Poverty and the Environment : Investment Poverty and the Role of Assets in Generating Welfare for Farmer Households in the Province of Herrera, Panama

Köyhiä maanviljelijöitä on usein syytetty kehitysmaiden ympäristöongelmista. On väitetty, että eloonjäämistaistelu pakottaa heidät käyttämään maata ja muita luonnonvaroja lyhytnäköisesti. Harva asiaa koskeva tutkimus on kuitenkaan tukenut tätä väitettä; perheiden köyhyyden astetta ja heidän aiheuttamaansa ympäristövaikutusta ei ole kyetty kytkemään toisiinsa. Selkeyttääkseen köyhyys-ympäristö –keskustelua, Thomas Reardon ja Steven Vosti kehittivät investointiköyhyyden käsitteen. Se tunnistaa sen kenties suuren joukon maanviljelijäperheitä, jotka eivät ole köyhiä perinteisten köyhyysmittareiden mukaan, mutta joiden hyvinvointi ei ole riittävästi köyhyysrajojen yläpuolella salliakseen perheen investoida kestävämpään maankäyttöön. Reardon ja Vosti korostivat myös omaisuuden vaikutusta perheiden hyvinvointiin, ja uskoivat sen vaikuttavan tuotanto- ja investointipäätöksiin. Tässä tutkimuksessa pyritään vastaamaan kahteen kysymykseen: Miten investointiköyhyyttä voidaan ymmärtää ja mitata? Ja, mikä on viljelijäperheiden omaisuuden hyvinvointia lisäävä vaikutus? Tätä tutkimusta varten haastateltiin 402 maanviljelijäperhettä Väli-Amerikassa, Panaman tasavallan Herreran läänissä. Näiden perheiden hyvinvointia mitattiin heidän kulutuksensa mukaan, ja paikalliset köyhyysrajat laskettiin paikallisen ruoan hinnan mukaan. Herrerassa ihminen tarvitsee keskimäärin 494 dollaria vuodessa saadakseen riittävän ravinnon, tai 876 dollaria vuodessa voidakseen ravinnon lisäksi kattaa muitakin välttämättömiä menoja. Ruoka- eli äärimmäisen köyhyyden rajan alle jäi 15,4% tutkituista perheistä, ja 33,6% oli jokseenkin köyhiä, eli saavutti kyllä riittävän ravitsemuksen, muttei kyennyt kustantamaan muita perustarpeitaan. Molempien köyhyysrajojen yläpuolelle ylsi siis 51% tutkituista perheistä. Näiden köyhyysryhmien välillä on merkittäviä eroavaisuuksia ei vain perheiden varallisuuden, tulojen ja investointistrategioiden välillä, mutta myös perheiden rakenteessa, elinympäristössä ja mahdollisuuksissa saada palveluja. Investointiköyhyyden mittaaminen osoittautui haastavaksi. Herrerassa viljelijät eivät tee investointeja puhtaasti ympäristönsuojeluun, eikä maankäytön kestävyyttä muutenkaan pystytty yhdistämään perheiden hyvinvoinnin tasoon. Siksi investointiköyhyyttä etsittiin sellaisena hyvinvoinnin tasona, jonka alapuolella elävien perheiden parissa tuottavat maanparannusinvestoinnit eivät enää ole suorassa suhteessa hyvinvointiin. Tällaisia investointeja ovat mm. istutetut aidat, lannoitus ja paranneltujen laiduntyyppien viljely. Havaittiin, että jos perheen hyvinvointi putoaa alle 1000 dollarin/henkilö/vuosi, tällaiset tuottavat maanparannusinvestoinnit muuttuvat erittäin harvinaisiksi. Investointiköyhyyden raja on siis noin kaksi kertaa riittävän ravitsemuksen hinta, ja sen ylitti 42,3% tutkituista perheistä. Heille on tyypillistä, että molemmat puolisot käyvät työssä, ovat korkeasti koulutettuja ja yhteisössään aktiivisia, maatila tuottaa paremmin, tilalla kasvatetaan vaativampia kasveja, ja että he ovat kerryttäneet enemmän omaisuutta kuin investointi-köyhyyden rajan alla elävät perheet. Tässä tutkimuksessa kyseenalaistettiin yleinen oletus, että omaisuudesta olisi poikkeuksetta hyötyä viljelijäperheelle. Niinpä omaisuuden vaikutusta perheiden hyvinvointiin tutkittiin selvittämällä, mitä reittejä pitkin perheiden omistama maa, karja, koulutus ja työikäiset perheenjäsenet voisivat lisätä perheen hyvinvointia. Näiden hyvinvointi-mekanismien ajateltiin myös riippuvan monista väliin tulevista tekijöistä. Esimerkiksi koulutus voisi lisätä hyvinvointia, jos sen avulla saataisiin paremmin palkattuja töitä tai perustettaisiin yritys; mutta näihin mekanismeihin saattaa vaikuttaa vaikkapa etäisyys kaupungeista tai se, omistaako perhe ajoneuvon. Köyhimpien perheiden parissa nimenomaan koulutus olikin ainoa tutkittu omaisuuden muoto, joka edisti perheen hyvinvointia, kun taas maasta, karjasta tai työvoimasta ei ollut apua köyhyydestä nousemiseen. Varakkaampien perheiden parissa sen sijaan korkeampaa hyvinvointia tuottivat koulutuksen lisäksi myös maa ja työvoima, joskin monesta väliin tulevasta muuttujasta, kuten tuotantopanoksista riippuen. Ei siis ole automaatiota, jolla omaisuus parantaisi perheiden hyvinvointia. Vaikka rikkailla onkin yleensä enemmän karjaa kuin köyhemmillä, ei tässä aineistossa löydetty yhtään mekanismia, jota kautta karjan määrä tuottaisi korkeampaa hyvinvointia viljelijäperheille. Omaisuuden keräämisen ja hyödyntämisen strategiat myös muuttuvat hyvinvoinnin kasvaessa ja niihin vaikuttavat monet ulkoiset tekijät. Ympäristön ja köyhyyden suhde on siis edelleen epäselvä. Köyhyyden voittaminen vaatii pitkällä tähtäimellä sitä, että viljelijäperheet nousisivat investointiköyhyyden rajan yläpuolelle. Näin heillä olisi varaa alkaa kartuttaa omaisuutta ja investoida kestävämpään maankäyttöön. Tällä hetkellä kuitenkin isolle osalle herreralaisia perheitä tuo raja on kaukana tavoittamattomissa. Miten päästä yli tuhannen dollarin kulutukseen perheenjäsentä kohden, mikäli elintaso ei yllä edes riittävään ravitsemukseen? Ja sittenkin, vaikka hyvinvointi kohenisi, ei ympäristön kannalta parannuksia ole välttämättä odotettavissa, mikäli karjalaumat kasvavat ja eroosioalttiit laitumet leviävät.

Stretching single DNA-molecules with temperature-stabilized optical tweezers

This thesis consists of two parts; in the first part we performed a single-molecule force extension measurement with 10kb long DNA-molecules from phage-λ to validate the calibration and single-molecule capability of our optical tweezers instrument. Fitting the worm-like chain interpolation formula to the data revealed that ca. 71% of the DNA tethers featured a contour length within ±15% of the expected value (3.38 µm). Only 25% of the found DNA had a persistence length between 30 and 60 nm. The correct value should be within 40 to 60 nm. In the second part we designed and built a precise temperature controller to remove thermal fluctuations that cause drifting of the optical trap. The controller uses feed-forward and PID (proportional-integral-derivative) feedback to achieve 1.58 mK precision and 0.3 K absolute accuracy. During a 5 min test run it reduced drifting of the trap from 1.4 nm/min in open-loop to 0.6 nm/min in closed-loop.

Bayesian Inference for Retrospective Population Genetics Models Using Markov Chain Monte Carlo Methods

Genetics, the science of heredity and variation in living organisms, has a central role in medicine, in breeding crops and livestock, and in studying fundamental topics of biological sciences such as evolution and cell functioning. Currently the field of genetics is under a rapid development because of the recent advances in technologies by which molecular data can be obtained from living organisms. In order that most information from such data can be extracted, the analyses need to be carried out using statistical models that are tailored to take account of the particular genetic processes. In this thesis we formulate and analyze Bayesian models for genetic marker data of contemporary individuals. The major focus is on the modeling of the unobserved recent ancestry of the sampled individuals (say, for tens of generations or so), which is carried out by using explicit probabilistic reconstructions of the pedigree structures accompanied by the gene flows at the marker loci. For such a recent history, the recombination process is the major genetic force that shapes the genomes of the individuals, and it is included in the model by assuming that the recombination fractions between the adjacent markers are known. The posterior distribution of the unobserved history of the individuals is studied conditionally on the observed marker data by using a Markov chain Monte Carlo algorithm (MCMC). The example analyses consider estimation of the population structure, relatedness structure (both at the level of whole genomes as well as at each marker separately), and haplotype configurations. For situations where the pedigree structure is partially known, an algorithm to create an initial state for the MCMC algorithm is given. Furthermore, the thesis includes an extension of the model for the recent genetic history to situations where also a quantitative phenotype has been measured from the contemporary individuals. In that case the goal is to identify positions on the genome that affect the observed phenotypic values. This task is carried out within the Bayesian framework, where the number and the relative effects of the quantitative trait loci are treated as random variables whose posterior distribution is studied conditionally on the observed genetic and phenotypic data. In addition, the thesis contains an extension of a widely-used haplotyping method, the PHASE algorithm, to settings where genetic material from several individuals has been pooled together, and the allele frequencies of each pool are determined in a single genotyping.

Homogeneous model theory of metric structures

This thesis studies homogeneous classes of complete metric spaces. Over the past few decades model theory has been extended to cover a variety of nonelementary frameworks. Shelah introduced the abstact elementary classes (AEC) in the 1980s as a common framework for the study of nonelementary classes. Another direction of extension has been the development of model theory for metric structures. This thesis takes a step in the direction of combining these two by introducing an AEC-like setting for studying metric structures. To find balance between generality and the possibility to develop stability theoretic tools, we work in a homogeneous context, thus extending the usual compact approach. The homogeneous context enables the application of stability theoretic tools developed in discrete homogeneous model theory. Using these we prove categoricity transfer theorems for homogeneous metric structures with respect to isometric isomorphisms. We also show how generalized isomorphisms can be added to the class, giving a model theoretic approach to, e.g., Banach space isomorphisms or operator approximations. The novelty is the built-in treatment of these generalized isomorphisms making, e.g., stability up to perturbation the natural stability notion. With respect to these generalized isomorphisms we develop a notion of independence. It behaves well already for structures which are omega-stable up to perturbation and coincides with the one from classical homogeneous model theory over saturated enough models. We also introduce a notion of isolation and prove dominance for it.

On the Geometry of Infinite-Dimensional Grassmannian Manifolds and Gauge Theory

This PhD Thesis is about certain infinite-dimensional Grassmannian manifolds that arise naturally in geometry, representation theory and mathematical physics. From the physics point of view one encounters these infinite-dimensional manifolds when trying to understand the second quantization of fermions. The many particle Hilbert space of the second quantized fermions is called the fermionic Fock space. A typical element of the fermionic Fock space can be thought to be a linear combination of the configurations m particles and n anti-particles . Geometrically the fermionic Fock space can be constructed as holomorphic sections of a certain (dual)determinant line bundle lying over the so called restricted Grassmannian manifold, which is a typical example of an infinite-dimensional Grassmannian manifold one encounters in QFT. The construction should be compared with its well-known finite-dimensional analogue, where one realizes an exterior power of a finite-dimensional vector space as the space of holomorphic sections of a determinant line bundle lying over a finite-dimensional Grassmannian manifold. The connection with infinite-dimensional representation theory stems from the fact that the restricted Grassmannian manifold is an infinite-dimensional homogeneous (Kähler) manifold, i.e. it is of the form G/H where G is a certain infinite-dimensional Lie group and H its subgroup. A central extension of G acts on the total space of the dual determinant line bundle and also on the space its holomorphic sections; thus G admits a (projective) representation on the fermionic Fock space. This construction also induces the so called basic representation for loop groups (of compact groups), which in turn are vitally important in string theory / conformal field theory. The Thesis consists of three chapters: the first chapter is an introduction to the backround material and the other two chapters are individually written research articles. The first article deals in a new way with the well-known question in Yang-Mills theory, when can one lift the action of the gauge transformation group on the space of connection one forms to the total space of the Fock bundle in a compatible way with the second quantized Dirac operator. In general there is an obstruction to this (called the Mickelsson-Faddeev anomaly) and various geometric interpretations for this anomaly, using such things as group extensions and bundle gerbes, have been given earlier. In this work we give a new geometric interpretation for the Faddeev-Mickelsson anomaly in terms of differentiable gerbes (certain sheaves of categories) and central extensions of Lie groupoids. The second research article deals with the question how to define a Dirac-like operator on the restricted Grassmannian manifold, which is an infinite-dimensional space and hence not in the landscape of standard Dirac operator theory. The construction relies heavily on infinite-dimensional representation theory and one of the most technically demanding challenges is to be able to introduce proper normal orderings for certain infinite sums of operators in such a way that all divergences will disappear and the infinite sum will make sense as a well-defined operator acting on a suitable Hilbert space of spinors. This research article was motivated by a more extensive ongoing project to construct twisted K-theory classes in Yang-Mills theory via a Dirac-like operator on the restricted Grassmannian manifold.

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.

Using Mathematical Morphology for Geometric Music Retrieval

The usual task in music information retrieval (MIR) is to find occurrences of a monophonic query pattern within a music database, which can contain both monophonic and polyphonic content. The so-called query-by-humming systems are a famous instance of content-based MIR. In such a system, the user's hummed query is converted into symbolic form to perform search operations in a similarly encoded database. The symbolic representation (e.g., textual, MIDI or vector data) is typically a quantized and simplified version of the sampled audio data, yielding to faster search algorithms and space requirements that can be met in real-life situations. In this thesis, we investigate geometric approaches to MIR. We first study some musicological properties often needed in MIR algorithms, and then give a literature review on traditional (e.g., string-matching-based) MIR algorithms and novel techniques based on geometry. We also introduce some concepts from digital image processing, namely the mathematical morphology, which we will use to develop and implement four algorithms for geometric music retrieval. The symbolic representation in the case of our algorithms is a binary 2-D image. We use various morphological pre- and post-processing operations on the query and the database images to perform template matching / pattern recognition for the images. The algorithms are basically extensions to classic image correlation and hit-or-miss transformation techniques used widely in template matching applications. They aim to be a future extension to the retrieval engine of C-BRAHMS, which is a research project of the Department of Computer Science at University of Helsinki.

Spirituality of Finnish peacekeepers

The previous academic research on Finnish peacekeeping has clarified the operative and historical aspects of Finnish peacekeeping lacking the view of an individual who does the actual peacekeeping work. This research is based on the underlying theoretical assumption of human beings possessing different kinds of talents and intelligences creating a holistic entity. In this broad perspective spirituality was explored as an umbrella concept, as a holistic ability or talent, that can be explored as the deepest aspect of defining what it means to be human. The theoretical framework incorporated the concept of an intelligence, which is defined in Gardner's theory of multiple intelligences as the ability to solve problems, or to create products, that are valued within one or more cultural settings (Gardner, 1993, x). The viability of this theory was studied in the sample of Finnish peacekeepers. Spirituality in the theoretical and conceptual horizon was viewed as an extension of Gardner's theory of intelligences as one potential Gardnerian intelligence candidate. In addition to Gardner's theory, spirituality was explored as sensitivity which includes capacities such as sensing awareness, sensing mystery and sensing value (Hay, 1998). Also the practical aspects of spirituality were taken in account as shown in our everyday lives giving us the direction and influencing our social responsibilities and concerns (Bradford, 1995). Spirituality was explored also involving the element of the peacekeepers' community, the element of personal moral orientations and in the domain of religion and coping. The purpose of this research aimed in two dimensions. First, the aim was to outline the intelligence profile and the spiritual sensitivity profile of peacekeepers. Second, the aim was to understand qualitatively the nature of peacekeepers' spirituality The research interests were studied with different kinds of peacekeepers. Applying the mixed methods approach the research was conducted in two phases: first the former SFOR peacekeepers (N=6) were interviewed and the data was analysed. Inspired by the primary findings of these interviews, the data for the case-study of one peacekeeper was collected in co-operation with one former SFOR peacekeeper (N=1). In the second phase the data was collected from KFOR peacekeepers through the quantitative MI-Survey and the spiritual sensitivity survey (N=195). The quantitative method was used to outline the intelligence profile and the spiritual sensitivity profile of peacekeepers (N=195). In the mixed methods approach this method highlighted the general overview of intelligence traits and spiritual sensitivity of peacekeepers. In the mixed methods approach the qualitative method including interviews (N=6) and a case-study of one peacekeeper (N=1) increased subjective, qualitative information of spirituality of peacekeepers. The intelligence profile of peacekeepers highlighted the bodily-kinesthetic and interpersonal dimensions as the practical and social aspects of peacekeepers. Strong inter-item dependencies in the intrapersonal intelligence profile meant that peacekeepers possess a self-reflection and self-knowledge component and they reflect on deep psychological and philosophical issues. Regarding the spiritual sensitivity, peacekeepers found awareness-sensing, mystery-sensing, value-sensing and community-sensing important. The community-sensing emphasised a strong will to advance peace and to help people who are in need: things that are close to the heart of the peacekeepers. These results depicted practicality, being socially capable, and reflecting one's inner world as essential to peacekeepers. Moreover, spirituality as peacekeepers' moral endeavour became clearer because the sub-model of their community-sensing described morally charged destinations: advancing peace and helping people in need. In the qualitative findings peacekeepers articulated justice orientation and rule-following characterising the nature of peacekeepers' moral attitude and moral call (Kohlberg, 1969). An ethic of care (Gilligan, 1982) describes mainly female moral orientation, but the findings revealed that an ethic of care is also an important agent supporting strongly male peacekeepers in their aim to carry out qualitatively good peacekeeping work. The moral endeavour was voiced, when the role of religion in coping meant the assessment of the a way of life, a way of conduct, a way of being truthful to one's own values in confusing surroundings. The practical level of spiritual and religious contemplation was voiced as morally charged inner motivation to fulfil one's duties and at the same time to cope with various peacekeeping challenges. The results of different data sets were combined and interpreted as the moral endeavour, which characterises peacekeepers' spirituality. As the combining result, the perspective of peacekeepers' spirituality is considered moral or at least morally charged.

Bending the Rules of Cell Protrusions : Molecular Mechanisms and Biological Roles of Inverse-BAR Proteins in Cell Morphogenesis

Plasma membrane adopts myriad of different shapes to carry out essential cellular processes such as nutrient uptake, immunological defence mechanisms and cell migration. Therefore, the details how different plasma membrane structures are made and remodelled are of the upmost importance. Bending of plasma membrane into different shapes requires substantial amount of force, which can be provided by the actin cytoskeleton, however, the molecules that regulate the interplay between the actin cytoskeleton and plasma membrane have remained elusive. Recent findings have placed new types of effectors at sites of plasma membrane remodelling, including BAR proteins, which can directly bind and deform plasma membrane into different shapes. In addition to their membrane-bending abilities, BAR proteins also harbor protein domains that intimately link them to the actin cytoskeleton. The ancient BAR domain fold has evolved into at least three structurally and functionally different sub-groups: the BAR, F-BAR and I-BAR domains. This thesis work describes the discovery and functional characterization of the Inverse-BAR domains (I-BARs). Using synthetic model membranes, we have shown that I-BAR domains bind and deform membranes into tubular structures through a binding-surface composed of positively charged amino acids. Importantly, the membrane-binding surface of I-BAR domains displays an inverse geometry to that of the BAR and F-BAR domains, and these structural differences explain why I-BAR domains induce cell protrusions whereas BAR and most F-BAR domains induce cell invaginations. In addition, our results indicate that the binding of I-BAR domains to membranes can alter the spatial organization of phosphoinositides within membranes. Intriguingly, we also found that some I-BAR domains can insert helical motifs into the membrane bilayer, which has important consequences for their membrane binding/bending functions. In mammals there are five I-BAR domain containing proteins. Cell biological studies on ABBA revealed that it is highly expressed in radial glial cells during the development of the central nervous system and plays an important role in the extension process of radial glia-like C6R cells by regulating lamellipodial dynamics through its I-BAR domain. To reveal the role of these proteins in the context of animals, we analyzed MIM knockout mice and found that MIM is required for proper renal functions in adult mice. MIM deficient mice displayed a severe urine concentration defect due to defective intercellular junctions of the kidney epithelia. Consistently, MIM localized to adherens junctions in cultured kidney epithelial cells, where it promoted actin assembly through its I-BAR andWH2 domains. In summary, this thesis describes the mechanism how I-BAR proteins deform membranes and provides information about the biological role of these proteins, which to our knowledge are the first proteins that have been shown to directly deform plasma membrane to make cell protrusions.

Folding and Selective Exit of Reporter Proteins from the Yeast Endoplasmic Reticulum

The present study analyses the traffic of Hsp150 fusion proteins through the endoplasmic reticulum (ER) of yeast cells, from their post-translational translocation and folding to their exit from the ER via a selective COPI-independent pathway. The reporter proteins used in the present work are: Hsp150p, an O-glycosylated natural secretory protein of Saccharomyces cerevisiae, as well as fusion proteins consisting of a fragment of Hsp150 that facilitates in the yeast ER proper folding of heterologous proteins fused to it. It is thought that newly synthesized polypeptides are kept in an unfolded form by cytosolic chaperones to facilitate the post-translational translocation across the ER membrane. However, beta-lactamase, fused to the Hsp150 fragment, folds in the cytosol into bioactive conformation. Irreversible binding of benzylpenicillin locked beta-lactamase into a globular conformation, and prevented the translocation of the fusion protein. This indicates that under normal conditions the beta-lactamase portion unfolds for translocation. Cytosolic machinery must be responsible for the unfolding. The unfolding is a prerequisite for translocation through the Sec61 channel into the lumen of the ER, where the polypeptide is again folded into a bioactive and secretion-competent conformation. Lhs1p is a member of the Hsp70 family, which functions in the conformational repair of misfolded proteins in the yeast ER. It contains Hsp70 motifs, thus it has been thought to be an ATPase, like other Hsp70 members. In order to understand its activity, authentic Lhs1p and its recombinant forms expressed in E. coli, were purified. However, no ATPase activity of Lhs1p could be detected. Nor could physical interaction between Lhs1p and activators of the ER Hsp70 chaperone Kar2p, such as the J-domain proteins Sec63p, Scj1p, and Jem1p and the nucleotide exchange factor Sil1p, be demonstrated. The domain structure of Lhs1p was modelled, and found to consist of an ATPase-like domain, a domain resembling the peptide-binding domain (PBD) of Hsp70 proteins, and a C-terminal extension. Crosslinking experiments showed that Lhs1p and Kar2p interact. The interacting domains were the C-terminal extension of Lhs1p and the ATPase domain of Kar2p, and this interaction was independent of ATPase activity of Kar2p. A model is presented where the C-terminal part of Lhs1p forms a Bag-like 3 helices bundle that might serve in the nucleotide exchange function for Kar2p in translocation and folding of secretory proteins in the ER. Exit of secretory proteins in COPII-coated vesicles is believed to be dependent of retrograde transport from the Golgi to the ER in COPI-coated vesicles. It is thought that receptors escaping to the Golgi must be recycled back to the ER exit sites to recruit cargo proteins. We found that Hsp150 leaves the ER even in the absence of functional COPI-traffic from the Golgi to the ER. Thus, an alternative, COPI-independent ER exit pathway must exists, and Hsp150 is recruited to this route. The region containing the signature guiding Hsp150 to this alternative pathway was mapped.

Spatial ecology of an oak-associated herbivore community : A metacommunity of herbivores

Habitat fragmentation is currently affecting many species throughout the world. As a consequence, an increasing number of species are structured as metapopulations, i.e. as local populations connected by dispersal. While excellent studies of metapopulations have accumulated over the past 20 years, the focus has recently shifted from single species to studies of multiple species. This has created the concept of metacommunities, where local communities are connected by the dispersal of one or several of their member species. To understand this higher level of organisation, we need to address not only the properties of single species, but also establish the importance of interspecific interactions. However, studies of metacommunities are so far heavily biased towards laboratory-based systems, and empirical data from natural systems are urgently needed. My thesis focuses on a metacommunity of insect herbivores on the pedunculate oak Quercus robur a tree species known for its high diversity of host-specific insects. Taking advantage of the amenability of this system to both observational and experimental studies, I quantify and compare the importance of local and regional factors in structuring herbivore communities. Most importantly, I contrast the impact of direct and indirect competition, host plant genotype and local adaptation (i.e. local factors) to that of regional processes (as reflected by the spatial context of the local community). As a key approach, I use general theory to generate testable hypotheses, controlled experiments to establish causal relations, and observational data to validate the role played by the pinpointed processes in nature. As the central outcome of my thesis, I am able to relegate local forces to a secondary role in structuring oak-based insect communities. While controlled experiments show that direct competition does occur among both conspecifics and heterospecifics, that indirect interactions can be mediated by both the host plant and the parasitoids, and that host plant genotype may affect local adaptation, the size of these effects is much smaller than that of spatial context. Hence, I conclude that dispersal between habitat patches plays a prime role in structuring the insect community, and that the distribution and abundance of the target species can only be understood in a spatial framework. By extension, I suggest that the majority of herbivore communities are dependent on the spatial structure of their landscape and urge fellow ecologists working on other herbivore systems to either support or refute my generalization.

Phylogenetics, taxon delimitation and phylogenetic diversity

Throughout the history of Linnean taxonomy, species have been described with varying degrees of justification. Many descriptions have been based on only a few ambiguous morphological characters. Moreover, species have been considered natural, well-defined units whereas higher taxa have been treated as disparate, non-existent creations. In the present thesis a few such cases were studied in detail. Often the species-level descriptions were based on only a few specimens and the variation previously thought to be interspecific was found to be intraspecific. In some cases morphological characters were sufficient to resolve the evolutionary relationships between the taxa, but generally more resolution was gained by the addition of molecular evidence. However, both morphological and molecular data were found to be deceptive in some cases. The DNA sequences of morphologically similar specimens were found to differ distinctly in some cases, whereas in other closely related species the morphology of specimens with identical DNA sequences differed substantially. This study counsels caution when evolutionary relationships are being studied utilizing only one source of evidence or a very limited number of characters (e.g. barcoding). Moreover, it emphasizes the importance of high quality data as well as the utilization of proper methods when making scientific inferences. Properly conducted analyses produce robust results that can be utilized in numerous interesting ways. The present thesis considered two such extensions of systematics. A novel hypothesis on the origin of bioluminescence in Elateriformia beetles is presented, tying it to the development of the clicking mechanism in the ancestors of these animals. An entirely different type of extension of systematics is the proposed high value of the white sand forests in maintaining the diversity of beetles in the Peruvian Amazon. White sand forests are under growing pressure from human activities that lead to deforestation. They were found to harbor an extremely diverse beetle fauna and many taxa were specialists living only in this unique habitat. In comparison to the predominant clay soil forests, considerably more elateroid beetles belonging to all studied taxonomic levels (species, genus, tribus, and subfamily) were collected in white sand forests. This evolutionary diversity is hypothesized to be due to a combination of factors: (1) the forest structure, which favors the fungus-plant interactions important for the elateroid beetles, (2) the old age of the forest type favoring survival of many evolutionary lineages and (3) the widespread distribution and fragmentation of the forests in the Miocene, favoring speciation.

Primary Dislocation of the Patella : A Clinical Study

A total of 177 patients with primary dislocation of the patella (PDP) were admitted to two trauma centers in Helsinki, Finland during 1991 to 1992. The inclusion criteria were: 1. Acute (≤14 days old) first-time lateral dislocation of the patella. 2. No previous knee operations or major knee injuries. 3. No ligament injuries to be repaired. 4. No osteochondral fractures requiring fixation. 50 patients were excluded. 30 of these excluded patients would have met the inclusion criteria, 19 patients received treatment by consultants not involved in the study, 7 refused to participate and 4 had an erroneous randomization. 127 patients including, 82 females, were then randomized to have either tailor-made operative procedure (group O) or conservative treatment (group C). The aftercare was similar for both groups. The mean age of the patients was 20 (9-47) years. All patients were subjected to analysis of trauma history (starting position and knee movement during the dislocation), examination under anesthesia (EUA) and arthroscopy. 70 patients (52 females) were randomized by their odd year of birth to operative group O and 57 patients (30 females) by their even year of birth to conservative group C. The diagnosis of PDP was based on locked dislocation in 68 patients, on dislocatability in EUA in 47 patients, and on subluxation in EUA combined with typical intra-articular lesions in 12 patients. In group O, 63 patients had exploration of the injuries on the medial side of the knee and tailor made reconstruction added with lateral release in 54 cases. The medial injury was operated by suturing in 39 patients, by duplication in 18 patients and by additional augmentation of the medial patellofemoral ligament (MPFL) with adductor magnus tenodesis in 6 patients. 7 patients, without locking in trauma history and only subluxation in EUA had only lateral release for realignment. In adductor magnus tenodesis the proximal end of the distal tendinous part was rerouted to the upper medial border of the patella. In the conservative group C, the treatment was adjusted to the extent of patellar displacement in EUA. Patients with dislocation in EUA had 3 weeks’ immobilization with the knee in slight flexion. Mobilization was started with a soft patellar stabilizing orthosis (PSO) used for additional three weeks. The patients with subluxation in EUA wore an orthosis for six weeks. The aftercare was similar in group O. The outcome was similar in both groups. After an average of 25 (20-45) months´ follow-up, the subjective result was better in group C in respect of the mean Hughston VAS knee score (87 for group O and 90 for group C, p=0.04, visual analog scale), but similar in terms of the patient’s own overall opinion and the mean Lysholm II knee score. Recurrent instability episodes occurred in 18 patients in group O and in 20 patients in group C. After an average of 7 (6-9) years´ follow-up, the groups did not show statistical difference either in respect of the patient’s own overall opinion, or the mean Hughston VAS and Kujala knee scores. The proportions of stable patellae was 25/70 (36%) in group O and 17/57 (30%) in group O (p=0.5). In a multivariate risk analysis, there was a correlation between low Kujala score (<90) as dependent parameter and female gender (OR: 3.5; 95% CI: 1.4-9.0), and loose body on primary radiographs (OR: 4.1; 95% CI: 1.2-15). Recurrent instability correlated with young age at the time of PDP (OR: 0.9; 95% CI: 0.8-1.0/year). Girls with open tibial apophysis had the worst prognosis for instability (88%; 95% CI: 77-98). The most common mechanisms in trauma history of the patients were movement to flexion from a straight start (78%) and movement to extension from a well-bent start (8%). Spontaneous relocation of the patella had taken place in 13/39 of girls, in 11/21 of boys, in 26/42 of women and in 17/24 of men with skeletal maturity of the tibia. The dislocation in EUA was non-rotating in 96/126 patients followed by outward rotating dislocation in 14/126 patients. Operative treatment policy in PDP is not recommended. Locking tendency of the patella in PDP depended on the skeletal maturation. Recurrence rate after PDP was higher than expected.

Long-term results of obstetric brachial plexus surgery

Background: Brachial plexus birth palsy (BPBP) most often occurs as a result of foetal-maternal disproportion. The C5 and C6 nerve roots of the brachial plexus are most frequently affected. In contrast, roots from the C7 to Th1 that result in total injury together with C5 and C6 injury, are affected in fewer than half of the patients. BPBP was first described by Smellie in 1764. Erb published his classical description of the injury in 1874 and his name became linked with the paralysis that is associated with upper root injury. Since then, early results of brachial plexus surgery have been reasonably well documented. However, from a clinical point of view not all primary results are maintained and there is also a need for later follow-up results. In addition most of the studies that are published emanate from highly specialized clinics and no nation wide epidemiological reports are available. One of the plexus injuries is the avulsion type, in which the nerve root or roots are ruptured at the neural cord. It has been speculated whether this might cause injury to the whole neural system or whether shoulder asymmetry and upper limb inequality results in postural deformities of the spine. Alternatively, avulsion could manifest as other signs and symptoms of the whole musculoskeletal system. In addition, there is no available information covering activities of daily living after obstetric brachial plexus surgery. Patients and methods: This was a population-based cross-sectional study on all patients who had undergone brachial plexus surgery with at least 5 years of follow-up. An incidence of 3.05/1000 for BPBP was obtained from the registers for this study period. A total of 1706 BPBP patients needing hospital treatment out of 1 717 057 newborns were registered in Finland between 1971 and 1997 inclusive. Of these BPBP patients, 124 (7.3%) underwent brachial plexus surgery at a mean age of 2.8 months (range: 0.4―13.2 months). Surgery was most often performed by direct neuroraphy after neuroma resection (53%). Depending on the phase of the study, 105 to 112 patients (85-90%) participated in a clinical and radiological follow-up assessment. The mean follow up time exceeded 13 years (range: 5.0―31.5 years). Functional status of the upper extremity was evaluated using Mallet, Gilbert and Raimondi scales. Isometric strength of the upper limb, sensation of the hand and stereognosis were evaluated for both the affected and unaffected sides then the differences and their ratios were calculated and recorded. In addition to the upper extremity, assessment of the spine and lower extremities were performed. Activities of daily living (ADL), participation in normal physical activities, and the use of physiotherapy and occupational therapy were recorded in a questionnaire. Results: The unaffected limb functioned as the dominant hand in all, except four patients. The mean length of the affected upper limb was 6 cm (range: 1-13.5 cm) shorter in 106 (95%) patients. Shoulder function was recorded as a mean Mallet score of 3 (range: 2―4) which was moderate. Both elbow function and hand function were good. The mean Gilbert elbow scale value was 3 (range: -1―5) and the mean Raimondi hand scale was 4 (range:1―5). One-third of the patients experienced pain in the affected limb including all those patients (n=9) who had clavicular non-union resulting from surgery. A total of 61 patients (57%) had an active shoulder external rotation of less than 0° and an active elbow extension deficiency was noted in 82 patients (77%) giving a mean of 26° (range: 5°―80°). In all, expect two patients, shoulder external rotation strength at a mean ratio 35% (range: 0―83%) and in all patients elbow flexion strength at a mean ratio of 41% (range: 0―79%) were impaired compared to the unaffected side. According to radiographs, incongruence of the glenohumeral joint was noted in 15 (16%) patients, whereas incongruence of the radiohumeral joint was found in 20 (21%) patients. Fine sensation was normal for 34/49 (69%) patients with C5-6 injury, for 15/31 (48%) with C5-7 and for only 8/25 (32%) of patients with total injury. Loss of protective sensation or absent sensation was noted in some palmar areas of the hand for 12/105 patients (11%). Normal stereognosis was recorded for 88/105 patients (84%). No significant inequalities in leg length were found and the incidence of structural scoliosis (1.7%) did not differ from that of the reference population. Nearly half of the patients (43%) had asynchronous motion of the upper limbs during gait, which was associated with impaired upper limb function. Data obtained from the completed questionnaires indicated that two thirds (63%) of the patients were satisfied with the functional outcome of the affected hand although one third of all patients needed help with ADL. Only a few patients were unable to participate in physical activities such as: bicycling, cross-country skiing or swimming. However, 71% of the patients reported problems related to the affected upper limb, such as muscle weakness and/or joint stiffness during the aforementioned activities. Incongruity of the radiohumeral joints, extent of the injury, avulsion type injury, age less than three months of age at the time of plexus surgery and inexperience of the surgeon was related to poor results as determined by multivariate analyses. Conclusions: Most of the patients had persistent sequelae, especially of shoulder function. Almost all measurements for the total injury group were poorer compared with those of the C5-6 type injury group. Most of the patients had asymmetry of the shoulder region and a shorter affected upper limb, which is a probable reason for having an abnormal gait. However, BPBP did not have an effect on normal growth of the lower extremities or the spine. Although, participation in physical activities was similar to that of the normal population, two-thirds of the patients reported problems. One-third of the patients needed help with ADL. During the period covered by this study, 7.3% BPBP of patients that needed hospital treatment had a brachial plexus operation, which amounts to fewer than 10 operations per year in Finland. It seems that better results of obstetric plexus surgery and more careful follow-up including opportunities for late reconstructive procedures will be expected, if the treatment is solely concentrated on by a few specialised teams.