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Helicobacter pylori infects over 50 % of the world’s population, causing gastritis, and in some cases, peptic ulcer disease and gastric cancer. Adherence to the gastric surface occurs primarily through H. pylori outer membrane proteins (HOPs) and is essential for bacterial survival and establishment of infection. The Blood group Antigen-Binding Adhesin (BabA) is the best-characterized attachment protein, mediating adherence by binding to fucosylated carbohydrate structures on the surface of the gastric epithelium. H. pylori is highly adaptable to environmental changes that occur during stomach longterm infection, however little is known about the effect of such changes on the adaptability and functionality of BabA adherence properties. The aim of this study was to evaluate how BabA-mediated binding properties of H. pylori isolates were affected during 20 years of chronic infection. Two H. pylori clinical isolates collected from a single individual, 20 years apart were studied for their Leb-binding properties using a combination of radioimmunoassay (RIA) and in situ histo- and cytochemistry. Our results demonstrated that H. pylori isolated after 20 years of infection had lost its Lewis b binding ability due to a nucleotide deletion in the babA gene, resulting in a translational frame shift and hence, a non-functional BabA protein. We also showed that the non-adherent isolate contains sub-populations of bacteria that express BabA and have therefore maintained the ability to bind to Leb-conjugate and adhere to human gastric mucosa in vitro.   An additional adherence pattern was revealed when H. pylori bacterial cells were applied to human buccal epithelium cells (BEC), with all the isolates demonstrating attachment. These results suggest that H. pylori can express additional binding properties for adherence in the oral cavity which may contribute to re-infection as well as further transmission of the H. pylori infection.

Helicobacter pylori (H. pylori) is a gram-negative, microaerophilic, spiral-shaped bacterium. It resides in the gastric mucous layer and epithelial lining of the stomach, often clustering at the junction of epithelial cells. H. pylori colonization usually occurs during childhood, and, when left untreated, generally persists for the host’s lifetime. Persistent H. pylori infection can cause chronic superficial gastritis and gastric duodenal ulcers, which is possibly linked to the development of gastric carcinoma and primary gastric lymphoma, especially of the mucosa-associated lymphoid tissue (MALT) type. It was recently defined as a class 1 carcinogen. The gastric inflammatory response to H. pylori infection is characterized by infiltration of the mucosa by neutrophils, T and B cells, plasma cells and macrophages. This reaction is initially induced by H. pylori attachment, followed by cytokine release by gastric epithelial cells. Epidemiological studies revealed that more than 50% of adults are infected with H. pylori all over the world. However, interestingly, only a subset of individuals develops serious H. pylori-related disease, while most infected individuals show no clinical symptoms. Gastric epithelial cells, like intestinal epithelial cells, express a subset of Toll-like receptors (TLRs) and similar pattern recognition receptors, which are important for the activation of the innate immune system. Bacterial components such as lipopeptides, peptidoglycan, LPS, flagellin, and CpG DNA are the ligands of TLRs. Thus, TLRs in gastric epithelial cells might be able to contribute to innate immune responses to H. pylori infection. However, there is scant knowledge about the mechanisms of innate immune response to acute and chronic H. pylori infection. This study is focused on host cell interaction with H. pylori flagellins, which are major components of the flagellar apparatus, and innate immune responses against them. The flagellins, which are essential for bacterial motility, are important for H. pylori to survive in the stomach mucus during the whole infectious cycle. Flagellins are known to act as the main determinant of many mucosal pathogenic bacteria that mediates proinflammatory signaling, including transcriptional factor NF-B activation via TLR5. In the first part of the study, we investigated the effects of H. pylori flagellins on TLR5 expression, NF-B activation and IL-8 production in various human intestinal and gastric epithelial cell lines by using Western blotting, semi-quantitative RT-PCR and ELISA. IL-8 is a potent neutrophil-activating chemokine expressed by gastric epithelial cells. When we stimulated the cells with the native form of or E. coli-expressed recombinant H. pylori flagellins, FlaA and FlaB, IL-8 was not induced in any case, while S. typhimurium flagellin (FliC) induced it significantly. H. pylori was able to modulate TLR5 protein expression and NF-B activation in epithelial cells regardless of the presence of flagellins. Having established the finding that H. pylori flagellins have unusually low immune-stimulatory properties, we further investigated to find out possible reasons why H. pylori flagellins are distinct from other flagellins of pathogenic bacteria in terms of immune-stimulatory activity. From amino acid sequence comparisons, we found that some regions in the terminal D0D1 protein domains of H. pylori flagellins are different from flagellins of other pathogenic bacteria. D0D1 is the domain which is known to interact with TLR5 in Salmonella FliC. To examine whether the differences endow H. pylori flagellins with low immune-stimulatory properties, we created several mutated H. pylori flagellins (FlaA and FlaB) by site-directed mutagenesis that contain one to four epitopes of Salmonella flagellin D0D1 domain amino acid sequences. The mutant flagellins expressed both in H. pylori and E. coli were used to determine their influence on TLR5-signaling mediators and cytokines, such as MAPkinases, (ERK, p38), NF-B, IL-8, and MIP-3. Salmonella FliC expressed in E. coli induced activation of p38, IB and NF-B leading to IL-8 and MIP-3 production in gastric epithelial cells. However, none of the H. pylori flagellin mutants activated MAP kinases or induced those cytokines. In a co-immunoprecipitation assay none of the recombinant wild type or mutated H. pylori flagellins showed any direct physical interaction with TLR5, while Salmonella FliC significantly co-precipitated with TLR5. Interestingly, we found H. pylori flagellins bind to the surface of gastric epithelial cells like FliC, although they do not bind to or stimulate TLR5. Based on the physical interaction of H. pylori flagellins and FliC with human gastric epithelial cells, we further analyzed transcriptional regulation by H. pylori flagellin in these host cells using microarray analysis. The result showed that H. pylori flagellins modulate host cell gene expression, and many of the identified regulation events overlap with the genes regulated by FliC. These findings imply that H. pylori flagellins do play a role in gene regulation of host cells probably through still unknown factors or receptors, although they do not trigger TLR5-related signaling pathways. The results of our study suggest that, in addition to the low immune-stimulatory activity of H. pylori LPS, the evolutionary reduction in stimulating activity of H. pylori flagellins on the local innate immune responses in the stomach in vivo might be a further strategy of this chronic mucosal pathogen to evade and minimize deleterious host responses, thereby promoting life-long persistence in the host, and possibly contributing to cancerogenesis. / Helicobacter pylori (H. pylori) ist ein gram-negatives, mikroaerophiles, spiralförmiges Bakterium. Es besiedelt die Schleimschicht und die Epitheloberfläche des Magens, wobei es sich besonders an den Kontaktstellen der Epithelzellen anlagert. Die Kolonisation mit H. pylori erfolgt normalerweise während der Kindheit und bleibt, wenn sie nicht behandelt wird, im allgemeinen während der gesamten Lebenszeit des Wirtes bestehen. Die persistierende H. pylori-Infektion kann chronische oberflächliche Gastritis und Zwöffingerdarmgeschwüre verursachen. Die Infektion kann auch zur Entwicklung von Magenkrebs und Lymphomen des Mukosa-assoziierten Lymphgewebes (MALT-Lymphom) führen. H. pylori ist seit 1994 als Typ I-Karzinogen klassifiziert. Die durch eine H. pylori-Infektion induzierte Entzündungsreaktion der Magenschleimhaut ist charakterisiert durch eine Infiltration der Schleimhaut mit neutrophilen Granulozyten, T- und B-Zellen, Plasmazellen und Makrophagen. Diese Reaktion wird ausgelöst durch die Anheftung von H. pylori gefolgt von der Freisetzung von Cytokinen durch die Magenepithelzellen. Epidemiologische Studien haben ergeben, dass weltweit mehr als 50% aller Erwachsenen mit H. pylori infiziert sind. Jedoch entwickelt interessanterweise nur eine Teilgruppe der infizierten Individuen eine ernsthafte H. pylori-assoziierte Krankheit, während die meisten Infizierten keine klinischen Symptome zeigen. Magenepithelzellen exprimieren, genauso wie Darmepithelzellen, eine Reihe von TOLL-like Rezeptoren (TLRs) und ähnliche Musterekennungsrezeptoren, die wichtig für die Aktivierung des angeborenen Immunsystems sind. Bakterielle Komponenten, wie z. B. Lipopeptide, Peptidoglycan, LPS, Flagellin und CpG-DNA sind die Liganden der TLRs. Auf diese Weise könnten die TLRs in den Magenepithelzellen in der Lage sein, zu der angeborenen Immunreaktion auf eine H. pylori-Infektion beizutragen. Jedoch ist bisher nur wenig über die Mechanismen der angeborenen Immunreaktion auf eine akute und chronische H. pylori-Infektion bekannt. Diese Studie befasst sich mit den Zellinteraktionen mit und den Antworten des Wirtsimmunsystems auf H. pylori-Flagelline, stark exprimierte Proteine des Flagellenapparats. Der Flagellenapparat ist essentiell für die Fähigkeit der Bakterien, im Magenschleim (Mukus) beweglich zu sein, und befähigt die Bakterien dazu, während des gesamten Infektionszyklus im Mukus und an der Magenmukosa zu überleben. Flagellin ist für viele pathogene Bakterien im Intestinaltrakt oder auch in der Lunge des Säuger-Wirts ein sehr wichtiger Faktor, der durch Bindung an TLR5 proinflammatorische Signalvorgänge, einschließlich der Aktivierung des Transkriptionsfaktors NF-B, herbeiführt. Im ersten Teil der vorliegenden Studie haben wir die Wirkungen von H. pylori-Flagellinen (FlaA, FlaB) auf TLR5-Expression, NF-B-Aktivierung und IL-8-Produktion in verschiedenen menschlichen Darm- und Magenepithelzelllinien mittels Western Blot, semi-quantitativer RT-PCR und ELISA untersucht. IL-8 ist ein hochwirksames Neutrophilen-aktivierendes Chemokin, welches von den Magenepithelzellen sezerniert wird und als ein Marker für die Zellaktivierung durch H. pylori, seine löslichen Produkte und Kontrollen diente. Nach Stimulation verschiedener Epithelzellen und humaner Makrophagen mit nativen oder in E. coli rekombinant hergestellten H. pylori-Flagellinen FlaA und FlaB wurde in keinem Fall IL-8 gebildet, während S. typhimurium-Flagellin (FliC) IL-8-Bildung und -Sekretion in signifikanter Menge induzierte. H. pylori war in der Lage, TLR5-Protein-Expression und die NF-B-Aktivierung in Epithelzellen zu modulieren, unabhängig von dem Vorhandensein von Flagellinen. Nachdem wir gezeigt hatten, dass H. pylori-Flagelline ungewöhnlich geringe immunstimulierende Eigenschaften besitzen, setzten wir unsere Untersuchungen fort, um mögliche Gründe herauszufinden, warum H. pylori-Flagelline sich von anderen Flagellinen pathogener Bakterien hinsichtlich der das Immunsystem stimulierenden Aktivitäten unterscheiden. Bei Vergleichen von Aminosäuresequenzen fanden wir heraus, dass einige Regionen in den terminalen D0D1-Domänen der H. pylori-Flagelline sich von Flagellinen anderer pathogener Bakterien unterscheiden. D0D1 ist der Funktionsbereich des Flagellins, von dem bekannt ist, dass er bei Salmonellen-FliC mit TLR5 interagiert. Um zu untersuchen, ob diese Unterschiede für die geringe immunstimulierende Wirkung von H. pylori-Flagellinen verantwortlich sind, generierten wir durch eine zielgerichtete Mutagenese mehrere mutierte H. pylori-Flagelline (FlaA und FlaB), die ein bis vier Epitope der Aminosäuresequenzen der D0D1-Domäne des Salmonella-Flagellins enthielten. Die mutierten Flagelline, die sowohl in H. pylori als auch in E. coli exprimiert wurden, wurden genutzt, um ihren Einfluss auf TLR5-Signal-Mediatoren und Cytokine, wie z. B. MAP-Kinasen (ERK, p38), NF-B, IL-8 und MIP-3α herauszufinden. In E. coli exprimiertes Salmonella-FliC bewirkte die Aktivierung von p38, IB, NF-B und ERK und führte zur Produktion von IL-8 und MIP-3α in den Magenepithelzellen. Im Gegensatz dazu aktivierte keine der H. pylori-Flagellinmutanten MAP-Kinasen oder induzierte diese Cytokine. Wir konnten durch Koimmunpräzipitationstechniken zeigen, dass wildtypische oder mutierte H. pylori-Flagelline nicht physisch mit TLR5 interagieren, während Salmonella-FliC spezifisch an TLR5 bindet. Interessanterweise fanden wir heraus, dass H. pylori-Flagelline wie FliC an die Oberfläche verschiedener humaner Epithelzellen binden, obwohl sie nicht TLR5 stimulieren oder an TLR5 binden. Basierend auf der physischen Interaktion von H. pylori-Flagellinen und FliC mit menschlichen Magenepithelzellen haben wir weiterhin die Transkriptionsregulation durch H. pylori-Flagellin in den Wirtszellen mit Hilfe der Microarray-Analyse untersucht. Die Ergebnisse zeigten, dass H. pylori-Flagelline die Gene der Wirtszelle modulieren, und viele der identifizierten Regulationsereignisse überschnitten sich mit den durch FliC regulierten Genen. Diese Ergebnisse implizieren, dass H. pylori-Flagelline doch eine Rolle bei der Genregulierung von Wirtszellen spielen, wahrscheinlich durch noch unbekannte Faktoren und Rezeptoren, obwohl sie keine mit TLR5 in Zusammenhang stehenden Signaltransduktionsketten auslösen. Die Resultate unserer Studien lassen darauf schließen, dass zusätzlich zu der das Immunsystem nur gering stimulierenden Aktivität von H. pylori-LPS die evolutionäre Reduzierung der stimulierenden Aktivität von H. pylori-Flagellinen auf lokale angeborene Immunreaktionen im Magen in vivo eine weitere Strategie dieses chronischen Schleimhautpathogens sein könnte, um schädliche Wirtsreaktionen zu verhindern und zu minimieren und hierdurch seine lebenslange Persistenz, jedoch auch die Krebsentstehung im Wirt zu fördern.

幽門螺桿菌感染在世界範圍內普遍存在，超過50%的世界人口都曾被感染。幽門螺桿菌與胃炎，胃潰瘍，胃癌和其他胃內疾病的發生密切相關。盡管目前已有多種有效除菌的抗生素，但耐藥菌的出現仍然不可忽視。防止幽門螺桿菌感染能有效的減緩疾病進程及其相關疾病引發的死亡率。因此，新藥物或者新的藥物劑型的研發十分重要。 / Cathelicidin是一種宿主免疫防禦系統用於抵抗不同種類病原微生物感染的生物肽。然而，其在幽門螺桿菌感染引發的炎癥中的作用仍未被揭示。本研究旨在發現Cathelicidin在幽門螺桿菌體內及體外感染中的可能抗菌作用及其機制。為了研究不同劑量Cathelicidin對幽門螺桿菌的直接抗菌作用，我們主要觀察了細菌生長，生物膜形成及細菌形態的改變。實驗結果表明，Cathelicidin可有效的抑制幽門螺桿菌的生長，破壞其生物膜形成，及在細菌胞膜形成孔狀結構，以改變其正常的超微形態。 / 在宿主抵禦幽門螺桿菌感染的機制中，自噬不僅具有抗菌活性，同時在清除胃上皮細胞內病原體的方面發揮著重要作用。然而，幽門螺桿菌則可能得益於自噬通路，並掌控自噬這一工具，進而幫助其自身的存活及感染。 / 研究發現，維生素D於體內的活性形式1,25 - 二羥維生素D3（1,25D3）可促進Cathelicidin的合成及激活自噬通路，從而發揮自身免疫來殺死在胃上皮細胞內定植的幽門螺桿菌。此外，通過RNAi沈默技術，與對照基因沈默的細胞相比，LL-37在人胃上皮細胞（HEF-145）中表達被抑制後，細胞內幽門螺桿菌的存活數量顯著上升。同樣的結果也被發現於動物模型中，在急性及慢性幽門螺桿菌感染的小鼠模型中，CRAMP基因敲除小鼠胃內的幽門螺桿菌數量比野生型小鼠胃內更多。 / 為了進一步研究Cathelicidin是否具有潛在的治療幽門螺桿菌感染的作用，本研究采用生物工程的方法將CRAMP轉入乳酸球菌中，再將這種分泌CRAMP型及對照組乳酸球菌餵給被幽門螺桿菌感染的小鼠。預防性和治療性的研究結果表明，這種能夠分泌CRAMP的益生菌可在胃黏膜表面存活和定植。更多的幽門螺桿菌能夠定植在CRAMP基因敲除小鼠的胃內，同時其胃內的促炎癥因子，IL-6，IL-1β及ICAM表達也高於野生型小鼠。此外，幽門螺桿菌感染上調了野生型小鼠胃上皮型來源的CRAMP表達，這一結果可部分解釋為什麽在野生型小鼠胃內只有少量幽門螺桿菌及輕度炎癥反應的原因。 / 重要的是，預防性及治療性的實驗顯著的提高了兩種小鼠胃黏膜中抗菌肽的水平，並降低了幽門螺桿菌感染及促炎癥因子mRNA的表達。值得注意的是，預防性的給藥還促進了胃粘液層的合成及防止表皮細胞雕亡，從而加強胃黏膜屏障的保護作用。 / 總結而言，本研究結果揭示Cathelicidin作為一種天然抗生素，在清除幽門螺桿菌及治療其引發的慢性胃炎中發揮重要的作用。分泌Cathelicidin型食用益生菌和幫助Cathelicidin內源性表達的1,25D3則有望發展成為新型的生物制劑用於防治動物和人體幽門螺桿菌感染及其引發的相關性胃炎。 / Helicobacter pylori (H. pylori) infection is one of the most prevalent infectious diseases, affecting more than 50% of the world’s population and responsible for gastritis, peptic ulcer, gastric cancer and other stomach disorders. / Although there are antibiotics which are effective to eradicate the bacteria, the worldwide appearance of drug resistance to H. pylori is common. It is therefore needed to search for new therapeutic agents or establish a new form of drug delivery system to prevent H. pylori infection at the early stage in order to reduce the disease progression and its associated morbidities. / Cathelicidin, a host defense antibacterial peptide in humans can eradicate different kinds of microbial infection. However, its roles in H. pylori infection and inflammation remain unexplored. This study sought to elucidate the possible actions and mechanisms for cathelicidin to protect against H. pylori infection and its associated inflammation both in vitro and in vivo. / To examine the direct antimicrobial action of cathelicidin, H. pylori survival, biofilm formation and morphology change were determined after exposure to different doses of cathelicidin in vitro. Results showed that exogenous cathelicidin could affect H. pylori growth, destroy bacteria biofilm and cause pore formation in H. pylori membranes. With respect to the host defense against H. pylori infection, autophagy plays a crucial role in antimicrobial activity, and contributes to clearance of intracellular pathogens in gastric cells. In this regard, H. pylori might benefit from autophagy pathway, and subvert the autophagy machinery in favor of its survival and infectious process. / The active form of vitamin D3, 1, 25-dihydroxyvitamin D3 (1, 25D3) activated LL-37, a human cathelicidin antimicrobial peptide and produced autophagy, which could contribute to host immune responses against intracellular survival of H. pylori in gastric cells. Additionally, we transfected gastric epithelial cells (HFE-145) with siRNA specific for LL-37 (siLL-37) to knockdown the expression of LL-37 in HFE-145 cells, which markedly increased the number of intracellular H. pylori when compared to cells transfected with a scrambled control siRNA (Csi). Consistent with these findings, cathelicidin knockout (Cnlp⁻/⁻) mice exhibited stronger H. pylori colonization in stomachs with acute and chronic H. pylori infection when compared to the stomachs in cathelicidin wild-type (Cnlp⁺/⁺) mice. / To further examine whether cathelicidin could be used as a therapeutic agent for H. pylori infection, we replenished exogenous CRAMP in H. pylori infected Cnlp⁺/⁺ and Cnlp⁻/⁻ mice with a bioengineered CRAMP-secreting strain of Lactococcus lactis (L. lactis) in a cost-effective manner. To this end, Cnlp⁺/⁺and Cnlp⁻/⁻ mice were pre-treated or post-treated with the control plasmid-encoded L. lactis or CRAMP-encoded L. lactis in H. pylori infected mice. They were then assessed for H. pylori infection and inflammatory responses in stomachs. Results showed that the probiotic L. lactis could survive in the gastric mucosa. In the absence of CRAMP, Cnlp⁻/⁻ mice exhibited more H. pylori harboring in the stomach together with marked expressions of IL-6, IL-1β and ICAM in the gastric mucosa when compared to wild type mice. Furthermore, in Cnlp⁺/⁺ mice, H. pylori infection stimulated gastric epithelium-derived CRAMP production but not in the Cnlp⁻/⁻ mice. These findings could partially explain why there were less bacterial infection and inflammatory responses in the wild type animals. Importantly, pre-treatment and post-treatment with CRAMP-encoded L. lactis significantly increased mucosal CRAMP level in both types of animals and reduced H. pylori infection and also pro-inflammatory cytokines mRNA expressions in these stomachs. It was noteworthy that delivering CRAMP intragastrically before H. pylori challenge strengthened the mucosal barrier by stimulating mucus layer synthesis and preventing epithelial cell apoptosis. / Collectively, these findings indicate that cathelicidin plays a significant role as a potential natural antibiotic for H. pylori clearance and a therapeutic agent for chronic gastritis. The increase of cathelicidin expression in the gastric mucosa either by the food-grade probiotic encoded with cathelicidin or the active form of vitamin D, could be promising biological preparations for the treatment of H. pylori infection and its associated gastritis in animals and perhaps also in humans. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Zhang, Lin. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2013. / Includes bibliographical references (leaves 144-170). / Abstract also in Chinese. / ABSTRACT --- p.I / 中文摘要 --- p.V / DECLARATION --- p.VII / ACKNOWLEDGEMENTS --- p.VIII / PUBLICATIONS --- p.XIV / LIST OF ILLUSTRATIONS --- p.XIX / INTRODUCTION --- p.1 / Chapter 1.1 --- Helicobacter pylori --- p.1 / Chapter 1.1.1 --- Overview --- p.1 / Chapter 1.1.2 --- Epidemiology of H. pylori infection --- p.2 / Chapter 1.1.3 --- Diagnosis and treatment strategies for H. pylori-induced diseases --- p.2 / Chapter 1.1.4 --- Bacteria autophagy: restriction or persistence of infection? --- p.3 / Chapter 1.1.5 --- Virulence factors of H. pylori related to autophagy --- p.8 / Chapter 1.1.6 --- Future research directions concerning H. pylori and autophagy --- p.11 / Chapter 1.2 --- Cathelicidins --- p.11 / Chapter 1.2.1 --- Overview --- p.11 / Chapter 1.2.2 --- Cathelicidin and its antimicrobial action and possible mechanisms --- p.12 / Chapter 1.2.3 --- Mouse cathelicidin deficient model --- p.16 / Chapter 1.2.4 --- Multiple receptors enable diversified activities of cathelicidins --- p.17 / Chapter 1.2.5 --- Endogenous cathelicidin induction --- p.23 / Chapter 1.2.5 --- New uses for old drugs --- p.26 / METHODS --- p.29 / Chapter 2.1 --- General Materials --- p.29 / Chapter 2.1.1 --- Chemicals and reagents --- p.29 / Chapter 2.1.2 --- Antibodies --- p.33 / Chapter 2.1.3 --- Commercial Kits --- p.34 / Chapter 2.1.4 --- Bacteria and culture conditions --- p.35 / Chapter 2.1.5 --- Animals --- p.36 / Chapter 2.1.6 --- Cell Line --- p.36 / Chapter 2.2 --- Experimental Designs --- p.37 / Chapter 2.2.1 --- In vitro studies --- p.37 / Chapter 2.2.2 --- In vivo studies --- p.44 / Chapter 2.3 --- Statistical analysis --- p.52 / RESULTS AND DISCUSSION --- p.53 / Chapter 3.1 --- Antimicrobial activity of cathelicidin on H. pylori in vitro --- p.53 / Chapter 3.2 --- Anti-biofilm formation activity of cathelicidin on H. pylori in vitro --- p.58 / Chapter 3.3 --- Manipulation of autophagy by H. pylori for their survival --- p.62 / Chapter 3.3.1 --- H. pylori stimulated dysfunctional autophagy --- p.62 / Chapter 3.3.2 --- H. pylori compromised the autophagic flux in cells and thereby promoting self-multiplication --- p.68 / Chapter 3.3.3 --- Autophagy is a host defense process in controlling intracellular survival of H. pylori --- p.71 / Chapter 3.4 --- Vitamin D3 inhibited H. pylori infection through the induction of autophagy --- p.76 / Chapter 3.4.1 --- 1,25D3 triggered the formation of autophagosomes and autophagolysosomes in gastric epithelial cells --- p.76 / Chapter 3.4.2 --- 1,25D3 treatment inhibited intracellular H. pylori survival through induction of autophagy by cathelicidin --- p.79 / Chapter 3.5 --- Discussion --- p.86 / Chapter 3.6 --- Elucidation of the role of endogenous and exogenous cathelicidin in H. pylori colonization and the associated gastritis --- p.94 / Chapter 3.6.1 --- H. pylori SS1 colonized in Cnlp⁺/⁺ and Cnlp⁻/⁻ mouse gastric epithelium --- p.94 / Chapter 3.6.2 --- Endogenous cathelicidin protects against H. pylori SS1 colonization in vitro and in vivo --- p.96 / Chapter 3.6.3 --- Endogenous cathelicidin protects against drug-resistant H. pylori 10783 colonization --- p.100 / Chapter 3.6.4 --- The bioengineered L. lactis encoded with CRAMP could localize in mouse stomachs and express CRAMP mRNA --- p.104 / Chapter 3.6.5 --- Effects of CRAMP secreting bioengineered L. lactis on H. pylori growth in vitro --- p.106 / Chapter 3.6.6 --- Post-treatment of CRAMP-encoded L.lactis on H. pylori colonization and its associated gastritis --- p.108 / Chapter 3.6.7 --- Pre-treatment of CRAMP-encoded L.lactis on H. pylori colonization and its associated gastritis --- p.118 / Chapter 3.7 --- Discussion --- p.129 / SUMMARY AND FUTURE PERSPECTIVES --- p.140 / REFERENCES --- p.144

預激活綜合體的形成對於脲酶的成熟是必需的。所以作為預激活綜合體一部份，UreF/UreG/UreG綜合體的形成也是脲酶成熟的關鍵之一。從幽門螺桿菌UreF/UreH的晶體結構顯示出是一個由異源二聚體形成的二聚體，這UreF/UreH二聚體和幽門螺桿菌的脲酶都有擁有個獨特的二重對稱性。而UreF/UreH二聚體的長度和幽門螺桿菌脲酶獨特的二次軸上那兩個催化中心的距離很接近。這讓我們聯想到UreF/UreH二聚體的二聚化是否與脲酶的活性有關。所以跟據UreF/UreH的晶體結構，計計了三個証實可以破壞UreF二聚化的突變體(F33D/Q37A, R179A/Y183D and F33D/Q37A/R179A/Y183D)。而這些突變體與UreH的結合體都保留了和脲酶結舍的能力卻失去了和UreG結合的能力，所以都不可以結合成完整的預激活綜合體來熟化脲酶。為了UreF/UreH二聚面的虛擬篩選，AutoDock Vina和Dock6.5,這兩個篩選程式用了DUD去做了一些基準。而基於一個百分比的富集值和首個已知配體的百分比值， Dock6.5比AutoDock Vina優勝，所以會用Dock6.5來篩選可以綁定UreF的二聚分介面的分子。最後，分析Dock6.5前1排名的分子，這些分子可以跟據它們和UreF殘基的接觸分類。 / The formation of the pre-activation complex is essential for the urease maturation. Being part of the pre-activation complex, the formation of theUreF/UreG/UreH complex is crucial for the formation of the complete preactivation complex. The crystal structures of Helicobacter pylor iUreF/UreH had been determined showing a dimer of heterodimer formation. The structure of UreF/UreH complex and H. pylori urease shared a unique two-fold symmetry. Moreover, the length of the UreF/UreH complex is similar to the distance of the two catalytic centres on the two-fold symmetry axis. This brought to the question: whether the dimerization of the UreF in the UreF/UreH complex has an effect on the H. pylori urease activity. According to the UreF/UreH crystal structure, three UreF mutants (F33D/Q37A, R179A/Y183D and F33D/Q37A/R179A/ Y183D) were designed and all were able to break the dimerization of UreF. These mutants were not able to interact with UreG, hence the complete pre-activation complex could not be formed and the maturation of urease was inhibited. Working towards to the virtual screening of the UreF/UreH complex dimerization surface, two docking programs, AutoDock Vina and Dock 6.5 were benchmarked using the DUD set. Dock 6.5 out performed AutoDock Vina by comparing the EF1 (Enrichment Factor of the top1% ranked ligands) and the percentage ranking of the first true hit. Using Dock 6.5, UreF residues that make the most contacts with the ligands had been identified using the top 1% of the ranked ligands. / Detailed summary in vernacular field only. / Yuen, Man Hon Nicholas. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2012. / Includes bibliographical references (leaves 72-74). / Abstracts also in Chinese. / Acknowledgements --- p.i / Abstract --- p.ii / 論文摘要 --- p.iii / Table of Content --- p.iv / Figures List --- p.vi / Tables List --- p.vi / Chapter Chapter 1 --- introduction --- p.1 / Chapter Introduction --- p.1 / Chapter 1.1 --- What is urease? --- p.1 / Chapter 1.2 --- Role of urease in H. pylori --- p.3 / Chapter 1.3 --- Structure of urease --- p.4 / Chapter 1.4 --- The active site of urease --- p.6 / Chapter 1.5 --- Accessory proteins are needed for urease maturation --- p.8 / Chapter 1.6 --- Crystal structure of H. pylori UreF/UreH complex --- p.12 / Chapter 1.7 --- Objective --- p.14 / Chapter Chapter 2: --- Material and Methods --- p.15 / Chapter 2.1 --- General Techniques --- p.15 / Chapter 2.1.1 --- Preparation and transformation of Escherichia coli competent cells --- p.15 / Chapter 2.1.2 --- Agarose gel electrophoresis of DNA --- p.16 / Chapter 2.1.3 --- Polymerase Chain reaction, PCR --- p.17 / Chapter 2.1.3.1 --- Basic protocol --- p.17 / Chapter 2.1.3.2 --- Generation of HisGST-UreF mutants --- p.18 / Chapter 2.1.4 --- Restriction digestion of DNA --- p.18 / Chapter 2.1.5 --- SDS-polyacryamide gel electrophoresis, SDS-PAGE --- p.19 / Chapter 2.1.6 --- Staining of polyacrylamide gel --- p.20 / Chapter 2.2 --- Expression and Purification of Recombinant Proteins --- p.21 / Chapter 2.2.1 --- General bacterial culturing, harvesting and lysis procedures --- p.21 / Chapter 2.2.2 --- Purification of wild type HisGST-UreF and mutants with UreH --- p.22 / Chapter 2.2.3 --- Purification of Urease (UreAC) --- p.23 / Chapter 2.2.4 --- Purification of His-SUMO-UreG --- p.24 / Chapter 2.3 --- Static light scattering, SLS --- p.25 / Chapter 2.4 --- In vitor Urease Activity --- p.26 / Chapter 2.5 --- In vitor Urease Activity --- p.27 / Chapter 2.6 --- Virtual Screening --- p.28 / Chapter 2.6.1 --- Docking with Dock 6.5 --- p.28 / Chapter 2.6.2 --- Docking with AutoDock Vina --- p.29 / Chapter 2.6.3 --- Enrichment factor calculation --- p.29 / Chapter 2.7 --- Reagents and Buffers --- p.30 / Chapter 2.7.1 --- Buffers for competent cells preparation --- p.30 / Chapter 2.7.2 --- Nucleic acid electrophoresis buffers --- p.30 / Chapter 2.7.3 --- Media fr bacterial culture --- p.30 / Chapter 2.7.4 --- Reagents for SDS-PAGE --- p.31 / Chapter 2.7.5 --- Reagents and Buffers for in vitro Urease Activity Assay --- p.32 / Chapter 2.7.6 --- Reagents and Buffers for in vitro Urease Activity Assay --- p.32 / Chapter Chapter 3 --- Dimerization of UreF is Essential for Urease Maturation --- p.33 / Chapter 3.1 --- Introduction --- p.33 / Chapter 3.2 --- Results --- p.34 / Chapter 3.2.1 --- Mutant design --- p.34 / Chapter 3.2.2 --- When expressed alone, the UreF mutants were found in the inclusion Body --- p.36 / Chapter 3.2.3 --- Co-expressing UreFmutants with UreH would solublize UreF mutants and the interactions between UreF mutants and UreH were retained --- p.36 / Chapter 3.2.4 --- UreF oligomerizationstate determination by size exclusion chromatography / static light scattering (SEC/LS) --- p.39 / Chapter 3.2.5 --- UreF dimerization is necessary for the interaction between the UreF/UreH complex and UreG --- p.41 / Chapter 3.2.6 --- UreF dimerization is not involved in the interaction between the UreF/UreH complex and Urease(UreA/UreC) --- p.43 / Chapter 3.2.7 --- UreF dimerization is essential for in vitro Urase Maturation --- p.45 / Chapter 3.2.8 --- UreF dimerization is essential for in vivo Urase Maturation --- p.47 / Chapter Chapter 4 --- Benchmarking Virtual Screening Performance of AUTODOCK VINA and DOCK 6.5 - Towards Virtual Screening of Inhibitors for Uref/UreH Complex Dimerization --- p.53 / Chapter 4.1 --- Introduction --- p.53 / Chapter 4.2 --- Benchmarking AutoDock Vina and Dock 6.5 --- p.54 / Chapter 4.2.1 --- Description of the Directory of Useful Decoys (DUD) set --- p.54 / Chapter 4.2.2 --- Benchmarking AutoDock Vina and Dock 6.5 shoewing Dock 6.5 has a better overall EF1 --- p.57 / Chapter 4.2.3 --- Dock 6.5 has a higher first hit percentile --- p.60 / Chapter 4.2.4 --- Analysis of the binding site for the top 1% ranked ligand for UreF Dimerization surface --- p.63 / Chapter 4.3 --- Discussion --- p.68 / Chapter Chapter 5 --- Conclusion --- p.71 / References --- p.72

This thesis examined the hypotheses that the mucus lining of the gastrointestinal tract (GIT) of Australian marsupials is colonised with large populations of spiral and fusiform shaped bacteria, many of which belong to the genus Helicobacter and that these Helicobacter species are likely be unique. The presence of spiral and fusiform shaped bacteria in the GIT of 8 Australian marsupial species (32 animals in total) was examined using microscopy, culture and Helicobacter genus specific PCR. The marsupials studied included the brushtail possum, ringtail possum, koala, wombat, Eastern grey kangaroo, Tasmanian devil, Eastern quoll and long nosed bandicoot. The spiral and fusiform shaped isolates were characterised and identified using morphological appearance, Helicobacter genus specific PCR and 16S rRNA gene sequence comparisons. The spatial distribution of Helicobacter species in the GIT sections was examined microscopically in silver stained sections of the GIT and using Fluorescent in situ hybridisation (FISH) with a Helicobacter genus specific probe. Spiral and/or fusiform shaped bacteria were detected and/or isolated from all marsupials studied. The prevalence and bacterial load of these organisms was found to differ in each marsupial species. These bacteria were found to belong to 3 different genera (Helicobacter, Campylobacter and Desulfovibrio). Each marsupial species appeared to be colonised with one or more unique Helicobacter species. Comparison of the detection of Helicobacter species in different groups of marsupials (herbivores, omnivores and carnivores) suggests that diet as well as the function and structure of the GIT may have a significant impact on their colonisation. Phylogenetic analysis of the new possum Helicobacters showed that they shared a common ancestor. Comparison of Helicobacter species isolated from different species of marsupial and placental mammals, as well as birds, showed that differences in environmental location i.e. gastric vs lower bowel had a major impact on the position of the Helicobacters on the phylogenetic tree.

Thesis (M.S.)--University of Hong Kong, 2001. / Includes bibliographical references (leaves 119-147).

Thesis (M.S.)--University of Toledo, 2009. / Typescript. "Submitted as partial fulfillment of the requirements for The Master of Science degree in Chemistry." "A thesis entitled"--at head of title. Bibliography: leaves 100-104.

Thesis (M.S.)--University of Hong Kong, 2001. / Includes bibliographical references (leaves 119-147).

Thesis (Ph. D.)--Ohio State University, 2003. / Title from first page of PDF file. Document formatted into pages; contains xxv, 330 p.; also includes graphics (some col.). Includes abstract and vita. Advisor: Kathryn A. Eaton, Dept. of Veterinary Bioscience. Includes bibliographical references (p. 297-330).