The Mechanisms of Hedgehog Signal Transduction

Studies in both vertebrates and invertebrates have identified proteins of the Hedgehog (Hh) family of secreted signaling molecules as key organizers of tissue patterning. Initially discovered in Drosophila in 1992, Hh family members have been discovered in animals with body plans as diverse as those of mammals, insects and echinoderms. In humans three related Hh genes have been identified: Sonic, Indian and Desert hedgehog (Shh, Ihh and Dhh). Transduction of the Hh signal to the cytoplasm utilizes an unusual mechanism involving consecutive repressive interactions between Hh and its receptor components, Patched (Ptc) and Smoothened (Smo). Several cytoplasmic proteins involved in Hh signal transduction are known in Drosophila, but mammalian homologs are known only for the Cubitus interruptus (Ci) transcription factor (GLI(1-3)) and for the Ci/GLI-associated protein, Suppressor of Fused (Su(fu)). In this study I analyzed the mechanisms of how the Hh receptor Ptc regulates the signal transducer Smo, and how Smo relays the Shh signal from the cell surface to the cytoplasm ultimately leading to the activation of GLI transcription factors. In Drosophila, the kinesin-like protein Costal2 (Cos2) is required for suppression of Hh target gene expression in the absence of ligand, and loss of Cos2 causes embryonic lethality. Cos2 acts by bridging Smo to the Ci. Another protein, Su(Fu) exerts a weak suppressive influence on Ci activity and loss of Su(Fu) causes subtle changes in Drosophila wing pattern. This study revealed that domains in Smo that are critical for Cos2 binding in Drosophila are dispensable for mammalian Smo function. Furthermore, by analyzing the function of Su(Fu) and the closest mouse homologs of Cos2 by protein overexpression and RNA interference I found that inhibition of the Hh response pathway in the absence of ligand does not require Cos2 activity, but instead critically depends on the activity of Su(Fu). These results indicate that a major change in the mechanism of action of a conserved signaling pathway occurred during evolution, probably through phenotypic drift made possible by the existence in some species of two parallel pathways acting between the Hh receptor and the Ci/GLI transcription factors. In a second approach to unravel Hh signaling we cloned > 90% of all human full-length protein kinase cDNAs and constructed the corresponding kinase-activity deficient mutants. Using this kinome resource as a screening tool, two kinases, MAP3K10 and DYRK2 were found to regulate Shh signaling. DYRK2 directly phosphorylated and induced the proteasome dependent degradation of the key Hh-pathway regulated transcription factor, GLI2. MAP3K10, in turn, affected GLI2 indirectly by modulating the activity of DYRK2.

Community forestry and environmental literacy in northern Thailand : Towards collaborative natural resource management and conservation

Conservation and sustainable management of tropical forests needs a holistic approach: in addition to ecological concerns, socio-economic issues including cultural aspects must be taken into consideration. An ability to adapt practices is a key to successful collaborative natural resource management. Achieving this requires local participation and understanding of local conceptions of the environment. This study examined these issues in the context of northern Thailand. Northern uplands are the home of much of the remaining natural forest in Thailand and several ethnic minority groups commonly referred to as hill tribes. The overall purpose of this study was to grasp a regional view of an ethnically diverse forested area and to elicit prospects to develop community forestry for conservation purposes and for securing people s livelihood. Conservation was a central goal of management as the forests in the area were largely designated as protected. The aim was to study local perceptions, objectives, values and practices of forest management, under the umbrella of the concept environmental literacy, as well as the effects of forest policy on community management goals and activities. Environmental literacy refers to holistic understanding of the environment. It was used as a tool to examine people s views, interests, knowledge and motivation associated to forests. The material for this study was gathered in six villages in Chiang Mai Province. Three minority groups were included in the study, the Karen, Hmong and Lawa, and also the Thai. Household and focus group interviews were conducted in the villages. In addition, officials at district, regional and national levels, workers of non-governmental organisations, and academics were interviewed, and some data were gathered from the students of a local school. The results showed that motivation for protecting the forests existed among each ethnic group studied. This was a result of culture and traditions evolved in the forest environment but also of a need to adapt to a changed situation and environment and to outside pressures. The consequences of deforestation were widely agreed on in the villages, and the impact of socio-economic changes on the forests and livelihood was also recognised. The forest was regarded as a source of livelihood providing land, products and services essential to the people inhabiting rural uplands. Traditions, fire control, cooperation, reforestation, separation of protected and utilisable areas, and rules were viewed as central for conservation. For the villagers, however, conservation meant sustainable use, whereas the government has tended to prefer strict restrictions on forest resource use. Thus, conflicts had arisen. Between communities, cooperation was more dominant than conflict. The results indicated that the heterogeneity of forest dwellers, although it has to be recognised, should not be overemphasised: ethnic diversity can be considered as no major obstacle for successful community forestry. Collaborative management is particularly important in protected areas in order to meet the conservation goals while providing opportunities for livelihood. Forest management needs more positive incentives and increased dialogue.

Management of multi-scale forest resource data over time

During the last decades there has been a global shift in forest management from a focus solely on timber management to ecosystem management that endorses all aspects of forest functions: ecological, economic and social. This has resulted in a shift in paradigm from sustained yield to sustained diversity of values, goods and benefits obtained at the same time, introducing new temporal and spatial scales into forest resource management. The purpose of the present dissertation was to develop methods that would enable spatial and temporal scales to be introduced into the storage, processing, access and utilization of forest resource data. The methods developed are based on a conceptual view of a forest as a hierarchically nested collection of objects that can have a dynamically changing set of attributes. The temporal aspect of the methods consists of lifetime management for the objects and their attributes and of a temporal succession linking the objects together. Development of the forest resource data processing method concentrated on the extensibility and configurability of the data content and model calculations, allowing for a diverse set of processing operations to be executed using the same framework. The contribution of this dissertation to the utilisation of multi-scale forest resource data lies in the development of a reference data generation method to support forest inventory methods in approaching single-tree resolution.

The success of the diversified farm : resource-based view

Farms and rural areas have many specific valuable resources that can be used to create non-agricultural products and services. Most of the research regarding on-farm diversification has hitherto concentrated on business start-up or farm survival strategies. Resource allocation and also financial success have not been the primary focus of investigations as yet. In this study these specific topics were investigated i.e. resource allocation and also the financial success of diversified farms from a farm management perspective. The key question addressed in this dissertation, is how tangible and intangible resources of the diversified farm affect the financial success. This study’s theoretical background deals with resource-based theory, and also certain themes of the theory of learning organisation and other decision-making theories. Two datasets were utilised in this study. First, data were collected by postal survey in 2001 (n = 663). Second, data were collected in a follow-up survey in 2006 (n = 439). Data were analysed using multivariate data analyses and path analyses. The study results reveal that, diversified farms performed differently. Success and resources were linked. Professional and management skills affected other resources, and hence directly or indirectly influenced success per se. In the light of empirical analyses of this study, tangible and intangible resources owned by the diversified farm impacted on its financial success. The findings of this study underline the importance of skills and networks for entrepreneur(s). Practically speaking all respondents of this study used either agricultural resources for non-farm businesses or non-farm resources for agricultural enterprises. To share resources in this way was seen as a pragmatic opportunity recognised by farmers. One of the downsides of diversification might be the phenomenon of over-diversification, which can be defined as the situation in which a farm diversifies beyond its optimal limit. The empirical findings of this study reveal that capital and labour resource constrains did have adverse effects on financial success. The evidence indicates that farms that were capital and labour resource constrained in 2001 were still less profitable than their ‘no problems’ counterparts five years later.

Enhanced processing of SPOT multispectral satellite imagery for environmental monitoring and modelling

The Taita Hills in southeastern Kenya form the northernmost part of Africa’s Eastern Arc Mountains, which have been identified by Conservation International as one of the top ten biodiversity hotspots on Earth. As with many areas of the developing world, over recent decades the Taita Hills have experienced significant population growth leading to associated major changes in land use and land cover (LULC), as well as escalating land degradation, particularly soil erosion. Multi-temporal medium resolution multispectral optical satellite data, such as imagery from the SPOT HRV, HRVIR, and HRG sensors, provides a valuable source of information for environmental monitoring and modelling at a landscape level at local and regional scales. However, utilization of multi-temporal SPOT data in quantitative remote sensing studies requires the removal of atmospheric effects and the derivation of surface reflectance factor. Furthermore, for areas of rugged terrain, such as the Taita Hills, topographic correction is necessary to derive comparable reflectance throughout a SPOT scene. Reliable monitoring of LULC change over time and modelling of land degradation and human population distribution and abundance are of crucial importance to sustainable development, natural resource management, biodiversity conservation, and understanding and mitigating climate change and its impacts. The main purpose of this thesis was to develop and validate enhanced processing of SPOT satellite imagery for use in environmental monitoring and modelling at a landscape level, in regions of the developing world with limited ancillary data availability. The Taita Hills formed the application study site, whilst the Helsinki metropolitan region was used as a control site for validation and assessment of the applied atmospheric correction techniques, where multiangular reflectance field measurements were taken and where horizontal visibility meteorological data concurrent with image acquisition were available. The proposed historical empirical line method (HELM) for absolute atmospheric correction was found to be the only applied technique that could derive surface reflectance factor within an RMSE of < 0.02 ps in the SPOT visible and near-infrared bands; an accuracy level identified as a benchmark for successful atmospheric correction. A multi-scale segmentation/object relationship modelling (MSS/ORM) approach was applied to map LULC in the Taita Hills from the multi-temporal SPOT imagery. This object-based procedure was shown to derive significant improvements over a uni-scale maximum-likelihood technique. The derived LULC data was used in combination with low cost GIS geospatial layers describing elevation, rainfall and soil type, to model degradation in the Taita Hills in the form of potential soil loss, utilizing the simple universal soil loss equation (USLE). Furthermore, human population distribution and abundance were modelled with satisfactory results using only SPOT and GIS derived data and non-Gaussian predictive modelling techniques. The SPOT derived LULC data was found to be unnecessary as a predictor because the first and second order image texture measurements had greater power to explain variation in dwelling unit occurrence and abundance. The ability of the procedures to be implemented locally in the developing world using low-cost or freely available data and software was considered. The techniques discussed in this thesis are considered equally applicable to other medium- and high-resolution optical satellite imagery, as well the utilized SPOT data.

Multi-user resource-sharing problem for the Internet

In this thesis we study a series of multi-user resource-sharing problems for the Internet, which involve distribution of a common resource among participants of multi-user systems (servers or networks). We study concurrently accessible resources, which for end-users may be exclusively accessible or non-exclusively. For all kinds we suggest a separate algorithm or a modification of common reputation scheme. Every algorithm or method is studied from different perspectives: optimality of protocols, selfishness of end users, fairness of the protocol for end users. On the one hand the multifaceted analysis allows us to select the most suited protocols among a set of various available ones based on trade-offs of optima criteria. On the other hand, the future Internet predictions dictate new rules for the optimality we should take into account and new properties of the networks that cannot be neglected anymore. In this thesis we have studied new protocols for such resource-sharing problems as the backoff protocol, defense mechanisms against Denial-of-Service, fairness and confidentiality for users in overlay networks. For backoff protocol we present analysis of a general backoff scheme, where an optimization is applied to a general-view backoff function. It leads to an optimality condition for backoff protocols in both slot times and continuous time models. Additionally we present an extension for the backoff scheme in order to achieve fairness for the participants in an unfair environment, such as wireless signal strengths. Finally, for the backoff algorithm we suggest a reputation scheme that deals with misbehaving nodes. For the next problem -- denial-of-service attacks, we suggest two schemes that deal with the malicious behavior for two conditions: forged identities and unspoofed identities. For the first one we suggest a novel most-knocked-first-served algorithm, while for the latter we apply a reputation mechanism in order to restrict resource access for misbehaving nodes. Finally, we study the reputation scheme for the overlays and peer-to-peer networks, where resource is not placed on a common station, but spread across the network. The theoretical analysis suggests what behavior will be selected by the end station under such a reputation mechanism.

Communities of wood-inhabiting fungi : Ecological requirements and responses to forest management and fragmentation

Despite much research on forest biodiversity in Fennoscandia, the exact mechanisms of species declines in dead-wood dependent fungi are still poorly understood. In particular, there is only limited information on why certain fungal species have responded negatively to habitat loss and fragmentation, while others have not. Understanding the mechanisms behind species declines would be essential for the design and development of ecologically effective and scientifically informed conservation measures, and management practices that would promote biodiversity in production forests. In this thesis I study the ecology of polypores and their responses to forest management, with a particular focus on why some species have declined more than others. The data considered in the thesis comprise altogether 98,318 dead-wood objects, with 43,085 observations of 174 fungal species. Out of these, 1,964 observations represent 58 red-listed species. The data were collected from 496 sites, including woodland key habitats, clear-cuts with retention trees, mature managed forests, and natural or natural-like forests in southern Finland and Russian Karelia. I show that the most relevant way of measuring resource availability can differ to a great extent between species seemingly sharing the same resources. It is thus critical to measure the availability of resources in a way that takes into account the ecological requirements of the species. The results show that connectivity at the local, landscape and regional scales is important especially for the highly specialized species, many of which are also red-listed. Habitat loss and fragmentation affect not only species diversity but also the relative abundances of the species and, consequently, species interactions and fungal successional pathways. Changes in species distributions and abundances are likely to affect the food chains in which wood-inhabiting fungi are involved, and thus the functioning of the whole forest ecosystem. The findings of my thesis highlight the importance of protecting well-connected, large and high-quality forest areas to maintain forest biodiversity. Small habitat patches distributed across the landscape are likely to contribute only marginally to protection of red-listed species, especially if habitat quality is not substantially higher than in ordinary managed forest, as is the case with woodland key habitats. Key habitats might supplement the forest protection network if they were delineated larger and if harvesting of individual trees was prohibited in them. Taking the landscape perspective into account in the design and development of conservation measures is critical while striving to halt the decline of forest biodiversity in an ecologically effective manner.

Disarming identities : Ethnic identities in conflict resolution: Hindrance or helpful resource?

This thesis proposes that national or ethnic identity is an important and overlooked resource in conflict resolution. Usually ethnic identity is seen both in international relations and in social psychology as something that fuels the conflict. Using grounded theory to analyze data from interactive problem-solving workshops between Palestinians and Israelis a theory about the role of national identity in turning conflict into protracted conflict is developed. Drawing upon research from, among others, social identity theory, just world theory and prejudice it is argued that national identity is a prime candidate to provide the justification of a conflict party’s goals and the dehumanization of the other necessary to make a conflict protracted. It is not the nature of national identity itself that lets it perform this role but rather the ability to mobilize a constituency for social action (see Stürmer, Simon, Loewy, & Jörger, 2003). Reicher & Hopkins (1996) have demonstrated that national identity is constructed by political entrepreneurs to further their cause, even if this construction is not a conscious one. Data from interactive problem-solving workshops suggest that the possibility of conflict resolution is actually seen by participants as a direct threat of annihilation. Understanding the investment necessary to make conflict protracted this reaction seems plausible. The justification for ones actions provided by national identity makes the conflict an integral part of a conflict party’s identity. Conflict resolution, it is argued, is therefore a threat to the very core of the current national identity. This may explain why so many peace agreements have failed to provide the hoped for resolution of conflict. But if national identity is being used in a constructionist way to attain political goals, a political project of conflict resolution, if it is conscious of the constructionist process, needs to develop a national identity that is independent of conflict and therefore able to accommodate conflict resolution. From this understanding it becomes clear why national identity needs to change, i.e. be disarmed, if conflict resolution is to be successful. This process of disarmament is theorized to be similar to the process of creating and sustaining protracted conflict. What shape and function this change should have is explored from the understanding of the role of national identity in supporting conflict. Ideas how track-two diplomacy efforts, such as the interactive problem-solving workshop, could integrate a process by both conflict parties to disarm their respective identities are developed.