibits mitochondrial aggregation and rearrangement of mitochondrial structure, leading to disorganization of the muscle fibrils. However, the molecular basis for this pathogenesis and the role of mitochondria in NoV infection remained unclear until now. We tested the hypoThesis that NoV establishes RCs in association with mitochondria in cultured mammalian cells at physiological temperature. We used immunofluorescence confocal microscopy and biochemical …

Iron Deficiency Increases Growth And Nitrogen-Fixation Rates Of Phosphorus-Deficient Marine Cyanobacteria, Nathan S. Garcia, Feixue Fu, Peter N. Sedwick, David A. Hutchins

OES Faculty Publications

Marine dinitrogen (N²)-fixing cyanobacteria have large impacts on global biogeochemistry as they fix carbon dioxide (CO₂) and fertilize oligotrophic ocean waters with new nitrogen. Iron (Fe) and phosphorus (P) are the two most important limiting nutrients for marine biological N₂ fixation, and their availabilities vary between major ocean basins and regions. A long-standing question concerns the ability of two globally dominant N₂-fixing cyanobacteria, unicellular Crocosphaera and filamentous Trichodesmium, to maintain relatively high N₂-fixation rates in these regimes where both Fe and P are typically scarce. We show that under P-deficient …

Heterotrophic And Autotrophic Contribution To Dinitrogen Fixation In The Gulf Of Aqaba, Eyal Rahav, Barak Herut, Margaret R. Mulholland, Natalia Belkin, Hila Elifantz, Ilana Berman-Frank

OES Faculty Publications

We evaluated the seasonal contribution of heterotrophic and autotrophic diazotrophy to the total dinitrogen (N₂) fixation in the photic zone of a pelagic station in the northern Gulf of Aqaba, Red Sea. N₂ fixation rates were highest during a Trichodesmium bloom in winter (0.7 nmol N l^-1 d^-1), decreased 7-fold 1 wk later throughout the upper 200 m (~0.1 nmol N l^-1) d^-1), and were significantly coupled with both primary and bacterial productivity. N₂ fixation rates were generally higher in the upper 200 m (~0.4 nmol N l^{-1 …}