Thesis Archives
Honors Thesis Archives
This search engine will let you explore the over 1800 theses written in Honors at The University of Maine since the Program’s inception in 1935. You may search our thesis archives based on any of the fields listed above. If the thesis is available at the Reynolds Library (Thomson Honors Center) or Fogler Library (Special Collections), the information will appear below the bibliographic data. At last count, we had about 1800 theses in the Reynolds Library.
Search Results
CHARACTERIZATION OF THE MYCOBACTERIOPHAGE UKULELE INTEGRATION SYSTEM; IDENTIFICATION OF INTEGRATION SITE ATTP AND THE ROLE OF THE INTEGRASE IN LYSOGENY REGULATION
Author:
Emily
E.
Whitaker
Major: Biochemistry Graduation Year: 2016 Thesis Advisor: Sally D. Molloy
Description of Publication:
Mycobacteriophage (phage) are a group of viruses that infect bacteria in the genus Mycobacterium. Two phage lifestyles are lytic and temperate. Lytic phage only carry out the lytic life cycle, resulting in host cell lysis. Temperate phage are capable of completing both lytic and lysogenic life cycles. During the lysogenic life cycle, a phage-encoded integrase facilitates integration at sites attP in the phage genome and attB in the host to form a lysogen. The cluster E mycobacteriophage integration system is poorly understood. Ukulele, a lysogenic cluster E phage, is being used to identify the Cluster E attP and characterize lysogeny regulation. A putative attP containing sequence was identified in the Ukulele genome by computational analysis. To confirm the presence of attP, this sequence will be inserted into a plasmid and transferred into integrase expressing M. smegmatis (pST-KT-int). Cells will be screened for plasmid integrated into the genome. To characterize the role of the integrase in lysogeny regulation, we will determine the impact of integrase expression levels on induction event frequency in M. smegmatis (pST-KT-int) – Ukulele lysogens.
Location of Publication: fogler reynolds
URL to Thesis: https://digitalcommons.library.umaine.edu/honors/414
Major: Biochemistry Graduation Year: 2016 Thesis Advisor: Sally D. Molloy
Description of Publication:
Mycobacteriophage (phage) are a group of viruses that infect bacteria in the genus Mycobacterium. Two phage lifestyles are lytic and temperate. Lytic phage only carry out the lytic life cycle, resulting in host cell lysis. Temperate phage are capable of completing both lytic and lysogenic life cycles. During the lysogenic life cycle, a phage-encoded integrase facilitates integration at sites attP in the phage genome and attB in the host to form a lysogen. The cluster E mycobacteriophage integration system is poorly understood. Ukulele, a lysogenic cluster E phage, is being used to identify the Cluster E attP and characterize lysogeny regulation. A putative attP containing sequence was identified in the Ukulele genome by computational analysis. To confirm the presence of attP, this sequence will be inserted into a plasmid and transferred into integrase expressing M. smegmatis (pST-KT-int). Cells will be screened for plasmid integrated into the genome. To characterize the role of the integrase in lysogeny regulation, we will determine the impact of integrase expression levels on induction event frequency in M. smegmatis (pST-KT-int) – Ukulele lysogens.
Location of Publication: fogler reynolds
URL to Thesis: https://digitalcommons.library.umaine.edu/honors/414
CHARACTERIZATION OF TRANSCRIPTIONAL CONTROL ELEMENTS IN CLUSTER E MYCOBACTERIOPHAGE UKULELE
Author:
Campbell
Belisle
Haley
Major: Biochemistry & Spanish Graduation Year: 2016 Thesis Advisor: Sally D. Molloy
Description of Publication:
Mycobacteriophage (phage) are a diverse group of viruses that infect Mycobacterium. Their study allows further understanding of viral evolution and genetics. Phage tightly control gene expression and transcribe their genes using host RNA polymerases. This project identifies potential transcriptional control elements in the genome of mycobacteriophage Ukulele. Promoters are sequences of the genome that allow binding of RNA polymerase and initiation of transcription. 21 putative promoters were identified in the Ukulele genome. To confirm transcriptional activity from putative promoters, a GFP reporter system was developed in mycobacterial cells. Intrinsic terminators are mRNA sequences that form secondary structure during transcription and stall the RNA polymerase. In Ukulele, 19 terminators were identified computationally. Future research includes confirmation of these terminators. Identification of elements that control transcription allows better understanding of phage gene expression.
Location of Publication: fogler reynolds
URL to Thesis: https://digitalcommons.library.umaine.edu/honors/397
Major: Biochemistry & Spanish Graduation Year: 2016 Thesis Advisor: Sally D. Molloy
Description of Publication:
Mycobacteriophage (phage) are a diverse group of viruses that infect Mycobacterium. Their study allows further understanding of viral evolution and genetics. Phage tightly control gene expression and transcribe their genes using host RNA polymerases. This project identifies potential transcriptional control elements in the genome of mycobacteriophage Ukulele. Promoters are sequences of the genome that allow binding of RNA polymerase and initiation of transcription. 21 putative promoters were identified in the Ukulele genome. To confirm transcriptional activity from putative promoters, a GFP reporter system was developed in mycobacterial cells. Intrinsic terminators are mRNA sequences that form secondary structure during transcription and stall the RNA polymerase. In Ukulele, 19 terminators were identified computationally. Future research includes confirmation of these terminators. Identification of elements that control transcription allows better understanding of phage gene expression.
Location of Publication: fogler reynolds
URL to Thesis: https://digitalcommons.library.umaine.edu/honors/397
Characterization Studies of Anti-Idiotype Antibodies that Molecularly Mimic the Antigenic Structure of a Universally Conserved Epitope on Aquatic Birnaviruses
Characterizing Mab Cluster R Prophage of Pathogen Mycobacterium abscessus (Mab)
Author:
Madeline
Kimble
Major: Biochemistry Graduation Year: 2021 Thesis Advisor: Sally D. Molloy
Description of Publication:
Mycobacterium abscessus (Mab) is an emerging pathogen that can cause pulmonary, skin and disseminating infections. It is one of the most drug-resistant pathogens and infections typically result in high morbidity and mortality. Understanding mechanisms of antibiotic resistance is critical for developing more effective treatments. Prophage, integrated viral genomes, are known to contribute to bacterial virulence and antibiotic resistance, yet Mab prophages remain largely uncharacterized.My research aims to characterize the diversity of the novel cluster MabR prophage genomes. The Molloy lab has demonstrated that the prophage McProf increases mycobacterial resistance to antibiotics. Using the McProf prophage genome sequence, we probed the PATRIC M. abscessus database to identify bacterial strains that carry prophage genomes related to McProf. We identified 25 related genomes, 8 of which were unique. This group of prophages are genetically distinct from prophages already described and we assigned them to a new cluster, MabR. Prophage genome ends were defined, and prophage sequences were extracted from bacterial genomes. MabR genomes are highly conserved, particularly across the structural genes in the right arm and the immunity cassette in the left arm.All nine genomes share a tyrosine-integrase and nearly identical attachment sites.All nine members share one of two types of Type VII secretion system polymorphic toxin systems, adjacent to the right attachment site that potentially improve fitness of the bacterial host. In future research we will investigate the role of MabR polymorphic toxins in drug resistance and bacterial fitness.
Location of Publication:
URL to Thesis: https://digitalcommons.library.umaine.edu/honors/669/
Major: Biochemistry Graduation Year: 2021 Thesis Advisor: Sally D. Molloy
Description of Publication:
Mycobacterium abscessus (Mab) is an emerging pathogen that can cause pulmonary, skin and disseminating infections. It is one of the most drug-resistant pathogens and infections typically result in high morbidity and mortality. Understanding mechanisms of antibiotic resistance is critical for developing more effective treatments. Prophage, integrated viral genomes, are known to contribute to bacterial virulence and antibiotic resistance, yet Mab prophages remain largely uncharacterized.My research aims to characterize the diversity of the novel cluster MabR prophage genomes. The Molloy lab has demonstrated that the prophage McProf increases mycobacterial resistance to antibiotics. Using the McProf prophage genome sequence, we probed the PATRIC M. abscessus database to identify bacterial strains that carry prophage genomes related to McProf. We identified 25 related genomes, 8 of which were unique. This group of prophages are genetically distinct from prophages already described and we assigned them to a new cluster, MabR. Prophage genome ends were defined, and prophage sequences were extracted from bacterial genomes. MabR genomes are highly conserved, particularly across the structural genes in the right arm and the immunity cassette in the left arm.All nine genomes share a tyrosine-integrase and nearly identical attachment sites.All nine members share one of two types of Type VII secretion system polymorphic toxin systems, adjacent to the right attachment site that potentially improve fitness of the bacterial host. In future research we will investigate the role of MabR polymorphic toxins in drug resistance and bacterial fitness.
Location of Publication:
URL to Thesis: https://digitalcommons.library.umaine.edu/honors/669/
CHARACTERIZING NEUTROPHIL BEHAVIOR IN ZEBRAFISH (DANIO RERIO) IN RESPONS TO ARSENIC AND CLUCOSE
Author:
Jacob
R.
Longfellow
Major: Microbiology Graduation Year: 2014 Thesis Advisor: Carol H. Kim
Description of Publication:
Location of Publication:
URL to Thesis: http://digitalcommons.library.umaine.edu/honors/202/
Major: Microbiology Graduation Year: 2014 Thesis Advisor: Carol H. Kim
Description of Publication:
Location of Publication:
URL to Thesis: http://digitalcommons.library.umaine.edu/honors/202/
Characterizing the Diversity of Cluster R Prophage in Mycobacterium abscessus
Author:
Colin
Welch
Major: Microbiology Graduation Year: 2021 Thesis Advisor: Sally D. Molloy
Description of Publication:
Mycobacterium abscessus is a mycobacterial pathogen responsible for pulmonary and disseminated infections in susceptible individuals and often is resistant to all antibiotic therapies, with cure rates ranging from 25% to 58% (Degiacomi et al., 2019). Investigating the mechanisms of extensive resistance in M. abscessus lends opportunities to develop more effective treatments. Prophage, viral sequences integrated into bacterial genomes, contribute to virulence and fitness in many bacterial pathogens including Escherichia coli O157:H7 and Vibrio cholerae (Fortier & Sekulovic, 2013). Yet, prophage in pathogenic mycobacteria are not well understood or studied. Recent work has demonstrated that the Mycobacterium chelonae prophage, McProf can function in concert with a second prophage to increase the expression of the conserved mycobacterial transcriptional regulator whiB7, which confers increased antibiotic resistance in mycobacteria (Cushman et al., Unpublished). To understand how prophage, like McProf, may influence resistance in M. abscessus, we bioinformatically identified and extracted eight novel prophage genomes with high sequence identity to McProf from M. abscessus sequences in the database PATRIC. The new prophages and McProf were assigned a novel M. abscessus (Mab) cluster, MabR. Strains carrying MabR prophage genomes were analyzed for cohabitating prophage sequences. Of the 25 strains, over 84% of them carried cohabitating prophages. There were 25 cohabiting prophages identified, with only six of those being unique. Three were clustered into MabD, and MabC, MabG, and MabA1 each received one prophage. One cohabiting prophage was identified in 16 of the 25 strains, all other cohabiting prophages were found either in one strain or two strains.
Location of Publication:
URL to Thesis: https://digitalcommons.library.umaine.edu/honors/694/
Major: Microbiology Graduation Year: 2021 Thesis Advisor: Sally D. Molloy
Description of Publication:
Mycobacterium abscessus is a mycobacterial pathogen responsible for pulmonary and disseminated infections in susceptible individuals and often is resistant to all antibiotic therapies, with cure rates ranging from 25% to 58% (Degiacomi et al., 2019). Investigating the mechanisms of extensive resistance in M. abscessus lends opportunities to develop more effective treatments. Prophage, viral sequences integrated into bacterial genomes, contribute to virulence and fitness in many bacterial pathogens including Escherichia coli O157:H7 and Vibrio cholerae (Fortier & Sekulovic, 2013). Yet, prophage in pathogenic mycobacteria are not well understood or studied. Recent work has demonstrated that the Mycobacterium chelonae prophage, McProf can function in concert with a second prophage to increase the expression of the conserved mycobacterial transcriptional regulator whiB7, which confers increased antibiotic resistance in mycobacteria (Cushman et al., Unpublished). To understand how prophage, like McProf, may influence resistance in M. abscessus, we bioinformatically identified and extracted eight novel prophage genomes with high sequence identity to McProf from M. abscessus sequences in the database PATRIC. The new prophages and McProf were assigned a novel M. abscessus (Mab) cluster, MabR. Strains carrying MabR prophage genomes were analyzed for cohabitating prophage sequences. Of the 25 strains, over 84% of them carried cohabitating prophages. There were 25 cohabiting prophages identified, with only six of those being unique. Three were clustered into MabD, and MabC, MabG, and MabA1 each received one prophage. One cohabiting prophage was identified in 16 of the 25 strains, all other cohabiting prophages were found either in one strain or two strains.
Location of Publication:
URL to Thesis: https://digitalcommons.library.umaine.edu/honors/694/
CHARACTERIZING THE INTACT PROPHAGE OF MYCOBACTERIUM CHELONAE BERGEY
Author:
Erica
Sewell
Major: Microbiology Graduation Year: 2017 Thesis Advisor: Keith W. Hutchinson
Description of Publication:
Mycobacteriophage (phage), are viruses that infect bacteria. All bacteria can be infected by phage, and each bacterial species has a unique set of phage that infect them, making phage prime candidates for studying viral diversity and evolution. Some phage integrate their genome into the host genome upon infection (prophage), where they may potentially remain indefinitely, coevolving with the host, and providing growth factors and other benefits to the host. The purpose of my research is to characterize a prophage within the genome of the bacterial host Mycobacterium chelonae Bergey to determine if it is still functional and potentially impacting the fitness of the host bacterium. Characterization of this prophage has revealed that multiple genes are conserved with regard to both the DNA and protein sequences. The integrase cassette is highly conserved, complete with integrase and two potential repressors, suggesting the phage may be capable of excising from the host genome. Multiple structural genes including capsid and tail proteins are also conserved, suggesting the prophage may be capable of producing intact virions. At least two prophage genes are transcriptionally active. These include a predicted repressor and transmembrane protein. Expression of these genes suggests that the prophage does indeed have some potential for affecting the biology of the host bacterium. Experiments are currently underway to determine if intact virion particles are being produced during bacterial growth.
Location of Publication: fogler reynolds
URL to Thesis: https://digitalcommons.library.umaine.edu/honors/265/
Major: Microbiology Graduation Year: 2017 Thesis Advisor: Keith W. Hutchinson
Description of Publication:
Mycobacteriophage (phage), are viruses that infect bacteria. All bacteria can be infected by phage, and each bacterial species has a unique set of phage that infect them, making phage prime candidates for studying viral diversity and evolution. Some phage integrate their genome into the host genome upon infection (prophage), where they may potentially remain indefinitely, coevolving with the host, and providing growth factors and other benefits to the host. The purpose of my research is to characterize a prophage within the genome of the bacterial host Mycobacterium chelonae Bergey to determine if it is still functional and potentially impacting the fitness of the host bacterium. Characterization of this prophage has revealed that multiple genes are conserved with regard to both the DNA and protein sequences. The integrase cassette is highly conserved, complete with integrase and two potential repressors, suggesting the phage may be capable of excising from the host genome. Multiple structural genes including capsid and tail proteins are also conserved, suggesting the prophage may be capable of producing intact virions. At least two prophage genes are transcriptionally active. These include a predicted repressor and transmembrane protein. Expression of these genes suggests that the prophage does indeed have some potential for affecting the biology of the host bacterium. Experiments are currently underway to determine if intact virion particles are being produced during bacterial growth.
Location of Publication: fogler reynolds
URL to Thesis: https://digitalcommons.library.umaine.edu/honors/265/
CHARACTERIZING THE NEUTROPHIL RESPONSE TO INFLUENZA A VIRUS INFECTION IN THE ZEBRAFISH MODEL
Author:
Alexis
Rae
Bowman
Major: Microbiology Graduation Year: 2016 Thesis Advisor: Carol H. Kim
Description of Publication:
Neutrophils are a type of innate immune cell that play a critical role in the acute inflammatory response by recognizing, phagocytizing and killing pathogens. Although their presence during infection is immensely significant for pathogen clearance, current research suggests that an overly robust neutrophil response may be detrimental to the host. Expression levels of the zebrafish chemokines Cxcl8-l1 and Cxcl8-l2, which are responsible for inducing neutrophil migration to a site of infection, have been shown to increase under inflammatory conditions caused by various PAMPs and infectious stimuli. Cxcl8 expression levels under inflammatory conditions caused by human viral infections, such as Influenza A virus infection, have yet to be studied. The aim of this study is to utilize the zebrafish as a model to characterize the neutrophil response to IAV infection. Using the MPX-mCherry transgenic zebrafish line (red fluorescence-tagged neutrophils) and IAV-GFP (green fluorescence-tagged Influenza A virus), we hope to quantify neutrophil migration to a localized IAV infection in the swimbladder. Localized infection with IAV-GFP resulted in increased numbers of neutrophils in the swimbladder region and surrounding tissues, suggesting that neutrophils do migrate to a localized IAV infection. Additionally, through the systemic infection of AB zebrafish embryos, we hope to investigate how levels of expression of neutrophil migratory genes: Cxcl8-l1 and Cxcl8-l2, may be altered upon IAV infection. Preliminary data have revealed that the Cxcl8 genes are up-regulated during IAV infection, particularly between 12 and 24 hpi.
Location of Publication: fogler
URL to Thesis: https://digitalcommons.library.umaine.edu/honors/373
Major: Microbiology Graduation Year: 2016 Thesis Advisor: Carol H. Kim
Description of Publication:
Neutrophils are a type of innate immune cell that play a critical role in the acute inflammatory response by recognizing, phagocytizing and killing pathogens. Although their presence during infection is immensely significant for pathogen clearance, current research suggests that an overly robust neutrophil response may be detrimental to the host. Expression levels of the zebrafish chemokines Cxcl8-l1 and Cxcl8-l2, which are responsible for inducing neutrophil migration to a site of infection, have been shown to increase under inflammatory conditions caused by various PAMPs and infectious stimuli. Cxcl8 expression levels under inflammatory conditions caused by human viral infections, such as Influenza A virus infection, have yet to be studied. The aim of this study is to utilize the zebrafish as a model to characterize the neutrophil response to IAV infection. Using the MPX-mCherry transgenic zebrafish line (red fluorescence-tagged neutrophils) and IAV-GFP (green fluorescence-tagged Influenza A virus), we hope to quantify neutrophil migration to a localized IAV infection in the swimbladder. Localized infection with IAV-GFP resulted in increased numbers of neutrophils in the swimbladder region and surrounding tissues, suggesting that neutrophils do migrate to a localized IAV infection. Additionally, through the systemic infection of AB zebrafish embryos, we hope to investigate how levels of expression of neutrophil migratory genes: Cxcl8-l1 and Cxcl8-l2, may be altered upon IAV infection. Preliminary data have revealed that the Cxcl8 genes are up-regulated during IAV infection, particularly between 12 and 24 hpi.
Location of Publication: fogler
URL to Thesis: https://digitalcommons.library.umaine.edu/honors/373
Characterizing the Range Shifts of Two Peromyscus Species in Maine
Author:
Molly
Bennett
Major: Wildlife Ecology Graduation Year: 2020 Thesis Advisor: Danielle Levesque
Description of Publication:
In a changing climate, two species of mice in Maine (Peromyscus maniculatus and Peromyscus leucopus) are currently undergoing range shifts. The objective of my thesis is to determine the historical and current range of each species within the state of Maine. I used two approaches. I assembled ear biopsies collected this summer in Acadia National Park and throughout the state by the Gardner and Levesque labs to genotype the mice as either P. maniculatus or P. leucopus. Additionally, I summarized research that denotes where the two species were historically present around the state. These species are functionally impossible to tell apart in the field, and projects that use small mammal trapping often simply choose one of the two species to identify all uncertain mice. A lack of genotyping and data from a current time frame hindered our understanding of the ranges of the species. However, knowledge of the ranges of the deer mouse and the white-footed mouse could yield information as to how the two species might differ as reservoirs for tick-borne disease, catalysts for forest community development, and models for mammalian range shifts.
Location of Publication:
URL to Thesis: https://digitalcommons.library.umaine.edu/honors/580/
Major: Wildlife Ecology Graduation Year: 2020 Thesis Advisor: Danielle Levesque
Description of Publication:
In a changing climate, two species of mice in Maine (Peromyscus maniculatus and Peromyscus leucopus) are currently undergoing range shifts. The objective of my thesis is to determine the historical and current range of each species within the state of Maine. I used two approaches. I assembled ear biopsies collected this summer in Acadia National Park and throughout the state by the Gardner and Levesque labs to genotype the mice as either P. maniculatus or P. leucopus. Additionally, I summarized research that denotes where the two species were historically present around the state. These species are functionally impossible to tell apart in the field, and projects that use small mammal trapping often simply choose one of the two species to identify all uncertain mice. A lack of genotyping and data from a current time frame hindered our understanding of the ranges of the species. However, knowledge of the ranges of the deer mouse and the white-footed mouse could yield information as to how the two species might differ as reservoirs for tick-borne disease, catalysts for forest community development, and models for mammalian range shifts.
Location of Publication:
URL to Thesis: https://digitalcommons.library.umaine.edu/honors/580/