The Significance of Wild Plants in the Evolutionary Ecology of Three Major Viruses Infecting Cultivated Sweetpotato in Uganda

The studies presented in this thesis contribute to the understanding of evolutionary ecology of three major viruses threatening cultivated sweetpotato (Ipomoea batatas Lam) in East Africa: Sweet potato feathery mottle virus (SPFMV; genus Potyvirus; Potyviridae), Sweet potato chlorotic stunt virus (SPCSV; genus Crinivirus; Closteroviridae) and Sweet potato mild mottle virus (SPMMV; genus Ipomovirus; Potyviridae). The viruses were serologically detected and the positive results confirmed by RT-PCR and sequencing. SPFMV was detected in 24 wild plant species of family Convolvulacea (genera Ipomoea, Lepistemon and Hewittia), of which 19 species were new natural hosts for SPFMV. SPMMV and SPCSV were detected in wild plants belonging to 21 and 12 species (genera Ipomoea, Lepistemon and Hewittia), respectively, all of which were previously unknown to be natural hosts of these viruses. SPFMV was the most abundant virus being detected in 17% of the plants, while SPMMV and SPCSV were detected in 9.8% and 5.4% of the assessed plants, respectively. Wild plants in Uganda were infected with the East African (EA), common (C), and the ordinary (O) strains, or co-infected with the EA and the C strain of SPFMV. The viruses and virus-like diseases were more frequent in the eastern agro-ecological zone than the western and central zones, which contrasted with known incidences of these viruses in sweetpotato crops, except for northern zone where incidences were lowest in wild plants as in sweetpotato. The NIb/CP junction in SPMMV was determined experimentally which facilitated CP-based phylogenetic and evolutionary analyses of SPMMV. Isolates of all the three viruses from wild plants were genetically similar to those found in cultivated sweetpotatoes in East Africa. There was no evidence of host-driven population genetic structures suggesting frequent transmission of these viruses between their wild and cultivated hosts. The p22 RNA silencing suppressor-encoding sequence was absent in a few SPCSV isolates, but regardless of this, SPCSV isolates incited sweet potato virus disease (SPVD) in sweetpotato plants co-infected with SPFMV, indicating that p22 is redundant for synergism between SCSV and SPFMV. Molecular evolutionary analysis revealed that isolates of strain EA of SPFMV that is largely restricted geographically in East Africa experience frequent recombination in comparison to isolates of strain C that is globally distributed. Moreover, non-homologous recombination events between strains EA and C were rare, despite frequent co-infections of these strains in wild plants, suggesting purifying selection against non-homologous recombinants between these strains or that such recombinants are mostly not infectious. Recombination was detected also in the 5 - and 3 -proximal regions of the SPMMV genome providing the first evidence of recombination in genus Ipomovirus, but no recombination events were detected in the characterized genomic regions of SPCSV. Strong purifying selection was implicated on evolution of majority of amino acids of the proteins encoded by the analyzed genomic regions of SPFMV, SPMMV and SPCSV. However, positive selection was predicted on 17 amino acids distributed over the whole the coat protein (CP) in the globally distributed strain C, as compared to only 4 amino acids in the multifunctional CP N-terminus (CP-NT) of strain EA largely restricted geographically to East Africa. A few amino acid sites in the N-terminus of SPMMV P1, the p7 protein and RNA silencing suppressor proteins p22 and RNase3 of SPCSV were also submitted to positive selection. Positively selected amino acids may constitute ligand-binding domains that determine interactions with plant host and/or insect vector factors. The P1 proteinase of SPMMV (genus Ipomovirus) seems to respond to needs of adaptation, which was not observed with the helper component proteinase (HC-Pro) of SPMMV, although the HC-Pro is responsible for many important molecular interactions in genus Potyvirus. Because the centre of origin of cultivated sweetpotato is in the Americas from where the crop was dispersed to other continents in recent history (except for the Australasia and South Pacific region), it would be expected that identical viruses and their strains occur worldwide, presuming virus dispersal with the host. Apparently, this seems not to be the case with SPMMV, the strain EA of SPFMV and the strain EA of SPCSV that are largely geographically confined in East Africa where they are predominant and occur both in natural and agro-ecosystems. The geographical distribution of plant viruses is constrained more by virus-vector relations than by virus-host interactions, which in accordance of the wide range of natural host species and the geographical confinement to East Africa suggest that these viruses existed in East African wild plants before the introduction of sweetpotato. Subsequently, these studies provide compelling evidence that East Africa constitutes a cradle of SPFMV strain EA, SPCSV strain EA, and SPMMV. Therefore, sweet potato virus disease (SPVD) in East Africa may be one of the examples of damaging virus diseases resulting from exchange of viruses between introduced crops and indigenous wild plant species. Keywords: Convolvulaceae, East Africa, epidemiology, evolution, genetic variability, Ipomoea, recombination, SPCSV, SPFMV, SPMMV, selection pressure, sweetpotato, wild plant species Author s Address: Arthur K. Tugume, Department of Agricultural Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Latokartanonkaari 7, P.O Box 27, FIN-00014, Helsinki, Finland. Email: tugume.arthur@helsinki.fi Author s Present Address: Arthur K. Tugume, Department of Botany, Faculty of Science, Makerere University, P.O. Box 7062, Kampala, Uganda. Email: aktugume@botany.mak.ac.ug, tugumeka@yahoo.com

A Floor Control Server in a Distributed Conference Service

The conferencing systems in IP Multimedia (IM) networks are going through restructuring, accomplished in the near future. One of the changes introduced is the concept of floors and floor control in its current form with matching entity roles. The Binary Floor Control Protocol (BFCP) is a novelty to be exploited in distributed tightly coupled conferencing services. The protocol defines the floor control server (FCS), which implements floor control giving access to shared resources. As the newest tendency is to distribute the conferencing services, the locations of different functionality units play an important role in developing the standards. The floor control server location is not yet single-mindedly fixed in different standardization bodies, and the debate goes on where to place it within the media server, providing the conferencing service. The thesis main objective is to evaluate two distinctive alternatives in respect the Mp interface protocol between the respective nodes, as the interface in relation to floor control is under standardization work at the moment. The thesis gives a straightforward preamble in IMS network, nodes of interest including floor control server and conferencing. Knowledge on several protocols – BFCP, SDP, SIP and H.248 provides an important background for understanding the functionality changes introduced in the Mp interface and therefore introductions on those protocols and how they are connected to the full picture is given. The actual analysis on the impact of the floor control server into the Mp reference point is concluded in relation to the locations, giving basic flows, requirements analysis including a limited implementation proposal on supporting protocol parameters. The overall conclusion of the thesis is that even if both choices are seemingly useful, not one of the locations is clearly the most suitable in the light of this work. The thesis suggests a solution having both possibilities available to be chosen from in separate circumstances, realized with consistent standardization. It is evident, that if the preliminary assumption for the analysis is kept regarding to only one right place for the floor control server, more work is to be done in connected areas to discover the one most appropriate location.

Collecting data from distributed FOSS projects

A key trait of Free and Open Source Software (FOSS) development is its distributed nature. Nevertheless, two project-level operations, the fork and the merge of program code, are among the least well understood events in the lifespan of a FOSS project. Some projects have explicitly adopted these operations as the primary means of concurrent development. In this study, we examine the effect of highly distributed software development, is found in the Linux kernel project, on collection and modelling of software development data. We find that distributed development calls for sophisticated temporal modelling techniques where several versions of the source code tree can exist at once. Attention must be turned towards the methods of quality assurance and peer review that projects employ to manage these parallel source trees. Our analysis indicates that two new metrics, fork rate and merge rate, could be useful for determining the role of distributed version control systems in FOSS projects. The study presents a preliminary data set consisting of version control and mailing list data.

Collecting data from distributed FOSS projects

A key trait of Free and Open Source Software (FOSS) development is its distributed nature. Nevertheless, two project-level operations, the fork and the merge of program code, are among the least well understood events in the lifespan of a FOSS project. Some projects have explicitly adopted these operations as the primary means of concurrent development. In this study, we examine the effect of highly distributed software development, is found in the Linux kernel project, on collection and modelling of software development data. We find that distributed development calls for sophisticated temporal modelling techniques where several versions of the source code tree can exist at once. Attention must be turned towards the methods of quality assurance and peer review that projects employ to manage these parallel source trees. Our analysis indicates that two new metrics, fork rate and merge rate, could be useful for determining the role of distributed version control systems in FOSS projects. The study presents a preliminary data set consisting of version control and mailing list data.

Exact bounds for distributed graph colouring

A distributed system is a collection of networked autonomous processing units which must work in a cooperative manner. Currently, large-scale distributed systems, such as various telecommunication and computer networks, are abundant and used in a multitude of tasks. The field of distributed computing studies what can be computed efficiently in such systems. Distributed systems are usually modelled as graphs where nodes represent the processors and edges denote communication links between processors. This thesis concentrates on the computational complexity of the distributed graph colouring problem. The objective of the graph colouring problem is to assign a colour to each node in such a way that no two nodes connected by an edge share the same colour. In particular, it is often desirable to use only a small number of colours. This task is a fundamental symmetry-breaking primitive in various distributed algorithms. A graph that has been coloured in this manner using at most k different colours is said to be k-coloured. This work examines the synchronous message-passing model of distributed computation: every node runs the same algorithm, and the system operates in discrete synchronous communication rounds. During each round, a node can communicate with its neighbours and perform local computation. In this model, the time complexity of a problem is the number of synchronous communication rounds required to solve the problem. It is known that 3-colouring any k-coloured directed cycle requires at least ½(log* k - 3) communication rounds and is possible in ½(log* k + 7) communication rounds for all k ≥ 3. This work shows that for any k ≥ 3, colouring a k-coloured directed cycle with at most three colours is possible in ½(log* k + 3) rounds. In contrast, it is also shown that for some values of k, colouring a directed cycle with at most three colours requires at least ½(log* k + 1) communication rounds. Furthermore, in the case of directed rooted trees, reducing a k-colouring into a 3-colouring requires at least log* k + 1 rounds for some k and possible in log* k + 3 rounds for all k ≥ 3. The new positive and negative results are derived using computational methods, as the existence of distributed colouring algorithms corresponds to the colourability of so-called neighbourhood graphs. The colourability of these graphs is analysed using Boolean satisfiability (SAT) solvers. Finally, this thesis shows that similar methods are applicable in capturing the existence of distributed algorithms for other graph problems, such as the maximal matching problem.

Distributed algorithms for edge dominating sets

An edge dominating set for a graph G is a set D of edges such that each edge of G is in D or adjacent to at least one edge in D. This work studies deterministic distributed approximation algorithms for finding minimum-size edge dominating sets. The focus is on anonymous port-numbered networks: there are no unique identifiers, but a node of degree d can refer to its neighbours by integers 1, 2, ..., d. The present work shows that in the port-numbering model, edge dominating sets can be approximated as follows: in d-regular graphs, to within 4 − 6/(d + 1) for an odd d and to within 4 − 2/d for an even d; and in graphs with maximum degree Δ, to within 4 − 2/(Δ − 1) for an odd Δ and to within 4 − 2/Δ for an even Δ. These approximation ratios are tight for all values of d and Δ: there are matching lower bounds.

Fast distributed approximation algorithms for vertex cover and set cover in anonymous networks

We present a distributed algorithm that finds a maximal edge packing in O(Δ + log* W) synchronous communication rounds in a weighted graph, independent of the number of nodes in the network; here Δ is the maximum degree of the graph and W is the maximum weight. As a direct application, we have a distributed 2-approximation algorithm for minimum-weight vertex cover, with the same running time. We also show how to find an f-approximation of minimum-weight set cover in O(f2k2 + fk log* W) rounds; here k is the maximum size of a subset in the set cover instance, f is the maximum frequency of an element, and W is the maximum weight of a subset. The algorithms are deterministic, and they can be applied in anonymous networks.