The genome packaging machinery of dsDNA bacteriophage PRD1

Viral genomes are encapsidated within protective protein shells. This encapsidation can be achieved either by a co-condensation reaction of the nucleic acid and coat proteins, or by first forming empty viral particles which are subsequently packaged with nucleic acid, the latter mechanism being typical for many dsDNA bacteriophages. Bacteriophage PRD1 is an icosahedral, non-tailed dsDNA virus that has an internal lipid membrane, the hallmark of the Tectiviridae family. Although PRD1 has been known to assemble empty particles into which the genome is subsequently packaged, the mechanism for this has been unknown, and there has been no evidence for a separate packaging vertex, similar to the portal structures used for packaging in the tailed bacteriophages and herpesviruses. In this study, a unique DNA packaging vertex was identified for PRD1, containing the packaging ATPase P9, packaging factor P6 and two small membrane proteins, P20 and P22, extending the packaging vertex to the internal membrane. Lack of small membrane protein P20 was shown to totally abolish packaging, making it an essential part of the PRD1 packaging mechanism. The minor capsid proteins P6 was shown to be an important packaging factor, its absence leading to greatly reduced packaging efficiency. An in vitro DNA packaging mechanism consisting of recombinant packaging ATPase P9, empty procapsids and mutant PRD1 DNA with a LacZ-insert was developed for the analysis of PRD1 packaging, the first such system ever for a virus containing an internal membrane. A new tectiviral sequence, a linear plasmid called pBClin15, was identified in Bacillus cereus, providing material for sequence analysis of the tectiviruses. Analysis of PRD1 P9 and other putative tectiviral ATPase sequences revealed several conserved sequence motifs, among them a new tectiviral packaging ATPase motif. Mutagenesis studies on PRD1 P9 were used to confirm the significance of the motifs. P9-type putative ATPase sequences carrying a similar sequence motif were identified in several other membrane containing dsDNA viruses of bacterial, archaeal and eukaryotic hosts, suggesting that these viruses may have similar packaging mechanisms. Interestingly, almost the same set of viruses that were found to have similar putative packaging ATPases had earlier been found to share similar coat protein folds and capsid structures, and a common origin for these viruses had been suggested. The finding in this study of similar packaging proteins further supports the idea that these viruses are descendants of a common ancestor.

Water Management in Cambodia Resources and Relations

In Cambodia, water has a special purpose as a source of life and livelihoods. Along with agriculture, fishing and forest use, industry, hydropower, navigation and tourism compete for the water resources. When rights and responsibilities related to essential and movable water are unclear, conflicts emerge easily. Therefore, water management is needed in order to plan and control the use of water resources. The international context is characterized by the Mekong River that flows through six countries. All of the countries by the river have very different roles and interests already depending on their geographical location. At the same time, water is also a tool for cooperation and peace. Locally, the water resources and related livelihoods create base for well-being, for economical and human resources in particular. They in turn are essential for the local people to participate and defend their rights to water use. They also help to construct the resource base of the state administration. Cambodia is highly dependent on the Mekong River. However, Cambodia has a volatile history whose effects can be seen for example in population structure, once suspended public institutions and weakened trust in the society. Relatively stable conditions came to the country as late as in the 1990s, therefore Cambodia for example has a weak status within the Mekong countries. This Master s thesis forms international, national and local interest groups of water use and analyzes their power relations and resources to affect water management. The state is seen as the salient actor as it has the formal responsibility of the water resources and of the coordination between the actions of different levels. In terms of water use this study focuses on production, in management on planning and in power relations on the resources. Water resources of Cambodia are seen consisting of the Mekong River and Tonle Sap Lake and the time span of the study is between the years 1991 and 2006. The material consists of semi-structured interviews collected during summer 2006 in Finland and in Cambodia as well as of literature and earlier studies. The results of the study show that the central state has difficulties to coordinate the actions of different actors because of its resource deficit and internal conflicts. The lessons of history and the vested interests of the actors of the state make it difficult to plan and to strengthen legislation. It seems that the most needed resources at the central state level are intangible as at the village level instead, the tangible resources (fulfilling the basic needs) are primarily important. The local decision-making bodies, NGOs and private sector mainly require legislation and legitimacy to support their role. However, the civil society and the international supporters are active and there are possibilities for new cooperation networks. Keywords: Water management, resources, participation, Cambodia, Mekong