Microbiology Commons^™

Phagephisher: A Pipeline For The Discovery Of Covert Viral Sequences In Complex Genomic Datasets, Thomas Hatzopoulos, Siobhan C. Watkins, Catherine Putonti

Bioinformatics Faculty Publications

Obtaining meaningful viral information from large sequencing datasets presents unique challenges distinct from prokaryotic and eukaryotic sequencing efforts. The difficulties surrounding this issue can be ascribed in part to the genomic plasticity of viruses themselves as well as the scarcity of existing information in genomic databases. The open-source software PhagePhisher (http://www.putonti-lab.com/phagephisher) has been designed as a simple pipeline to extract relevant information from complex and mixed datasets, and will improve the examination of bacteriophages, viruses, and virally related sequences, in a range of environments. Key aspects of the software include speed and ease of use; PhagePhisher can be used with …

18s Rdna Dataset Profiling Microeukaryotic Populations Within Chicago Area Nearshore Waters, Daniel Searle, Emily Sible, Alexandria Cooper, Catherine Putonti

Bioinformatics Faculty Publications

Despite their critical role in the aquatic food web and nutrient cycling, microeukaryotes within freshwater environments are under-studied. Herein we present the first high-throughput molecular survey of microeukaryotes within Lake Michigan. Every two weeks from May 13 to August 5, 2014, we collected surface water samples from the nearshore waters of four Chicago area beaches: Gillson Park, Montrose Beach, 57th Street Beach, and Calumet Beach. Four biological replicates were collected for each sampling date and location, resulting in 112 samples. Eighty-nine of these samples were surveyed through targeted sequencing of the V7 and V8 regions of the 18S rDNA gene. …

Investigation Of A Ubiquitous Spore Surface Protein, Justyna Kordzikowska

Master's Theses

All bacterial spores are comprised of concentric shells. All spores are encased in a layer called the coat. Some spores have an additional layer outside of the coat called the exosporium. Presumably, this morphological variation is an adaptation to variation in the environments in which these species can be found. However, spores from species with and without exosporia can often be found in the same niche. We hypothesize, therefore, that spores with and without exosporia share a common surface protein. Bacillus anthracis possess a well characterized surface protein called BclA. A BclA homologue is also present on the surface of …

Lipoate Metabolism In Staphylococcus Aureus Pathogenesis, Maria Azul Zorzoli

Master's Theses

Lipoate is an essential cofactor of several proteins involved in cellular energy homeostasis and catabolism. Lipoate metabolism has been linked to pathogenesis in some microbial species, but its role in Staphylococcus aureus infections had not been explored. In this thesis, we tested the hypothesis that lipoate acquisition mechanisms promote S. aureus infectivity. We used a bacterial genetics approach to elucidate the biological function of the S. aureus genes involved in lipoate metabolism. Our findings allowed us to propose a model for lipoic acid de novo biosynthesis and salvage pathways in S. aureus. Moreover, we detail hitherto undescribed genetic arrangements of …

Adenovirus Evasion Of Cell-Intrinsic Immunity, Andrew Michael Burrage

Dissertations

Virus cell entry represents one of the earliest opportunities for a host to respond to infection. Understanding the processes of pathogen detection and restriction employed by the host, as well as strategies utilized by the virus itself to evade such processes, is critical in developing therapeutics to counter pathogenesis. Adenovirus (Ad) infections are self-limiting in healthy populations, but can be devastating to individuals with compromised immune systems. Currently, no specific antiviral treatments exist to combat Ad infections in susceptible populations. However, because Ad infections are not severe in healthy individuals, employing replication-defective Ads as vaccine vectors is generally regarded as …

Draft Genome For A Urinary Isolate Of Lactobacillus Crispatus, Travis Kyle Price, Majed Shaheen, Laurynas Kalesinskas, Kema Malki, Evann Elizabeth Hilt, Catherine Putonti, Alan J. Wolfe

Bioinformatics Faculty Publications

While Lactobacillus crispatus contributes to the stability of normal vaginal microbiota, its role in urinary health remains unclear. As part of an on-going attempt to characterize the female urinary microbiota, we report the genome sequence of an L. crispatus strain isolated from a woman displaying no lower urinary tract symptoms.

Land-Use And Algal Species Influence Bacterial Community Composition And Activity In Streams, Miguel Rojas

Master's Theses

Microbial biofilms can be found on virtually all submerged surfaces in aquatic habitats, including rivers and streams. Biofilms are complex, taxonomically diverse communities of microorganisms (including algae and bacteria) that colonize solid surfaces and support a wide range of metabolic activities. Biofilms are critical components of river and stream ecosystems because they are key drivers of nutrient cycling processes (including nitrogen cycling) and because they serve as an important food source for higher trophic levels. Biofilms in urban streams are subject to a number of anthropogenic stressors, but research on the ecology of urban biofilms and their response to stressors …

Lactobacillus Crispatus Produces A Bacteridical Molecule That Kills Uropathogenic E. Coli, Katherine Diebel

Master's Theses

As many as 1 in 2 women will have at least one urinary tract infection (UTI) in their lifetime. UTIs can cause complications in pregnancy and decrease quality of life, and their treatment and prevention are expensive. Uropathogenic E. coli (UPEC) is the primary cause of UTI. The probiotic and bactericidal capacities of gut and vaginal Lactobacillus isolates have been studied, but the same attention has not been paid to urinary strains. These urinary isolates of L. crispatus appear to have a greater killing capacity against UPEC and this bactericidal activity does not depend on the cells themselves, consistent with …

Investigating The Regulatory Mechanisms By Which Arabinose And Sypa Control Biofilm Formation In Vibrio Fischeri, Sheila Paris

Master's Theses

Biofilms are surface-associated microbial communities surrounded by an extracellular matrix. Through biofilm formation, many pathogens and symbionts are able to colonize, survive, and persist in their host. A model system used to study biofilm formation is the symbiotic bacterium Vibrio fischeri, which colonizes its host, the squid Euprymna scolopes. Complex signaling between the squid and the bacteria is essential for the proper regulation of biofilm formation as well as for persistent colonization.

The signal(s) that promote host-relevant biofilm formation are as-yet unknown, but recently it was discovered that the sugar, L-arabinose, serves as a unique signal to promote biofilm formation …

Bacteriophages Isolated From Lake Michigan Demonstrate Broad Host-Range Across Several Bacterial Phyla, Kema Malki, Alex Kula, Katherine Bruder, Emily Sible, Thomas Hatzopoulos, Stephanie Steidel, Siobhan C. Watkins, Catherine Putonti

Biology: Faculty Publications and Other Works

BACKGROUND:

The study of bacteriophages continues to generate key information about microbial interactions in the environment. Many phenotypic characteristics of bacteriophages cannot be examined by sequencing alone, further highlighting the necessity for isolation and examination of phages from environmental samples. While much of our current knowledge base has been generated by the study of marine phages, freshwater viruses are understudied in comparison. Our group has previously conducted metagenomics-based studies samples collected from Lake Michigan - the data presented in this study relate to four phages that were extracted from the same samples.

FINDINGS:

Four phages were extracted from Lake Michigan …

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 Pidd Protein In Adenoviral Induction Of Apoptosis, Iris Teresa Figueroa

Master's Theses

The Adenovirus E1A gene sensitizes cells to genetic insults and apoptosis, most notably in response to cytotoxic factors from innate immune cells. The mechanisms by which E1A sensitizes cells to apoptotic stressors have not been fully elucidated, however E1A actively represses NF-κB anti-apoptotic defenses, thereby sensitizing cells to alternative apoptotic cascades. Recent studies alternatively indicate that E1A also actively induces Caspase-2 activation and mitochondrial injury in the presence of certain cytotoxic injuries.

Caspase-2 is cleaved and activated in a large complex consisting of p53-inducible protein with a death domain (PIDD), an adaptor protein RAIDD, and pro-caspase 2. PIDD auto-proteolyzes into …

The Effects Of Stress And Alcohol On Hiv-1 Latency, Sarah Ilene Talley

Master's Theses

A major barrier to HIV eradication is the persistence of latent viral reservoirs that exist despite antiretroviral therapy. In order to develop effective therapeutics, a comprehensive understanding of latency and factors driving the formation of the latent reservoir is needed. As stress and alcohol are common comorbidities associated with HIV infection, the goal of this research was to determine how stress and alcohol could affect HIV-latency. Specifically, we hypothesized that the ability of latent proviruses to be reactivated by “shock and kill” approaches would be altered by glucocorticoid and ethanol treatments, and prolonged ethanol exposure would affect the size of …

The Role Of Central Metabolism And Electron Transport In Biofilm Formation By Vibrio Fischeri, Jakob Michael Ondrey

Master's Theses

Biofilms protect bacteria from environmental threats, including antibiotics; thus, biofilms formed during infections pose an increasing threat to human health. A natural model used to study biofilm formation in the context of a host is the symbiosis between Vibrio fischeri and its host, the squid Euprymna scolopes. Successful colonization depends on the formation of a biofilm and genes involved in making the polysaccharide matrix component, syp. In culture, biofilm phenotypes, including the formation of wrinkled colonies, similarly depend on syp. However, little is known about other factors that contribute to this phenotype. To expand the utility of currently available genetic …

The Contribution Of The Female Urinary Microbiota To Lower Urinary Tract Symptoms, Travis Kyle Price

Master's Theses

The recent finding that urine is not sterile raises a lot of questions: first and foremost, what microorganisms are present, and are these microorganisms correlated with clinical urinary symptoms? Recent work on the female urinary microbiota (FUM) found that the communities of microorganisms differ between women with no lower urinary tract symptoms (LUTS) and those with Urgency Urinary Incontinence (UUI) a form of over-active bladder syndrome. Specifically, a diverse or dysbiotic urinary microbiota was found to be associated with symptomatic women. This suggests the possibility that the FUM can be contributing to urinary symptoms. Conversely, it could also suggest that …

Malaria Transmission Blocking Vaccines, Lukasz Jacek Sewera

Master's Theses

Malaria affects 198 million people and kills 584,000 each year, predominantly in Sub-Saharan Africa (WHO). The most severe form of malaria is caused by the protozoan parasite Plasmodium falciparum. Development of a vaccine against P. falciparum has been hindered by its complex life cycle with multiple antigenically distinct human and mosquito stages. To effectively prevent disease and reduce the parasite burden in populations, a vaccine will need to target multiple stages, including blocking transmission at the mosquito stage.

Antibodies generated against P. falciparum mosquito stage antigen Pfs25 can prevent parasite transmission from humans to mosquitoes. However, Pfs25 is poorly immunogenic …

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 …

Anthropogenic Litter In Urban Freshwater Ecosystems: Distribution And Microbial Interactions, Timothy Hoellein, Miguel Rojas, Adam Pink, Joseph Gasior, John J. Kelly

Biology: Faculty Publications and Other Works

Accumulation of anthropogenic litter (i.e. garbage; AL) and its ecosystem effects in marine environments are well documented. Rivers receive AL from terrestrial habitats and represent a major source of AL to marine environments, but AL is rarely studied within freshwater ecosystems. Our objectives were to 1) quantify AL density in urban freshwaters, 2) compare AL abundance among freshwater, terrestrial, and marine ecosystems, and 3) characterize the activity and composition of AL biofilms in freshwater habitats. We quantified AL from the Chicago River and Chicago's Lake Michigan shoreline, and found that AL abundance in Chicago freshwater ecosystems was comparable to previously …

Temporal Variations In The Abundance And Composition Of Biofilm Communities Colonizing Drinking Water Distribution Pipes, John J. Kelly, Nicole Minalt, Alessandro Culotti, Marsha Pryor, Aaron Packman

Biology: Faculty Publications and Other Works

Pipes that transport drinking water through municipal drinking water distribution systems (DWDS) are challenging habitats for microorganisms. Distribution networks are dark, oligotrophic and contain disinfectants; yet microbes frequently form biofilms attached to interior surfaces of DWDS pipes. Relatively little is known about the species composition and ecology of these biofilms due to challenges associated with sample acquisition from actual DWDS. We report the analysis of biofilms from five pipe samples collected from the same region of a DWDS in Florida, USA, over an 18 month period between February 2011 and August 2012. The bacterial abundance and composition of biofilm communities …

Effects Of Urbanization On Sediment Microbial Communities In Lotic Ecosystems, Bradley Drury

Master's Theses

The world is becoming increasingly urbanized, with the majority of the world's population now living in urban areas. Urbanization has the potential to significantly alter lotic ecosystems and the services they provide. Benthic microbial communities are key components of lotic ecosystems due to their contributions to primary production and nutrient cycling. Two types of human inputs associated with urbanization that may impact benthic microbial communities in lotic ecosystems are the input of wastewater treatment effluent and the input of emerging contaminants, including pharmaceuticals and personal care products. This work examines the effects of treated WWTP effluent on benthic microbial communities …

Coronavirus Proteases As Therapeutic Targets: Development Of Biosensors To Detect Inhibition Of Protease Activity And Separation Of The Multiple Functions Of Coronavirus Papain-Like Proteases, Andrew Kilianski

Dissertations

Coronaviruses are important human pathogens and have the potential to severely impact public health on an international scale. The emergence of SARS-CoV and MERS-CoV highlight the need for research to identify antivirals and vaccines against coronaviruses. To develop therapeutics against current and potentially emergent coronaviruses, I utilized two approaches targeting the proteases encoded within all coronaviruses. The papain-like protease and 3C-like protease of coronaviruses are responsible for cleaving viral polyproteins early during infection, and this step is required for viral replication. To quantitatively assess the inhibition by small-molecule compounds on MERS-CoV protease activity, I developed a luciferase-based biosensor to monitor …

Identification Of Clinical Markers That Predict The Outcomes Of Methicillin-Resistant Staphylococcus Aureus Infections And Identification Of Synergistic Antibiotic Combinations For The Treatment Of These Infections, Virginia Long

Master's Theses

Methicillin-resistant Staphylococcus aureus(MRSA) is a prominent nosocomial infection. Vancomycin is the mainstay of treatment, but it has a high rate of failure. Combination therapies can be used, but synergy is often not tested in clinical laboratories. Physicians are at a disadvantage because they cannot predict MRSA outcomes. The first aim of the study was to identify clinical and demographic markers that could predict infection recurrence or prolonged bacteremia. This was accomplished using retrospective chart review and statistical analysis. The second aim of the study was to identify which combinations, of those commonly used for MRSA treatment at Loyola, demonstrate the …

Host Proteins Interact With The Hiv-1 Core To Facilitate And Restrict, Zana Lukic

Dissertations

Host cell proteins, termed restriction factors, which inhibit viral replication at various stages of the viral life cycle, determine the species-specific tropism of numerous retroviruses. Many members of the TRIM family of proteins act as viral restriction factors. One well-characterized example is the ability of TRIM5á from rhesus macaques (rhTRIM5á) to inhibit human immunodeficiency virus type-1 (HIV-1) soon after viral entry but prior to reverse transcription (RT). It is well established that the restriction requires an interaction between the viral capsid lattice and the B30.2/SPRY domain of TRIM5á. Following the binding of the viral core, TRIM5á mediates an event or …

Adenovirus Vectors As Potent Adjuvants In Vaccine Development, Kathleen Ann Mcguire

Dissertations

Due to their ability to activate the immune system, replication-defective Adenoviruses (Ad) are potential vaccine vectors for several pathogens. The proinflammatory response to Ad contributes to the response to vaccine antigens. We found that reactive oxygen species (ROS) are an important signal in the proinflammatory response to Ad. We identified that serotype 5 adenovirus (Ad5) elicits ROS by inducing mitochondrial membrane damage, a process that is dependent on endosomal membrane rupture and Cathepsin release. This mitochondrial dysfunction contributes to NLRP3 inflammasome- and NFκB-dependent innate immune activation. The ROS-dependent inflammatory response likely contributes to the adaptive immune response by supporting DC …

Reconsidering The Model Of Trim5Α Assembly: The Role Of The Linker2 (L2) Region In Trim5Α Assembly, Laura Johnsen

Master's Theses

The TRIM5α protein from rhesus macaques (TRIM5αrh) exhibits a remarkable ability to potently inhibit infection by Human Immunodeficiency Virus Type-1 (HIV-1). Extensive studies have shown that TRIM5α is capable of self-associating at many levels, eventually leading to the formation of a hexameric assembly that can superimpose on the hexameric lattice of the HIV-1 capsid. The mechanism underlying the self-association of TRIM5α and the molecular determinants of self-association remain to be completely understood. In this study, we show that the Linker 2 (L2) region of TRIM5rh is important for dimerization and higher order self-association, both of which are independent processes. Additionally, …

Characterization Of The Female Urinary Microbiota And Their Association With The Female Bladder Uroepithelium, Evann Elizabeth Hilt

Master's Theses

The current clinical dogma assumes that urine is sterile in the absence of clinically relevant infection. However, recent evidence has demonstrated the existence of a female urinary microbiota in women with and without lower urinary tract symptoms. With the knowledge that the lower urinary tract possesses its own unique microbiota, I hypothesize that certain bacterial species of the female microbiota may be the cause or play a role in lower urinary tract syndromes such as overactive bladder syndrome (OAB). About 40-50% of OAB patients do not respond to conventional anti-muscarinic and beta-3 adrenergic agonist drug treatment. One possible explanation for …

An Investigation Of The Role Of Vibrio Vulnificus Rbda And Vibrio Parahaemolyticus Sypa In Biofilm Formation, Cecilia Thompson

Master's Theses

Vibrio vulnificus and Vibrio parahaemolyticus are both bacteria that cause human infection. V. vulnificus has a polysaccharide locus, rbd, responsible for bacterial aggregation, a form of biofilm. This locus is conserved in V. parahaemolyticus and in the non-pathogen V. fischeri.

In V. fischeri, the polysaccharide locus, syp, has been extensively characterized and shown to be important for biofilm formation. In V. fischeri, the first gene, sypA, is critical for biofilm formation. V. fischeri biofilm-proficient strains form wrinkled colonies. In contrast, sypA mutants form smooth colonies, indicating a lack of biofilm formation.

To understand the function of RbdA and SypAVP, proteins …

Host Entry Factors For Human Coronaviruses, Taylor Heald-Sargent

Dissertations

Coronaviruses infect a diverse range of animals from birds to pigs and cats to humans. Coronaviruses employ RNA-based replicative processes and as such are genetically adaptable to acquire novel host ranges. A coronavirus from one species can jump to another by shifting its entry requirements. As we learned from the Severe Acute Respiratory Syndrome (SARS) pandemic, this shift in species can have detrimental consequences. Thus, it is imperative that we understand the virus-host interaction during the entry process.

This dissertation focuses on host entry factors that influence human coronavirus entry. Recently, a new class of proteases, the type II transmembrane …

Identifying Novel Factors Involved In Biofilm Formation By Vibrio Fischeri, Valerie Ray

Dissertations

Biofilm formation by bacteria provides them with a means to survive harsh environmental conditions and promote colonization of a particular surface (biotic or abiotic). Due to the resistance properties of biofilms, biofilm-forming bacteria are difficult to treat in the context of host infections. Thus, investigating the processes that control biofilm formation will promote the development of novel therapeutics. To study biofilm formation in the context of a host, I utilized as a model system the marine bacterium Vibrio fischeri, which must be competent to form a biofilm to colonize its squid host Euprymna scolopes. Biofilm formation by V. fischeri requires …

Multifunctional Coronavirus Papain-Like Proteases As Targets For Antiviral Therapeutics And Vaccines, Anna Maria Mielech

Dissertations

Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) and Middle Ease Respiratory Syndrome coronavirus (MERS-CoV) pose a severe threat to humans because of high mortality. Despite the risk of coronavirus (CoV) emerging in the human population there are no antiviral drugs or vaccines to combat coronavirus infection. The focus of my dissertation was to study the multifunctionality of papain-like proteases (PLPs) encoded within coronavirus genomes to facilitate the development of antiviral drugs and vaccines. The viral PLPs are critical for processing the amino-terminal end of the replicase during virus replication and are attractive targets for antiviral therapies.

In my research, I analyzed …