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Dissertations / Theses on the topic 'Bacteriophages Bacteriophage lambda'

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Published: 4 June 2021

Last updated: 6 February 2022

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1

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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2

Grayson, Paul Politzer David. "The DNA ejection process in bacteriophage lambda /." Diss., Pasadena, Calif. : California Institute of Technology, 2007. http://resolver.caltech.edu/CaltechETD:etd-05252007-103551.

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3

Mosaico, Maria Luisa. "The utility of bacteriophage lambda in gene targeting." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2000. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape2/PQDD_0021/MQ55228.pdf.

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4

Cassell, Geoffrey. "Analysis of bacteriophage [lambda] site-specific recombination intermediates /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2000. http://wwwlib.umi.com/cr/ucsd/fullcit?p9979967.

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5

Kamadurai, Hari Bascar. "Mechanistic insights into catalysis and allosteric enzyme activation in bacteriophage lambda integrase." Columbus, Ohio : Ohio State University, 2007. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1172778957.

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6

Pakula, Andrew Arnold. "A genetic and biochemical analysis of the bacteriophage [lambda] cro protein." Thesis, Massachusetts Institute of Technology, 1988. http://hdl.handle.net/1721.1/14612.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 1988.
On t.p. [lambda] appears as the original Greek letter.
Includes bibliographical references.
by Andrew Arnold Pakula.
Ph.D.

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7

Bankhead, Troy M. "Characterization and structure-function analysis of the integrase recombinase of bacteriophage lambda /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2002. http://wwwlib.umi.com/cr/ucsd/fullcit?p3064447.

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8

Babbar, Baljeet Kaur. "Identification of ATP-reactive sites in the bacteriophage lambda packaging enzyme, terminase." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp01/MQ34054.pdf.

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9

Ortega, Marcos Eduardo. "Biophysical and structural characterization of bacteriophage lambda terminase : a DNA packaging enzyme /." Connect to full text via ProQuest. IP filtered, 2006.

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Thesis (Ph.D. in Biochemistry) -- University of Colorado, 2006.
Typescript. Includes bibliographical references (leaves 118-126). Free to UCDHSC affiliates. Online version available via ProQuest Digital Dissertations;

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10

Jia, Haifeng. "Equilibrium dimerization and DNA binding studies of the bacteriophage lambda Cro repressor variants /." Full text available from ProQuest UM Digital Dissertations, 2006. http://0-proquest.umi.com.umiss.lib.olemiss.edu/pqdweb?index=0&did=1379527481&SrchMode=2&sid=1&Fmt=2&VInst=PROD&VType=PQD&RQT=309&VName=PQD&TS=1217432334&clientId=22256.

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11

Patience, Trudy. "Sequence analysis of a Cowdria ruminantium lamdba (sic) GEM-11 clone." Thesis, Stellenbosch : Stellenbosch University, 2002. http://hdl.handle.net/10019.1/53052.

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Thesis (MSc)--Stellenbosch University, 2002.
ENGLISH ABSTRACT: Heartwater is a major threat to livestock in Africa due to its high mortality rate. The intracellular nature of the causative organism, Cowdria ruminantium, makes it difficult to study, hence an effective and user-friendly vaccine has been extremely difficult to obtain. Two C. ruminantium DNA libraries have recently been constructed, the lambda GEM11 bacteriophage DNA library and the lambda ZAPII bacteriophage DNA library, and this has lead to a renewed search for protective genes that could be used as a vaccine against heartwater. In this study, several molecular techniques including PCR, cloning and sequencing were used to identify genes in the lambda GEM11 bacteriophage DNA library that code for proteins, which could be used as vaccines to protect susceptible animals against heartwater. The lambda GEM11 library was screened with a rickettsial secretory protein gene sequence, known as seeD. One positive colony was selected from which the bacteriophage DNA was isolated. The C. ruminantium DNA was amplified from the bacteriophage DNA by using PCR and C. ruminantium-specific primers. The C. ruminantium DNA was screened with Mycoplasma, bovine and Cowdria DNA probes. The amplified DNA was subeloned into two vectors and the clones were screened by restriction analysis to identify clones containing inserts. The appropriate clones were sequenced and overlapping sequences matched, ordered and aligned. Two sequences were continuous with a short sequence of unidentified bases in between. Oligonucleotide primers were designed to amplify the DNA sequence between the two contiguous sequences. This led to the identification of the entire sequence of the C. ruminantium genome contained within the bacteriophage plaque. The single contiguous sequence was analysed and the putative protein-coding sequences were obtained and compared to DNA sequences of known organisms using the BLAST program. Five open reading frames were identified with homology to genes encoding specific proteins in bacteria. Two open reading frames showed homology to the genes encoding the transporter proteins, FtsY and the ABC transporter, and three open reading frames were found to be homologous to genes encoding the essential enzymes dethiobiotin synthetase, pro lipoprotein diacylglycerol transferase and the putative NADH-ubiquinone oxidoreductase subunit. The five open reading frames encode for genes, which are essential for the normal functioning of the C. ruminantium organism. However, these open reading frames might not be effective for use in a DNA vaccine since none of the open reading frames showed homology to obvious genes that could play a role in immunity and therefore confer protection. The open reading frames can be used in mutagenesis studies to produce attenuated strains of the organism that possess mutated versions of these proteins. These attentuated strains could be used for the vaccination of cattle, and thereby confer protection against viable pathogenic C. ruminantium isolates.
AFRIKAANSE OPSOMMING: Hartwater is 'n bedreiging vir vee in Afrika weens die hoë mortaliteitssyfer verbonde aan die siekte. Die intrasellulêre aard van die organisme wat hartwater veroorsaak, Cowdria ruminantium, bemoeilik navorsing aangaande die organisme. Dit het tot gevolg dat 'n effektiewe en gebruikersvriendelike entstof moeilik bekombaar is. Daar is onlangs sukses behaal met die konstruksie van twee C. ruminantium DNA genoteke, die lambda GEM11 bakteriofaag genoteek en die lambda ZAPII bakteriofaag genoteek. Dit het gelei tot 'n herlewing in die soektog na beskermende gene, wat in 'n entstof teen hartwater gebruik kan word. In hierdie studie is verskeie molekulêre tegnieke insluitende PKR, klonering en geenopeenvolging bepaling, gebruik om gene te identifiseer in die lambda GEM11 bakteriofaag genoteek wat kodeer vir proteïene wat in entstowwe gebruik kan word as beskerming teen hartwater. Die secD geen is gebruik om die lambda GEM11 bakteriofaag genoteek te sif. Een positiewe plaak is gevind waarna die DNA uit die bakteriofaag plaak geïsoleer en die C. ruminantium DNA vanuit die bakteriofaag plaak geamplifiseer is deur gebruik te maak van PKR en spesifieke C. ruminantium inleiers. Die C. ruminantium DNA is gesif met Mycoplasma, bees en Cowdria radioaktief gemerkte DNA peilers. Die C. ruminantium DNA is vervolgens in twee vektore gekloneer. Die klone is gesif deur middel van restriksie analise. Die DNA volgorde van die klone is bepaal en twee ononderbroke sekwense is geïdentifiseer met 'n gaping in die middel tussen die twee sekwense. Oligonukleotied inleiers is daarna ontwerp om die geenopeenvolging van die gaping tussen die twee sekwense te vul. Hierdeur kon die volledige geenopeenvolging van die genoom van C. ruminantium wat in die lambda GEM 11 bakteriofaag plaak voorkom, bepaal word. Hierdie volledige geenopeenvolging is vervolgens geanaliseer en die oop leesrame wat daarin voorkom geïdentifiseer. Vyf leesrame is gevind om homologie met gene wat kodeer vir proteïene wat in bakterieë voorkom, te toon. Twee leesrame het homologie met die gene wat kodeer vir transport proteïene, FtsYen die ABC transporter getoon, en drie leesrame het homologie met gene wat kodeer vir die essensiële ensieme detiobiotin sintetase, prolipoproteïen diasielgliserol transferase en die NADHubikinoon oksidoreduktase subeenheid getoon. Dié vyf leesrame het die potensiaal om as entstowwe gebruik te word aangesien al vyf leesrame kodeer vir gene wat 'n belangrike rol speel in die oorlewing van die C. ruminantium organisme. Alhoewel die leesrame moontlik nie so effektief sal wees in 'n DNA entstof nie, toon dit potensiaal om in mutasieeksperimente gebruik te word. Organismes wat die gemuteerde weergawe van die geen besit sal nie-funksionele proteïene produseer, wat 'n invloed kan hê op die normale fisiologiese funksies van die organisme en dus sal lei tot 'n minder virulente organisme. Die geattenueerde organisme kan moontlik gebruik word om diere te immuniseer en daardeur immuniteit aan diere lewer wat beskerming sal bied teen patogeniese C. ruminantium isolate.

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12

Burcica, Cristina Irina. "Modeling a Class of Naturally Occurring Mechanisms for Use in Synthetic Biology." University of Cincinnati / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1218772646.

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13

Maxwell, Karen Lee. "Structural, biophysical, and functional studies on the head-tail joining reaction of bacteriophage [lambda]." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/NQ59024.pdf.

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14

Conant, Clarke Robert. "Binding and CIS-RNA looping interactions that determine activity of the N antitermination protein of bacteriophage lambda /." view abstract or download file of text, 2004. http://wwwlib.umi.com/cr/uoregon/fullcit?p3136407.

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Thesis (Ph. D.)--University of Oregon, 2004.
Typescript. Includes vita and abstract. Includes bibliographical references (leaves 163-172). Also available for download via the World Wide Web; free to University of Oregon users.

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15

Meays, Mary Elizabeth. "A study of the effects of polyamines on restriction endonuclease cleavage of bacteriophage lambda DNA." Scholarly Commons, 1990. https://scholarlycommons.pacific.edu/uop_etds/2193.

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This study provides information about the effects of polyamines on the restriction enzymatic cleavage of bacteriophage lambda DNA. The polyamines studied were spermine, spermidine, Nl-acetylspermidine and N8- acetylspermidine. The restriction enzymes studied were Xhoi, BamHI, EcoRI, and Hindiii. The electrophoretic pattern of lambda DNA digests by these enzymes were recorded photographically. These results were further analyzed by spectrographic digitization and replotting. Polyamines affect the electrophoretic pattern of restriction fragments in two ways: by causing DNA streaking and by decreasing ethidium bromide binding to DNA, which in turn affects DNA staining properties. The polyamines studied have effects which are increasingly dependent on the charge of the polyamine. The concentration necssary to alter the electrophoretic pattern decreases with increased positive charge of the polyamines. Spermine, the most highly charged polyamine studied, resulted in alterations at a lower concentration than any other polyamines studied. Following spermine was spermidine, and then the two acetylated polyamines, Nl-acetylspermidine, and N8- acetylspermidine.

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16

Subramaniam, Srisunder. "Studies of conformational changes and dynamics accompanying substrate recognition, allostery and catalysis in bacteriophage lambda integrase." The Ohio State University, 2005. http://rave.ohiolink.edu/etdc/view?acc_num=osu1111655332.

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17

Jessop, Lea. "Architecture of the synaptic intermediates of the site-specific recombination pathways mediated by the bacteriophage Lambda integrase /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2000. http://wwwlib.umi.com/cr/ucsd/fullcit?p9981973.

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18

Smith, Christopher E. "Insights into the structure and function of Red beta: the unique single-strand annealing protein of bacteriophage lambda." The Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1449183321.

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19

Coates, Nicholas John Hewlett. "On the nature of the UV-inhibition of oriC and oriCc allele /." Title page, contents and summary only, 1996. http://web4.library.adelaide.edu.au/theses/09PH/09phc652.pdf.

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20

Tessier, Luc-Henri. "Expression dans e. Coli de deux proteines d'origine humaine : l'interferon-gamma et l'alpha-antitrypsine." Université Louis Pasteur (Strasbourg) (1971-2008), 1986. http://www.theses.fr/1986STR13010.

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21

Zhang, Yaofang. "Elemental Detection with ICPMS - Implications from Warfare Agents to Metallomics." University of Cincinnati / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1335463155.

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22

Lohman, Kenton L. "Isolation and Characterization of Temperature-sensitive Protein Synthesis Mutants of Escherichia Coli by Directed Mutagenesis of the Defective Bacteriophage Lambda Fus2." Digital Commons @ East Tennessee State University, 1985. https://dc.etsu.edu/etd/2722.

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Mutagenesis of the defective transducing bacteriophage lambda fus2 was used to isolate a collection of temperature-sensitive mutants of E. coli in the major ribosomal protein gene cluster. Four mutants were examined in detail. Two of the mutants were resistant to the ribosomal antibiotics neamine and spectinomycin. Another mutant was defective in 50S ribosomal subunit assembly at 42(DEGREES)C. The 30S subunit proteins S17 and S19 were changed in two different mutants. Each protein migrated as a more basic species in two-dimensional gels of ribosomal proteins. Ribosomes from each of the four mutants examined showed a temperature-dependent reduction in translational activity in cell-free assays. The kinetic assays showed declines in both the rate and extent of translation at three temperatures. Ribosomes from three of the four mutants were also found to have an increased rate of heat inactivation at 45(DEGREES)C compared to control particles. Mixed subunit assays idendtified a t.s. subunit in each mutant. A defect in reassociation at high temperature was found for the subunits from one mutant. Another mutant showed significantly high levels of misreading at 32(DEGREES)C and 42(DEGREES)C. Two mutants showed a decreased ability to bind 14C-phenylalanine tRNA at the two temperatures tested. The increased efficiency and utility of this mutagenesis method for the isolation of protein synthesis mutants is discussed.

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23

Salloum, Mazen. "Les infections à "Streptococus agalactiae" chez l'adulte : emergence et impact de la lysogénie." Thesis, Tours, 2010. http://www.theses.fr/2010TOUR3144/document.

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Streptococcus Agalactiae est depuis les années 1990, responsable d'infections invasives émergentes chez l'adulte. Nous montrons queles souches responsables de ces infections appartiennent majoritairement aux sérotypes V et Ia et aux deux clones phylogénétiquement éloignés, CC1 et CC23. L'étude du contenu prophagique montre une lysogénie fréquente suggérant l'importance de la lysogénie dans la spécialisation de ces souches particulièrement aptes à infecter l'adulte. Dans un deuxième temps, nous avons isolé sept phages tempérés de souches associées à des infections cutanées et ostéo-articulaires. Ces phages appartiennent à la famille des SIPHOVIRIDAE. L’analyse par restriction enzymatique de l’ADN phagique et l’amplification par PCR de fragments d’ADN prophagique a montré la diversité de ces phages et leurdifférence des phages isolés de souches associées aux infections materno-foetales. Les phagesisolés de souches lysogènes de CC1 ont présenté un spectre lytique étendu aux souches de tous les clones intra-species
Streptococcus agalactiae has emerged since 1990 in infections in nonpregnant adults, We showed that the strains isolated from adult infections were mainly of serotypes V and Ia., and mainly belonged to the two phylogenetically distant clones, CC1 and CC23. The prophagic content study showed a frequent lysogeny, suggesting a role of lysegeny in the specialization of these strains able to infect adult. Also, we isolated seven phages from strains associated with cutaneous and osteoarticular infections in adult. Ces phages classified among SIPHOVIRIDAE. Restriction analysis of phagic DNA and PCR for prophagic DNA showed genetiacally diverse phages, distinct from the phages isolated from strains responsible for materno-foetal infections. Phages isolated from lysogenic strains of CC1 had a wide lytic spectrum and were able to lyse strains belonging to all clones intra-species

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24

Thébaud, Olivier. "Emploi des chaînes de Markov dérivantes dans l'étude du génome." Paris 5, 2001. http://www.theses.fr/2001PA05S008.

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Ce travail de recherche consiste à décrire des modèles statistiques capables d'expliquer au mieux l'hétérogénéité et tenter d'identifier des régions distinctes du génome. Nous travaillons dans trois directions : statistique en utilisant des chaines de Markov, biologique puisque nous appliquons notre modèle à des données réelles et informatique car l'un de nos buts est de créer des outils informatiques à partir de nos modèles statistiques. Depuis quelques années, au sein du laboratoire de statistique médicale de Paris V, un travail de thèse a été poursuivi par le maître de conférence Florence Muri, qui utilise des modèles de chaînes de Markov cachées pour délimiter les régions homogènes de la séquence d'ADN étudiée. Ces modèles supposent l'existence de plages homogènes dont on ignore a priori la taille et la position, et que l'on dispose d'un nombre fini de modèles (typiquement 2, 3 ou 4) qui s'ajustent de façon satisfaisante sur chacune de ces plages. Ici nous cherchons à établir la théorie mathématique et statistique qui permettra de faire évoluer de façon continue la chaine de Markov. On parle de chaines de Markov dérivantes. Pour donner un exemple simple du type de modèle, considérons une matrice de transition de départ 0, une d'arrivée 1 et une matrice de transition t évoluant tout au long de la séquence de taille n selon l'équation suivante : t = (1t/n) 0 + t/n 1. Ainsi nous éviterons les ruptures brutales observées entre deux plages successives dans l'optique chaines de Markov cachées en dérivant continument entre ces deux plages. Notre priorité est bien entendu la meilleure estimation possible de 0 et 1. Nous développons d'abord mathématiquement le modèle, puis nous procédons à des simulations pour assimiler son comportement et l'appliquons enfin sur les deux organismes e. Coli et le phage ou la comparaison de nos résultats avec ceux obtenus grâce aux chaines de Markov cachées a grand intérêt.

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25

Wigginton, Krista Rule. "Surface Enhanced Raman Spectroscopy as a Tool for Waterborne Pathogen Testing." Diss., Virginia Tech, 2008. http://hdl.handle.net/10919/29330.

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The development of a waterborne pathogen detection method that is rapid, multiplex, sensitive, and specific, would be of great assistance for water treatment facilities and would help protect water consumers from harmful pathogens. Here we have utilized surface enhanced Raman spectroscopy (SERS) in a sensitive multiplex pathogen detection method. Two strategies are proposed herein, one that utilizes SERS antibody labels and one that measures the intrinsic SERS signal of organisms. For the SERS label strategy, gold nanoparticles are conjugated with antibodies specific to Cryptosporidium parvum and Giardia lamblia and with organic dye molecules. The dye molecules, rhodamine B isothiocyanate (RBITC) and malachite green isothiocyanate (MGITC) were surface enhanced by the gold nanoparticles resulting in unique fingerprint SERS spectra. The SERS label method was successful in detecting G. lamblia and C. parvum simultaneously. The method was subsequently coupled with a filtration step to both concentrate and capture cysts on a flat surface for detection. Raman mapping across the filter membrane detected ~95% of the spiked cysts in the optimized system. In the second type of strategy, intrinsic virus SERS signals were detected with silver nanoparticles for enhancement. Principal component analysis performed on the spectra data set resulted in the successful differentiation of MS2 and PhiX174 species and also for the differentiation of viable virus samples and inactivated virus samples.
Ph. D.

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26

Domelier, Anne-Sophie. "Etude des phages de streptococcus agalactiae en lien avec l'origine anatomique, la phylogénie et les propriétés métaboliques des isolats." Thesis, Tours, 2009. http://www.theses.fr/2009TOUR3137/document.

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Notre travail a consisté à rechercher des éléments génétiques nouveaux associés aux souchesde Streptococcus agalactiae (SGB) responsables de méningites néonatales (MNN).L'amplification au hasard des ADN génomiques a identifié 3 fragments prophagiquesassociés aux souches à haut risque de MNN. Trente-six phages ont été isolés à partir desouches invasives et non invasives de SGB. La caractérisation moléculaire a défini sixgroupes moléculaires. L'étude du spectre lytique a montré des particularités pour chacun dessix groupes moléculaires. L'étude des capacités métaboliques de souches de SGB a montréque les souches lysogènes appartenant aux lignées phylogénétiques impliquées dans les MNNet présentent des pertes cataboliques. Les transferts génétiques horizontaux qui marquent lesclones des MNN ne semblent pas jouer un rôle dans la résistance aux macrolides. Desmécanismes de transduction ont joué un rôle important dans l'émergence de lignéesphylogénétiques impliquées dans les MNN
We tried to identify new genetic elements in the genome of Streptotoccus agalactiae (SGB)strains responsible for neonatal meningitis (MNN). Three prophage-related DNA elementswere identified by randomly amplified polymorphie DNA analysis significantly associatedwith SGB strains presented a high risk of causing MNN. Thirty-six phages were isolated from invasive and non invasive SGB strains. Molecular characterization of phage DNA identified six distantly related molecular groups. The various phage groups had specifie lytic activities.The lysogenic strains belonging to phylogenetic lineages most involved in MNN presented catabolic losses. The horizontal gene transfers that mediate mobile genetic elementsrecognized as markers of highly virulent clones do not seem to be have played a role in theemergence of macrolide resistance. Ali our results indicate that transduction may have play arole in the emergence of phylogenetic lineages implicated in MNN

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27

Henry, Matthew S. "Characterization of a lambdoid phage gene encoding a host cell attachment spike." Bowling Green, Ohio : Bowling Green State University, 2008. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=bgsu1214189208.

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28

Ivanov, Yury V. "The Roles of Moron Genes in the Escherichia Coli Enterobacteria Phage Phi-80." Bowling Green State University / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1350778152.

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29

Xing, Xu. "Structural studies of homologous recombination in bacteria." Columbus, Ohio : Ohio State University, 2007. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1186680748.

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30

Hyder, Batool. "Biochemical Investigation into the HNH Motif of HK97 gp74." Thesis, 2014. http://hdl.handle.net/1807/44026.

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Bacteriophages are viruses that infect bacteria. This thesis describes studies of gp74 from the bacteriophage HK97, which functions as an HNH endonuclease. HNH endonucleases are DNA digestion proteins characterized by two highly conserved His residues and an Asn residue. Like other HNH endonucleases, the activity of gp74 is dependent on binding of divalent metal ions to the HNH motif. Current work focused on confirming the identity of conserved HNH motif residues of gp74. We hypothesized the catalytic His residue is H43, the structural Asn residue is N73, and that H82 is involved in metal–binding. Additional residues in the ββα–fold, such as D42, may also bind the metal. Our bound metal analysis and the sequence of gp74 also suggest the presence of a Zn2+–finger motif. Mutations of D42 and H82 decrease the activity of gp74, without affecting the structure. These studies advance our understanding of the gp74 activity.

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31

Grayson, Paul. "The DNA ejection process in bacteriophage lambda." Thesis, 2007. https://thesis.library.caltech.edu/2069/1/paul-20070524-7.pdf.

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Bacteriophages have long served as model systems through which the nature of life may be explored. From a physical or mechanical point of view, phages are excellent examples of natural nanotechnology: they are nanometer-scale systems which depend critically on forces, pressures, velocities, and other fundamentally physical quantities for their biological functions. The study of the physical properties of phages has therefore provided an arena for application of physics to biology. In particular, recent studies of the motor responsible for packaging a phage gnome into a capsid showed a buildup of pressure within the capsid of tens of atmospheres. This thesis reports a combined theoretical and experimental study on various aspects of the genome ejection process, so that a comparison may be drawn with the packaging experiments. In particular, we examine various theoretical models of the forces within a phage capsid, deriving formulas both for the force driving genome ejection and for the velocity at which the genome is translocated into a host cell. We describe an experiment in which the force was measured as a function of the amount of genome within the phage capsid, and another where the genome ejection velocity was measured for single phages under the microscope. We make direct quantitative comparisons between the theory and experiments, stringently testing the extent to which we are able to model the genome ejection process.

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32

Dewey, Jill Sayes. "Characterization of the Bacteriophage Lambda Holin and Its Membrane Lesion." Thesis, 2010. http://hdl.handle.net/1969.1/ETD-TAMU-2010-08-8275.

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Bacteriophage holins are a diverse group of proteins that are responsible for the spontaneous and specifically-timed triggering of host cell lysis. The best-studied holin, S105 of phage lambda, is known to form lesions, or “holes”, in the inner membrane of E. coli which are large enough to allow the endolysin through to the periplasm. S105 has been studied extensively by both genetic and biochemical approaches; however, little is known about the mechanism of hole formation or the structure of the lambda holin and its inner membrane lesion. An in vitro system for reconstituting hole formation by S105 was developed in which liposomes containing a self-quenched fluorophore served as artificial cell membranes (1-2). Upon delivery of solubilized S105 to the liposomes, an increase in fluorescence was observed, indicating that the fluorophore within the liposomes had escaped into the surrounding media via an S105-mediated hole in the membrane. This in vitro system, which has been optimized in this work, has been a valuable biochemical tool for analysis and reconstitution of the pathway to S105 hole formation in the cell membrane. Due to the difficulty associated with over-expression and purification of toxic membrane proteins, there are no solved structures of bacteriophage holins. Sample preparation and experimental conditions for NMR spectroscopy were optimized and structural information about a lambda holin mutant protein was obtained. Specifically, micellar contacts of transmembrane domain regions versus water contacts of the C-terminal region, secondary structure, and backbone dynamics were determined. Cryo-electron microscopy was used to visualize the inner membrane lesions formed by phage holins [lambda] S105, P2 Y, and T4 T. Therefore, the large holes initially seen in cells expressing S105 are not specific to the lambda holin, nor to class I holins. The S105 holes average ~340 nm (3), and are the largest membrane lesions ever observed in biology. They are stable at their original size, and are not localized to a specific region of the membrane. In addition, missense mutants of S105 were used to correlate hole size, protein accumulation, and lysis timing in a current model for the S105 hole formation pathway.

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33

Zahn, Kenneth. "Structure and function of the bacteriophage [lambda] origin of replication." 1987. http://catalog.hathitrust.org/api/volumes/oclc/18099484.html.

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White, Rebecca Lynn. "What makes the lysis clock tick? A study of the bacteriophage holin." 2008. http://hdl.handle.net/1969.1/ETD-TAMU-2766.

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The timing of host lysis is the only decision made in the bacteriophage lytic cycle. To optimize timing, double-stranded DNA phages use a 2-component lysis system consisting of a muralytic enzyme, the endolysin, and a small membrane protein, the holin, which controls the timing of lysis. The best characterized holin gene to date is the S gene of bacteriophage λ. One unusual feature of the S gene is that it produces two proteins of opposing function: the holin, S105, and the antiholin, S107. Raab et al isolated and characterized a number of S mutants, but all of them expressed both the holin and the antiholin; it is possible, then, that the true extent of the holin-holin interactions were masked by interactions with the antiholin. Thus, a large number of S105 mutants were created, and their phenotypes characterized in the absence of the antiholin. The interaction between those mutants and the wild-type were examined in an attempt to better understand what determines the timing of hole formation by S105. S105 and S107 differ only by two amino acids at the N-terminus; S107 has an additional Met-Lys sequence. Previous studies have shown that S107 may have a different topology to S105, where the N-terminus of S107 is located in the cytoplasm and is cannot flip through the membrane because of the extra cationic side chain. This study investigates the role of the N-terminal transmembrane domain of the S proteins in terms of hole formation and its role in the antiholin character of S107. Previous results suggest that S105 forms hole via a large oligomeric structure termed the “death raft”. The death raft model states that after S105 is inserted into the membrane, it forms “rafts”, which grow in size until a spontaneous channel forms leading to depolarization of the membrane and hole formation. This study investigates the pathway of hole formation at the single-cell level, using a C-terminal fusion of S105 and green fluorescent protein, and attempts to address several of the predictions posed by the death raft model.

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Edmonds, Lizbeth. "Structural determination and analysis of the tail terminator protein, GPU, from lambda bacteriophage /." 2005.

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Thesis (M.Sc.)--York University, 2005. Graduate Programme in Biology.
Typescript. Includes bibliographical references (leaves 49-54). Also available on the Internet. MODE OF ACCESS via web browser by entering the following URL: http://gateway.proquest.com/openurl?url%5Fver=Z39.88-2004&res%5Fdat=xri:pqdiss &rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&rft_dat=xri:pqdiss:MR11779

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Hensel, Linda L. "Both Escherichia coli himA and lambda packaging gene expression alter normal bacteriophage lambda DNA replication rates." 1991. http://catalog.hathitrust.org/api/volumes/oclc/24397435.html.

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Thesis (Ph. D.)--University of Wisconsin--Madison, 1991.
Typescript. Vita. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references (leaves 152-165).

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37

Savva, George Christos. "Structural studies of the bacteriophage lambda holin and M. tuberculosis secA translocase." Thesis, 2007. http://hdl.handle.net/1969.1/ETD-TAMU-2438.

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Double stranded DNA bacteriophages achieve release of phage progeny by disrupting the cell envelope of the host cell. This is accomplished by two phage-encoded proteins, the holin and the endolysin. In bacteriophage lambda, the S holin is a small three TMD membrane protein that creates a lesion in the inner membrane of the host at a specific time, programmed in its primary structure. Lesion formation permits the cytoplasmic endolysin R access to the murein cell wall for degradation and cell lysis. Although it has been shown that S oligomerizes in the membrane, the structural nature of this complex has not been elucidated. In this study the S holin was purified using a mild non-ionic detergent and the structure of a ring complex formed by the holin was determined by electron microscopy and single particle analysis at a resolution of 2.6 nm. Biochemical characterization of the rings suggests that such a complex might represent the assembly formed by S in the membrane. Protein translocation in all organisms allows the export of proteins destined for localization outside the cytoplasm. In eubacteria, newly synthesized proteins are directed to the heterotrimeric membrane complex SecYEG by signals embedded in their sequence. The driving force through this complex is provided by the cytoplasmic ATPase SecA which combines ATP hydrolysis to mechanically insert proteins through the protein conducting channel. Using electron microscopy and single particle analysis we have obtained the structure of SecA from M. tuberculosis. The structure indicates that four SecA monomers assemble to form an elongated molecule with D2 symmetry. Docking of the EM map to the crystal structure of tb SecA confirms this arrangement of the subunits. This finding, that M. tuberculosis SecA forms a tetramer raises intriguing possibilities about SecA function.

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Coburn, David Lawson. "The Role of Bacteriophage Lambda gpK in Tail Assembly and Host Cell Entry." Thesis, 2011. http://hdl.handle.net/1807/30554.

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The bacteriophage lambda tail protein gpK is required for tail assembly. The activity of the protein can be found at the assembling tail tip and is believed to be localized to this structure. GpK is a 27 kDa protein that has sequence identity to two families of proteins: the Mov34 family of peptidases and the NlpC/P60 family of peptidoglycan endopeptidases. Point substitutions and complementation data confirm that gpK possesses each of these domains and that they can function in trans. When the Mov34 domain is inactivated tail assembly is disrupted whereas when the NlpC/P60 domain is inactivated tails assemble but are inactive. Evidence is presented here that the C-terminal domain possesses lytic activity in isolation but not when part of the full-length protein.

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Coburn, David. "The Role of Bacteriophage Lambda gpK in Tail Assembly and Host Cell Entry." Thesis, 2011. http://hdl.handle.net/1807/32130.

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The bacteriophage lambda tail protein gpK is required for tail assembly. The activity of the protein can be found at the assembling tail tip and is believed to be localized to this structure. GpK is a 27 kDa protein that has sequence identity to two families of proteins: the Mov34 family of peptidases and the NlpC/P60 family of peptidoglycan endopeptidases. Point substitutions and complementation data confirm that gpK possesses each of these domains and that they can function in trans. When the Mov34 domain is inactivated tail assembly is disrupted whereas when the NlpC/P60 domain is inactivated tails assemble but are inactive. Evidence is presented here that the C-terminal domain possesses lytic activity in isolation but not when part of the full-length protein.

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Tam, William. "Characterization of an Iron-Sulfur Binding Protein in the Tail Tip Complex of Bacteriophage Lambda." Thesis, 2012. http://hdl.handle.net/1807/42907.

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The assembly of λ tail requires the action of 11 gene products which must interact in an organized fashion to assemble infectious tail particles. GpL is an essential protein for the formation of the tail tip complex and necessary for the assembly of λ tail. The work described here has shown that gpL and its homologues contain two domains where the C-terminal domain coordinates an oxygen-sensitive [4Fe-4S] 2+ cluster using 4 highly conserved cysteines. This is the first report of a bacteriophage morphogenetic protein to coordinate a [4Fe-4S]2+ cluster. Through two individual cysteine mutants, C184A and C228A, it was determined that these mutant proteins coordinate a [2Fe-2S]2+ cluster also using 4 cysteines; the fourth cysteine being non-conserved. λ tails assembled with cysteine mutant gpL resulted in a 1000-fold decrease in the titer of active tails and tail particles could not be detected by TEM indicating that λ tails cannot be assembled with cysteine mutant gpL. I propose that the coordination of a [4Fe-4S] cluster with the four conserved cysteines maintains a conformation in gpL that can optimally interact with other tail proteins for efficient tail assembly.

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Glasgow, Anna C. "Bacteriophage Mu sites, functions, and processes involved in growth inhibition of lambda::mini-Mu phages." 1986. http://catalog.hathitrust.org/api/volumes/oclc/14184254.html.

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Berry, Joel Dallas. "The Final Step in Phage Lysis: The Role of the Rz-Rz1 Spanin Complex in the Disruption of the Outer Membrane." Thesis, 2010. http://hdl.handle.net/1969.1/ETD-TAMU-2010-05-7685.

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The purpose of the work described in this dissertation is to better understand the role of Rz and Rz1 function with respect to phage lysis. We determined using both a genetic and biochemical approach that the Rz protein is an inner membrane protein containing a single N-terminal transmembrane domain (TMD) with an Nin/Cout topology. Consistent with previous work on Rz1, the Rz1 lipoprotein was found to be localized to the outer membrane (OM). Following localization, both Rz and Rz1 form homodimers in vivo due to intermolecular disulfide formation. Despite being localized to apposing membranes, the two proteins form a complex. A small number of phages encode a potential single protein equivalent of Rz-Rz1. This protein, termed a spanin, is predicted to tether the inner and outer membranes by a single polypeptide chain. Based on complementation, it was concluded that gp11 from the phage T1 is a functional equivalent of Rz-Rz1. Gp11, and by analogy the Rz-Rz1 two-component spanin complex, threads the meshwork of the PG layer. The presence of an Rz-Rz1 complex, which forms in the presence of peptidoglycan (PG), is supported by in vivo results. The soluble periplasmic domains of Rz and Rz1, which are dimeric and monomeric respectively, were purified. Circular dichroism analysis indicates that Rz is structured, with significant α-helical content, whereas Rz1, in which 10 out 39 residues are proline, is unstructured. Mixing the proteins results in the formation of a complex with significant new α-helical content. Negative-stain images reveal ~ 25 nm x ~ 4 nm rod-shaped structures. Holin independent activity of Rz and Rz1 is found to disrupt whole cells. Furthermore, time lapse microscopy of λ and λRzam lysis allows us to conclude that Rz and Rz1 are essential for lysis. These results suggest a model for Rz-Rz1 function which begins with Rz and Rz1 forming a complex through direct interaction prior to holin and endolysin function. Holin-mediated hole formation allows the endolysin to degrade PG which sterically hinders Rz-Rz1 activity. Removal of PG by endolysin degradation thus triggers Rz-Rz1 OM disruption via fusion of the inner and outer membranes.

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Sheldon, Katlyn. "Two Dimensional Genetic Approach to the Development of a Controllable Lytic Phage Display System." Thesis, 2013. http://hdl.handle.net/10012/7371.

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Bacteriophage Lambda (λ) has played a historical role as an essential model contributing to our current understanding of molecular genetics. Lambda’s major capsid protein “gpD” occurs on each capsid at 405 to 420 copies per phage in homotrimeric form and functions to stabilize the head and likely to compact the genomic DNA. The interesting conformation of this protein allows for its exploitation through the genetic fusion of peptides or proteins to either the amino or carboxy terminal end of gpD, while retaining phage assembly functionality and viability. The lytic nature of λ and the conformation of gpD in capsid assembly makes this display system superior to other display options. Despite previous reports of λ as a phage display candidate, decorative control of the phage remains an elusive concept. The primary goal of this study was to design and construct a highly controllable head decoration system governed by two genetic conditional regulation systems; plasmid-mediated temperature sensitive repressor expression and bacterial conditional amber mutation suppression. The historical λ Dam15 conditional allele results in a truncated gpD fragment when translated in nonsuppressor, wild-type E. coli cells, resulting in unassembled, nonviable progeny. I sequenced the Dam15 allele, identifying an amber (UAG) translational stop at the 68th codon. Employing this mutant in combination with a newly created isogenic cellular background utilizing the amber suppressors SupD (Serine), SupE (Glutamine), SupF (Tyrosine) and Sup— (wild type), we sought to control the level of incorporation of undecorated gpD products. As a second dimension, I constructed two separate temperature-inducile plasmids whereby expression of either D or D::eGFP was governed by the λ strong λ CI[Ts]857 temperature-sensitive repressor and expressed from the λ PL strong promoter. Our aim was to measure the decoration of the λ capsid by a D::gfp fusion under varying conditions regulated by both temperature and presence of suppression. This was achieved utilizing this controllable system, enabling the measurement of a variable number of fusions per phage based on diverse genetic and physical environments without significantly compromising phage viability. Surprisingly, both SupE and SupF showed similar levels of Dam15 suppression, even though sequencing data indicated that only SupE could restore the native gpD sequence at amino acid 68 (Q). In contrast, SupD (S), conferred very weak levels of suppression, but imparted an environment for very high decoration of gpD::eGFP per capsid, even at lower (repressed) temperatures. The presence of albeit few wild-type gpD molecules allowed for an even greater display than that of the perceived “100%” decoration scenario provided by the nonsuppressor strain. It appears that the lack of wild-type gpD does not allow for the space required to display the maximum number of fusions and in turn creates an environment that affects both phage assembly and therefore phage viability. Finally, the use of Western blotting, confirmed the presence of gpD::eGFP fusion decoration by employing a polyclonal anti-eGFP antibody. The significance of this work relates to the unique structure of λ’s capsid and its ability to exploit gpD in the design of controlled expression, which is guiding future research examining the fusion of different therapeutic peptides and proteins. Furthermore this approach has important implications specifically for the design of novel vaccines and delivery vehicles for targeted gene therapy in which steric hindrance and avidity are important concerns. The execution of this project employed basic bacterial genetics, phage biology and molecular biology techniques in the construction of bacterial strains and plasmids and the characterization of the phage display system.

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Gebura, Myroslav. "Nanobodies as new tools for studying large cargo transport and lamina organization." Doctoral thesis, 2017. http://hdl.handle.net/11858/00-1735-0000-002E-E42F-E.

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Berkane, Emir [Verfasser]. "Etude de l'interaction entre GpJ, une proteine du bacteriophage lambda, et LamB, une proteine de la membrane externe des bacteries gram-negatives / présentée et soutenue par Emir Berkane." 2005. http://d-nb.info/976081555/34.

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