Computational Methods for Detecting Large-Scale Chromosome Rearrangements in SNP Data

Large-scale chromosome rearrangements such as copy number variants (CNVs) and inversions encompass a considerable proportion of the genetic variation between human individuals. In a number of cases, they have been closely linked with various inheritable diseases. Single-nucleotide polymorphisms (SNPs) are another large part of the genetic variance between individuals. They are also typically abundant and their measuring is straightforward and cheap. This thesis presents computational means of using SNPs to detect the presence of inversions and deletions, a particular variety of CNVs. Technically, the inversion-detection algorithm detects the suppressed recombination rate between inverted and non-inverted haplotype populations whereas the deletion-detection algorithm uses the EM-algorithm to estimate the haplotype frequencies of a window with and without a deletion haplotype. As a contribution to population biology, a coalescent simulator for simulating inversion polymorphisms has been developed. Coalescent simulation is a backward-in-time method of modelling population ancestry. Technically, the simulator also models multiple crossovers by using the Counting model as the chiasma interference model. Finally, this thesis includes an experimental section. The aforementioned methods were tested on synthetic data to evaluate their power and specificity. They were also applied to the HapMap Phase II and Phase III data sets, yielding a number of candidates for previously unknown inversions, deletions and also correctly detecting known such rearrangements.

A Decentralized Session Management Framework for Heterogeneous Ad-Hoc and Fixed Networks

Wireless technologies are continuously evolving. Second generation cellular networks have gained worldwide acceptance. Wireless LANs are commonly deployed in corporations or university campuses, and their diffusion in public hotspots is growing. Third generation cellular systems are yet to affirm everywhere; still, there is an impressive amount of research ongoing for deploying beyond 3G systems. These new wireless technologies combine the characteristics of WLAN based and cellular networks to provide increased bandwidth. The common direction where all the efforts in wireless technologies are headed is towards an IP-based communication. Telephony services have been the killer application for cellular systems; their evolution to packet-switched networks is a natural path. Effective IP telephony signaling protocols, such as the Session Initiation Protocol (SIP) and the H 323 protocol are needed to establish IP-based telephony sessions. However, IP telephony is just one service example of IP-based communication. IP-based multimedia sessions are expected to become popular and offer a wider range of communication capabilities than pure telephony. In order to conjoin the advances of the future wireless technologies with the potential of IP-based multimedia communication, the next step would be to obtain ubiquitous communication capabilities. According to this vision, people must be able to communicate also when no support from an infrastructured network is available, needed or desired. In order to achieve ubiquitous communication, end devices must integrate all the capabilities necessary for IP-based distributed and decentralized communication. Such capabilities are currently missing. For example, it is not possible to utilize native IP telephony signaling protocols in a totally decentralized way. This dissertation presents a solution for deploying the SIP protocol in a decentralized fashion without support of infrastructure servers. The proposed solution is mainly designed to fit the needs of decentralized mobile environments, and can be applied to small scale ad-hoc networks or also bigger networks with hundreds of nodes. A framework allowing discovery of SIP users in ad-hoc networks and the establishment of SIP sessions among them, in a fully distributed and secure way, is described and evaluated. Security support allows ad-hoc users to authenticate the sender of a message, and to verify the integrity of a received message. The distributed session management framework has been extended in order to achieve interoperability with the Internet, and the native Internet applications. With limited extensions to the SIP protocol, we have designed and experimentally validated a SIP gateway allowing SIP signaling between ad-hoc networks with private addressing space and native SIP applications in the Internet. The design is completed by an application level relay that permits instant messaging sessions to be established in heterogeneous environments. The resulting framework constitutes a flexible and effective approach for the pervasive deployment of real time applications.

Offloading content routing cost from routers

The publish/subscribe paradigm has lately received much attention. In publish/subscribe systems, a specialized event-based middleware delivers notifications of events created by producers (publishers) to consumers (subscribers) interested in that particular event. It is considered a good approach for implementing Internet-wide distributed systems as it provides full decoupling of the communicating parties in time, space and synchronization. One flavor of the paradigm is content-based publish/subscribe which allows the subscribers to express their interests very accurately. In order to implement a content-based publish/subscribe middleware in way suitable for Internet scale, its underlying architecture must be organized as a peer-to-peer network of content-based routers that take care of forwarding the event notifications to all interested subscribers. A communication infrastructure that provides such service is called a content-based network. A content-based network is an application-level overlay network. Unfortunately, the expressiveness of the content-based interaction scheme comes with a price - compiling and maintaining the content-based forwarding and routing tables is very expensive when the amount of nodes in the network is large. The routing tables are usually partially-ordered set (poset) -based data structures. In this work, we present an algorithm that aims to improve scalability in content-based networks by reducing the workload of content-based routers by offloading some of their content routing cost to clients. We also provide experimental results of the performance of the algorithm. Additionally, we give an introduction to the publish/subscribe paradigm and content-based networking and discuss alternative ways of improving scalability in content-based networks. ACM Computing Classification System (CCS): C.2.4 [Computer-Communication Networks]: Distributed Systems - Distributed applications

The Gerbera cDNA Microarray: A Tool for Large-Scale Identification of Genes Involved in Flower Development

During the past ten years, large-scale transcript analysis using microarrays has become a powerful tool to identify and predict functions for new genes. It allows simultaneous monitoring of the expression of thousands of genes and has become a routinely used tool in laboratories worldwide. Microarray analysis will, together with other functional genomics tools, take us closer to understanding the functions of all genes in genomes of living organisms. Flower development is a genetically regulated process which has mostly been studied in the traditional model species Arabidopsis thaliana, Antirrhinum majus and Petunia hybrida. The molecular mechanisms behind flower development in them are partly applicable in other plant systems. However, not all biological phenomena can be approached with just a few model systems. In order to understand and apply the knowledge to ecologically and economically important plants, other species also need to be studied. Sequencing of 17 000 ESTs from nine different cDNA libraries of the ornamental plant Gerbera hybrida made it possible to construct a cDNA microarray with 9000 probes. The probes of the microarray represent all different ESTs in the database. From the gerbera ESTs 20% were unique to gerbera while 373 were specific to the Asteraceae family of flowering plants. Gerbera has composite inflorescences with three different types of flowers that vary from each other morphologically. The marginal ray flowers are large, often pigmented and female, while the central disc flowers are smaller and more radially symmetrical perfect flowers. Intermediate trans flowers are similar to ray flowers but smaller in size. This feature together with the molecular tools applied to gerbera, make gerbera a unique system in comparison to the common model plants with only a single kind of flowers in their inflorescence. In the first part of this thesis, conditions for gerbera microarray analysis were optimised including experimental design, sample preparation and hybridization, as well as data analysis and verification. Moreover, in the first study, the flower and flower organ-specific genes were identified. After the reliability and reproducibility of the method were confirmed, the microarrays were utilized to investigate transcriptional differences between ray and disc flowers. This study revealed novel information about the morphological development as well as the transcriptional regulation of early stages of development in various flower types of gerbera. The most interesting finding was differential expression of MADS-box genes, suggesting the existence of flower type-specific regulatory complexes in the specification of different types of flowers. The gerbera microarray was further used to profile changes in expression during petal development. Gerbera ray flower petals are large, which makes them an ideal model to study organogenesis. Six different stages were compared and specifically analysed. Expression profiles of genes related to cell structure and growth implied that during stage two, cells divide, a process which is marked by expression of histones, cyclins and tubulins. Stage 4 was found to be a transition stage between cell division and expansion and by stage 6 cells had stopped division and instead underwent expansion. Interestingly, at the last analysed stage, stage 9, when cells did not grow any more, the highest number of upregulated genes was detected. The gerbera microarray is a fully-functioning tool for large-scale studies of flower development and correlation with real-time RT-PCR results show that it is also highly sensitive and reliable. Gene expression data presented here will be a source for gene expression mining or marker gene discovery in the future studies that will be performed in the Gerbera Laboratory. The publicly available data will also serve the plant research community world-wide.

Ecological communities in variable environments : dynamics and diversity under coloured environmental stochasticity

While environmental variation is an ubiquitous phenomenon in the natural world which has for long been appreciated by the scientific community recent changes in global climatic conditions have begun to raise consciousness about the economical, political and sociological ramifications of global climate change. Climate warming has already resulted in documented changes in ecosystem functioning, with direct repercussions on ecosystem services. While predicting the influence of ecosystem changes on vital ecosystem services can be extremely difficult, knowledge of the organisation of ecological interactions within natural communities can help us better understand climate driven changes in ecosystems. The role of environmental variation as an agent mediating population extinctions is likely to become increasingly important in the future. In previous studies population extinction risk in stochastic environmental conditions has been tied to an interaction between population density dependence and the temporal autocorrelation of environmental fluctuations. When populations interact with each other, forming ecological communities, the response of such species assemblages to environmental stochasticity can depend, e.g., on trophic structure in the food web and the similarity in species-specific responses to environmental conditions. The results presented in this thesis indicate that variation in the correlation structure between species-specific environmental responses (environmental correlation) can have important qualitative and quantitative effects on community persistence and biomass stability in autocorrelated (coloured) environments. In addition, reddened environmental stochasticity and ecological drift processes (such as demographic stochasticity and dispersal limitation) have important implications for patterns in species relative abundances and community dynamics over time and space. Our understanding of patterns in biodiversity at local and global scale can be enhanced by considering the relevance of different drift processes for community organisation and dynamics. Although the results laid out in this thesis are based on mathematical simulation models, they can be valuable in planning effective empirical studies as well as in interpreting existing empirical results. Most of the metrics considered here are directly applicable to empirical data.

Nitrous oxide emissions from selected natural and managed northern ecosystems

Microbial activity in soils is the main source of nitrous oxide (N2O) to the atmosphere. Nitrous oxide is a strong greenhouse gas in the troposphere and participates in ozone destructive reactions in the stratosphere. The constant increase in the atmospheric concentration, as well as uncertainties in the known sources and sinks of N2O underline the need to better understand the processes and pathways of N2O in terrestrial ecosystems. This study aimed at quantifying N2O emissions from soils in northern Europe and at investigating the processes and pathways of N2O from agricultural and forest ecosystems. Emissions were measured in forest ecosystems, agricultural soils and a landfill, using the soil gradient, chamber and eddy covariance methods. Processes responsible for N2O production, and the pathways of N2O from the soil to the atmosphere, were studied in the laboratory and in the field. These ecosystems were chosen for their potential importance to the national and global budget of N2O. Laboratory experiments with boreal agricultural soils revealed that N2O production increases drastically with soil moisture content, and that the contribution of the nitrification and denitrification processes to N2O emissions depends on soil type. Laboratory study with beech (Fagus sylvatica) seedlings demonstrated that trees can serve as conduits for N2O from the soil to the atmosphere. If this mechanism is important in forest ecosystems, the current emission estimates from forest soils may underestimate the total N2O emissions from forest ecosystems. Further field and laboratory studies are needed to evaluate the importance of this mechanism in forest ecosystems. The emissions of N2O from northern forest ecosystems and a municipal landfill were highly variable in time and space. The emissions of N2O from boreal upland forest soil were among the smallest reported in the world. Despite the low emission rates, the soil gradient method revealed a clear seasonal variation in N2O production. The organic topsoil was responsible for most of the N2O production and consumption in this forest soil. Emissions from the municipal landfill were one to two orders of magnitude higher than those from agricultural soils, which are the most important source of N2O to the atmosphere. Due to their small areal coverage, landfills only contribute minimally to national N2O emissions in Finland. The eddy covariance technique was demonstrated to be useful for measuring ecosystem-scale emissions of N2O in forest and landfill ecosystems. Overall, more measurements and integration between different measurement techniques are needed to capture the large variability in N2O emissions from natural and managed northern ecosystems.

Country-scale carbon accounting of the vegetation and mineral soils of Finland

The increase in global temperature has been attributed to increased atmospheric concentrations of greenhouse gases (GHG), mainly that of CO2. The threat of severe and complex socio-economic and ecological implications of climate change have initiated an international process that aims to reduce emissions, to increase C sinks, and to protect existing C reservoirs. The famous Kyoto protocol is an offspring of this process. The Kyoto protocol and its accords state that signatory countries need to monitor their forest C pools, and to follow the guidelines set by the IPCC in the preparation, reporting and quality assessment of the C pool change estimates. The aims of this thesis were i) to estimate the changes in carbon stocks vegetation and soil in the forests in Finnish forests from 1922 to 2004, ii) to evaluate the applied methodology by using empirical data, iii) to assess the reliability of the estimates by means of uncertainty analysis, iv) to assess the effect of forest C sinks on the reliability of the entire national GHG inventory, and finally, v) to present an application of model-based stratification to a large-scale sampling design of soil C stock changes. The applied methodology builds on the forest inventory measured data (or modelled stand data), and uses statistical modelling to predict biomasses and litter productions, as well as a dynamic soil C model to predict the decomposition of litter. The mean vegetation C sink of Finnish forests from 1922 to 2004 was 3.3 Tg C a-1, and in soil was 0.7 Tg C a-1. Soil is slowly accumulating C as a consequence of increased growing stock and unsaturated soil C stocks in relation to current detritus input to soil that is higher than in the beginning of the period. Annual estimates of vegetation and soil C stock changes fluctuated considerably during the period, were frequently opposite (e.g. vegetation was a sink but soil was a source). The inclusion of vegetation sinks into the national GHG inventory of 2003 increased its uncertainty from between -4% and 9% to ± 19% (95% CI), and further inclusion of upland mineral soils increased it to ± 24%. The uncertainties of annual sinks can be reduced most efficiently by concentrating on the quality of the model input data. Despite the decreased precision of the national GHG inventory, the inclusion of uncertain sinks improves its accuracy due to the larger sectoral coverage of the inventory. If the national soil sink estimates were prepared by repeated soil sampling of model-stratified sample plots, the uncertainties would be accounted for in the stratum formation and sample allocation. Otherwise, the increases of sampling efficiency by stratification remain smaller. The highly variable and frequently opposite annual changes in ecosystem C pools imply the importance of full ecosystem C accounting. If forest C sink estimates will be used in practice average sink estimates seem a more reasonable basis than the annual estimates. This is due to the fact that annual forest sinks vary considerably and annual estimates are uncertain, and they have severe consequences for the reliability of the total national GHG balance. The estimation of average sinks should still be based on annual or even more frequent data due to the non-linear decomposition process that is influenced by the annual climate. The methodology used in this study to predict forest C sinks can be transferred to other countries with some modifications. The ultimate verification of sink estimates should be based on comparison to empirical data, in which case the model-based stratification presented in this study can serve to improve the efficiency of the sampling design.

Effects of large-scale human land use on Capercaillie (Tetrao urogallus L.) populations in Finland

The Capercaillie (Tetrao urogallus L.) is often used as a focal species for landscape ecological studies: the minimum size for its lekking area is 300 ha, and the annual home range for an individual may cover 30 80 km2. In Finland, Capercaillie populations have decreased by approximately 40 85%, with the declines likely to have started in the 1940s. Although the declines have partly stabilized from the 1990s onwards, it is obvious that the negative population trend was at least partly caused by changes in human land use. The aim of this thesis was to study the connections between human land use and Capercaillie populations in Finland, using several spatial and temporal scales. First, the effect of forest age structure on Capercaillie population trends was studied in 18 forestry board districts in Finland, during 1965 1988. Second, the abundances of Capercaillie and Moose (Alces alces L.) were compared in terms of several land-use variables on a scale of 50 × 50 km grids and in five regions in Finland. Third, the effects of forest cover and fine-grain forest fragmentation on Capercaillie lekking area persistence were studied in three study locations in Finland, on 1000 and 3000 m spatial scales surrounding the leks. The analyses considering lekking areas were performed with two definitions for forest: > 60 and > 152 m3ha 1 of timber volume. The results show that patterns and processes at large spatial scales strongly influence Capercaillie in Finland. In particular, in southwestern and eastern Finland, high forest cover and low human impact were found to be beneficial for this species. Forest cover (> 60 m3ha 1 of timber) surrounding the lekking sites positively affected lekking area persistence only at the larger landscape scale (3000 m radius). The effects of older forest classes were hard to assess due to scarcity of older forests in several study areas. Young and middle-aged forest classes were common in the vicinity of areas with high Capercaillie abundances especially in northern Finland. The increase in the amount of younger forest classes did not provide a good explanation for Capercaillie population decline in 1965 1988. In addition, there was no significant connection between mature forests (> 152 m3ha 1 of timber) and lekking area persistence in Finland. It seems that in present-day Finnish landscapes, area covered with old forest is either too scarce to efficiently explain the abundance of Capercaillie and the persistence of the lekking areas, or the effect of forest age is only important when considering smaller spatial scales than the ones studied in this thesis. In conclusion, larger spatial scales should be considered for assessing the future Capercaillie management. According to the proposed multi-level planning, the first priority should be to secure the large, regional-scale forest cover, and the second priority should be to maintain fine-grained, heterogeneous structure within the separate forest patches. A management unit covering hundreds of hectares, or even tens or hundreds of square kilometers, should be covered, which requires regional-level land-use planning and co-operation between forest owners.