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In order to examine the potential of HSV-1 as a vector to study the expression of DNA repair genes in mammalian cells, a recombinant virus containing the den V gene from bacteriophage T4 has been constructed. This gene encodes a pyrimidine dimer-specific endonuclease that has the capacity to initiate excision repair of DNA. Transfection studies indicate that excision repair deficient xeroderma pigmentosum (XP) group A cells are able to carry out excision repair initiated by the den V gene product. This gene along with the 3' LTR of Rous Sarcoma Virus and the SV40 polyadenylation signals were inserted into the non-essential glycoprotein I gene of HSV-1. Immunoprecipitation studies confirmed the production of the den V protein in virus infected cells. The uv survival of this HSV-1:den V recombinant virus was examined in various primary cell types. The cells examined in this study were primary fibroblasts from a normal individual, a Trichothiodystrophy patient and five XP patients as well as a mouse L cell line. The ability of the virally encoded den V gene to restore the excision repair deficiency in these cells was measured by monitoring the uv survival of HSV-1:den V as compared to wildtype HSV-1. Increased survival of HSV-1:den V was detected in Trichothiodystrophy cells, and in cells from XP complementation groups A, C and D, but not in XP cells from complementation groups E and F or in mouse L cells. These results demonstrate that HSV can be effectively used to study the expression of a cloned DNA repair gene in a variety of cell types. HSV has a substantial capacity of gene insertion and a wide host range including cells of human and rodent origin. / Thesis / Master of Science (MS)

The den V gene from bacteriophage T4 codes for a small, pyrimidine dimer specific, endonuclease. Recent studies have shown that transfection of the gene into DNA excision repair deficient, Xeroderma Pigmentosum cells, can partially restore the excision repair ability of the cells and results in an increased resistance to UV light. In this study the den V gene has been inserted into Herpes Simplex Virus type 1 (HSV 1) in order to determine if HSV 1 can be used as a suitable vector for studying DNA repair genes. A 1.9 kb cartridge containing the den V gene, the 3' LTR of Rous Sarcoma Virus as the promoter, and the SV40 polyadenylation signals was inserted as the thymidine kinase locus of the virus. Properly initiated transcription form the construct, HDV 1, was verified by primer extension analysis. The Host cell reactivation of this virus and several other strains of HSV 1 were examined in normal and Xeroderma Pigmentosum cells. The results from these experiments suggest that both the viral DNA polymerase and thymidine kinase genes play important roles for the survival of UV irradiated HSV 1. / Thesis / Master of Science (MS)

Histophilus somni is a commensal of the mucosal surfaces of respiratory and reproductive tracts of cattle and sheep. However, as an opportunistic pathogen, H. somni can cause diseases such as pneumonia, myocarditis, abortion, arthritis, and meningo-encephalitis. Previously, several virulence factors/mechanisms had been identified in H. somni of which the phase-variable lipooligosaccharide, induction of host cell apoptosis, intraphagocytic survival, and immunoglobulin Fc binding proteins were well characterized. To further understand the biological properties of H. somni, the genomes of pneumonia strain 2336 and preputial strain 129Pt have been sequenced. Using the genome sequence data and comparative analyses with other members of the Pasteurellaceae, putative genes that encode proteases, restriction-modification enzymes, hemagglutinins, glycosyltransferases, kinases, helicases, and adhesins have been identified in H. somni. Most of the H. somni strain-specific genes were found to be associated with prophage-like sequences, plasmids, and/or transposons. Therefore, it is likely that these mobile genetic elements played a significant role in creating genomic diversity and phenotypic variability among strains of H. somni. Functional characterization of H. somni luxS in the genomic context revealed that the gene encodes S-ribosylhomocysteinase that can complement biosynthesis of AI-2 quorum sensing signal molecules in Escherichia coli DH5alpha. It was also found that several pathogenic isolates of H. somni form a prominent biofilm and that luxS as well as phosphorylcholine expression can influence biofilm formation by H. somni. In conclusion, comparative analyses of the genomes and functional characterization of putative genes have shed new light on the versatility and evolution of H. somni. / Ph. D.

The number of illnesses attributable to antibiotic resistant bacterial infections are on the rise. According to the CDC, by 2050, complications due to antibiotic resistant infections are set to become the most prevalent cause of death worldwide, overtaking both cancer and heart disease in number. We are required to look for supplements to aid antibiotics in the fight against bacteria because it's becoming increasingly clear that antibiotics alone will fail in the face of multidrug-resistant strains. Bacteriophages are natural killers of bacteria and can thus be weaponized to treat multidrug-resistant infections. When a phage is discovered, our databases need to contain as much information about that family of phage as possible, including genomic analysis and host range. The Vi01-like phage family is an important family of Enterobacteriaceae phages that infect many clinically relevant bacterial species like Salmonella typhimurium, Cronobacter sakazaki, Citrobacter freundii, and Shigella boydii, but were heretofore highly uncharacterized. This research began with the isolation, genome assembly, and annotation of six phages within a single family, the Vi01-like phage family, which had previously been described in the work of other researchers. The following research is a careful look into the genomic identity of the Vi01-like phages. The phages were analyzed using standard -omic approaches, focusing on genomic and proteomic characterization. While their proteomes are largely uncharacterized, mass spectrometry analysis confirmed the presence of five hypothetical proteins in the virion. Several of these proteins form a putative operon that suggests a ferritin-mediated entry system on the Vi01-like phage family tail. No dependence on this pathway was observed, however. While unable to infect every genus of Enterobacteriaceae tested, these phages are extraordinarily broad ranged, demonstrating the ability to infect Salmonella enterica, Citrobacter freundii, and Erwinia amylora with generally high efficiency. Upon inspection, the tail spike proteins of the Vi01-like phages, unique in their number within each genome, may be an important contributor to the wide range of bacterial hosts. The results of this research are currently being prepared for submission or are under review for publication.

The purpose of this research was to determine if bacteriophage (phage) could be used to treat and reduce the incidence of Listeria in food manufacturing facilities, and thereby reduce the risk of food products being cross-contaminated with Listeria monocytogenes. Listeria incidence in food manufacturing ready-to-eat environments was surveyed at 31 ready-to-eat (RTE) food plants. A total 4,829 samples were collected from all locations. Nine (29%) facilities had zero samples positive for Listeria spp., whereas 22 (71%) had one or more samples positive. The total incidence of Listeria spp. in all RTE food plants was 4.5%. The effectiveness of phage against Listeria was determined when applied to stainless steel, polyurethane thermoplastic, and epoxy. Each material was inoculated with a cocktail containing L. monocytogenes and L. innocua (4 to 5-log10 CFU/cm2) and treated with two different concentrations of phage (2x10^7 and 1x10^8 PFU/cm2). Treated samples were held at 4 or 20°C for 1 and 3h. After treatment with phage, Listeria reductions ranged from 1.27–3.33 log10 CFU/cm2 on stainless steel, 1.17–2.76 log10 CFU/cm2 on polyurethane thermoplastic, and 1.19–1.76 log10 CFU/cm2 on epoxy. Listeria reduction occurred on all materials tested, under all conditions. Higher phage concentration, longer time, and higher environmental temperatures led to significantly (P<0.05) greater reduction of Listeria on stainless-steel and polyurethane thermoplastic. The effectiveness of a phage against Listeria spp. was evaluated in two food manufacturing facilities, operating at either 4°C or 20°C. First, a moderate application of a 2x10^7 PFU/mL phage was applied once per day over three days and samples were collected and analyzed for Listeria at 0, 24, 48 and 72 h. This phage treatment led to a decrease in the incidence of Listeria by 67%. A second application method was studied with phage being applied in the food manufacturing environment in an intensified manner (3 times in 18 hours) at a higher concentration of phage (1x10^8 pfu/mL). This intensified application led to a 32% overall reduction in the incidence of Listeria in the production environment. Applications of Listeria specific phage can be an additional intervention strategy for controlling pathogenic Listeria organisms in food production facilities. / Doctor of Philosophy / Listeriosis is a serious illness caused by the bacterium Listeria monocytogenes. Annually in the United States it is estimated that 95.7% of all listeriosis illnesses are caused by the consumption of contaminated food, and it is generally recognized that L. monocytogenes is caused by cross contamination of ready-to-eat foods from an environmental source. The purpose of this research was to determine if food manufacturing facilities could use bacteriophage (phage) to treat and reduce the incidence of Listeria in food manufacturing plant, and thereby reduce the risk of food products being cross-contaminated with L. monocytogenes. The incident rate of Listeria was surveyed by collecting 4,829 samples from 31 ready-to-eat (RTE) food plants across the United States. Nine (29%) facilities had zero samples positive for Listeria spp., whereas 22 (71%) plants had one or more samples positive. The total incidence of Listeria spp. in all RTE food plant samples was 4.5%. Second, research was completed to determine if phage at different levels reduced Listeria on three common food manufacturing plant materials (stainless steel, polyurethane belting and epoxy flooring). After Listeria was attached to each material (4 to 5-log10 CFU/cm2), they were treated with two different levels of phage (2x10^7 and 1x10^8 PFU/cm2) at two temperatures (4 or 20°C) for 1 and 3 hours. After treatment with phage, Listeria reduction of 93.2 to 99.9% occurred on all materials tested, under all conditions. Finally, two different methods of applying phage (moderate and intensified) in a food manufacturing plant was studied. The moderate application was a single treatment with lower concentration of phage (2x10^7 PFU/mL) once per day for three days, while the intensified treatment was the application of high phage concentrations (1x10^8 pfu/mL) three different times, all in a single day. Both application methods reduced the incidence of Listeria in the food manufacturing plant. The total reduction across all trials was 67% using the moderate application method and 32% using the intensified application of phage.

Since phages use the host resources to replicate themselves after infection, the different sizes of the phage genome should influence the replication rate. We, therefore, hypothesized that the smaller genomes should burst the cell faster than the larger ones. As well, the shorter genomes would have greater burst sizes because they should replicate faster. Here, we obtained 16 phages of various genome length. All phages were isolated on Streptomyces griseus and available in our phage bank at the University of North Texas. We performed one-step growth studies for the 16 phages, as well as determined the host doubling time from its growth curve. The results show that S. griseus grown in nutrient broth has a doubling time of 5 hours and 22 minutes. This doubling time is used as a guideline for the phage growth studies. Because the filamentous nature of the host caused several difficulties during the experiment, we isolated single cells by sonication and centrifugation. After the cell number was determined by viable cell count, the cells were infected with each type of phage using a multiplicity of infection (MOI) of 0.5. The results show that phages' burst times range between 45 (±0, standard error) and 420 (±30) minutes and burst sizes from 12 (±0) to 1500 (±60) The statistical analyses show that there is no correlation between either genome size and burst time (R= -0.01800, P=0.97894) or genome size and burst size (R= -0.32678, P=0.21670). We further performed the comparative genomics studies to investigate whether the phages with similar burst times and burst sizes show similar genome structures. The studies show that Eddasa and Lorelei have similar burst times of 45 to 60 minutes and share 52 homologs. For burst size, only Tribute and Blueeyedbeauty that have similar burst sizes of 21-30, and they are genetically related because of the 48 shared homologs. Although this study did not find any correlation between genome size and burst time/burst size, it provides a foundation for further studies to determine what regulates these two traits.

京都大学 / 新制・論文博士 / 博士(農学) / 乙第13623号 / 論農博第2919号 / 新制||農||1110(附属図書館) / 学位論文||R6||N5483 / 京都大学大学院生命科学研究科統合生命科学専攻 / (主査)教授 小川 順, 教授 井上 善晴, 教授 木岡 紀幸 / 学位規則第4条第2項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

No description available.

The seed germination process during sprout production provides suitable environmental conditions for the growth of pathogenic bacteria, such as Listeria monocytogenes. A potential way to control this bacterial growth is through the use of bacteriophages, which are naturally occurring viruses that specifically attack bacterial targets and have been shown to be effective antimicrobials in some foods. Therefore, the objective of this study was to evaluate the antimicrobial susceptibility of L. monocytogenes to bacteriophage on alfalfa sprouts during seed germination and subsequent refrigerated storage at 4 °C. Alfalfa sprout seeds were dip-inoculated with 5.5 x 105 CFU/ml L. monocytogenes serogroups 1 and 4. This was followed by treatment with the commercial bacteriophage LISTEX™ P100 at a concentration of 5.3 x 107 PFU/ml. The seeds were then soaked and germinated for 80 h using the glass jar method. The concentration of L. monocytogenes was determined every 24 h using PALCAM agar plated in triplicate. When compared to the spiked, untreated control, treatment of sprout seeds with LISTEX™ P100 resulted in a statistically significant (p < 0.05) reduction of 1.6 log10 CFU/g L. monocytogenes after the initial 24 h of germination. However, the bacteriophage did not show a lasting inhibitory effect, with no statistically significant reductions in L. monocytogenes growth as compared to the control at subsequent time points. The bacteriophage remained stable over the entire germination and storage period. Although biocontrol of Listeria with bacteriophages has high potential to serve as an alternative strategy to control foodborne illnesses, factors such as phage delivery and dose optimization in sprouts need to be further investigated.