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Bacteriophage

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Articles 31 - 57 of 57

Full-Text Articles in Microbiology

Isolation, Characterization, And Genomic Comparison Of Bacteriophages Of Enterobacteriales Order, Ruchira Sharma Jul 2019

Isolation, Characterization, And Genomic Comparison Of Bacteriophages Of Enterobacteriales Order, Ruchira Sharma

Theses and Dissertations

According to CDC, every year at least 2 million people are affected and 23,000 dies as a result of antibiotic resistance in U.S. It is considered one of the biggest threats to global health. More and more bacterial infections are becoming harder to treat. One such infection is fire blight, one of the most destructive disease of apple and pear trees. It is caused by bacteria Erwinia amylovora and its outbreaks have been known to destroy entire orchards in a single season. The conventional method of treatments includes use of antibiotics like streptomycin and oxytetracycline but the incidences like presence …

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Further Understanding Of Bacteriophages That Infect The Bacterial Family Enterobacteriaceae, Paul Flake Mar 2019

Further Understanding Of Bacteriophages That Infect The Bacterial Family Enterobacteriaceae, Paul Flake

Undergraduate Honors Theses

Despite the eclectic nature of bacteriophage genomes, nucleotide comparison is an effective method for grouping phages into cluster and subcluster classifications. This process is facilitated by making preliminary cluster assignations based on the identity of the major capsid protein. As more phages continue to be sequenced and integrated into cluster/subcluster groupings, adjustments may need to be made to the genomic similarity percentages that have previously defined cluster/subcluster classifications. Implementing proteomic comparison in addition to nucleotide homology may provide added clarity to this process. Protein conservation and diversity among lytic phages that infect the bacterial family Enterobacteriaceae is discussed and the …

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Crystallographic Studies On Host-Interacting Proteins Of Phage K Virion, Antonio Pichel Beleiro Jan 2019

Crystallographic Studies On Host-Interacting Proteins Of Phage K Virion, Antonio Pichel Beleiro

Theses

Phage K is a lytic bacteriophage that infects a broad range of staphylococci, including some methicillin-resistant Staphylococcus aureus strains. Phage K attaches to its host via a baseplate. The contracted conformation of the baseplate contains a fiber and two receptorbinding proteins responsible for the interaction with the host. The native conformation of the baseplate also includes a tail central spike that shears off after contraction. The aim of the thesis is the structural characterization of phage K receptor-binding proteins and tail central spike. Experimentally, the thesis relies on crystallographic methods, which encompass: production of suitable sample, crystallization, diffraction, and data …

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Bacteriophages For Treating American Foulbrood And The Neutralization Of Paenibacillus Larvae Spores, Thomas Scott Brady Jul 2018

Bacteriophages For Treating American Foulbrood And The Neutralization Of Paenibacillus Larvae Spores, Thomas Scott Brady

Theses and Dissertations

The causative agent of the most devastating honeybee disease, American foulbrood (AFB), is the spore-forming bacterium Paenibacillus larvae. To prevent AFB outbreaks beekeepers prophylactically treat their hives with antibiotics even though it decreases the overall health of uninfected hives. A new treatment for AFB is needed due to recent legislation against using antibiotics, antibiotic resistance developing in P. larvae, and the resilience of P. larvae spores. Bacteriophages, or phages, are an attractive alternative to traditional antibiotics because of their specificity and ability to evolve alongside their target bacterium. In this study, two phage cocktails were developed for the …

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Pseudomonas Pb1-Like Phages: Whole Genomes From Metagenomes Offer Insight Into An Abundant Group Of Bacteriophages, Siobhan C. Watkins, Emily Sible, Catherine Putonti Jun 2018

Pseudomonas Pb1-Like Phages: Whole Genomes From Metagenomes Offer Insight Into An Abundant Group Of Bacteriophages, Siobhan C. Watkins, Emily Sible, Catherine Putonti

Biology: Faculty Publications and Other Works

Despite the abundance, ubiquity and impact of environmental viruses, their inherent genomic plasticity and extreme diversity pose significant challenges for the examination of bacteriophages on Earth. Viral metagenomic studies have offered insight into broader aspects of phage ecology and repeatedly uncover genes to which we are currently unable to assign function. A combined effort of phage isolation and metagenomic survey of Chicago’s nearshore waters of Lake Michigan revealed the presence of Pbunaviruses, relatives of the Pseudomonas phage PB1. This prompted our expansive investigation of PB1-like phages. Genomic signatures of PB1-like phages and Pbunaviruses were identified, permitting the unambiguous distinction between …

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Mechanism Of Virus Inactivation By Cold Atmospheric-Pressure Plasma And Plasma-Activated Water, Li Guo, Ruobing Xu, Lu Gou, Zhichao Liu, Yiming Zhao, Dingxin Liu, Lei Zhang, Hailan Chen, Michael G. Kong Jun 2018

Mechanism Of Virus Inactivation By Cold Atmospheric-Pressure Plasma And Plasma-Activated Water, Li Guo, Ruobing Xu, Lu Gou, Zhichao Liu, Yiming Zhao, Dingxin Liu, Lei Zhang, Hailan Chen, Michael G. Kong

Bioelectrics Publications

ABSTRACT Viruses cause serious pathogenic contamination that severely affects the environment and human health. Cold atmospheric-pressure plasma efficiently inactivates pathogenic bacteria; however, the mechanism of virus inactivation by plasma is not fully understood. In this study, surface plasma in argon mixed with 1% air and plasma-activated water was used to treat water containing bacteriophages. Both agents efficiently inactivated bacteriophages T4, ϕ174, and MS2 in a time-dependent manner. Prolonged storage had marginal effects on the antiviral activity of plasma-activated water. DNA and protein analysis revealed that the reactive species generated by plasma damaged both nucleic acids and proteins, consistent with the …

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The Evolution Of Molecular Compatibility Between Bacteriophage Φx174 And Its Host, Alexander Kula, Joseph Saelens, Jennifer Cox, Alyxandria M. Schubert, Michael Travisano, Catherine Putonti May 2018

The Evolution Of Molecular Compatibility Between Bacteriophage Φx174 And Its Host, Alexander Kula, Joseph Saelens, Jennifer Cox, Alyxandria M. Schubert, Michael Travisano, Catherine Putonti

Biology: Faculty Publications and Other Works

Viruses rely upon their hosts for biosynthesis of viral RNA, DNA and protein. This dependency frequently engenders strong selection for virus genome compatibility with potential hosts, appropriate gene regulation and expression necessary for a successful infection. While bioinformatic studies have shown strong correlations between codon usage in viral and host genomes, the selective factors by which this compatibility evolves remain a matter of conjecture. Engineered to include codons with a lesser usage and/or tRNA abundance within the host, three different attenuated strains of the bacterial virus ФX174 were created and propagated via serial transfers. Molecular sequence data indicate that biosynthetic …

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Enhancing The Sea-Phages App To Collect Weather-Related Metadata From Soil Sampling Locations, Kelly M. Degnon May 2018

Enhancing The Sea-Phages App To Collect Weather-Related Metadata From Soil Sampling Locations, Kelly M. Degnon

Senior Honors Projects, 2010-2019

The bacteriophage population is extremely diverse and abundant, with a seemingly limitless number of phages that have yet to be isolated and sequenced. The SEA-PHAGES program discovers and completely sequences the genome of hundreds of phages every year, contributing to the ever-growing database of phage sequences. However, there is little data about the conditions in which these phages are collected and if weather conditions can have an effect on the likelihood of isolating a phage. The SEA-PHAGES app, when used by students in the SEA- PHAGES program, will collect data on the location and weather conditions in which a soil …

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Restoration Of Phage Growth On A Non-Permissive Host By Bypassing Transcription Termination Signals, Millicent Ronkainen Apr 2018

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 …

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Role Of Viruses Within Metaorganisms: Ciona Intestinalis As A Model System, Brittany A. Leigh Sep 2017

Role Of Viruses Within Metaorganisms: Ciona Intestinalis As A Model System, Brittany A. Leigh

USF Tampa Graduate Theses and Dissertations

Marine animals live and thrive in a literal sea of microorganisms, yet are often able to maintain specific associations that are largely dictated by the environment, host immunity and microbial interactions. Animal-associated microbiomes include bacteria and viruses that vastly outnumber host cells, especially in the gut environment, and are considered to be integral parts of healthy, functioning animals that act as a metaorganism. However, the processes underlying the initial establishment of these microbial communities are not very well understood. This dissertation focuses on the establishment of a well-known developmental animal model, Ciona intestinalis (sea squirt), to study the establishment and …

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The Use Of Informativity In The Development Of Robust Viromics-Based Examinations, Siobhan C. Watkins, Catherine Putonti Jan 2017

The Use Of Informativity In The Development Of Robust Viromics-Based Examinations, Siobhan C. Watkins, Catherine Putonti

Bioinformatics Faculty Publications

Metagenomics-based studies have provided insight into many of the complex microbial communities responsible for maintaining life on this planet. Sequencing efforts often uncover novel genetic content; this is most evident for phage communities, in which upwards of 90% of all sequences exhibit no similarity to any sequence in current data repositories. For the small fraction that can be identified, the top BLAST hit is generally posited as being representative of a viral taxon present in the sample of origin. Homology-based classification, however, can be misleading as sequence repositories capture but a small fraction of phage diversity. Furthermore, lateral gene transfer …

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Comparative Genomics Of 9 Novel Paenibacillus Larvae Bacteriophages, Casey Stamereilers, Lucy Leblanc, Diane Yost, Penny S. Amy, Philippos K. Tsourkas Aug 2016

Comparative Genomics Of 9 Novel Paenibacillus Larvae Bacteriophages, Casey Stamereilers, Lucy Leblanc, Diane Yost, Penny S. Amy, Philippos K. Tsourkas

Life Sciences Faculty Research

American Foulbrood Disease, caused by the bacterium Paenibacillus larvae, is one of the most destructive diseases of the honeybee, Apis mellifera. Our group recently published the sequences of 9 new phages with the ability to infect and lyse P. larvae. Here, we characterize the genomes of these P. larvae phages, compare them to each other and to other sequenced P. larvae phages, and putatively identify protein function. The phage genomes are 38–45 kb in size and contain 68–86 genes, most of which appear to be unique to P. larvae phages. We classify P. larvae phages into 2 main clusters and …

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Characterization Of Five Brevibacillus Bacteriophages And Their Genomes, Michael Allen Sheflo Jun 2016

Characterization Of Five Brevibacillus Bacteriophages And Their Genomes, Michael Allen Sheflo

Theses and Dissertations

Brevibacillus laterosporus (B. laterosporus) is a pathogen difficult to distinguish from Paenibacillus larvae (P. larvae), and contributes to Colony Collapse Disorder (CCD) of honeybees. To develop a biocontrol agent to limit its presence, bacteriophages were isolated from Utah County soil samples and used to infect B. laterosporus isolated from Utah County honey and larvae samples. Since CCD is prevalent in Utah beehives, bacteriophage that infect and lyse B. laterosporus may be isolated and characterized. Pathogens were isolated from soil samples, and 16S rRNA gene tests initially identified the strains as P. larvae. Bacteriophages were isolated, purified, and amplified sufficiently to …

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Discovery And Characterization Of Bacteriophage To Control Mrsa, Jacob B. Hatch, Bradford Berges Feb 2016

Discovery And Characterization Of Bacteriophage To Control Mrsa, Jacob B. Hatch, Bradford Berges

Journal of Undergraduate Research

About 20% of humans are carriers of Staphylococcus aureus (SA). There were an estimated 11,000 deaths in the United States in 2005 attributed to SA, with the majority caused by MRSA (Methicillin Resistant Staphylococcus Aureus) isolates [1]. Many MRSA isolates have developed resistance to all but one antibiotic drug: vancomycin. However, other bacteria have developed resistance to vancomycin, suggesting that in time MRSA will likewise become non-responsive to this last available drug and MRSA infections will be untreatable. This project looks to find an alternate method of MRSA treatment. Bacteriophage (phage) are viruses that infect bacterial cells in order …

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The Use Of Bacteriophage For Surface Sterilization Of Methicillin-Resistant Staphylococcus Aureus In Poultry Facilities, Trevor Wienclaw, Bradford Berges Feb 2016

The Use Of Bacteriophage For Surface Sterilization Of Methicillin-Resistant Staphylococcus Aureus In Poultry Facilities, Trevor Wienclaw, Bradford Berges

Journal of Undergraduate Research

Staphylococcus aureus (SA) is potentially dangerous pathogen that can infect humans and animals alike1. The primary treatment for such infections has been antibiotics, but even shortly after antibiotics began to be used, antibiotic-resistant strains, known as MRSA, were discovered. These resistant strains have since spread, and now account for over half of all clinical isolates4. A similar scenario developed in the livestock industry. Antibiotics have been used to treat diseased animals and to promote growth in healthy animals. This use lead to development of MRSA among these animals. These animals may merely be carriers or they …

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Interactomics-Based Functional Analysis: Using Interaction Conservation To Probe Bacterial Protein Functions, J. Harry Caufield Jan 2016

Interactomics-Based Functional Analysis: Using Interaction Conservation To Probe Bacterial Protein Functions, J. Harry Caufield

Theses and Dissertations

The emergence of genomics as a discrete field of biology has changed humanity’s understanding of our relationship with bacteria. Sequencing the genome of each newly-discovered bacterial species can reveal novel gene sequences, though the genome may contain genes coding for hundreds or thousands of proteins of unknown function (PUFs). In some cases, these coding sequences appear to be conserved across nearly all bacteria. Exploring the functional roles of these cases ideally requires an integrative, cross-species approach involving not only gene sequences but knowledge of interactions among their products. Protein interactions, studied at genome scale, extend genomics into the field of …

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Isolation And Host Range Of Staphylococcus Aureus Bacteriophages And Use For Decontamination Of Fomites, Kyle C. Jensen Jun 2015

Isolation And Host Range Of Staphylococcus Aureus Bacteriophages And Use For Decontamination Of Fomites, Kyle C. Jensen

Theses and Dissertations

Staphylococcus aureus is a common bacterium found on the skin and mucosal membranes of about 20% of the population. S. aureus growth on the skin is harmless, but if it bypasses the skin it can causes life-threatening diseases such as pneumonia, meningitis, bacteremia, and sepsis. Antibiotic-resistant strains of S. aureus, called Methicillin Resistant S. aureus (MRSA), are resistant to most antibiotics except vancomycin. However, vancomycin resistant strains of MRSA are becoming more common. In this study, 12 phages were isolated capable of infecting human S. aureus and/or MRSA strains. Five phages were discovered through mitomycin C induction of prophages and …

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Advancing Phage Genomics And Honeybee Health Through Discovery And Characterization Of Paenibacillaceae Bacteriophages, Bryan Douglas Merrill Jun 2015

Advancing Phage Genomics And Honeybee Health Through Discovery And Characterization Of Paenibacillaceae Bacteriophages, Bryan Douglas Merrill

Theses and Dissertations

The Paenibacillaceae family of bacteria includes two species known to infect the hives of honeybees, Paenibacillus larvae and Brevibacillus laterosporus. P. larvae, the causative agent of American Foulbrood (AFB) causes a lethal infection of honeybee larvae, while B. laterosporus is a secondary invader following European Foulbrood (EFB) infection. Increasing antibiotic resistance of P. larvae bacteria has prompted a search for alternative treatment methods for this disease. Bacteriophages are the most diverse life forms on earth and can provide important insights about the bacterial hosts they infect. However, few Paenibacillaceae phages have been isolated or characterized. In this study, the first …

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Discovery And Characterization Of Bacteriophage To Control Mrsa, Jacob B. Hatch, Bradford Berges May 2015

Discovery And Characterization Of Bacteriophage To Control Mrsa, Jacob B. Hatch, Bradford Berges

Journal of Undergraduate Research

About 20% of humans are carriers of Staphylococcus aureus (SA). There were an estimated 11,000 deaths in the United States in 2005 attributed to SA, with the majority caused by MRSA (Methicillin Resistant Staphylococcus Aureus) isolates [1]. Many MRSA isolates have developed resistance to all but one antibiotic drug: vancomycin. However, other bacteria have developed resistance to vancomycin, suggesting that in time MRSA will likewise become non-responsive to this last available drug and MRSA infections will be untreatable. This project looks to find an alternate method of MRSA treatment. Bacteriophage (phage) are viruses that infect bacterial cells in order …

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Addressing The Black Box Phenomenon Of Genome Sequencing And Assembly, Brandon Carter May 2015

Addressing The Black Box Phenomenon Of Genome Sequencing And Assembly, Brandon Carter

Senior Honors Projects, 2010-2019

Genomics, a study of all genetic material in an organism, is a new discipline having a great impact on medicine, agriculture, and environmental phenomena. Most undergraduate faculty members were not formally trained in genomics and must retool themselves in order to stay current with these evolving technologies. Advances in sequencing technology have resulted in an explosion of “big data” that can only be managed and analyzed using digital methods. Multiple complex computer programs are required to teach students the concepts using hands-on methods. These programs are challenging to use, especially since the same faculty members lacking genomics training were not …

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Transduction As The Method Of Horizontal Gene Transfer Of The Staphylococcal Chromosomal Cassette Mec (Sccmec), Amber B. Sauder May 2015

Transduction As The Method Of Horizontal Gene Transfer Of The Staphylococcal Chromosomal Cassette Mec (Sccmec), Amber B. Sauder

Senior Honors Projects, 2010-2019

Methicillin-resistant Staphylococcus aureus (MRSA) gains resistance to β-lactam antibiotics through a mutated penicillin binding protein (PBP2a) encoded on the SCCmec element. In combination with the recombinase encoded by ccr, these two genes are used as markers of the mobile genetic element (SCCmec). Due to recent increases in community acquired MRSA infections, the mechanisms of antibiotic resistance gene transfer have gained attention. Transduction, a method of horizontal gene transfer mediated by bacteriophage, is believed to be responsible for the movement of the SCCmec element. Recent studies have shown the transduction of the SCCmec element in clinical isolates; however, this study is …

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Comparative Genome Analysis Of Novel Paenibacillus Larvae Bacteriophage, Bryan Merrill, Dr. Sandra Burnett Apr 2014

Comparative Genome Analysis Of Novel Paenibacillus Larvae Bacteriophage, Bryan Merrill, Dr. Sandra Burnett

Journal of Undergraduate Research

Honey bees pollinate one third of the crops in the U.S. diet. The spore-forming bacterium Paenibacillus larvae causes American Foulbrood (AFB), a highly contagious disease that is lethal in honey bee larvae. P. larvae is the most serious pathogen affecting honey bees. The spores can be found in any healthy beehive, are stable for 40 years or more, and cannot be killed by antibiotics. The disease manifests itself when worker bees feed P. larvae spores to larvae and the spores germinate. The bacteria then consume the larvae and turns back into a spore that the worker bees then transfer throughout …

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Growth Of Lactic Acid Bacteria: Influence Of Protocooperation, Bacteriophage Infection, And Prebiotic Carbohydrates, Caitlin D. Goin Oct 2010

Growth Of Lactic Acid Bacteria: Influence Of Protocooperation, Bacteriophage Infection, And Prebiotic Carbohydrates, Caitlin D. Goin

School of Biological Sciences: Dissertations, Theses, and Student Research

Lactic acid bacteria are a vital part of the fermented food industry and are the subject of much interest and research. Industry is especially interested in using modern molecular approaches to maintain and improve selected strains; several industrial uses could be improved by closer investigation, namely the protocooperation of S. thermophilus and L. bulgaricus, the role of CRISPRs in phage resistance, and the utilization of prebiotic carbohydrates. Questions such as what genes and pathways are shared during milk fermentation between S. thermophilus and L. bulgaricus, when and what genes are active during bacteriophage infection, and how and where …

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Prevalence And Biological Control Of Salmonella Contamination In Rendering Plant Environments And The Finished Rendered Meals, Brandon Kinley Dec 2009

Prevalence And Biological Control Of Salmonella Contamination In Rendering Plant Environments And The Finished Rendered Meals, Brandon Kinley

All Dissertations

Although the rendering process serves as invaluable means for the disposal of inedible animal by-products, the finished products often harbor pathogenic and opportunistic microorganisms such as Salmonella and enterococci, respectively. The temperatures used during the rendering process far exceed the heat tolerance threshold of most bacterial species, so cross-contamination from the environment and/or from the incoming raw material is the proposed source of the contamination. Research has demonstrated that the raw material coming into the rendering facility is highly contaminated with pathogenic bacteria including Salmonella. While not in a rendering facility, studies have also demonstrated that bacteria such as Salmonella …

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Oriented Cell Growth On Self-Assembled Bacteriophage M13 Thin Films, Jianhua Rong, L. Andrew Lee, Kai Li, Brandon Harp, Charlene M. Mello, Zhongwei Niu, Qian Wang Sep 2008

Oriented Cell Growth On Self-Assembled Bacteriophage M13 Thin Films, Jianhua Rong, L. Andrew Lee, Kai Li, Brandon Harp, Charlene M. Mello, Zhongwei Niu, Qian Wang

Faculty Publications

Fibrillar M13 bacteriophages were used as basic building blocks to generate thin films with aligned nanogrooves, which, upon chemical grafting with RGD peptides, guide cell alignment and orient the cell outgrowth along defined directions.

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The Application Of Bacteriophage For The Elimination Of Pathogenic Bacteria In Compost, Spencer Heringa Jul 2008

The Application Of Bacteriophage For The Elimination Of Pathogenic Bacteria In Compost, Spencer Heringa

All Theses

The demand for organically grown produce is rapidly rising in the United States, resulting in a resurgence of natural fertilizers, such as animal waste, being used in agriculture. Currently, there are guidelines set by the USDA for the proper processing of fecal materials through composting; however food-borne illnesses associated with fresh-produce have become more and more common. Research is being conducted toward developing more effective treatments of fecal waste to reduce the survival of harmful bacteria. One possible form of treatment is through the use of bacteriophages that are able to 'seek and destroy' specific bacteria. The objectives of this …

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Characterization Of Dairy Milk House Waste Water In Kentucky, Anshu Singh, Czarena L. Crofcheck, Gail M. Brion Mar 2007

Characterization Of Dairy Milk House Waste Water In Kentucky, Anshu Singh, Czarena L. Crofcheck, Gail M. Brion

Biosystems and Agricultural Engineering Faculty Publications

This study focuses on characterization of milk house waste water from eight different farms in Kentucky. The farms were separated into three groups based on the number of cows: small (20-30), medium (30-60), and large (over 60 cows). Samples were collected once a month from four farms and twice a month from the remainder. Samples were analyzed for chemical, biochemical, and microbiological characteristics. Results indicated a large and significant variation in the chemical and microbiological characteristics between the farms. Farm size had a significant effect on the nutrient content of the waste water. Though samples exhibited seasonal variation, there was …

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