Дисертації: "Bacteriophages Genetics"

1

Dibbens, Justin Andrew. "Studies on the control of late gene transcription in coliphage 186 /." Title page, contents and summary only, 1990. http://web4.library.adelaide.edu.au/theses/09PH/09phd543.pdf.

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2

Brathwaite, Kelly Janelle. "Interactions between Campylobacters and their bacteriophages." Thesis, University of Nottingham, 2015. http://eprints.nottingham.ac.uk/28422/.

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Campylobacter jejuni is a leading cause of human bacterial enteritis worldwide. Consumption of contaminated poultry meat is considered a major source of infection. The use of virulent bacteriophages as a form of biocontrol to specifically reduce this pathogen in poultry (phage therapy) is a promising intervention that does not rely on antimicrobials and therefore circumvents the emergence of antibiotic-resistant Campylobacter strains. In order to achieve this, a better understanding of the mechanisms involved in phage-host interactions at the molecular level would assist in the development of the strategy and the selection of bacteriophages. The main objective of this study was to therefore examine such interactions between Campylobacter and its virulent phages. To achieve this, the transcriptional response of C. jejuni to phage infection was investigated, along with the role of a Type II restriction-modification system during phage infection of Campylobacter. These studies were conducted using the highly phage-sensitive Campylobacter strain, C. jejuni PT14, in conjunction with a number of group II and III bacteriophages (Eucampyvirinae). Transcriptome studies (RNA-Seq) revealed a phage-induced host response that included a demand for iron and oxygen. This was highlighted by the up-regulation of several siderophore-based iron acquisition genes and down-regulation of genes associated with a number of anaerobic electron transport pathways that utilise alternative electron acceptors to oxygen. In addition, the pattern of gene regulation also suggested apo-Fur regulation of the iron-responsive and flagellar biogenesis genes. This host response has been proposed to occur as a consequence of the reduction of ribonucleotides to form deoxyribonucleotides during phage DNA replication. This process is catalysed by the enzyme ribonucleotide reductase and requires iron and oxygen during the formation of a reactive di-iron centre within the β-subunit of the enzyme. Unusually knock-out mutants of a Type II restriction-modification system had a negative impact on phage replication. The A911_00150 mutant displayed pleiotropic changes in motility, cell based invasion and the ability to colonise chickens. Transcriptome analysis highlighted down-regulation of the genes required for the synthesis of the bacterial flagellum.

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3

Mmolawa, Princess Tlou. "Molecular analysis of temperate phages in Salmonella enterica serovar Typhimurium DT 64 isolated in Australia." Title page, contents and summary only, 2001. http://web4.library.adelaide.edu.au/theses/09PH/09phm6855.pdf.

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Files on accompanying CD-ROM: Appendix III Phages ST64T and ST64B sequences, are in rtf format. Bibliography: leaves 279-324. System requirements for accompanying CD-ROM: IBM or compatible ; Microsoft Word or compatible to read rtf files.

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4

GARVEY, KEVIN JAMES. "DNA SEQUENCE ANALYSIS OF BACILLUS PHAGE PHI29 RIGHT EARLY REGION AND LATE GENES 14, 15 AND 16 (LYSOZYME)." Diss., The University of Arizona, 1986. http://hdl.handle.net/10150/183839.

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The sequence of the rightmost 4,626 bp of the Bacillus phage φ29 genome is presented and analyzed. Nine large open reading frames (ORF's) have been found. Three of these ORF's are correlated with the late genes 14, 15 and 16. The remaining six ORF's are in the right early region. One of these early ORF's has been identified as gene 17 (g17), the only early gene to have been genetically mapped in this region. The remaining ORF's (16.5, 16.6, 16.7, 16.8 and 16.9) were previously unknown. The biological efficacies of some of these putative early ORF's were demonstrated using an in vitro E. coli transcription-translation system. The primary amino acid sequences, molecular weights, translational initiation sequences and genetic organization of these nine genes are presented and discussed. Gene product 15 (gp15) was found to have strong homology with Salmonella phage P22 gp19, a lysozyme. gp15 also has a lesser but possibly significant homology with T4 gene product e (gpe), also a lysozyme. Using a clone containing φ29 g15 it was shown that gp15 can complement T4 gene e (ge) mutant infections, leading to the conclusion that φ29 g15 encodes a lysozyme. Three transcriptional initiation sites (P(E)3, P(EC)3 and B2) were previously mapped in this region. The sequences of the putative P(EC)3 and B2 promoter sites are presented and shown to have homology with the Bacillus σ⁵⁵ concensus sequence. Sequences having homology to a minor Bacillus sigma factor recognition site, σ³², are also presented and discussed. The region between the last late gene (g16) and the last early gene (ORF-16.5) consists of only 30 bp. Analysis of potential secondary structures of transcripts across this region suggests that the same sequences may be involved in the termination of both late and early transcription.

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5

Goh, Shan. "Phenotypic and genotypic characterisation of bacteriophages of Clostridium difficile." University of Western Australia. Microbiology Discipline Group, 2003. http://theses.library.uwa.edu.au/adt-WU2004.0018.

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Clostridium difficile is an important hospital-acquired pathogen causing C. difficile-associated diarrhoea (CDAD) in patients exposed to antibiotics. The lack of information on bacteriophages of C. difficile, and the potential of phages as therapeutic agents for the treatment of CDAD, prompted the isolation and characterisation of phages active against clinical isolates of C. difficile in order to determine the prevalence and significance of phages of this anaerobe. Three (5.4 %) of 56 clinical C. difficile isolates induced by mitomycin C yielded dsDNA phages C2, C5, C6 and C8. The four phages differed from previously described C. difficile phages in particle morphology, burst size and host range. C2, C5 and C8 particles were members of the family Myoviridae, while C6 belonged to Siphoviridae. The burst sizes were 5 for C2, 7 for C5, 19 for C6 and 33 for C8. C8 had the broadest host range, lysing 27 out of 56 (48 %) C. difficile isolates, followed by C6 (43 %), C5 (20 %) and C2 (20 %). Superinfection experiments, restriction enzyme analysis and Southern hybridisation showed C2 and C5 to be closely related with C8 somewhat related to them, however, C6 was distantly related to the other three phages. C2 was further characterised as a representative phage. Its genome did not possess cohesive ends, and was shown to integrate chromosomally via an attP site identified within a 1.9 kb HindIII fragment. However, an integrase gene, which is typically close to the attP region, was not located. Nine of 16 HindIII fragments of C2, including the 1.9 kb fragment, were cloned into pUC18. Approximately 9 kb of the estimated 43 kb genome of C2 was sequenced and analysed. Seven of the nine translated sequences were homologous to phage structural proteins, two sequences were not homologous to any relevant protein in the Genbank and EMBL databases, and one was homologous to proteins of Clostridium species. Nucleotide homology between the C2 sequences and the recently sequenced C. difficile strain CD630 was found in three regions within CD630 genome. Seven of the nine sequences, including the 1.9 kb fragment, were clustered in one region. These data suggest that the genes constitute a phage structural gene module. The presence of C2-like sequences in CD630, and Southern hybridisation of C. difficile strains using phage probes, suggested related prophage sequences may be commonly present in this bacterial species. An investigation was carried out to determine the presence of toxin genes tcdA and tcdB, and PaLoc-associated gene tcdE, in phage DNA. In addition, the effect of phage infection on toxin production of toxigenic C. difficile strains was studied. Of the three genes, tcdE only was detected in phages C2, C5 and C8, but not in C6. Strains that maintained phages in a stable manner (lysogens) were isolated and used in toxin studies. The amount of toxin B produced was measured by cytotoxic assays using Vero cells, and toxin A production was measured by ELISA. Although phages did not encode toxin A or B genes, there was a significant increase in toxin B production in some lysogens. There was no increase in toxin A production. Transcriptional analyses of tcdA and tcdB in lysogens and parental strains was performed by real-time RT-PCR and Northern hybridisation to determine whether phage was affecting regulation of toxin transcription. Phage did not appear to affect toxin gene transcription, although results from real-time RT-PCR and Northern hybridisation were conflicting. A phage induced from the highly toxigenic reference strain VPI 10463 was also briefly characterised and investigated for its effect on toxin production in VPI 10463. The phage, ΦCV, had similar particle morphology to C2, C5 and C8, and had some HindIII bands in common with C2 and C5. Two cured variant strains produced significantly less toxin B compared to VPI 10463. In conclusion, several important properties of C. difficile phages were characterised. It appears these temperate phages may play a role in toxin production making them unsuitable as therapeutic agents for the treatment of CDAD. However, C2 phage may have potential as the basis for an integrative vector that will add to the genetic tools available for clostridia.

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6

Harrison, Sharon Jane. "Targeted transgenesis and the 186 site-specific recombination system /." Title page, summary and contents only, 1999. http://web4.library.adelaide.edu.au/theses/09PH/09phh322.pdf.

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7

Huen, Shing-yan Michael, and 禤承恩. "A mechanistic study of lambdaphage-mediated recombination in E. coli." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2006. http://hub.hku.hk/bib/B35321854.

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8

Swanson, Rhett. "Cloning and expression of the genes encoding bacteriophage T7 & SP6 RNA polymerase /." Title page, table of contents and summary only, 1990. http://web4.library.adelaide.edu.au/theses/09PH/09phs9722.pdf.

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9

Chang, Jenny Ren-Jye. "Scaffolding-mediated capsid size determination in bacteriophages." Birmingham, Ala. : University of Alabama at Birmingham, 2009. https://www.mhsl.uab.edu/dt/2009p/changj.pdf.

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Thesis (Ph. D.)--University of Alabama at Birmingham, 2009.
Title from PDF title page (viewed Jan. 26, 2010). Additional advisors: Asim K. Bej, Gail E. Christie, Peter E. Prevelige, Jr., R. Douglas Watson. Includes bibliographical references.

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10

Brumby, Anthony Mansfield. "The control of prophage induction in coliphage 186 /." Title page, contents and summary only, 1994. http://web4.library.adelaide.edu.au/theses/09PH/09phb893.pdf.

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11

Seo, Sang Beom. "The isolation and characterization of mutations in the deoxyguanosine triphosphate triphosphohydrolase (dgt) gene of ESCHERICHIA COLI." Thesis, Georgia Institute of Technology, 1990. http://hdl.handle.net/1853/25334.

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12

Gerendasy, Dan Douglas. "The genomic organization and right early transcription of bacteriophage PRD1." Diss., The University of Arizona, 1989. http://hdl.handle.net/10150/184884.

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The bacteriophage PRD1 is a lipid bearing phage that infects a wide variety of gram-negative bacteria, including Escherichia coli and Salmonella typhimurium when they harbor the appropriate plasmid. It contains a linear duplex DNA molecule that is covalently bound by its 5' ends to a terminal protein. Like adenovirus and the Bacillus phage φ29, PRD1 specifies its own DNA polymerase which is able to utilize the phage encoded terminal protein to prime DNA synthesis. In addition to these two proteins, PRD1 also specifies an additional replication protein (p12) of unknown function. We have sequenced the origins of replication (termini of the genome) as well as the right most 1700 bp of the bacteriophage PRD1 genome. The right most 1700 bp encompasses the right early region and completes the sequence of all PRD1 early functions. We report here that the PRD1 genome contains a perfect 111 bp inverted terminal repeat. Furthermore, statistical analyses of the right 1700 bp, as well as the examination of transcription and translation signals has allowed us to assign gene XII to an open reading frame and to infer the direction of both early and late transcription. Gene XII, which has been implicated in the replication process and the regulation of gene expression is predicted to encode a 16.7 Kdal protein. Data base searches have revealed a possible evolutionary relationship between this protein and the ε-subunit of E. coli DNA polymerase III. We have also mapped right, early transcription of the PRD1 genome. This has corroborated our inference concerning the direction of right early transcription and confirmed our assignment of gene XII to an open reading frame. It has also revealed that two putative rho-independent terminators are functional in vitro and that the putative right early promoter is utilized in vivo and in vitro. The data presented here have permitted us to ascertain the general genomic and transcriptional organization of PRD1 and to predict the primary structure of the product of gene XII. These results, in turn, have allowed us to develop hypotheses concerning the evolution of linear, protein primed DNA's and the function of gene XII.

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13

Fehrsen, Jeanni. "Isolation of antigenic peptides of Cowdria ruminantium and their encoding genes using a genome-derived phage display library." Thesis, Rhodes University, 2003. http://hdl.handle.net/10962/d1003979.

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The development of new and effective vaccines and immunodiagnostic reagents requires the characterisation of antigenically relevant proteins and their interactions with the products of the immune system. Phage display technology was investigated as a means of elucidating some of the antigenic properties of the rickettsial parasite, Cowdria ruminantium (Cowdria). Randomly fragmented gene-derived libraries have been useful in elucidating viral and other epitopes, but only limited work has been done with entire genomes. A phage display library expressing a repertoire of Cowdria peptides was constructed. It was sufficiently large to represent the organism's genome, but lacked phages displaying peptides coded for by genes containing a Pvu II restriction enzyme site, including the one coding for the major antigenic protein 1 (MAP1). This was considered advantageous since MAP1 is immunodominant and has already been well characterised. Affinity selection with antibodies against Cowdria proteins other than MAP1 allowed several antibody-reactive peptides to be isolated. These selected sequences were placed in the context of the genome by screening a lambda bacteriophage library and by comparison with Cowdria DNA sequences. Apart from showing that antigenic mimics were present in the phage display library, six open reading frames encoding putative Cowdria proteins were identified. All had similarities to, or motifs in common with, membrane proteins and are thus likely to be exposed to the host's humoral immune system. Some of the proteins identified were larger than the antigens used to elicit the antibodies used for selection, probably as a result of the presence of cross-reactive epitopes. Despite limitations experienced when extending a fragmented-gene approach for epitope location to genomes, it was possible to identify an antigenic region on MAP1 by comparison with selected mimics. In addition, binding peptide sequences were identified with two monoclonal antibodies that had been raised against non-Cowdria antigens. An epitope on the VP7 protein of bluetongue virus was identified and peptides were found that reacted with a monoclonal antibody directed against malignant catarrhal fever virus. Thus, apart from being able to identify several potentially important Cowdria epitopes and genes, the fragmented-genome library holds promise as a universal reagent for identifying useful mimics.

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14

Huen, Shing-yan Michael. "A mechanistic study of lambdaphage-mediated recombination in E. coli." Click to view the E-thesis via HKUTO, 2006. http://sunzi.lib.hku.hk/hkuto/record/B35321854.

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15

Kalionis, Bill. "The early control region of temperate coliphage 186 : sequence and transcription studies /." Title page, contents and summary only, 1985. http://web4.library.adelaide.edu.au/theses/09PH/09phk14.pdf.

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16

Hsieh, Jui-Cheng. "Structure-function analysis of the bacteriophage PRD1 DNA terminal protein: Nucleotide sequence, overexpression, and site-directed mutagenesis of the terminal protein gene." Diss., The University of Arizona, 1990. http://hdl.handle.net/10150/184974.

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The nucleotide sequence of the PRD1 terminal protein gene has been determined. The coding region for PRD1 terminal protein is 777 base pairs long and encodes 259 amino acid residues (29,326 daltons). The deduced amino acid sequence of PRD1 terminal protein reveals no overall homology with other known terminal proteins or related proteins. A closer examination revealed a highly conserved amino acid sequence, YSRLRT, exist among all identified DNA terminal proteins including PRD1, PZA, Nf, φ29 and adenovirus. This is the first conserved amino acid sequence that has been found in all identified DNA terminal proteins. Not only is the YSRLRT sequence conserved, but its spatial location is similar as well. Therefore, the significance of the YSRLRT conserved sequence is suggested by both its conservative spatial location and high degree of homology across species. To study the structure-function relationship of the YSRLRT sequence of PRD1 terminal protein, in vitro site-directed mutagenesis was performed to determine the role of each amino acid in this conserved region. The PRD1 terminal protein and DNA polymerase genes were cloned into phagemid pEMBLex3, and the recombinant plasmid used for constructing mutants. Eleven PRD1 terminal protein mutant clones were examined for their priming complex formation activities. Our results have strongly demonstrated that the positive charge residue of arginine-174 plays an important role for PRD1 terminal protein function. There are 13 tyrosine residues in the predicted PRD1 terminal protein. It was of interest to known which tyrosine is actually linked to terminal nucleotide of the PRD1 DNA. We used a new approach involving replacing the tyrosine residues with phenylalanine residues in the carboxyl terminal portion of the protein. From analyses, the tyrosine-190 has been determined to be the most likely linkage site between terminal protein and PRD1 DNA.

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17

Hallewell, Jennyka, and University of Lethbridge Faculty of Arts and Science. "Shiga toxin-producing bacteriophage in Escherichia coli O157:H7." Thesis, Lethbridge, Alta. : University of Lethbridge, Deptartment of Biochemistry, 2008, 2008. http://hdl.handle.net/10133/776.

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Shiga toxin-producing E. coli (STEC) including E. coli O157:H7 are potential food and water borne zoonotic bacterial pathogens capable of causing outbreaks of severe illness in humans. The virulence of E. coli O157:H7 strains may be related to the type of Stx produced and several Stx2 variants have been identified which appear to differ in their ability to cause disease. Two lineages exist within O157 strains where lineage I is associated mainly with human and bovine isolates and lineage II is associated mainly with bovine isolates. The goal of this study was to identify and characterize a lineage II EC970520 Stx2c phage and determine if variations in the phage compared to Stx2 phage found within the lineage I strain, EDL933, can result in differences in virulence observed between the lineages. This study suggests: 1) that the lineage II strain EC970520 contains a highly heterogeneous Stx2c variant phage; 2) that location of integration of the phage within the genome of a bacterium may be important for host selection; 3) that EC970520 Stx2c phage genes are lineage II specific but only a subset of EDL933 phage genes are lineage I specific; 4) that differences in the stability of phages within bacteria contribute to the evolution of new pathogens; 5) that variation in phage genes can be used to detect different strains of E. coli O157:H7 and other STEC; and 6)that the type of phage may result in phenotypic differences between lineages and occurrence of human disease. Results of this study indicate that lineage II strains may be less virulent than lineage I strains due to specific genetic differences and the ability to release phage which is important to the evolution of new pathogenic strains.
xv, 162 leaves : ill. ; 29 cm.

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18

Hsu, Yu-Hung. "Characterization of Mannheimia haemolytica-specific bacteriophages." Thesis, Lethbridge, Alta. : University of Lethbridge, Dept. of Biological Sciences, c2011, 2011. http://hdl.handle.net/10133/3150.

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Mannheimia haemolytica is the principal bacterial agent associated with bovine respiratory disease (BRD). It has a significant economic impact on the beef feedlot industry. The current methods for BRD prevention and treatment have various problems and limitations, especially with reports of increased antimicrobial resistance in M. haemolytica. Bacteriophage therapy presents a novel method to mitigate M. haemolytica. This study aimed to isolate strictly lytic M. haemolytica-specific bacteriophages from bovine nasopharyngeal swabs and feedlot trough water. This was accompanied by an extensive characterization of temperate bacteriophages induced from representative strains of a M. haemolytica collection. Phage morphology, host specificity, genomic diversity, and comparative genomics were determined. Even though temperate bacteriophages are not ideal candidates for phage therapy, they can be engineered or modified to serve this function. Genome sequences of selected temperate bacteriophages also provide a foundation for future studies on the biology of these microorganisms.
viii, 107 leaves : ill. ; 29 cm

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19

Kunapuli, Phani Chandrika. "Analysis of the Clear Plaque Phenotype of the Bacteriophage HK75." TopSCHOLAR®, 2010. http://digitalcommons.wku.edu/theses/219.

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The growth of bacteriophage HK75 is inhibited by specific mutations in the zinc binding domain of the host RNA polymerase beta prime subunit. It shares this rare property with bacteriophage HK022 and other phages that use RNA mediated antitermination to promote early gene expression. Recent genomic analysis of HK75 and HK022 has confirmed the relatedness of these two phages and place HK75 in the lambdoid family of bacteriophages. Lambdoid phages are temperate and can adopt a lytic or lysogenic lifestyle upon infection of a suitable host. However, HK75 only forms clear plaques and thus appears to be defective in its ability to form lysogens. Based on published analyses of other lambdoid phages, a clear plaque phenotype is commonly due to a mutation in one of 5 phage genes: cI, cII, cIII, int, xis or the phage repressor DNA binding sites. To determine which mutation is responsible for the clear plaque phenotype of HK75, we cloned the cI and cIII genes and assayed their activities. The HK75 cI gene clone prevented super-infection by HK75. This result demonstrated repressor functionality and thus the clear plaque phenotype cannot be due to a mutation in the HK75 cI gene. Several amino acid differences were noted between the HK022 and HK75 CIII proteins. To determine if the clear plaque phenotype was due to mutations in the HK75 cIII gene, we cloned it into an expression vector. Only under conditions of cIII gene overexpression were lysogens of HK75 recovered. The phage CIII protein normally protects CII from proteolysis. Stabilization of CII by mutations in specific host proteases has been shown to suppress a clear plaque phenotype caused by mutations in the cIII gene. When HK75 was plated on a protease deficient strain of E. coli, turbid plaques were formed and lysogens were recovered. These results support the idea that the clear plaque phenotype of HK75 is due to a defect in the expression of the phage cIII gene.

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20

Iyer, Kartik. "Interaction of bacteriophage mu middle transcription activator protein mor with promoter DNA." View the abstract Download the full-text PDF version (on campus access only), 2008. http://etd.utmem.edu/ABSTRACTS/2008-033-Iyer-index.html.

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Thesis (M.S.)--University of Tennessee Health Science Center, 2008.
Title from title page screen (viewed on July 31, 2008). Research advisor: Martha M Howe, Ph.D. Document formatted into pages (vii, 127 p. : ill.). Vita. Abstract. Includes bibliographical references (p. 103-116).

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21

Lima, Mendez Gipsi. "Towards in silico detection and classification of prokaryotic Mobile Genetic Elements." Doctoral thesis, Universite Libre de Bruxelles, 2008. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/210578.

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Bacteriophage genomes show pervasive mosaicism, indicating that horizontal gene exchange plays a crucial role in their evolution. Phage genomes represent unique combinations of modules, each of them with a different phylogenetic history. Thus, a web-like, rather than a hierarchical scheme is needed for an appropriate representation of phage evolutionary relationships. Part of the virology community has long recognized this fact and calls for changing the traditional taxonomy that classifies tailed phages according to the type of genetic materials and phage tail and head/capsid morphologies. Moreover, based on morphological features, the current system depends on inspection of phage virions under the electron microscope and cannot directly classify prophages. With the genomic era, many phages have been sequenced that are not classified, calling for development of an automatic classification procedure that can cope with the sequencing pace. The ACLAME database provides a classification of phage proteins into families and assigns the families with at least 3 members to one or several functions.

In the first contribution of this work, the relative contribution of those different protein families to the similarities between the phages is assessed using pair-wise similarity matrices. The modular character of phage genomes is readily visualized using heatmaps, which differ depending on the function of the proteins used to measure the similarity.

Next, I propose a framework that allows for a reticulate classification of phages based on gene content (with statistical assessment of the significance of number of shared genes). Starting from gene/protein families, we built a weighted graph, where nodes represent phages and edges represent phage-phage similarities in terms of shared families. The topology of the network shows that most dsDNA phages form an interconnected group, confirming that dsDNA phages share a common gene pool, as proposed earlier. Differences are observed between temperate and virulent phages in the values of several centrality measures, which may correlate with different constraints to rampant recombination dictated by the phage lifestyle, and thus with a distinct evolutionary role in the phage population.

To this graph I applied a two-step clustering method to generate a fuzzy classification of phages. Using this methodology, each phage is associated with a membership vector, which quantitatively characterizes the membership of the phage to the clusters. Alternatively, genes were clustered based on their ‘phylogenetic profiles’ to define ‘evolutionary cohesive modules’. Phages can then be described as composite of a set of modules from the collection of modules of the whole phage population. The relationships between phages define a network based on module sharing. Unlike the first network built from statistical significant number of shared genes, this second network allows for a direct exploration of the nature of the functions shared between the connected phages. This functionality of the module-based network runs at the expense of missing links due to genes that are not part of modules, but which are encoded in the first network.

These approaches can easily focus on pre-defined modules for tracing one or several traits across the population. They provide an automatic and dynamic way to study relationships within the phage population. Moreover, they can be extended to the representation of populations of other mobile genetic elements or even to the entire mobilome.

Finally, to enrich the phage sequence space, which in turn allows for a better assessment of phage diversity and evolution, I devise a prophage prediction tool. With this methodology, approximately 800 prophages are predicted in 266 among 800 replicons screened. The comparison of a subset of these predictions with a manually annotated set shows a sensitivity of 79% and a positive predictive value of 91%, this later value suggesting that the procedure makes few false predictions. The preliminary analysis of the predicted prophages indicates that many may constitute novel phage types.

This work allows tracing guidelines for the classification and analysis of other mobile genetic elements. One can foresee that a pool of putative mobile genetic elements sequences can be extracted from the prokaryotic genomes and be further broken down in groups of related elements and evolutionary conserved modules. This would allow widening the picture of the evolutionary and functional relationships between these elements.

Doctorat en Sciences
info:eu-repo/semantics/nonPublished

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22

Jonnalagadda, Madhuri. "Site Directed Mutagensis of Bacteriophage HK639 and Identification of Its Integration Site." TopSCHOLAR®, 2008. http://digitalcommons.wku.edu/theses/42.

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Bacteriophages affect bacterial evolution, pathogenesis and global nutrient cycling. They are also the most numerous and diverse group of biological entities on the planet [1, 2, 3, 4, 5, 6]. Members of the Lambda phage family share a similar genetic organization and control early gene expression by suppressing transcription, a process known as antitermination. Transcription antitermination in Lambda is mediated by a phage-encoded protein whereas in lambdoid phage HK022, antitermination is mediated by a phage-encoded RNA molecules. Recent results suggest that another bacteriophage called HK639 also appears to use RNA-mediated antitermination. To characterize this newly identified phage we generated site directed mutations and identified where the phage integrates into the chromosome of its bacterial host.

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23

Mavris, Maria. "Bacteriophage SfII mediated serotype conversion in Shigella flexneri /." Title page, abstract and contents only, 1998. http://web4.library.adelaide.edu.au/theses/09PH/09phm4608.pdf.

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24

Cramer, Todd James Lucas. "Genetic mosaicism between the bacteriophage [phi]80 and bacteriophage [lambda]." Bowling Green, Ohio : Bowling Green State University, 2008. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=bgsu1223514067.

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25

Povinelli, Christine Marie. "Genetic analysis of the dihydrofolate reductase and thymidylate synthase genes of bacteriophage T4." Diss., Georgia Institute of Technology, 1987. http://hdl.handle.net/1853/25347.

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26

Lee, Se Il. "Statistical thermodynamics of virus assembly." Diss., Georgia Institute of Technology, 2010. http://hdl.handle.net/1853/33900.

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Experiments show that MgSO4 salt has a non-monotonic effect as a function of MgSO4 concentration on the ejection of DNA from bacteriophage lambda. There is a concentration, N0, at which the minimum amount of DNA is ejected. At lower or higher concentrations, more DNA is ejected. We propose that this non-monotonic behavior is due to the overcharging of DNA at high concentration of Mg⁺² counterions. As the Mg⁺² concentration increases from zero, the net charge of ejected DNA changes its sign from negative to positive. N0 corresponds to the concentration at which DNA is neutral. Our theory fits experimental data well. The DNA-DNA electrostatic attraction is found to be -0.004 kBT/nucleotide. Simulations of DNA-DNA interaction of a hexagonal DNA bundle support our theory. They also show the non-monotonic DNA-DNA interaction and reentrant behavior of DNA condensation by divalent counterions. Three problems in understanding the capsid assembly for a retrovirus are studied: First, the way in which the viral membrane affects the structure of in vivo assembled HIV-1 capsid is studied. We show that conical and cylindrical capsids have similar energy at high surface tension of the viral membrane, which leads to the various shapes of HIV-1 capsids. Secondly, the problem of RNA genome packaging inside spherical viruses is studied using RNA condensation theory. For weak adsorption strength of capsid protein, most RNA genomes are located at the center of the capsid. For strong adsorption strength, RNA genomes peak near the capsid surface and the amount of RNA packaged is proportional to the capsid area instead its volume. Theory fits experimental data reasonably well. Thirdly, the condensation of RNA molecules by nucleocapsid (NC) protein is studied. The interaction between RNA molecules and NC proteins is important for the reverse transcription of viral RNA which relates to the viral infectivity. For strong adsorption strength of the NC protein, there is a screening effect by RNA molecules around a single NC protein.

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27

Cramer, Todd James. "Genetic Mosaicism Between The Bacteriophage φ80 And Bacteriophage λ". Bowling Green State University / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1223514067.

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28

Eriksson, Jesper. "Structure-Function Studies of Bacteriophage P2 Integrase and Cox protein." Doctoral thesis, Stockholm University, Department of Genetics, Microbiology and Toxicology, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-683.

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Probably no group of organisms has been as important as bacteriophages when it comes to the understanding of fundamental biological processes like transcriptional control, DNA replication, site-specific recombination, e.t.c.

The work presented in this thesis is a contribution towards the complete understanding of these organisms. Two proteins, integrase, and Cox, which are important for the choice of the life mode of bacteriophage P2, are investigated. P2 is a temperate phage, i.e. it can either insert its DNA into the host chromosome (by site-specific recombination) and wait (lysogeny), or it can produce new progeny with the help of the host protein machinery and thereafter lyse the cell (lytic cycle). The integrase protein is necessary for the integration and excision of the phage genome. The Cox protein is involved as a directional factor in the site-specific recombination, where it stimulates excision and inhibits integration. It has been shown that the Cox protein also is important for the choice of the lytic cycle. The choice of life mode is regulated on a transcriptional level, where two mutually exclusive promoters direct whether the lytic cycle (Pe) or lysogeny (Pc) is chosen. The Cox pro-tein has been shown to repress the Pc promoter and thereby making tran-scription from the Pe promoter possible, leading to the lytic cycle. Further, the Cox protein can function as a transcriptional activator on the parasite phage, P4. P4 has gained the ability to adopt the P2 protein machinery to its own purposes.

In this work the importance of the native size for biologically active integrase and Cox proteins has been determined. Further, structure-function analyses of the two proteins have been performed with focus on the protein-protein interfaces. In addition it is shown that P2 Cox and the P2 relative Wphi Cox changes the DNA topology upon specific binding. From the obtained results a mechanism for P2 Cox-DNA interaction is discussed.

The results from this thesis can be used in the development of a gene delivery system based on the P2 site-specific recombination system.

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29

Wright, Alice Ann. "The Genomic Sequence and Annotation of Bacteriophage HK239." TopSCHOLAR®, 2010. http://digitalcommons.wku.edu/theses/208.

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Bacteriophages are viruses that infect bacteria and they are the most numerous biological entities on Earth. Temperate phage can adopt two different lifestyles. In the lytic lifestyle, a phage injects its genome into the host and a controlled developmental program ensues. The phage DNA is replicated, phage genes are expressed and new viral particles are assembled. Ultimately, the host cell lyses and the phage particles are released into the environment. In the lysogenic lifestyle, a phage integrates its genome into the host chromosome, creating a prophage. The cell containing the prophage is known as a lysogen. Most prophage genes are not expressed. However, those that are encode a wide variety of functions. One function is exclusion, or the prevention of a different phage type from successfully infecting the lysogenic cell. Most exclusion systems are limited to a specific phage. Bacteriophage HK239 is unique in that it has a wide range of exclusion including Lambda, P1vir, P2, HK022, and T4rII. To learn more about HK239, the genome was sequenced and annotated. The genome is 41,538 bp in length and there are 71 open reading frames. It has a genomic organization similar to other lambda phage and is most closely related to bacteriophage HK022. No additional genes that share homology with known exclusion functions were identified through the sequence analysis of the HK239 genome. It is possible that an open reading frame for which no database matches were found may indeed encode an exclusion function.

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30

Long, Graham Stanley. "Molecular cloning of bacteriophage K1E endosialidase." Thesis, University of Cambridge, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.339539.

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31

Arap, Marco Antonio. "Estudo da proteína de choque térmico GRP78 para o desenvolvimento de um sistema de receptor-ligante para o câncer de próstata." Universidade de São Paulo, 2003. http://www.teses.usp.br/teses/disponiveis/5/5153/tde-31052007-122749/.

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Introdução: Apesar dos avanços nas técnicas de diagnóstico e tratamento, o câncer de próstata avançado ainda é uma condição letal. Terapêuticas mais eficazes são necessárias para reduzir as taxas de morbi-mortalidade associadas à doença. A Proteína-78 regulada pela glicose (GRP78), uma proteína de choque térmico envolvida na apresentação de antígenos, foi recentemente descrita como sendo um possível marcador molecular para o câncer de próstata. Ainda mais, a resposta imune a essa proteína mostrou correlação com o desenvolvimento de doença hormônio-independente e com pior sobrevida para a doença. Objetivos: Neste estudo, avaliou-se a hipótese de que a GRP78 poderia ser usada como marcador molecular em câncer de próstata no desenvolvimento de um sistema de receptor-ligante, através do uso da tecnologia de apresentação de fagos. Casuística e métodos: Inicialmente, foram clonados dois peptídeos que apresentam afinidade à proteína regulada pela GRP78 (os peptídeos WIFPWIQL e WDLAWMFRLPVG) no vetor fUSE5, criando-se fagos com capacidade teórica de ligação à mesma proteína. Posteriormente foi testada a capacidade de ligação desses fagos à GRP78 na membrana de células prostáticas malignas em solução, em xeno-tumores in vivo e em metástases ósseas de câncer de próstata humano. Resultados: Demonstrou-se que ambos os fagos se ligam especificamente à GRP78 in vitro, em comparação à proteínas com seqüência semelhante (proteínas de choque térmico 70 e 90) e não semelhante (albumina sérica bovina). Em seguida, mostrou-se que esses fagos se ligam com afinidade pelo menos 30 vezes maior à células de câncer de próstata que o fago controle, e que os fagos são internalizados por essas células. Posteriormente, mostrou-se que os fagos rastrearam xeno-tumores prostáticos quando injetados in vivo num modelo animal de câncer de próstata. Finalmente, mostrou-se que os fagos ligam-se especificamente à GRP78 expressa em metástases ósseas de adenocarcinoma prostático humano. Conclusões: Os fagos criados apresentam capacidade de ligação específica à GRP78 in vitro, em células em suspensão e in vivo. A estratégia e o sistema de receptor-ligante definidos no presente estudo podem ter implicacões relevantes no desenvolvimento de terapias dirigidas para o tratamento do câncer de próstata.
Introduction: Despite the advances in diagnosis and treatment, advanced prostate cancer remains a lethal condition. Improved methods of therapy are needed to reduce the morbidity and mortality rates associated with this disease. The Glucose-regulated protein-78 (GRP78), a stress-responsive heat-shock protein involved in antigen presentation, was recently described as a possible molecular marker for prostate cancer. Moreover, immune response against this protein was shown to have correlation with the development of androgen-independent prostate cancer and shorter overall survival. Objectives: We hipothesized that GRP78 could be used as a molecular marker for prostate cancer in the development of a receptor-ligand system, by using phage display technology. Patients and methods: We initially cloned two GRP78-targeting peptides (WIFPWIQL and WDLAWMFRLPVG) into a fUSE5-based phage. We then tested binding capacity of the phage to GRP78 in vitro, to GRP78 expressed in intact prostate cancer cell membranes, to a prostate cancer xenograft and to human bone metastases. Results: We showed that both phage created bound specifically to GRP78 in vitro, in comparison to related (Heat-shock proteins 70 and 90) and unrelated control proteins (bovine serum albumin). Next, we showed that these phage bound at least 30 times more to prostate cancer cells than the control phage, and were also internalized into these cells. Both GRP78-binding phage showed a strong homing in vivo to a human prostate cancer xenograft in a mouse model. Finally, we showed that both phage bound specifically to GRP78 expressed in human prostate cancer bone metastases. Conclusions: Both phage are capable of binding specifically to GRP78 in vitro, in the context of intact prostate cancer cells and in vivo. The strategy and the ligand-receptor system we have defined in this study may have relevant implications in the development of targeted therapies for the treatment of prostate cancer.

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32

Poon, Pui-wah Alice. "Genetical study of HK253 and related temperate coliphages /." [Hong Kong : University of Hong Kong], 1988. http://sunzi.lib.hku.hk/hkuto/record.jsp?B12358393.

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33

OBRINGER, JOHN WILLIAM. "GENETIC EXCLUSION IN BACTERIOPHAGE-T4 (EXONUCLEASES)." Diss., The University of Arizona, 1987. http://hdl.handle.net/10150/184090.

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Genetic exclusion in phage T4 is the prime responsibility of the imm and sp genes. The map region containing imm does not allow sufficient bps to encode for proteins the size reported for the imm gp. After assaying 30 mutants of the genes adjacent to imm, I found 7 in gene 42 that were defective in the imm phenotype. Upon reverting amNG411(42), the mutant most defective exclusion, for its gene 42 phenotype the exclusion phenotype also changed. When assayed in UGA suppressor hosts, imm+ phage showed a decreased exclusion ability indicating that an opal codon was involved in production of the functional imm gp. I concluded that imm and gene 42 overlap in an out-of-phase orientation with the involvement of an opal readthrough. This overlap has implications in the genetic regulation of this region. This region of T4 also encodes several other genes important in phage intra- and interspecific competition. They are B-gt, 42 and sp. Using recombinant DNA techniques, I precisely located the sp gene to a region between 21.647 and 22.014 kbp on the T4 restriction map and determined its molecular weight as approximately 15 kDa. This same region of T4 was purported to contain gene 40. Complementation and marker rescue experiments with sp+ plasmids indicated that genes sp and 40 are the same. Gene 40 mutants also were found to be defective in sp function. Genes sp and 40 were redesignated gene sp/40 thus linking an early expressing gene with the morphogenic pathway of prohead assembly. Functionally, host enzymes exo III and exo V were found as participants in gp imm mediated exclusion. Presumably gp imm alters the pilot protein of the superinfecting DNA thus exposing it. Gp sp functions by an anti-lysozyme action. But the pleiotrophic effects of sp/40 are best explained by a temperature induced conformational rearrangement hypothesis. This work links molecular genetics to the ecological concept of competition and provides insights into the function and the evolutionary significance of the competition cluster genes. The competition cluster encodes fundamental adaptive strategies found universally in nature.

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34

Short, Nicholas J. "The DNA sequence of the filamentous bacteriophage Pf1." Thesis, University of Cambridge, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.305822.

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35

Deyoung, Katherine Leigh. "Genetic studies of self-splicing RNAs in bacteriophage T4." Diss., Georgia Institute of Technology, 1993. http://hdl.handle.net/1853/25434.

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36

潘佩華 and Pui-wah Alice Poon. "Genetical study of HK253 and related temperate coliphages." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1988. http://hub.hku.hk/bib/B31231329.

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37

Richardson, Helena Elizabeth. "Defining the early lythic region of coliphage 186 and the control of middle gene transcription /." Title page, contents and summary only, 1987. http://web4.library.adelaide.edu.au/theses/09PH/09phr522.pdf.

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38

Forghani, Farnaz. "Protein engineering of bacteriophage Mu transposase." Thesis, McGill University, 1990. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=60444.

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Bacteriophage Mu is an ideal system to study DNA transposition. The 70-KDa protein product of the phage early gene A, termed transposase, is absolutely required for transposition. Transposase binds specifically at sites located at both ends of the phage genome, termed attL and attR, and at an enhancer-like element at the left end of the genome, called IAS (internal activation sequence). It then nicks at these ends, and nicks a random target DNA sequence in a 5 base pair staggered fashion with 5$ sp prime$ extensions and promotes strand transfer between the Mu ends and the target DNA. The transposase protein can be roughly divided into three domains. The other activities of the protein have not been mapped even at the domain level. To further define the different functional domains of this complex enzyme, a series of insertion mutants at 8 different sites along the transposase protein were constructed using TAB linker mutagenesis. In this study, 1 and 2 TAB linkers were inserted into 8 HpaII sites in the Mu A gene, generating a set of 2 and 4 amino acid insertion mutants. Examination of these mutants for specific DNA-binding activity of transposase to the ends of the phage genome in vitro revealed temperature sensitive proteins. Transpositional activity of the mutant proteins revealed that the mutant proteins, which are temperature sensitive in specific DNA-binding activity, are deficient in transpositional activity.

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39

Hyman, Paul Lawrence. "The genetics of bacteriophage T4 DNA repair during infection." Diss., The University of Arizona, 1991. http://hdl.handle.net/10150/185380.

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Recombinational repair is a widespread mechanism for dealing with DNA damage. It is found in both prokaryotes and eukaryotes which implies that it is an ancient process which arose early in the evolutionary history of life on Earth. In addition, it has been implicated as a driving force in the evolution of sexual reproduction. In this dissertation I report experimental results which clarify the role of recombinational repair in bacteriophage (phage) T4. The Luria-Latarjet effect is an increase in resistance to DNA damage by phage T4 during infection. It has often been assumed to involve recombinational repair, but this has never been actually demonstrated. Using eleven phage T4 mutants, I have obtained evidence that the Luria-Latarjet effect is due to three repair pathways--excision repair, post-replication-recombinational-repair (PRRR) and multiplicity reactivation (MR), a form of recombinational repair. My results show that the Luria-Latarjet effect develops in two stages. The first stage starts soon after infection. Damage which occurs during the first stage can be repaired by excision repair or PRRR. The second stage appears to start after the first round of DNA replication is complete. Damage which occurs during this stage can apparently be repaired by MR as well as the other two repair pathways. I have also transferred the yeast RAD50 gene, which is required for recombinational repair, into an E. coli expression vector. After demonstrating expression of the protein, I used this construct to test for complementation by the RAD50 gene of E. coli and phage T4 mutants defective in recombinational repair. I was unable to demonstrate complementation in five different assays. Based on the results discussed above and what is known about the phage T4 life cycle, I propose a model for the Luria-Latarjet effect in phage T4. Further, I propose that recombinational repair has been selected to ensure progeny phage genomes are packaged with minimum damage. Since numerous other viruses also show a Luria-Latarjet effect type resistance to DNA damage, I suggest that the conclusions from this phage T4 study may have wide applicability to other viruses.

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40

Talbot, Simon John. "Structural studies of RNA-protein interactions in the bacteriophage MS2." Thesis, University of Leeds, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.303328.

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41

Davison, P. J. "In vitro packaging and recombination of DNA in bacteriophage T1." Thesis, University of Liverpool, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.370842.

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42

Olubuyide, Temitope Kehinde. "Investigation of the MutT2 gene." Thesis, Georgia Institute of Technology, 1999. http://hdl.handle.net/1853/31013.

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43

Sinclair, R. B. "The repressor (c) gene of Streptomyces phage #PHI#c31." Thesis, University of East Anglia, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.378897.

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44

Reed, Patricia. "Function of bacteriophage Orf recombinases in genetic exchange." Thesis, Durham University, 2006. http://etheses.dur.ac.uk/4917/.

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Recombination events in bacteriophages frequently occur by illegitimate exchange at short tracts of sequence homology, enabling these viruses to acquire novel genes and serve as vehicles for horizontal gene transfer. The emergence of new pathogenic organisms due to the acquisition of virulence determinants from bacterial viruses has stimulated considerable interest in the mechanisms of phage recombination. Bacteriophage λ encodes its own recombination system, consisting of Exo, β and γ proteins. An additional λ recombinase, Orf, participates in the early stages of exchange, supplying a function equivalent to the Escherichia coli RecFOR complex. The host enzyme complex promotes the loading of the RecA strand exchange protein onto SSB-coated ssDNA. This thesis describes the purification and biochemical analysis of the λ Orf protein, in parallel with two distantly related homologs from E. coli cryptic prophage DLP12 and Staphylococcus aureus phage ɸETA.X Orf was found to belong to a family of proteins originating from diverse lambdoid phage and prophage sources. Members of this family reside within a conserved genetic module located between phage replication and cell lysis functions. Orf exists as a homodimer, arranged as a toroid with a shallow cleft running perpendicular to the central cavity. K binds preferentially to DNA containing single- stranded regions, and associates with E. coli SSB protein in the presence of ssDNA. The Orf homolog from E. coli DLP12 displayed similar properties. This work suggests that members of the Orf family function as recombination mediator proteins, stimulating the assembly of strand exchange proteins onto ssDNA, and highlights the importance of overcoming the barrier presented by SSB proteins during lambdoid phage recombination.

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45

Whichard, Jean Marie. "Bacteriophage Felix O1: Genetic Characterization and Bioremedial Application." Diss., Virginia Tech, 2000. http://hdl.handle.net/10919/29591.

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Bacteriophage Felix O1 was studied for applicability as a Salmonella intervention. Felix O1's potential as a Salmonella therapeutic was explored, as was its utility as a food application. Felix O1 is specific for and infects most serovars within the genus Salmonella. The entire 86.155-kb sequence of the phage's linear, double-stranded chromosome was determined. 213 open reading frames (ORFs) were found, including 23 homologues of phage genes (e<0.008). Homology searches do not indicate genes that would be expected to increase virulence of Salmonella. Thirteen T4 homologues were found, including rIIA and rIIB, rapid lysis genes of T-even phages. Site-directed mutagenesis of the rIIB region was attempted by homologous recombination with plasmids containing luxAB of Vibrio harveyi. No DrIIB luxAB+ recombinants resulted from the methods tried. Serial in vivo passage was used to select for a longer-circulating Felix O1 mutant using the modified methods of Merril et al., (1996). No difference was found in the clearance of wild-type (WT) and Felix O1 following nine serial passages. Injection of 10⁹pfus yielded 24-hour concentrations of 6.5 and 4.9 log10 pfus/ml plasma for WT and 9th passage, respectively. Both isolates were undetectable in plasma by 72 hours, but remained in spleens at 96 hours. A large-plaque Felix O1 variant (LP) isolated during in vivo serial passage was compared with WT for Salmonella growth suppression. Spectrophotometric measurement of BHI cultures indicated greater suppression of S. typhi by LP than by WT, a difference not seen with S. typhimurium DT104. Both isolates suppressed 24-hour S. typhimurium DT104 growth on experimentally-contaminated chicken frankfurters at 22Â°C. Untreated frankfurters yielded 6.81 log10 Salmonella cfus/g, whereas WT and LP-treated samples yielded 5.01 and 4.70 log10 cfus/g, respectively. Both phages suppressed the Salmonella typhimurium DT104 growth (p<0.0001), but the isolates did not perform differently (p=0.5088). Presence of Salmonella caused a higher yield of WT phage than from the uninoculated group (p=0.0011), but did not affect LP yield (p=0.4416). With Salmonella present, the 24-hour LP concentration was lower than WT concentration. This supports the surmised LP rapid-lysis phenotype since T4 rapid-lysis mutants typically exhibit lower burst sizes than wild-type phage.
Ph. D.

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46

com, shawnseet@gmail, and Shawn Ginn Ming Seet. "Genome sequence of bacteriophage ÖAR29 : a basis for integrative plasmid vectors." Murdoch University, 2005. http://wwwlib.murdoch.edu.au/adt/browse/view/adt-MU20060615.135718.

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The initial aim of this project was to characterise the integrative recombination mechanism of bacteriophage ÖAR29 , to provide a better understanding for development of the shuttle plasmid pBA as a site-specific Bacteroides integration vector. RT-PCR showed that the previously identified ÖAR29 recombination genes, integrase (Int) and excisionase (Xis), were transcribed from pBA in E. coli SCS110, B. thetaiotaomicron AR29 and B. uniformis AR20. In silico derived amino acid sequences from both genes showed only very low levels of similarity to other known Int and Xis in GenBank. To improve understanding of the phage recombination system, the ÖAR29 genome was sequenced. This revealed a 35,558 bp double-stranded DNA genome with GC content of 39.11%. Bioinformatic analysis identified 53 open reading frames (>30 codons) and gene promoters and terminators that allowed the genome arrangement to be compared with other phages. Comparison of deduced gene products with proteins from other phages identified 6 reading frames, allowed tentative identification of 7 others, but left 40 ORFs unidentified. Those with strong homology to known genes were: large terminase subunit (44.66 kDa), dnaC (27.94 kDa), helix-turn-helix (HTH) transcription regulator (14.69 kDa), cI repressor (26.48 kDa), amidase (18.42kDa) and a novel integrase (54.22 kDa). The integrase gene is located 162 base-pairs downstream of the phage attachment (attP) core site, rather than the previously suggested location upstream of the integration site. The ÖAR29 attP was shown to include a 16-bp att core region, 117 bp upstream of the previously suggested location. Integration of ÖAR29 was found to occur at the 3end of an arg-tRNA gene on the AR29 genome (attB). Imperfect direct repeats with a consensus sequence (ANGTTGTGCAA) were found surrounding the attP core. A review of pBA sequence showed that only the 5 end (435 bp) of the newly identified Int gene was cloned in pBA. Despite this, PCR analysis revealed integration of pBA into the AR29 genome. Serial subculturing of pBA transformed AR29 was able to cure AR29 of the ÖAR29 prophage, providing an improved host for integrative plasmids, and for detailed studies of AR29 physiology and ÖAR29 life cycles.

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47

Seet, Shawn Ginn Ming. "Genome sequence of bacteriophage €AR29 : a basis for integrative plasmid vectors /." Access via Murdoch University Digital Theses Project, 2005. http://wwwlib.murdoch.edu.au/adt/browse/view/adt-MU20060615.135718.

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48

Amin, M. K. A. "The ecology and genetics of Pseudomonas bacteriophage in freshwater systems." Thesis, Cardiff University, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.381224.

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49

Petty, Nicola Karen. "New bacteriophages for two animal pathogens : tools for genetic manipulation." Thesis, University of Cambridge, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.612529.

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50

Garforth, Scott John. "Structure-specific DNA cleavage and binding by bacteriophage T5 5'-3' exonuclease." Thesis, University of Sheffield, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.287351.

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