Thesis (Ph. D.)--University of Texas at Austin, 1998. / Vita. Includes bibliographical references (leaves 76-81). Available also in a digital version from Dissertation Abstracts.

Thesis (Ph. D.)--Illinois State University, 1995. / Title from title page screen, viewed May 12, 2006. Dissertation Committee: Radheshyam K. Jayaswal (chair), Brian J. Wilkinson, Alan J. Katz, Herman E. Brockman, Anthony J. Otsuka. Includes bibliographical references (leaves 112-118) and abstract. Also available in print.

>Magister Scientiae - MSc / There are limited reports on virus population in haloalkaline environments; therefore the aim of this study was to investigate the genetic diversity and biology of bacteriophage communities in these environments. Bacteria were isolated to be used as phage hosts. One bacterium from Lake Magadi and four bacteria from Lake Shala were successfully isolated from sediment samples. A further two Lake Shala bacterial hosts from the IMBM culture collection were also used to isolate bacteriophages. Bacterial isolates were identified to be most closely related to Bacillius halodurans, Halomonas axialensis, Virgibacillus salarius, Bacillus licheniformis, Halomonas venusta, Bacillus pseudofirmus and Paracoccus aminovorans. Bacteriophages were screened using all bacteria against sediment samples from both Lake Shala and Lake Magadi. One phage was identified from Lake Magadi sediments (MGBH1) and two phages from Lake Shala sediments (SHBH1 and SHPA). TEM analysis showed that these phages belong to three different dsDNA phage families; Siphoviridae (MGBH1), Myoviridae (SHBH1) and Podoviridae (SHPA). All phages showed different genome sizes on agarose gel. Due to the small genome size, phage SHPA was chosen for further investigation. Partial, genome sequence analysis showed homology to both bacterial and phage proteins. A further investigation of phage diversity in this environment is essential using metagenomic approaches to understand these unique communities.

Escherichia coli 0157:H7 is classified as a member of the enterohaemorrhagic E. coli (EHEC) family. These organisms are responsible for a variety of clinical manifestations ranging from non-bloody diarrhoea to gross bloody diarrhoea with complications that include haemorrhagic colitis (HC), haemolytic uraemic syndrome (HUS) and thrombotic thrombocytopaenic purpura (TTP). Infection occurs by the ingestion of faecally contaminated food products, water sources and through person-to-person contact. Outbreaks of E. coli O157:H7 have been reported worldwide although most outbreaks seem to be from countries in the Northern hemisphere. Very little information is available on the prevalence of E. coli O157:H7 in South Africa. The only data available on E. coli O157:H7 were from a 1992 outbreak in Swaziland with some cases spreading to the adjacent provinces of South Africa. Selective methods were assessed and optimised to identify and isolate E. coli O157:H7 from food, water and faeces. These methods included culture techniques, immunomagnetic separation, immunoassays and molecular confirmation techniques. The methods optimised and assessed in this study proved to be suitable for the detection and isolation of E. coli O157:H7 from environmental water, food and faecal samples. In addition to the isolation of E. coli O157:H7 from these sources, methods were also optimised for the characterisation of E. coli O157:H7 using repetitive sequence analysis and induction of shiga toxin (Stx)¬converting phages which carry the genes coding for Stx from strains of E. coli O157:H7. The prevalence of E. coli O157:H7 in human-, bovine- and porcine faeces, sewage and recreational waters was investigated in a selected region of South Africa. Data suggested a low prevalence in sewage (0.76%), recreational waters (0%) and human faecal (0%) samples with a higher prevalence among carriers such as cattle (12.5%) and pigs (14.29%). UV-induced Stx-converting phages were examined and found to have different phage morphologies to the previously described lambdoid structure. In order to establish the host range susceptibility of these phages, all induced phages were subjected to conditions favourable for infecting E. coli O157:H7, non-O157 E. coli and other members of the enterobacteriaceae family including Salmonella, Shigella, Enterobacter, Klebsiella, and Proteus. These results have shown that Stx-phages were able to infect Salmonella cholerasuis and produce infectious progeny from these strains. Stx-converting phages propagated in Salmonella cholerasuis were able to re-infect strains of E. coli O157:H7. This study has shown that IMS in combination with molecular techniques was a sensitive tool for the isolation, identification and characterisation of E. coli O157:H7 from different sources. Results indicated that Stx-phages induced from E. coli O157:H7 demonstrated lambdoid structure as well as phages with long hexagonal heads and long non-contractile tails. / Dissertation (MSc (Medical Virology))--University of Pretoria, 2005. / Medical Virology / unrestricted

Chapter 1: Introduction and Literature Review; Chapter 2: A retrospective study of anthrax on the Ghaap plateau, Northern Cape Province of South Africa, with special reference to the 2007 - 2008 outbreaks; Chapter 3: Insights gained from sample diagnostics during anthrax outbreaks in the Kruger National Park, South Africa; Chapter 4: Through the lens: a microscopic and molecular evaluation of archival blood smears from the 2010 anthrax outbreaks in Kruger National Park, South Africa; Chapter 5: A distribution snapshot of anthrax in South Africa: multiple locus variable number of tandem repeats analyses of Bacillus anthracis isolates from epizootics spanning 4 decades across southern Africa; Chapter 6: Isolation and Whole Genome Analysis of a Lytic Bacteriophage Infected Bacillus anthracis Isolate from Pafuri, South Africa; Chapter 7: Characterisation of temperate bacteriophages infecting Bacillus cereus sensu stricto group in the anthrax endemic regions of South Africa; Chapter 8: General discussion, conclusions and recommendations. / Thesis (PhD)--University of Pretoria, 2016. / German Research Foundation (DFG) / National Research Foundation (NRF) of South Africa. / Veterinary Tropical Diseases / PhD / Unrestricted

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, Division of Biochemistry, 1966 / In title on t.p., "[epsilon]" appears as the lower-case Greek letter. "September, 1966." / Includes bibliographical references (leaves 157-165). / by John Mahlon Keller. / Ph. D. / Ph. D. Massachusetts Institute of Technology, Department of Biology, Division of Biochemistry

<p>  </p> <p>There is an increasing global awareness of the threat posed by antimicrobial resistance. Measures are being taken by non-government organizations, nations and individual entities to address this intensely pressing issue which ultimately threatens human lives. The One Health initiative provides a framework which may advance public understanding of and willingness to address antimicrobial resistance. One Health seeks to identify alternative solutions to problems through an understanding of the human-animal-ecological interconnection. There are several alternatives to antibiotics that have been proposed in livestock (and specifically poultry) production systems. This work focused specifically on the prospect of bacteriophages as a tool for microbial control. A sample of 1,497 respondents targeted to be representative of the population of Pakistan completed a survey providing data about knowledge of antibiotics, the threats of antimicrobial resistance, and their food shopping behaviors. A hypothetical discrete choice experiment was used to elicit survey respondent’s choices amongst various chicken products which varied according to purchase location (supermarket versus wet market) and were labeled with regard to the use of antibiotics in production. Respondents were randomly assigned into one or two groups. One group saw in-depth information about antibiotics and bacteriophage technology alongside basic information about poultry prices, purchase location, and product labeling. The other group saw only basic information about purchase location, pricing, and product labeling, but were not provided the additional information about antibiotics or bacteriophage technology and its potential effectiveness for microbial control. In addition to the estimation of consumer willingness to pay for poultry production processes, respondent’s food shopping behavior, familiarity with antibiotic use, and familiarity with bacteriophages or phages was assessed. A random parameters logit model was used to estimate Pakistan poultry consumer’s willingness to pay for bacteriophage technology as an alternative to antibiotics in poultry production. </p>

As antibiotic resistance has become a major global threat, the World Health Organization has urgently called scientists for alternative strategies for control of bacterial infections. Endolysin, a protein encoded by a phage gene, can degrade bacterial peptidoglycan (PG). Currently, there are three endolysin products in the clinical phase. We, thus, are interested in exploring novel endolysins from Streptomyces phages as only a few of them have been experimentally characterized. Using bioinformatics tools, we identified nine functional domain groups from 250 Streptomyces phages putative endolysins. NootNoot gp34 (transglycosylase; Nt34lys), Nabi gp26 (amidase; Nb26lys), Tribute gp42 (PGRP; Tb42lys), and LazerLemon gp35 (CHAP; LL35lys) were selected for experimental studies. We hypothesized that (1) the proteins of interest will have the ability to degrade PG, and (2) the proteins will be potential antimicrobial agents against ESKAPE safe relatives. The results showed that LL35lys, Nb26lys and Tb42lys exhibit PG-degrading activity on zymography and hydrolysis assay. The enzymes (400 µg/mL) can reduce PG turbidity to 32-40%. The killing assay suggested that Tb42lys possess a boarder range (Escherichia coli, Pseudomonas putida, Acinetobacter baylyi and Klebsiella aerogenes). While Nb26lys can attack Gram-negative bacteria, LL35lys can only reduce the growth of the Gram-positive strains with an MIC90 of 2 µg/mL. A higher concentration (≥300 µg/mL) of Nb26lys is needed to treat P. putida and K. aerogenes. Therefore, endolysins from Streptomyces phage have potential as possible antimicrobial agents against ESKAPE bacteria.

A Colorimetric Coliphage Assay Detection System (CCADS) that is composed of a Liquid Colorimetric Presence-Absence (LCPA) method and a Colorimetric Agar-Based (CAB) method was developed to overcome the limitations imposed by the Standard Methods for the Examination of Water and Wastewater agar-based coliphage method (APHA method). Both CCADS methods are based on the induction of β-galactosidase in Escherichia coli and the release of the enzyme through a lytic cell infection. The released enzyme then cleaves a chromogenic substrate which produces a colored reaction product. The CCADS was evaluated against the APHA method under laboratory conditions using a common sewage coliphage strain as a model (American Type Culture Collection- 13706-B2), and under field conditions using water samples collected from four different sources. During the laboratory evaluation, both the LCPA and CAB methods were found to be superior in coliphage detection to the APHA method because: 1) the LCPA and CAB methods were easier to read and interpret than the APHA method, 2) the LCPA and CAB methods were not subject to false positive results, 3) the LCPA method theoretically detected fewer coliphage particles than the APHA method, and 4) the CAB method detected roughly twice the number of coliphage particles than the APHA method. During the field evaluation, the results indicated: 1) the LCP A method was as reliable as either the CAB or APHA methods in coliphage detection, 2) the LCP A and CAB methods were easier to read and interpret than the APHA method, 3) neither the LCPA method nor the CAB method were subject to false positive results, 4) the CAB method detected more coliphages than the APHA method under conditions of high fecal pollution, but both methods performed equally well in coliphage detection under conditions of low fecal contamination, and 5) the LCPA and CAB methods were equally as sensitive in coliphage detection as the APHA method. Finally, the coliphage group proved to be a useful indicator of fecal pollution in nonpotable water supplies that exhibited a high degree of fecal pollution, whereas they were not shown to be useful indicators in potable water supplies that exhibited low levels of fecal contamination. The lack of coliphage detection sensitivity under conditions of low fecal contamination does not appear to be method limited, but rather the result of inefficiencies in processing environmental samples using the concentration methods currently available. / Ph. D.

An in vitro initiation of a DNA replication system was developed to study the function of Ø29 terminal protein. Cell free extracts prepared from Bacillus phage Ø29-infected cells catalyzed the formation of a complex between a 30,000 dalton protein and dAMP in the presence of MgCl₂, Ø29 DNA-protein template and α-³²P dATP. Uninfected cell extracts did not support this reaction. The molecular weight of this complex, the nature of linkage between dAMP and 30,000 dalton protein as well as nucleotide specificity for this reaction suggest that the protein moiety of this complex is the terminal protein of Ø29. Similar results were obtained with phages GA-1 and M2Y infected cell extracts. The similar requirements for complex formation and DNA replication in vitro implies that the complex formation is an initiation step in DNA replication. This notion was supported by characterizing the elongation product which formed in the presence of ddCTP. Two distinct antibodies were prepared for analyse the function of the terminal protein in Ø29 DNA replication. These antibodies react with native terminal protein as assayed by immunoprecipitation and ELISA methods. The inhibition of complex formation by these antibodies provides strong evidence that the terminal protein is involved in complex formation. The notion that complex formation is an initial step of DNA replication was demonstrated conclusively by inhibition of anti-TP on DNA replication in vitro. The results presented in this dissertation provide evidence supporting the protein-priming mode of linear Ø29 DNA replication.