Functional and cellular analysis of autoimmune regulator (AIRE) protein

Autoimmune diseases are a major health problem. Usually autoimmune disorders are multifactorial and their pathogenesis involves a combination of predisposing variations in the genome and other factors such as environmental triggers. APECED (autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy) is a rare, recessively inherited, autoimmune disease caused by mutations in a single gene. Patients with APECED suffer from several organ-specific autoimmune disorders, often affecting the endocrine glands. The defective gene, AIRE, codes for a transcriptional regulator. The AIRE (autoimmune regulator) protein controls the expression of hundreds of genes, representing a substantial subset of tissue-specific antigens which are presented to developing T cells in the thymus and has proven to be a key molecule in the establishment of immunological tolerance. However, the molecular mechanisms by which AIRE mediates its functions are still largely obscure. The aim of this thesis has been to elucidate the functions of AIRE by studying the molecular interactions it is involved in by utilizing different cultured cell models. A potential molecular mechanism for exceptional, dominant, inheritance of APECED in one family, carrying a glycine 228 to tryptophan (G228W) mutation, was described in this thesis. It was shown that the AIRE polypeptide with G228W mutation has a dominant negative effect by binding the wild type AIRE and inhibiting its transactivation capacity in vitro. The data also emphasizes the importance of homomultimerization of AIRE in vivo. Furthermore, two novel protein families interacting with AIRE were identified. The importin alpha molecules regulate the nuclear import of AIRE by binding to the nuclear localization signal of AIRE, delineated as a classical monopartite signal sequence. The interaction of AIRE with PIAS E3 SUMO ligases, indicates a link to the sumoylation pathway, which plays an important role in the regulation of nuclear architecture. It was shown that AIRE is not a target for SUMO modification but enhances the localization of SUMO1 and PIAS1 proteins to nuclear bodies. Additional support for the suggestion that AIRE would preferably up-regulate genes with tissue-specific expression pattern and down-regulate housekeeping genes was obtained from transactivation studies performed with two models: human insulin and cystatin B promoters. Furthermore, AIRE and PIAS activate the insulin promoter concurrently in a transactivation assay, indicating that their interaction is biologically relevant. Identification of novel interaction partners for AIRE provides us information about the molecular pathways involved in the establishment of immunological tolerance and deepens our understanding of the role played by AIRE not only in APECED but possibly also in several other autoimmune diseases.

Invertebrate predation and trophic cascades in a pelagic food web : The multiple roles of Chaoborus flavicans (Meigen) in a clay-turbid lake

In lake ecosystems, both fish and invertebrate predators have dramatic effects on their prey communities. Fish predation selects large cladocerans while invertebrate predators prefer prey of smaller size. Since invertebrate predators are the preferred food items for fish, their occurrence at high densities is often connected with the absence or low number of fish. It is generally believed that invertebrate predators can play a significant role only if the density of planktivorous fish is low. However, in eutrophic clay-turbid Lake Hiidenvesi (southern Finland), a dense population of predatory Chaoborus flavicans larvae coexists with an abundant fish population. The population covers the stratifying area of the lake and attains a maximum population density of 23000 ind. m-2. This thesis aims to clarify the effects of Chaoborus flavicans on the zooplankton community and the environmental factors facilitating the coexistence of fish and invertebrate predators. In the stratifying area of Lake Hiidenvesi, the seasonal succession of cladocerans was exceptional. The spring biomass peak of cladocerans was missing and the highest biomass occurred in midsummer. In early summer, the consumption rate by chaoborids clearly exceeded the production rate of cladocerans and each year the biomass peak of cladocerans coincided with the minimum chaoborid density. In contrast, consumption by fish was very low and each study year cladocerans attained maximum biomass simultaneously with the highest consumption by smelt (Osmerus eperlanus). The results indicated that Chaoborus flavicans was the main predator of cladocerans in the stratifying area of Lake Hiidenvesi. The clay turbidity strongly contributed to the coexistence of chaoborids and smelt at high densities. Turbidity exceeding 30 NTU combined with light intensity below 0.1 μE m-2 s-1provides an efficient daytime refuge for chaoborids, but turbidity alone is not an adequate refuge unless combined with low light intensity. In the non-stratifying shallow basins of Lake Hiidenvesi, light intensity exceeds this level during summer days at the bottom of the lake, preventing Chaoborus forming a dense population in the shallow parts of the lake. Chaoborus can be successful particularly in deep, clay-turbid lakes where they can remain high in the water column close to their epilimnetic prey. Suspended clay alters the trophic interactions by weakening the link between fish and Chaoborus, which in turn strengthens the effect of Chaoborus predation on crustacean zooplankton. Since food web management largely relies on manipulations of fish stocks and the cascading effects of such actions, the validity of the method in deep clay-turbid lakes may be questioned.

Distribution of non-biting midges (Diptera, Chironomidae) in subarctic lakes of Finnish Lapland applications in lake classification and palaeolimnology

Climate change contributes directly or indirectly to changes in species distributions, and there is very high confidence that recent climate warming is already affecting ecosystems. The Arctic has already experienced the greatest regional warming in recent decades, and the trend is continuing. However, studies on the northern ecosystems are scarce compared to more southerly regions. Better understanding of the past and present environmental change is needed to be able to forecast the future. Multivariate methods were used to explore the distributional patterns of chironomids in 50 shallow (≤ 10m) lakes in relation to 24 variables determined in northern Fennoscandia at the ecotonal area from the boreal forest in the south to the orohemiarctic zone in the north. Highest taxon richness was noted at middle elevations around 400 m a.s.l. Significantly lower values were observed from cold lakes situated in the tundra zone. Lake water alkalinity had the strongest positive correlation with the taxon richness. Many taxa had preference for lakes either on tundra area or forested area. The variation in the chironomid abundance data was best correlated with sediment organic content (LOI), lake water total organic carbon content, pH and air temperature, with LOI being the strongest variable. Three major lake groups were separated on the basis of their chironomid assemblages: (i) small and shallow organic-rich lakes, (ii) large and base-rich lakes, and (iii) cold and clear oligotrophic tundra lakes. Environmental variables best discriminating the lake groups were LOI, taxon richness, and Mg. When repeated, this kind of an approach could be useful and efficient in monitoring the effects of global change on species ranges. Many species of fast spreading insects, including chironomids, show a remarkable ability to track environmental changes. Based on this ability, past environmental conditions have been reconstructed using their chitinous remains in the lake sediment profiles. In order to study the Holocene environmental history of subarctic aquatic systems, and quantitatively reconstruct the past temperatures at or near the treeline, long sediment cores covering the last 10000 years (the Holocene) were collected from three lakes. Lower temperature values than expected based on the presence of pine in the catchment during the mid-Holocene were reconstructed from a lake with great water volume and depth. The lake provided thermal refuge for profundal, cold adapted taxa during the warm period. In a shallow lake, the decrease in the reconstructed temperatures during the late Holocene may reflect the indirect response of the midges to climate change through, e.g., pH change. The results from three lakes indicated that the response of chironomids to climate have been more or less indirect. However, concurrent shifts in assemblages of chironomids and vegetation in two lakes during the Holocene time period indicated that the midges together with the terrestrial vegetation had responded to the same ultimate cause, which most likely was the Holocene climate change. This was also supported by the similarity in the long-term trends in faunal succession for the chironomid assemblages in several lakes in the area. In northern Finnish Lapland the distribution of chironomids were significantly correlated with physical and limnological factors that are most likely to change as a result of future climate change. The indirect and individualistic response of aquatic systems, as reconstructed using the chironomid assemblages, to the climate change in the past suggests that in the future, the lake ecosystems in the north do not respond in one predictable way to the global climate change. Lakes in the north may respond to global climate change in various ways that are dependent on the initial characters of the catchment area and the lake.

Risk factors for open angle glaucoma; a clinical and molecular genetic study

Glaucoma, optic neuropathy with excavation in the optic nerve head and corresponding visual field defect, is one of the leading causes for blindness worldwide. However, visual disability can often be avoided or delayed if the disease is diagnosed at an early stage. Therefore, recognising the risk factors for development and progression of glaucoma may prevent further damage. The purpose of the present study was to evaluate factors associated with visual disability caused by glaucoma and the genetic features of two risk factors, exfoliation syndrome (ES) and a positive family history of glaucoma. The present study material consisted of three study groups 1) deceased glaucoma patients from the Ekenäs practice 2) glaucoma families from the Ekenäs region and 3) population based families with and without exfoliation syndrome from Kökar Island. For the retrospective study, 106 patients with open angle glaucoma (OAG) were identified. At the last visit, 17 patients were visually impaired. Blindness induced by glaucoma was found in one or both eyes in 16 patients and in both eyes in six patients. The cumulative incidence of glaucoma caused blindness for one eye was 6% at 5 years, 9% at 10 years, and 15% at 15 years from initialising the treatment. The factors associated with blindness caused by glaucoma were an advanced stage of glaucoma at diagnosis, fluctuation in intraocular pressure during treatment, the presence of exfoliation syndrome, and poor patient compliance. A cross-sectional population based study performed in 1960-1962 on Kökar Island and the same population was followed until 2002. In total 965 subjects (530 over 50 years) have been examined at least once. The prevalence of exfoliation syndrome (ES) was 18% among subjects older than 50 years. Seventy-five of all 78 ES-positives belonged to the same extended pedigree. According to the segregation and family analysis, exfoliation syndrome seemed to be inherited as an autosomal dominant trait with reduced penetrance. The penetrance was more reduced for males, but the risk for glaucoma was higher in males than in females. To find the gene or genes associated with exfoliation syndrome, a genome wide scan was performed for 64 members (28 ES affected and 36 controls) of the Kökar pedigree. A promising result was found: the highest two-point LOD score of 3.45 (θ=0.04) in chromosome18q12.1-21.33. The presence of mutations in glaucoma genes TIGR/MYOC (myocilin) and OPTN (optineurin) was analysed in eight glaucoma families from the Ekenäs region. An inheritance pattern resembling autosomal dominant mode was detected in all these families. Primary open angle glaucoma or exfoliation glaucoma was found in 35% of 136 family members and 28% were suspected to have glaucoma. No mutations were detected in these families.

Neighborhood Shopkeepers in Contemporary South Korea: Household, Work, and Locality

This is an ethnographic study of the lived worlds of the keepers of small shops in a residential neighborhood in Seoul, South Korea. It outlines, discusses, and analyses the categories and conceptualizations of South Korean capitalism at the level of households, neighborhoods, and Korean society. These cultural categories were investigated through the neighborhood shopkeepers practices of work and reciprocal interaction as well as through the shopkeepers articulations of their lived experience. In South Korea, the keepers of small businesses have continued to be a large occupational category despite of societal and economic changes, occupying approximately one fourth of the population in active work force. In spite of that, these people, their livelihoods and their cultural and social worlds have rarely been in the focus of social science inquiry. The ethnographic field research for this study was conducted during a 14-month period between November 1998 and December 1999 and in three subsequent short visits to Korea and to the research neighborhood. The fieldwork was conducted during the aftermath of the Asian currency crisis, colloquially termed at the time as the IMF crisis, which highlighted the social and cultural circumstances of small businesskeeper in a specific way. The livelihoods of small-scale entrepreneurs became even more precarious than before; self-employment became an involuntary choice for many middle-class salaried employees who were laid off; and the cultural categories and concepts of society and economy South Korean capitalism were articulated more sharply than before. This study begins with an overview of the contemporary setting, the Korean society under the socially and economically painful outcomes of the economic crisis, and continues with an overview of relevant literature. After introducing the research area and the informants, I discuss the Korean notion of neighborhood, which incorporates both the notions of culturally valued Koreanness and deficiency in the sense of modernity and development. This study further analyses the ways in which the businesskeepers appropriate and reproduce the Korean ideas of men s and women s gender roles and spheres of work. As the appropriation of children s labor is conditional to intergenerational family trajectories which aim not to reproduce parents occupational status but to gain entry to salaried occupations via educational credentials, the work of a married couple is the most common organization of work in small businesses, to which the Korean ideas of family and kin continuity are not applied. While the lack of generational businesskeeping succession suggests that the proprietors mainly subscribe to the notions of familial status that emanate from the practices of the white-collar middle class, the cases of certain women shopkeepers show that their proprietorship and the ensuing economic standing in the family prompts and invites inversed interpretations and uses of common cultural notions of gender. After discussing and analyzing the concept of money and the cultural categorization of leisure and work, topics that emerged as very significant in the lived world of the shopkeepers, this study charts and analyses the categories of identification which the shopkeepers employ for their cultural and social locations and identities. Particular attention is paid to the idea of ordinary people (seomin), which shopkeepers are commonly considered to be most representative of, and which also sums up the ambivalence of neighborhood shopkeepers as a social category: they are not committed to familial reproduction and continuity of the business but aspire non-entrepreneurial careers for their children, while they occupy a significant position in the elaborations of culturally valued notions and ideologies defining Koreanness such as warmheartedness and sociability.

How Kings are Made, How Kingship Changes : A Study of Ritual and Ritual Change in Pre-Colonial Owamboland, Namibia

This study discusses the legitimacy basis of political power and its changes in historical African societies. It starts from Luc de Heusch s tenet that political power required a legitimacy basis of a spiritual kind, often formulated as sacred kingship. In ancient and pre-literate societies such kings were held to be responsible for the fertility of man, land and cattle. The king was a paradoxical figure, symbolising society, but standing above it, while simultaneously being its victim by being ritually killed at old age. This was also how Owambo sacred kings were conceived. De Heusch suggested that African kings derived their power over fertility from having been made sacred monsters in the rituals of installation. With the example of Owambo kingship, this study argues that the transgressive and monstrous aspect is only one of several dimension of a king s sacredness and brings out the nurturing and symbolically female aspect, identified but not analysed further by de Heusch. In the Owambo kingly installation a king-elect was made sacred, and part of it was that a link was ritually created to the early owners of the land. Their consent made it possible for the king to promote fertility and to appropriate power emblems needed for ruling. In the kingdom of Ondonga the early owners of the land were the spirits of early Bushman inhabitants and those of an early kingly clan, both neglected in public memory. The sacred dimension of kingship was further augmented when kings manipulated and appropriated rain rituals and initiation rituals, both of which were related to fertility. The study argues that even though there were aspects of the sacred monster in Owambo kingship, its manifestation was, in part, a distortion of the reciprocal aspect of kingship that was expressed in the homage paid to various ancestor spirits. A change in succession practices from ritual regicide to political assassination took place concomitant with the introduction of firearms, and this broke the sacrificial aspect of sacred kingship paving the way for a more predatory form of kingship while the sacred status of the king was retained.

Phytoplankton succession from 1968 to 1990 in the subarctic Lokka reservoir

Tiivistelmä: Kasviplanktonin kehitys vuosina 1968-1990 subarktisessa Lokan tekoaltaassa

Effect of soil preparation of boreal spruce forest on air and soil temperature conditions in forest regeneration areas.

The effect of scarification, ploughing and cross-directional plouhing on temperature conditions in the soil and adjacent air layer have been studied during 11 consecutive growth periods by using an unprepared clear-cut area as a control site. The maximum and minimum temperatures were measured daily in the summer months, and other temperature observations were made at four-hour intervals by means of a Grant measuring instrument. The development of the seedling stand was also followed in order to determine its shading effect on the soil surface. Soil preparation decreased the daily temperature amplitude of the air at the height of 10 cm. The maximum temperatures on sunny days were lower in the tilts of the ploughed and in the humps of the cross-directional ploughed sites compared with the unprepared area. Correspondingly, the night temperatures were higher and so the soil preparation considerably reduced the risk of night frost. In the soil at the depth of 5 cm, soil preparation increased daytime temperatures and reduced night temperatures compared with unprepared area. The maximum increase in monthly mean temperatures was almost 5 °C, and the daily variation in the surface parts of the tilts and humps increased so that excessively high temperatures for the optimal growth of the root system were measured from time to time. The temperature also rose at the depths of 50 and 100 cm. Soil preparation also increased the cumulative temperature sum. The highest sums accumulated during the summer months were recorded at the depth of 5 cm in the humps of cross-directional ploughed area (1127 dd.) and in the tilts of the ploughed area (1106 dd.), while the corresponding figure in the unprepared soil was 718 dd. At the height of 10 cm the highest temperature sum was 1020 dd. in the hump, the corresponding figure in the unprepared area being 925 dd. The incidence of high temperature amplitudes and percentage of high temperatures at the depth of 5 cm decreased most rapidly in the humps of cross-directional ploughed area and in the ploughing tilts towards the end of the measurement period. The decrease was attributed principally to the compressing of tilts, the ground vegetation succession and the growth of seedlings. The mean summer temperature in the unprepared area was lower than in the prepared area and the difference did not diminish during the period studied. The increase in temperature brought about by soil preparation thus lasts at least more than 10 years.

Position and Feed-Rate Control for Contouring Numerical-Control Systems

Numerical control (NC) for contouring operations requires precise control of position and feed rate for approximating the contour by linear moves of the cutter. A control scheme, for generating linear moves with desired slopes for the cutter, is described. This scheme provides for nine successive linear moves, and may be either expanded or implemented in succession, for approximating a contour.

A Genetic Study of Immunoglobulin E and Atopic Disease Based on Families Ascertained through Asthmatic Children

In order to investigate the modes of inheritance of serum immunoglobulin E (IgE) levels and atopic disease, serum IgE levels and data on allergic disease were obtained from 42 families ascertained through asthmatic children visiting an allergy clinic. Although the mean IgE levels were elevated (mean 637 U/ml), the prevalence of atopic disease in this population was surprisingly low. When the data were analyzed using complex segregation analysis, no major locus could be detected. Moreover, the polygenic heritability was unexpectedly small even though the correlation between serum IgE levels and the liability to atopic disease was around 0.4. Given this unusual set of findings, it is postulated that parasitic infections in this population have (in accordance with well-established results of parasitic disease) caused both elevated levels of serum IgE and a decreased prevalence of allergic disease with the possible masking of the various genetic components of serum IgE levels and atopic disease.

Potential and economics of forestry options for carbon sequestration in India

There is a need to understand the carbon (C) sequestration potential of the forestry option and its financial implications for each country.In India the C emissions from deforestation are estimated to be nearly offset by C sequestration in forests under succession and tree plantations. India has nearly succeeded in stabilizing the area under forests and has adequate forest conservation strategies. Biomass demands for softwood, hardwood and firewood are estimated to double or treble by the year 2020. A set of forestry options were developed to meet the projected biomass needs, and keeping in mind the features of land categories available, three scenarios were developed: potential; demand-driven; and programme-driven scenarios. Adoption of the demand-driven scenario, targeted at meeting the projected biomass needs, is estimated to sequester 78 Mt of C annually after accounting for all emissions resulting from clearfelling and end use of biomass. The demand-driven scenario is estimated to offset 50% of national C emission at 1990 level. The cost per t of C sequestered for forestry options is lower than the energy options considered. The annual investment required for implementing the demand-driven scenario is estimated to be US$ 2.1 billion for six years and is shown to be feasible. Among forestry options, the ranking based on investment cost per t of C sequestered from least cost to highest cost is; natural regeneration-agro-forestry-enhanced natural regeneration (< US$ 2.5/t C)-timber-community-softwood forestry (US$ 3.3 to 7.3 per t of C).

Recovery of tropical rainforest avifauna in relation to vegetation succession following shifting cultivation in Mizoram, north-east India

1. Recovery of rainforest bird community structure and composition, in relation to forest succession after slash-and-burn shifting cultivation or jhum was studied in Mizoram, north-east India. Replicate fallow sites abandoned after shifting cultivation 1, 5, 10, 25 and approximate to 100 years ago, were compared with primary evergreen and semi-evergreen forest using transect and quadrat sampling. 2. Vegetation variables such as woody plant species richness, tree density and vertical stratification increased with fallow age in a rapid. nun-linear, asymptotic manner. Principal components analysis of vegetation variables summarized 92.8% of the variation into two axes: PC1 reflecting forest development and woody plant succession (variables such as tree density, woody plant species richness), and PC2 depicting bamboo density, which increased from 1 to 25 years and declined thereafter. 3. Bird species richness, abundance and diversity, increased rapidly and asymptotically during succession paralleling vegetation recovery as shown by positive correlations with fallow age and PC1 scores of sites. Bamboo density reflected by PC2 had a negative effect on bird species richness and abundance. 4. The bird community similarity (Morisita index) of sites with primary forest also increased asymptotically with fallow age indicating sequential species turnover during succession. Bird community similarity of sites with primary forest (or between sites) was positively correlated with both physiognomic and floristic similarities with primary forest (or between sites). 5. The number of bird species in guilds associated with forest development and woody plants (canopy insectivores, frugivores: bark feeders) was correlated with PCI scores of the sites. Species in other guilds (e. g. granivores, understorey insectivores) appeared to dominate during early and mid-succession. 6. The non-linear relationships imply that fallow periods less than a threshold of 25 years for birds, and about 50-75 years for woody plants, are likely to cause substantial community alteration. 7. As 5-10-year rotation periods or jhum cycles prevail in many parts of north-east India. there is a need to protect and conserve tracts of late-successional and primary forest.

Field emission properties of carbon nanotube arrays with defects and impurities

Field emission from carbon nanotubes (CNTs) in the form of arrays or thin films give rise to several strongly correlated process of electromechanical interaction and degradation. Such processes are mainly due to (1) electron-phonon interaction (2) electromechanical force field leading to stretching of CNTs (3) ballistic transport induced thermal spikes, coupled with high dynamic stress, leading to degradation of emission performance at the device scale. Fairly detailed physics based models of CNTs considering the aspects (1) and (2) above have already been developed by these authors, and numerical results indicate good agreement with experimental results. What is missing in such a system level modeling approach is the incorporation of structural defects and vacancies or charge impurities. This is a practical and important problem due to the fact that degradation of field emission performance is indeed observed in experimental I-V curves. What is not clear from these experiments is whether such degradation in the I-V response is due to dynamic reorientation of the CNTs or due to the defects or due to both of these effects combined. Non-equilibrium Green’s function based simulations using a tight-binding Hamiltonian for single CNT segment show up the localization of carrier density at various locations of the CNTs. About 11% decrease in the drive current with steady difference in the drain current in the range of 0.2-0.4V of the gate voltage was reported in literature when negative charge impurity was introduced at various locations of the CNT over a length of ~20nm. In the context of field emission from CNT tips, a simplistic estimate of defects have been introduced by a correction factor in the Fowler-Nordheim formulae. However, a more detailed physics based treatment is required, while at the same time the device-scale simulation is necessary. The novelty of our present approach is the following. We employ a concept of effective stiffness degradation for segments of CNTs, which is due to structural defects, and subsequently, we incorporate the vacancy defects and charge impurity effects in the Green’s function based approach. Field emission induced current-voltage characteristics of a vertically aligned CNT array on a Cu-Cr substrate is then simulated using a detailed nonlinear mechanistic model of CNTs coupled with quantum hydrodynamics. An array of 10 vertically aligned and each 12 m long CNTs is considered for the device scale analysis. Defect regions are introduced randomly over the CNT length. The result shows the decrease in the longitudinal strain due to defects. Contrary to the expected influence of purely mechanical degradation, this result indicates that the charge impurity and hence weaker transport can lead to a different electromechanical force field, which ultimately can reduce the strain. However, there could be significant fluctuation in such strain field due to electron-phonon coupling. The effect of such fluctuations (with defects) is clearly evident in the field emission current history. The average current also decreases significantly due to such defects.

Effect of capillarity and heterogeneity in the numerical modelling of multiphase flow of fluids in unsaturated porous medium

The multiphase flow of fluids in the unsaturated porous medium is considered as a three phase flow of water, NAPL, and air simultaneously in the porous medium. The adaptive solution fully implicit modified sequential method is used for the numerical modelling. The effect of capillarity and heterogeneity effect at the interface between the media is studied and it is observed that the interface criteria has to be taken into account for the correct prediction of NAPL migration especially in heterogeneous media. The modified Newton Raphson method is used for the linearization and Hestines and Steifel Conjugate Gradient method is used as the solver.