Autophagy is a conserved cellular process that is responsible for degrading and recycling cytoplasmic constituents and has also emerged as a significant factor in modulating immune responses during enteric infections. This study investigates the role of autophagy in host defense during enteric parasitic infection, Trichuris muris, by focusing on the host defense, expulsion of worms, infection pathogenesis, and gut microbiota composition. Using C57BL/6 mice that are resistant and AKR mice that are susceptible to T. muris infection, we confirmed that when infected with T. muris, C57BL/6 mice can clear the infection almost completely by day 21 post-infection (p.i.). In contrast, AKR mice cannot, and therefore harbor a chronic infection within. Moreover, autophagy gene 7 floxed mice (Atg7fl/fl) and mice that are deficient in the autophagy protein, autophagy 7, in their intestinal epithelial cells (Atg7ΔIEC), were infected with T. muris and sacrificed on different time points. We observed that the Atg7fl/fl mice were able to almost clear the infection by day 21 p.i. but the Atg7ΔIEC mice were unable to clear infection by day 21 p.i. In vitro experiments consisted of exposing intestinal epithelial (HT-29) cell lines to T. muris excretory secretory products (ESPs) at different concentrations and also for different time-points, however, autophagy protein levels remained unchanged in those concentrations and time-points. Microbiota from uninfected and infected Atg7fl/fl and Atg7ΔIEC, analyzed by 16s rRNA sequencing revealed no significant differences in microbial composition among uninfected mice and minor differences in microbiota composition among T. muris infected mice. / Thesis / Master of Science in Medical Sciences (MSMS)

This thesis addresses the threat that personal computer faced from malware when the personal computer is connected to the Internet. Traditional host-based security approaches, such as anti-virus scanning protect the host from virus, worms, Trojans and other malwares. One of the issues of the host-based security approaches is that when the operating system is compromised by the malware, the antivirus software also becomes vulnerable. In this thesis, we present a novel approach through using an external device to enhance the host security by offloading the security solution from the host to the external device. We describe the design of the DeviceGuard framework that separate the security solution from the host and offload it to the external device, a Trusted Device. The architecture of the DeviceGuard consists of two components, the DeviceGuard application on the Trusted Device and a DeviceGuard daemon on the host. Our prototype based on Android Development Phone (ADP) shows the feasibilities and efficiency of our approach to provide security features including system file and user data integrity monitoring, secure signing and secure decryption. We use Bluetooth as the communication protocol between the host and the Trusted Device. Our experiment results indicates a practical Bluetooth throughput at about 2M Bytes per second is sufficient for short range communication between the host and the Trusted Device; Message digest with SHA-512, digital signing with 1024 bits signature and secure decryption with AES 256 bits on the Trusted device takes only the scale of 10? and 10? ms for 1K bytes and 1M bytes respectively which are also shows the feasibility and efficiency of the DeviceGuard solution. We also investigated the use of embedded system as the Trusted Device. Our solution takes advantage of the proliferation of devices, such as Smartphone, for stronger system and data security. / Master of Science

Comparative analysis of multiple genomes presents many challenges ranging from management of information about thousands of local similarities to definition of features by combination of evidence from multiple analyses and experiments. This research represents the development stage of a database-backed pipeline for comparative analysis of multiple genomes. The genomes of three recently sequenced species of Brucella were compared and a superset of known and hypothetical coding sequences was identified to be used in design of a discriminatory genomic cDNA array for comparative functional genomics experiments. Comparisons were made of coding regions from the public, annotated sequence of B. melitensis (GenBank) to the annotated sequence of B. suis (TIGR) and to the newly-sequenced B. abortus (personal communication, S. Halling, National Animal Disease Center, USDA). A systematic approach to analysis of multiple genome sequences is described including a data model for storage of defined features is presented along with necessary descriptive information such as input parameters and scores from the methods used to define features. A collection of adjacency relationships between features is also stored, creating a unified database that can be mined for patterns of features which repeat among or within genomes. The biological utility of the data model was demonstrated by a detailed analysis of the multiple genome comparison used to create the sample data set. This examination of genetic differences between three Brucella species with different virulence patterns and host preferences enabled investigation of the genomic basis of virulence. In the B. suis genome, seventy-one differentiating genes were found, including a contiguous 17.6 kb region unique to the species. Although only one unique species-specific gene was identified in the B. melitensis genome and none in the B. abortus genome, seventy-nine differentiating genes were found to be present in only two of the three Brucella species. These differentiating features may be significant in explaining differences in virulence or host specificity. RT-PCR analysis was performed to determine whether these genes are transcribed in vitro. Detailed comparisons were performed on a putative B. suis pathogenicity island (PAI). An overview of these genomic differences and discussion of their significance in the context of host preference and virulence is presented. / Master of Science

Challenges exist in higher education networks with host inventory and identification. Any student, staff, faculty, or dedicated IT administrator can be the primary responsible personnel for devices on the network. Confounding the problem is that there is also a large mix of personally-owned devices. These network environments are a hybrid of corporate enterprise, federated network, and Internet service provider. This management model has survived for decades based on the ability to identify responsible personnel when a host, system, or user account is suspected to have been compromised or is disrupting network availability for others. Mobile devices, roaming wireless access, and users accessing services from multiple devices has made the task of identification onerous. With increasing numbers of hosts on networks of higher education institutions, strategies such as dynamic addressing and address translation become necessary. The proliferation of the Internet of Things (IoT) makes this identification task even more difficult. Loss of intellectual property, extortion, theft, and reputational damage are all significant risks to research institution networks. Quickly responding to and remediating incidents reduces exposure and risk. This research evaluates what universities are doing for host inventory and creates a working prototype of a system for associating relevant log events to one or more responsible people. The prototype reduces the need for human-driven updates while enriching the dynamic host inventory with additional information. It also shows the value of associating application and service authentications to hosts. The prototype uses live network data which is de-identified to protect privacy. / Master of Science / Keeping track of computers or hosts on a network has become increasingly difficult. In the past, most of the hosts were owned by the institution, but now more hosts are owned by the end users. The management of institution networks has become a mix of corporate enterprise, federated network, and Internet service provider. This model has survived for decades based on the ability to identify someone responsible when a host or system is suspected to be infected with malware or is disrupting network availability for others. Mobile devices, roaming wireless access, and users accessing services from multiple devices has made the task of identification more difficult. With increasing numbers of hosts on networks of higher education institutions, strategies such as dynamic addressing and address translation become necessary. The proliferation of the Internet of Things (IoT) makes identification even more difficult. Loss of intellectual property, theft, and reputational damage are all significant risks to institution networks. Quickly responding to and remediating cybersecurity incidents reduces exposure and risk. This research considers what universities are doing for host inventory and creates a working prototype of a system for associating relevant log events to one or more responsible people. The prototype reduces the need for human-driven updates while incorporating additional information for the dynamic host inventory. It also shows the value of associating application and service authentications to hosts. The prototype uses real network data which is de-identified to protect privacy.

This study investigated a system comprised of entomopathogenic nematodes (EPN) (Steinernematidae and Heterorhabditidae), their symbiotic bacteria (Xenorhabdus, Photorhabdus) and an insect host, M. sexta. The focus of this investigation was to examine the effects insect host condition on the nematode-bacterium mutualistic partnership as a whole. The EPN used in the study had varying host-searching strategies: an ambusher, Steinernema carpocapsae, and a cruiser, Heterorhabditis sonorensis. Insect host age and diet were evaluated as factors that affect insect host condition. Wandering 5th instar M. sexta were much less susceptible to EPN infection compared to non-wandering 5th instar larvae, regardless of EPN species. Insect host diet had a significant impact on H. sonorensis susceptibility to EPN infection, and a non-significant trend was observed for S. carpocapsae. EPN and bacterial symbiont fitness were unaffected by insect host condition. This is the first record of the effect of insect host condition on both EPN and their symbiotic bacteria.

When tourism is growing fast it is important to develop it in a sustainable way which benefits the communities involved as much as possible. Homestay tourism can benefit local communities such as mass tourism has been widely criticized for failing to do. Homestay has shown to be successful as a tool for building sustainable tourism and contributing to locals involved in other countries. The concept has given hosts an opportunity to gain from their local resources. This gives the resources importance thereby locals preserve them. Although, there is a lack of studies on how the homestay concept can contribute to sustainable tourism development and how the concept is implemented in the Philippines. The aim with the research is to explore impacts of the homestay concept in sustainable tourism development through following perspectives: assess the social and economic impacts of having a homestay, identify motivational factors behind local peoples' decisions to put up a homestay, explore further ways of developing homestays in a developing country with focus on the central part of The Philippines. In the research, several challanges for implementing the homestay concept in a sustainable way have been identified and given suggestions on. The biggest challenge identified is that hosts do not have the skills and knowledge for the purpose of the homestay concept. The study argue that this challenge could be overcome by host-training to a large extent. This host-training should preferably be facilitated by the government, which in the Philippines has internal challenges such as reversed hierarchy and low commitment to overcome before being able to facilitate the homestays for a more sustainable tourism development.

Unionoid mussels are globally threatened and their conservation requires species-specific knowledge on their ecology and parasite-host interaction. Unio crassus is one of Europe’s most threatened unionoid species and has a temporary obligate parasitic life stage (glochidia) on fish. A lack of suitable hosts is probably a major limitation for mussel recruitment, but host species composition, suitability and availability in time and space have yet to be fully explored. This thesis examines different aspects of the host fish species, including their composition, suitability and ecological importance, in relation to U. crassus, using both field and laboratory studies. The effects of mussel and host density on mussel reproductive potential were considered, as were aspects of evolutionary adaptations between mussels and fish and how climate change may affect their interaction. The results show that U. crassus is a host generalist, parasitizing a variety of fish species. Host suitability and density, which varied among fish species and rivers, affected the level of glochidia encapsulation, hence mussel reproductive potential, more so than the density of mussels taking part in reproduction. Ecologically important hosts included both highly suitable primary hosts, and less suitable hosts that were highly abundant. Whether or not U. crassus has specific adaptations to its hosts to enhance juvenile transformation remains unclear. No distinct pattern of local adaptation was found, nor was there an effect of host fish presence on the timing of glochidia release by adult mussels. Instead, temperature played a major role, with results suggesting that changes in spring water temperature regimes can cause temporal and spatial mismatches in the mussel-host interaction. This thesis indicates that investigations of local mussel-host interactions help in identifying mechanisms important for unionoid conservation management and prioritization. / Många sötvattenmusslor har en komplex livscykel där larverna (glochidier) under sin utveckling till frilevande musslor parasiterar på gälarna hos lämpliga värdfiskar. Flera av våra musslor, såsom den tjockskaliga målarmusslan (Unio crassus), är globalt hotade och för att kunna bevara och förvalta dessa arter på bästa sätt behöver vi lära oss mer om deras ekologi och samspelet mellan musslan och dess värdfiskar. Avsaknaden av värdfiskar innebär förmodligen en stor begränsning för rekryteringen av juvenila musslor, men det finns trots detta en begränsad kunskap om hur artsammansättningen i fisksamhället och dess tillgänglighet påverkar musselpopulationer.  Min avhandling undersöker olika aspekter av interaktioner mellan U. crassus och dess värdfiskar, som hur värdfisksamhällen och fiskarters värdlämplighet påverkar musslans reproduktionspotential. Jag har även studerat hur tätheter av olika fiskarter och vuxna musslor påverkar rekryteringen, eventuella evolutionära anpassningar samt om en förhöjd temperatur skulle kunna påverka interaktionen mellan U. crassus och dess värdfiskar. Resultaten visar att U. crassus är en generalist som parasiterar på en mängd olika fiskarter. Jag fann dock en stor variation i dominerande fiskarter och lämpliga värdar mellan olika åar, vilket påverkade reproduktionspotentialen hos musslorna mer än vad tätheten vuxna musslor som deltog i reproduktionen gjorde. Som ekologiskt viktiga värdar fanns således både särskilt lämpliga, primära värdarter, men också mindre lämpliga arter som förekom i höga tätheter. Ingen tydlig lokal anpassning kunde observeras, och fiskens närvaro påverkade inte tidpunkten för när de vuxna musslorna släppte sina glochidielarver. Däremot fann jag att temperaturen spelade en viktig roll för musslans reproduktion, där ökad temperatur föreslås ha negativa effekter på interaktionen mellan musslan och dess värdfiskar. Avhandlingen visar på vikten av att studera interaktioner mellan den tjockskaliga målarmusslan och dess värdar på lokal skala för att bättre kunna identifiera och prioritera viktiga naturvårdsåtgärder. / UnioCrassusforLIFE (European LIFE+ project: LIFE10 NAT/SE/000046)

Doctor of Philosophy / Department of Biology / Stefan Rothenburg / Vaccinia virus is the prototypic poxvirus that has been widely used as a model for investigating poxvirus biology and genetics. Like several members of the Poxviridae family, vaccinia virus can infect several different species including mice, cows and humans. Because the entry of poxviruses into a host cell relies on ubiquitously expressed surface molecules, which are found in many species, the ability of poxviruses to infect and replicate in different host cells primarily depends on their ability to subvert the host’s innate immune response. One critical barrier to infection is overcoming the general shutdown of protein translation initiated by the cellular protein kinase PKR. PKR detects cytoplasmic double-stranded (ds) RNA generated during infection by the replicating virus, which activates it to phosphorylate the alpha-subunit of the eukaryotic translation initiation factor 2 (eIF2) and suppress general translation. Poxviruses are large viruses with dsDNA genomes that encode around 200 genes. Several of these genes are known as host range genes and are important for replication in different host species and many interact with components of the host immune response to promote viral replication. Two genes in vaccinia virus, called E3L and K3L, are known inhibitors of PKR and have previously been shown to be important for virus replication in cells from different species. The molecular explanation behind their host range function, however, is unknown. The main goal of the research presented in this thesis is to determine the molecular mechanisms for the host range function of vaccinia virus E3L and K3L, particularly in different hamster host cells. Along with an analysis of vaccinia virus host range genes, we have used genome-wide comparisons between host-restricted poxviruses in the Leporipoxvirus genus to parse out the potential genomic determinants of host range restriction in this clade of poxviruses. The overarching aim of this thesis work is to better understand the molecular mechanisms for host range in poxviruses.

Insects are host to a diverse range of vertically transmitted micro-organisms, but while their bacterial symbionts are well-studied, little is known about their vertically transmitted viruses. The sigma virus (DMelSV) is currently the only natural hostspecific pathogen to be described in Drosophila melanogaster. In this thesis I have examined; the diversity and evolution of sigma viruses in Drosophila, their transmission and population dynamics, and their ability to host shift. I have described six new rhabdoviruses in five Drosophila species — D. affinis, D. obscura, D. tristis, D. immigrans and D. ananassae — and one in a member of the Muscidae, Muscina stabulans (Chapters two and four). These viruses have been tentatively named as DAffSV, DObsSV, DTriSV, DImmSV, DAnaSV and MStaSV respectively. I sequenced the complete genomes of DObsSV and DMelSV, the L gene from DAffSV and partial L gene sequences from the other viruses. Using this new sequence data I created a phylogeny of the rhabdoviruses (Chapter two). The sigma viruses form a distinct clade which is closely related to the Dimarhabdovirus supergroup, and the high levels of divergence between these viruses suggest that they may deserve to be recognised as a new genus. Furthermore, this analysis produced the most robustly supported phylogeny of the Rhabdoviridae to date, allowing me to reconstruct the major transitions that have occurred during the evolution of the family. This data suggests that the bias towards research into plants and vertebrates means that much of the diversity of rhabdoviruses has been missed, and rhabdoviruses may be common pathogens of insects. In Chapter three I examined whether the new sigma viruses in Drosophila affinis and Drosophila obscura are both vertically transmitted. As is the case for DMelSV, both males and females can transmit these viruses to their offspring. Males transmit lower viral titres through sperm than females transmit through eggs, and a lower proportion of their offspring become infected. I then examined natural populations of D. obscura in the UK; 39% of flies were infected and the viral population shows clear evidence of a recent expansion, with extremely low genetic diversity and a large excess of rare polymorphisms. Using sequence data I estimate that the virus has swept across the UK within the last ~11 years, during which time the viral population size doubled approximately every 9 months. Using simulations based on lab estimates of transmission rates, I show that the biparental mode of transmission allows the virus to invade and rapidly spread through populations, at rates consistent with those measured in the field. Therefore, as predicted by the simulations, the virus has undergone an extremely rapid and recent increase in population size. In Chapter four I investigated for the first time whether vertically transmitted viruses undergo host shifts or cospeciate with their hosts. Using a phylogenetic approach I show that sigma viruses have switched between hosts during their evolutionary history. These results suggest that sigma virus infections may be short-lived in a given host lineage, so that their long-term persistence relies on rare horizontal transmission events between hosts. In Chapter five I examined the ability of three Drosophila sigma viruses to persist and replicate in 51 hosts sampled across the Drosophilidae phylogeny. I used a phylogenetic mixed model to account for the non-independence of host taxa due to common ancestry, which additionally allows integration over the uncertainty in the host phylogeny. In two out of the three viruses there was a negative correlation between viral titre and genetic distance from the natural host. Additionally the host phylogeny explains an extremely high proportion of the variation (after considering genetic distance from the natural host) in the ability of these viruses to replicate in novel hosts (>0.8 for all viruses). There were strong phylogenetic correlations between all the viruses (>0.65 for all pairs), suggesting a given species’ level of resistance to one virus is strongly correlated with its resistance to other viruses. This suggests the host phylogeny, and genetic distance from the natural host, may be important in determining viruses ability to host switch. This work has aimed to address fundamental questions relating to host-parasite coevolution and pathogen emergence. The data presented suggests that sigma viruses are likely to be widespread vertically transmitted insect viruses, which have dynamic interactions with their hosts. These viruses appear to have switched between hosts during their evolutionary history and it is likely the host phylogeny is a determinant of such host shifts.

Further functional investigation revealed that knockdown of GRP78 expression by RNA interference resulted in a significant increase of both intracellular and extracellular HBV virions in the transient HBV-producing HepG2 cells, concomitant with enhanced levels of hepatitis B surface antigen and e antigen in the culture medium Conversely, overexpression of GRP78 in HepG2 cells led to HBV suppression concomitant with induction of the positive regulatory circuit of GRP78 and interferon-beta 1 (IFN-beta1). In this connection, IFN-beta1-mediated 2', 5'-oligoadenylate synthetase (OAS) and ribonuclease L (RNase L) signaling pathway was noted to be activated in GRP78-overexpressing HepG2 cells. Moreover, GRP78 was significantly down-regulated in the livers of chronic hepatitis B patients after effective anti-HBV treatment (p= 0.019) as compared with their counterpart pre-treatment liver biopsies. / Hepatitis B virus (HBV) infection is a global public health problem, which plays a crucial role in the pathogenesis of chronic hepatitis, cirrhosis and hepatocellular carcinoma. Although considerable progress has been made over the past decade, the pathogenesis of HBV infection and the mechanisms of host-virus interactions are still elusive. / In conclusion, the present study demonstrates for the first time that GRP78 functions as an endogenous anti-HBV factor via IFN-beta1-OAS-RNase L pathway in hepatocytes. Induction of hepatic GRP78 may provide a novel therapeutic approach in treating HBV infection. / In this study, we applied a two-dimensional gel electrophoresis and mass spectrometry-based comparative proteomic approach to globally analyze the host early response to HBV by using an inducible HBV-producing cell line HepAD38. Twenty-three proteins were identified as differentially expressed, with glucose-regulated protein 78 (GRP78) as one of the most significantly up-regulated proteins induced by HBV replication. This induction was further confirmed in both HepAD38 and HepG2 cells transfected with HBV-producing plasmids by real-time reverse transcription-polymerase chain reaction (RT-PCR) and Western blotting, as well as in HBV-infected human liver biopsies by immunohistochemistry. / Ma, Yan. / Adviser: Ming-Liang He. / Source: Dissertation Abstracts International, Volume: 72-01, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 111-129). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. Ann Arbor, MI : ProQuest Information and Learning Company, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.