Microbiology Commons^™

Characterizing The Virulence Factor Yape In Yersinia Pestis., Tiva Templeton Vancleave

Electronic Theses and Dissertations

Yersinia pestis is the causative agent of bubonic plague and is primarily transmitted by fleas. Upon infection, the bacteria rapidly travel to the regional lymph nodes causing inflammation and cellulitis in these tissues (referred to as buboes). Two outer membrane proteins, YapE and Pla, have been implicated to have roles in dissemination to the lymph nodes. Their adhesive properties have shown that they are able to interact with host macrophages thereby increasing their ability to disseminate to regional lymph nodes. More recently, we have shown that YapE is cleaved by another virulence factor important for lymph node colonization, Pla, to …

Ictv Virus Taxonomy Profile: Hypoviridae, Nobuhiro Suzuki, Said A. Ghabrial, Kook-Hyung Kim, Michael Pearson, Shin-Yi L. Marzano, Hajime Yaegashi, Jiatao Xie, Lihua Guo, Hideki Kondo, Igor Koloniuk, Bradley I. Hillman, Ictv Report Consortium

Plant Pathology Faculty Publications

The Hypoviridae, comprising one genus, Hypovirus, is a family of capsidless viruses with positive-sense, ssRNA genomes of 9.1–12.7 kb that possess either a single large ORF or two ORFs. The ORFs appear to be translated from genomic RNA by non-canonical mechanisms, i.e. internal ribosome entry site-mediated and stop/restart translation. Hypoviruses have been detected in ascomycetous or basidiomycetous filamentous fungi, and are considered to be replicated in host Golgi-derived, lipid vesicles that contain their dsRNA as a replicative form. Some hypoviruses induce hypovirulence to host fungi, while others do not. This is a summary of the current ICTV report …

Characterization Of Type Ii Toxin Anti-Toxin Systems In Aggregatibacter Actinomycetemcomitans., Blair W. Schneider

Electronic Theses and Dissertations

Microbes express many protective mechanisms in response to environmental stress. Toxin/anti-toxin systems encode a biologically active toxin and a labile anti-toxin that inhibits the toxin’s activity. These systems are known to contribute to persister cell and biofilm formation. A. actinomycetemcomitans thrives in the complex oral microbial community and is subjected to continual environmental flux. Little is known regarding the presence and function of TA systems in this organism or their contribution survival in the oral environment. Using BLAST searches and other informatics tools, we identified 11 intact TA systems that are conserved across all seven serotypes of A. actinomycetemcomitans and …

The Involvement Of Epithelial Cells In Arenavirus-Induced Pathogenesis., Nikole Leslie Margaret Warner

Electronic Theses and Dissertations

Mammalian Arenaviruses are a geographically and genetically diverse family of viruses, which is separated into two sub-groups; the Old World (OW) and New World (NW) groups. Of the OW viruses, Lassa virus (LASV), found endemically in Western Africa, is an important human pathogen, causing hundreds of thousands of infections, and several thousand deaths annually. Interestingly, some villages in endemic regions, up to 45% of the population show seropositivity for the virus. It is hypothesized that seropositivity is a result of natural infection through inhalation or ingestion of infectious particles. However, the exact mechanism is still unknown. LASV’s natural reservoir is …

Nutritional Virulence Of Legionella Pneumophila., Ashley M. Best

Electronic Theses and Dissertations

Legionella pneumophila is an environment organism that parasitizes a wide range of protozoa. Growth within the environmental host primes L. pneumophila for infection of human alveolar macrophages when contaminated aerosols are inhaled. Intracellular replication within either host requires the establishment a replicative niche, known as the Legionella-containing vacuole (LCV). Biogenesis of the LCV depends on the type IVb translocation system, the Dot/Icm, to translocation >320 effectors into the host cytosol. Effectors are responsible for preventing lysosome fusion to the LCV, recruitment of ER-derived vesicles to the LCV, and modulation of a plethora of host processes to promote the intracellular …

Comparing Microbiome Sampling Methods In A Wild Mammal: Fecal And Intestinal Samples Record Different Signals Of Host Ecology, Evolution, Melissa R. Ingala, Nancy B. Simmons, Claudia Wultsch, Konstantinos Krampis, Kelly A. Speer, Susan L. Perkins

Publications and Research

Processing of multimodal information is essential for an organism to respond to environmental events. However, how multimodal integration in neurons translates into behavior is far from clear. Here, we investigate integration of biologically relevant visual and auditory information in the goldfish startle escape system in which paired Mauthner-cells (M-cells) initiate the behavior. Sound pips and visual looms as well as multimodal combinations of these stimuli were tested for their effectiveness of evoking the startle response. Results showed that adding a low intensity sound early during a visual loom (low visual effectiveness) produced a supralinear increase in startle responsiveness as compared …

Characterizing Cultivable Bacteria From Trachymyrmex Septentrionalis Fungus Gardens, Hannah Beatty

Honors Scholar Theses

The relationship between the fungus-growing ant Trachymyrmex septentrionalis, its symbiotic cultivar fungus, and the transient and residential community of microorganisms is a diverse and complex symbiosis that has evolved over space and time. The fungus garden, comprised primarily of the cultivar fungus belonging to the family Leucocoprineae,provides an environment that hosts many bacteria, which may also play an important role in this symbiosis. Although it is known that Pseudonocardia bacteria defend the ant host against fungal pathogens, other species of bacteria that are present in these fungus gardens also likely contribute to this symbiosis. Previous studies of this …

Binding Of Maize Necrotic Streak Virus (Mnesv) 3’ I-Shaped Structure (3’ Iss) To Eukaryotic Translation Factors (Eifs) And Implication In Eif4f Mediated Translation Initiation, Qiao Liu

Dissertations, Theses, and Capstone Projects

5' m⁷GpppN cap and the 3' poly adenosine (A) tail of eukaryotic mRNAs are key elements for recruiting translation initiation machinery in canonical translation initiation. Unlike host mRNAs, many viruses lack these elements and yet they are translated efficiently. Plant viruses, in particular, have complex structures within their untranslated regions (UTR) that allow them to bypass some cellular translation control steps. In Maize necrotic streak virus (MNeSV) 3' UTR, an I-Shaped RNA Structure (ISS) has been reported to mediate the virus translation initiation progress. 3’ ISS binding with eIF4F has been shown to facilitate translation. 5’ -3’ kissing …

Regulation Of The Tubulin Homolog Ftsz In Escherichia Coli, Monika S. Buczek

Dissertations, Theses, and Capstone Projects

Escherichia coli is a well-known pathogen, and importantly, a widely used model organism in all fields of biological sciences for cloning, protein purification, and as a model for Gram-negative bacterial species. And yet, researchers do not fully understand how this bacterium replicates and divides. Every year additional division proteins are discovered, which adds complexity to how we understand E. coli undergoes cell division. Due to their specific roles in cytokinesis, some of these proteins may be potential targets for development of antibacterials or bacteriostatics, which are much needed for fighting the current global antibacterial deficit. My thesis work focuses on …

The Effect Of Cellular Dehydration On Glucose Regulation In Lean And Obese Females, Chunbo Yang

Graduate Theses and Dissertations

A chronically elevated vasopressin level has been associated with an impaired glucose regulation system in humans. A recent study in patients with diabetes suggested that low water intake is associated with impaired glucose regulation. The aim of this study was to examine the effect of hypertonic saline infusion on glucose regulation in healthy females. Thirty healthy, non-diabetic females performed a 2-h infusion followed by a 4-h oral glucose tolerance test (OGTT). Every subject participated in two trials separated by one month, in a counterbalanced order. Two trials were identical in the procedure, differing in the concentration of saline infusion, with …

Evolution Via Gene Duplication And Alternative Splicing In The Eukaryotic Ski7 And Hbs1 Genes, Alexandra Marshall

Dissertations and Theses (Open Access)

Gene duplication and alternative splicing are both recognized as important drivers of proteomic diversity and innovation during evolution, but the evolutionary changes over long periods of time or the interrelations of the two processes has not been extensively studied. Here I study these phenomena for the SKI7 and HBS1 gene pair. These Saccharomyces cerevisiae genes were created as part of a whole genome duplication (WGD) event and have since functionally diverged. Although both genes function in mRNA surveillance pathways, the two genes act on different RNAs and have different effects on the target mRNAs. Ski7 brings the Ski complex and …

Functional Similarity Of Prd-Containing Virulence Regulators In Bacillus Anthracis, Malik Raynor

Dissertations and Theses (Open Access)

Bacillus anthracis produces three regulators, AtxA, AcpA, and AcpB, that control virulence gene expression and are members of an emerging class of regulators termed “PCVRs” (Phosphoenolpyruvate-dependent phosphotransferase regulation Domain-Containing Virulence Regulators). AtxA controls expression of the toxin genes; lef, cya, and pag, and is the master virulence regulator and archetype PCVR. AcpA and AcpB are less well studied. AcpA and AcpB independently positively control transcription of the capsule biosynthetic operon capBCADE, and culture conditions that enhance AtxA activity result in capBCADE transcription in strains lacking acpA and acpB. RNA-Seq was used to assess the regulons of the …

Identification Of “Fhua” Like Genes In Rhizobium Leguminosarum Atcc 14479 And Its Role In Vicibactin Transport And Investigation Of Heme Bound Iron Uptake System, Sushant Khanal

Electronic Theses and Dissertations

Siderophores are low molecular weight, iron chelating compounds produced by many bacteria for uptake of iron in case of iron scarcity. Vicibactin is a trihydroxamate type siderophore produced by Rhizobium leguminosarum bv. trifolii ATCC 14479. This work focuses on identifying an outer membrane receptor involved in the transport of vicibactin. We have confirmed the presence of the putative fhuA gene in R. leguminosarum bv. trifolii ATCC 14479. This bacteria shows mutualistic symbiosis with the red clover plant Trifoliium prantense. Leghemoglobin, with its cofactor heme is present in the plant root nodules that surrounds the infecting organism present in the nodules. …

Calvin Avenue Basin Project Description And Analysis, Calvin University

Faculty and Professional Research

The existing detention basin, Calvin Avenue Basin was modified in 2017 to include a two-stage ditch, level spreaders, and micro- and macrotopography with the goal of reducing the volume of stormwater leaving the basin, resulting in less stormwater, less flashiness, and improved water quality in the downstream, impaired waterway of Silver Creek. The total storage increase at a reference elevation of 690 is 348,615 gallons (1.07 acre-feet) for all modifications (two-stage ditch and microtopography). This equates to 4.35 million gallons of stormwater that will be stored and slowly released. Of this, 2.46 million gallons of stormwater will be infiltrated annually. …

Physician Suicide: An Overlooked Epidemic, Emily Gallagher

Senior Honors Projects

Suicide, in general, can be a challenging topic to approach and dissect. It can be complicated and uncomfortable and is perpetuated as taboo. Physician suicide in particular can be even more complicated, confusing, and uncomfortable. The topic of physician suicide (as well as medical student suicide) is understudied and the literature available is underwhelming. The research I conducted focuses on the big picture of physician suicide. From the first year of medical school, to a new doctor’s residency, and on through their practice, physicians face a unique set of obstacles and adversities that shape their experience and ultimately lend to …

Microbiome Of Commercial Broilers Through Evisceration And Immersion Chilling, John A. Handley

Graduate Theses and Dissertations

The United States poultry industry generated 38.6 billion pounds (17,500 metric ton) of meat in 2014 which averaged to 121 pounds (55 kg) per individual of the U.S that same year. Of that meat generated by the poultry industry, an estimated 1 million cases of Salmonellosis will occur. Out of the 1 million cases approximately 40, 000 to 50,000 will be confirmed cases by the CDC. Recently, the USDA has requested changes in the inspection process and are currently allowing processors more freedom to utilize innovation to drive the increase in safer and more desirable foods. The new standards set …

Optimizing Genetic Manipulation Of Methanogens Through Faster Cloning Techniques, Merrisa Jennings

Biological and Agricultural Engineering Undergraduate Honors Theses

Methanogenesis is the biological production of methane. Only anaerobic archaea known as methanogens are capable of such a metabolic feat. They have strict living conditions and substrate sources which determine their rate of metabolism. This is of particular importance from a greenhouse gas reduction perspective or biogas capturing perspective. One of the best ways to optimize methanogen methane production is via genetic manipulation. The current procedures are timely though, therefore a faster cloning processes should be developed. The objective of this study was to optimize a premade genetic transformation kit known as the Gibson Kit. The Gibson Kit was supposed …

Chloride Salt Inhibition On Lipid Production In Wastewater-Grown Algae For Biofuel Production, Will Richardson

Biological and Agricultural Engineering Undergraduate Honors Theses

Algae are increasingly being recognized as useful organisms for many applications in today’s world. Their ability to remove nitrogen, phosphorus, and trace metals from water while adding oxygen to water makes them an attractive tertiary treatment technology in municipal wastewater treatment facilities. At the same time, algae produce lipids and carbohydrates that are useful for biofuel production, and they are not a human food crop unlike many biofuel feedstocks. In this study the effect of increased chloride concentrations in wastewater was assessed on the ability of two species of algae, Chlorella vulgaris and Scenedesmus dimorphus, to function as a …

Bioprospecting Deep-Sea Actinobacteria For Novel Anti-Infective Natural Products, Dongbo Xu, Linna Han, Chunhui Li, Qi Cao, Duolong Zhu, Nolan H. Barrett, Dedra Harmody, Jing Chen, Haining Zhu, Peter J. Mccarthy, Xingmin Sun, Guojun Wang

Molecular and Cellular Biochemistry Faculty Publications

The global prevalence of drug resistance has created an urgent need for the discovery of novel anti-infective drugs. The major source of antibiotics in current clinical practice is terrestrial actinobacteria; the less-exploited deep-sea actinobacteria may serve as an unprecedented source of novel natural products. In this study, we evaluated 50 actinobacteria strains derived from diverse deep water sponges and environmental niches for their anti-microbial activities against a panel of pathogens including Candida albicans, Clostridium difficile, Staphylococcus aureus, and methicillin-resistant S. aureus (MRSA), and Pseudomonas aeruginosa. More than half of the tested strains (27) were identified as …

Comparison Of Staphylococcus Phage K With Close Phage Relatives Commonly Employed In Phage Therapeutics, Jude Ajuebor, Colin Buttimer, Sara Arroyo-Moreno, Nina Chanishvili, Emma M. Gabriel, Jim O'Mahony, Olivia Mcauliffe, Horst Neve, Charles Franz, Aidan Coffey

Department of Biological Sciences Publications

The increase in antibiotic resistance in pathogenic bacteria is a public health danger requiring alternative treatment options, and this has led to renewed interest in phage therapy. In this respect, we describe the distinct host ranges of Staphylococcus phage K, and two other K-like phages against 23 isolates, including 21 methicillin-resistant S. aureus (MRSA) representative sequence types representing the Irish National MRSA Reference Laboratory collection. The two K-like phages were isolated from the Fersisi therapeutic phage mix from the Tbilisi Eliava Institute, and were designated B1 (vB_SauM_B1) and JA1 (vB_SauM_JA1). The sequence relatedness of B1 and JA1 to phage K …

Investigation Into The Causes And Severity Of The 1918 Influenza Pandemic, Alex T. Freedenberg

The Review: A Journal of Undergraduate Student Research

The 1918 Influenza outbreak is regarded as one of the worst pandemics in human history due to its widespread effects across the globe and its high death rate. This death rate was unusual among influenza infections as most strains do not cause the amount of death that is seen in this outbreak, with 20 million dead as a conservative estimate and 100 million by other estimations. This pandemic was not very well contained for a plethora of reasons. Two main reasons are that it came at a time when understanding viral mechanics still escaped medical professionals, and due to the …

Investigation Of Bacteria From The Trachymyrmex Septentrionalis Fungus Garden For Potential Antibacterial Drug Leads, Brendan Stewart

University Scholar Projects

Bacterial and fungal strains are growing resistance to antibiotics and antifungal agents at an alarming rate. According to the Centers for Disease Control and Prevention, over two million people in the United States in 2016 were diagnosed with an infection resistant to antibiotics. As such, there has been increased interest in natural products as sources of novel compounds that are essential to the development of new drugs and treatment methods. Within the environment, there are various host-microbe symbioses, one of which is the Trachymyrmex septentrionalis leaf-cutter ant community. The microbes in symbioses like the T. septentrionalis community are hypothesized to …

Investigation Of Bacteria From The Trachymyrmex Septentrionalis Fungus Garden For Potential Antibacterial Drug Leads, Brendan Stewart

Honors Scholar Theses

Bacterial and fungal strains are growing resistance to antibiotics and antifungal agents at an alarming rate. According to the Centers for Disease Control and Prevention, over two million people in the United States in 2016 were diagnosed with an infection resistant to antibiotics. As such, there has been increased interest in natural products as sources of novel compounds that are essential to the development of new drugs and treatment methods. Within the environment, there are various host-microbe symbioses, one of which is the Trachymyrmex septentrionalis leaf-cutter ant community. The microbes in symbioses like the T. septentrionalis community are hypothesized to …

Predator-By-Environment Interactions Mediate Bacterial Competition In The Dictyostelium Discoideum Microbiome, R Fredrik Inglis, Odion Asikhia, Erica Ryu, David C. Queller, Joan E. Strassmann

Biology Faculty Research

Interactions between species and their environment play a key role in the evolution of diverse communities, and numerous studies have emphasized that interactions among microbes and among trophic levels play an important role in maintaining microbial diversity and ecosystem functioning. In this study, we investigate how two of these types of interactions, public goods cooperation through the production of iron scavenging siderophores and predation by the social amoeba Dictyostelium discoideum, mediate competition between two strains of Pseudomonas fluorescens that were co-isolated from D. discoideum. We find that although we are able to generally predict the competitive outcomes between …

2018 3rd Place: The Growth And Characterization Of Psychromonas Aquimarina, A New Model Organism For Climate Change, Carrie Carpenter, Catherine Santai

Harrisburg University Research Symposium (2018 & 2019)

Climate change is currently affecting the Earth and will only increase with time1. A change to the environment means that wildlife will need to adapt. Adaptation occurs when an organism changes physiologically or otherwise to permit continued growth in the environment in which it resides. Scientists do not completely understand adaptation mechanisms. Psychromonas aquimarinais a novel bacterium, with little known. This bacteria will first be characterized and studied before conducting temperature studies. Psychromonas aquimarina is a psychrophile, a bacterium able to survive in colder regions where most bacteria would not. P. aquimarinais an ideal bacterium to study because climate change …

A Recurrent Silent Mutation Implicates Feca In Ethanol Tolerance By Escherichia Coli., Katherine M Lupino, Kymberleigh A Romano, Matthew J Simons, John T Gregg, Leanna Panepinto, Ghislaine M Cruz, Lauren Grajek, Gregory A. Caputo, Mark J. Hickman, Gregory B. Hecht

College of Science & Mathematics Departmental Research

BACKGROUND: An issue associated with efficient bioethanol production is the fact that the desired product is toxic to the biocatalyst. Among other effects, ethanol has previously been found to influence the membrane of E. coli in a dose-dependent manner and induce changes in the lipid composition of the plasma membrane. We describe here the characterization of a collection of ethanol-tolerant strains derived from the ethanologenic Escherichia coli strain FBR5.

RESULTS: Membrane permeability assays indicate that many of the strains in the collection have alterations in membrane permeability and/or responsiveness of the membrane to environmental changes such as temperature shifts or …

Transmembrane Domains Of Highly Pathogenic Viral Fusion Proteins Exhibit Trimeric Association In Vitro, Stacy R. Webb, Stacy E. Smith, Michael G. Fried, Rebecca Ellis Dutch

Molecular and Cellular Biochemistry Faculty Publications

Enveloped viruses require viral fusion proteins to promote fusion of the viral envelope with a target cell membrane. To drive fusion, these proteins undergo large conformational changes that must occur at the right place and at the right time. Understanding the elements which control the stability of the prefusion state and the initiation of conformational changes is key to understanding the function of these important proteins. The construction of mutations in the fusion protein transmembrane domains (TMDs) or the replacement of these domains with lipid anchors has implicated the TMD in the fusion process. However, the structural and molecular details …

Restoration Of Phage Growth On A Non-Permissive Host By Bypassing Transcription Termination Signals, Millicent Ronkainen

Mahurin Honors College Capstone Experience/Thesis Projects

RNA polymerase is the central enzyme in all gene expression. The rpoCY75N mutation in the zinc-binding domain of the β’ subunit of E. coli RNA polymerase blocks a unique RNA-based mechanism of transcription antitermination utilized by bacteriophage HK022 and its relatives. Here, we describe the characterization of mutant phage, orc0368, which overcomes the rpoCY75N mutation. The orc0368 genome varies from the wild type phage genome by 4 single base pair mutations. Three of these mutations were not characterized because they occur in intergenic regions but the fourth was chosen for study because of its location between a series …

Pengaruh Jenis Media Tanam Dan Aplikasi Pupuk Hayati Mikoriza Terhadap Pertumbuhan, Pembungaan Dan Infeksi Mikoriza Pada Tanaman Anggrek Dendrobium Sp, Okti Herliana, E Rokhminarsi, S Mardini, M Jannah

Jurnal Kultivasi

The research aimed to find out 1) the best growing media for growth and flowering of Dendrobium orchid, 2) the best dosage of mycorrhizal biofertilizer for growth and flowering of Dendrobium orchid, 3) the best combination type of growing media and mycorrhizal biofertilizer for growth and flowering of Dendrobium orchid. The research was conducted at Screen house of Datar Village, Sumbang Subdistrict, Banyumas Regency from May 2017 to November 2017. The research design was using Randomized Block Design (RBD) method with 2 factors and 3 replicates:(1) Growing media with 3 treatment types; wood charcoal, fern (Cyathea contaminans), root of the …

A Biofilm Matrix-Associated Protease Inhibitor Protects Pseudomonas Aeruginosa From Proteolytic Attack, Boo Shan Tseng, Courtney Reichhardt, Gennifer E. Merrihew, Sophia A. Araujo-Hernandez, Joe J. Harrison, Michael J. Maccoss, Matthew R. Parsek

Life Sciences Faculty Research

Pseudomonas aeruginosa produces an extracellular biofilm matrix that consists of nucleic acids, exopolysaccharides, lipid vesicles, and proteins. In general, the protein component of the biofilm matrix is poorly defined and understudied relative to the other major matrix constituents. While matrix proteins have been suggested to provide many functions to the biofilm, only proteins that play a structural role have been characterized thus far. Here we identify proteins enriched in the matrix of P. aeruginosa biofilms. We then focused on a candidate matrix protein, the serine protease inhibitor ecotin (PA2755). This protein is able to inhibit neutrophil elastase, a bactericidal enzyme …