Phylogenetics of Myrmica ants and their social parasites

Understanding the overwhelming diversity of life calls for complex organisational schemes. The field of systematics may thus be seen as the cornerstone of evolutionary biology. In the last few decades, systematics has been rejuvenated through the introduction of molecular methods such as DNA barcoding and multi-gene phylogenetic approaches. These methods may shed new light on established taxonomic ideas and problems. For example, the classification of ants has aroused much debate due to reinterpretation of morphological characters or contradictions between molecular data and morphology. Only in the last few years a consensus was reached regarding the phylogeny of ant subfamilies. However, the situation remains deplorable for lower taxonomic ranks such as subfamilies, tribes and genera. This thesis describes the systematics and evolution of the Holarctic ant genus Myrmica and the tribe to which it belongs, Myrmicini. Using barcoding, molecular-phylogenetic data and divergence time estimations, it addresses questions regarding the taxonomy, morphology and biogeography of this group. Furthermore, the interrelationships between socially parasitic Myrmica species and their hosts (other species in the genus) were inferred. The phylogeny suggests that social parasitism evolved several times in Myrmica. Finally, this thesis investigated whether coevolution shaped the phylogeny of socially parasitic Maculinea butterflies that live inside Myrmica colonies. No evidence was found for coevolution.

Dung beetle radiations in Madagascar

Speciation on islands is affected by island size and the range of habitats and resources available and often also by limited interactions with other taxa. An ancestral population may evolve into a large number of species via an adaptive radiation. In Madagascar, most groups of animals and plants have radiated on the island, having arrived via oceanic dispersal during the long isolation of Madagascar. Characteristic features of Malagasy biota are exceptionally high level of endemism, high species richness as well as lack of many higher taxa that are dominant on the African mainland. Malagasy dung beetles are dominated by two tribes, Canthonini and Helictopleurina, with more than 250 endemic species. In this thesis I have reconstructed molecular phylogenies for the two tribes using several gene regions and different phylogenetic methods. Evolution of closely related species and among populations of the same species was examined with haplotype networks. The Malagasy Canthonini consists of three large lineages, while Helictopleurina forms a monophyletic group. The ancestors of each of the four clades colonised Madagascar at different times during Cenozoic. The subsequent radiations differ in terms of the number of extant species (from 37 to more than 100) and the level of ecological differentiation. In addition, Onthophagini (6 species) and Scarabaeini (3) have colonised Madagascar several times, but they have not radiated and the few species have not entered forests where Canthonini and Helictopleurina mostly occur. Among the three Canthonini radiations, speciation appears to have been mostly allopatric in the oldest and the youngest clades, while in the Epactoides clade sister species have diverged in their ecologies but have similar geographical distributions, indicating that speciation may have occurred in regional sympatry. The most likely isolating mechanisms have been rivers and forest refugia during dry and cool geological periods. Most species are generalists feeding on both carrion and dung, and competition among ecologically similar species may prevent their coexistence in the same communities. Some species have evolved to forage in the canopy and a few species have shifted to use cattle dung, a new resource in the open habitats following the introduction of cattle 1500 years ago. The latter shift has allowed species to expand their geographical ranges.

Substrate Selectivity and Molecular Adaptation in the Outer Membrane Proteases of Yersinia pestis and Salmonella enterica

Proteolysis is important in bacterial pathogenesis and colonization of animal and plant hosts. In this work I have investigated the functions of the bacterial outer membrane proteases, omptins, of Yersinia pestis and Salmonella enterica. Y. pestis is a zoonotic pathogen that causes plague and has evolved from gastroenteritis-causing Yersinia pseudotuberculosis about 13 000 years ago. S. enterica causes gastroenteritis and typhoid fever in humans. Omptins are transmembrane β-barrels with ten antiparallel β-strands and five surface-exposed loops. The loops are important in substrate recognition, and variation in the loop sequences leads to different substrate selectivities between omptins, which makes omptins an ideal platform to investigate functional adaptation and to alter their polypeptide substrate preferences. The omptins Pla of Y. pestis and PgtE of S. enterica are 75% identical in their amino acid sequences. Pla is a multifunctional protein with proteolytic and non-proteolytic functions, and it increases bacterial penetration and proliferation in the host. Functions of PgtE increase migration of S. enterica in vivo and bacterial survival in mouse macrophages, thus enhancing bacterial spread within the host. Mammalian plasminogen/fibrinolytic system maintains the balance between coagulation and fibrinolysis and participates in several cellular processes, e.g., cell migration and degradation of extracellular matrix proteins. This system consists of activation cascades, which are strictly controlled by several regulators, such as plasminogen activator inhibitor 1 (PAI-1), α2-antiplasmin (α2AP), and thrombin-activatable fibrinolysis inhibitor (TAFI). This work reveals novel interactions of the omptins of Y. pestis and S. enterica with the regulators of the plasminogen/fibrinolytic system: Pla and PgtE inactivate PAI-1 by cleavage at the reactive site peptide bond, and degrade TAFI, preventing its activation to TAFIa. Structure-function relationship studies with Pla showed that threonine 259 of Pla is crucial in plasminogen activation, as it prevents degradation of the plasmin catalytic domain by the omptin and thus maintains plasmin stability. In this work I constructed chimeric proteins between Pla and Epo of Erwinia pyrifoliae that share 78% sequence identity to find out which amino acids and regions in Pla are important for its functions. Epo is neither a plasminogen activator nor an invasin, but it degrades α2AP and PAI-1. Cumulative substitutions towards Pla sequence turned Epo into a Pla-like protein. In addition to threonine 259, loops 3 and 5 are critical in plasminogen activation by Pla. Turning Epo into an invasin required substitution of 31 residues located at the extracellular side of the Epo protein above the lipid bilayer, and also of the β1-strand in the N-terminal transmembrane region of the protein. These studies give an example of how omptins adapt to novel functions that advantage their host bacteria in different ecological niches.

Population structure and evolution in the ant Plagiolepis pygmaea and its two social parasites Plagiolepis xene and Plagiolepis grassei

Social behaviour affects dispersal of animals and is an important modifier of genetic population structures. The female sex is often philopatric, which maintains coancestry within the breeding groups and promotes cooperative behaviours. This enables also inclusive fitness returns from altruism and explains why some individuals sacrifice personal reproduction for the good of others in social insects such as ants. However, reduced dispersal and population substructuring at the level of colonies may also entail inbreeding, loss of genetic diversity, and vulnerability. In addition, the most vulnerable ants are species that are evolved to parasitize colonies of other ants, and which compromise between abilities to disperse and the efficiency to parasitize the host. On the other hand, certain social organisations of ant colonies may facilitate a species to disperse outside its natural range and become a pest. Altogether, knowledge on genetic structuring of ant populations, as well as the evolution of their life histories can contribute to conservation biology and population management. The aim of this thesis was to investigate population structures and phylogenetic evolution of the ant Plagiolepis pygmaea and its two obligatory, workerless social parasites (inquilines) P. xene and P. grassei with genetic markers and DNA sequence data. The results support the general assumption that populations of inquiline parasites are highly fragmented and genetically vulnerable. Comparison of the two parasites suggests that differences in their relative abundance may follow from their interaction with the host, i.e. how well the species is adapted to reproduce in the host colonies. The results also indicate that the most recent free living ancestor to these two parasite species is their common host. This is considered to provide evidence for the controversial issue of sympatric speciation. Further, given that the level of adaptations to parasitic life history depends on the evolutionary time since the free-living ancestor, the results establish a link between species rarity and its evolutionary age. The populations of the host species P. pygmaea displayed significantly reduced dispersal both among the females (queens) and males, and high levels of inbreeding which may enhance worker altruism. In addition, the queens were found to mate with multiple males. Given the high relatedness between the queens and their mates, this occurs probably for non-genetic reasons, e.g. without benefits associated in genetically more diverse offspring. The results hence caution that the contribution of non-genetic factors to the prevailing mating patterns and genetic population structures should not be underestimated.

Molecular Tuning of Rhodopsins for High Visual Sensitivity in Different Light Environments : Variation in Absorbance Spectrum and Opsin Sequence within and between Species

Visual pigments of different animal species must have evolved at some stage to match the prevailing light environments, since all visual functions depend on their ability to absorb available photons and transduce the event into a reliable neural signal. There is a large literature on correlation between the light environment and spectral sensitivity between different fish species. However, little work has been done on evolutionary adaptation between separated populations within species. More generally, little is known about the rate of evolutionary adaptation to changing spectral environments. The objective of this thesis is to illuminate the constraints under which the evolutionary tuning of visual pigments works as evident in: scope, tempo, available molecular routes, and signal/noise trade-offs. Aquatic environments offer Nature s own laboratories for research on visual pigment properties, as naturally occurring light environments offer an enormous range of variation in both spectral composition and intensity. The present thesis focuses on the visual pigments that serve dim-light vision in two groups of model species, teleost fishes and mysid crustaceans. The geographical emphasis is in the brackish Baltic Sea area with its well-known postglacial isolation history and its aquatic fauna of both marine and fresh-water origin. The absorbance spectrum of the (single) dim-light visual pigment were recorded by microspectrophotometry (MSP) in single rods of 26 fish species and single rhabdoms of 8 opossum shrimp populations of the genus Mysis inhabiting marine, brackish or freshwater environments. Additionally, spectral sensitivity was determined from six Mysis populations by electroretinogram (ERG) recording. The rod opsin gene was sequenced in individuals of four allopatric populations of the sand goby (Pomatoschistus minutus). Rod opsins of two other goby species were investigated as outgroups for comparison. Rod absorbance spectra of the Baltic subspecies or populations of the primarily marine species herring (Clupea harengus membras), sand goby (P. minutus), and flounder (Platichthys flesus) were long-wavelength-shifted compared to their marine populations. The spectral shifts are consistent with adaptation for improved quantum catch (QC) as well as improved signal-to-noise ratio (SNR) of vision in the Baltic light environment. Since the chromophore of the pigment was pure A1 in all cases, this has apparently been achieved by evolutionary tuning of the opsin visual pigment. By contrast, no opsin-based differences were evident between lake and sea populations of species of fresh-water origin, which can tune their pigment by varying chromophore ratios. A more detailed analysis of differences in absorbance spectra and opsin sequence between and within populations was conducted using the sand goby as model species. Four allopatric populations from the Baltic Sea (B), Swedish west coast (S), English Channel (E), and Adriatic Sea (A) were examined. Rod absorbance spectra, characterized by the wavelength of maximum absorbance (λmax), differed between populations and correlated with differences in the spectral light transmission of the respective water bodies. The greatest λmax shift as well as the greatest opsin sequence difference was between the Baltic and the Adriatic populations. The significant within-population variation of the Baltic λmax values (506-511 nm) was analyzed on the level of individuals and was shown to correlate well with opsin sequence substitutions. The sequences of individuals with λmax at shorter wavelengths were identical to that of the Swedish population, whereas those with λmax at longer wavelengths additionally had substitution F261F/Y in the sixth transmembrane helix of the protein. This substitution (Y261) was also present in the Baltic common gobies and is known to redshift spectra. The tuning mechanism of the long-wavelength type Baltic sand gobies is assumed to be the co-expression of F261 and Y261 in all rods to produce ≈ 5 nm redshift. The polymorphism of the Baltic sand goby population possibly indicates ambiguous selection pressures in the Baltic Sea. The visual pigments of all lake populations of the opossum shrimp (Mysis relicta) were red-shifted by 25 nm compared with all Baltic Sea populations. This is calculated to confer a significant advantage in both QC and SNR in many humus-rich lakes with reddish water. Since only A2 chromophore was present, the differences obviously reflect evolutionary tuning of the visual protein, the opsin. The changes have occurred within the ca. 9000 years that the lakes have been isolated from the Sea after the most recent glaciation. At present, it seems that the mechanism explaining the spectral differences between lake and sea populations is not an amino acid substitution at any other conventional tuning site, but the mechanism is yet to be found.

Recovery of Yeast Saccharomyces cerevisiae after Thermal Insult

All organisms have evolved mechanisms to acquire thermotolerance. A moderately high temperature activates heat shock genes and triggers thermotolerance towards otherwise lethal high temperature. The focus of this work is the recovery mechanisms ensuring survival of Saccharomyces cerevisiae yeast cells after thermal insult. Yeast cells, first preconditioned at 37˚C, can survive a short thermal insult at 48-50˚C and are able to refold heat-denatured proteins when allowed to recover at physiological temperature 24˚C. The cytoplasmic chaperone Hsp104 is required for the acquisition of thermotolerance and dissolving protein aggregates in the cytosol with the assistance of disaccharide trehalose. In the present study, Hsp104 and trehalose were shown to be required for conformational repair of heat-denatured secretory proteins in the endoplasmic reticulum. A reporter protein was first accumulated in the lumen of endoplasmic reticulum and heat-denatured by thermal insult, and then failed to be repaired to enzymatically active and secretion-competent conformation in the absence of Hsp104 or trehalose. The efficient transport of a glycoprotein CPY, accumulated in the endoplasmic reticulum, to the vacuole after thermal insult also needed the presence of Hsp104 and trehalose. However, proteins synthesized after thermal insult at physiological temperature were secreted with similar kinetics both in the absence and in the presence of Hsp104 or trehalose, demonstrating that the secretion machinery itself was functional. As both Hsp104 and trehalose are cytosolic, a cross-talk between cytosolic and luminal chaperone machineries across the endoplasmic reticulum membrane appears to take place. Global expression profiles, obtained with the DNA microarray technique, revealed that the gene expression was shut down during thermal insult and the majority of transcripts were destroyed. However, the transcripts of small cytosolic chaperones Hsp12 and Hsp26 survived. The first genes induced during recovery were related to refolding of denatured proteins and resumption of de novo protein synthesis. Transcription factors Spt3p and Med3p appeared to be essential for acquisition of full thermotolerance. The transcription factor Hac1p was found to be subject to delayed up-regulation at mRNA level and this up-regulation was diminished or delayed in the absence of Spt3p or Med3p. Consequently, production of the chaperone BiP/Kar2p, a target gene of Hac1p, was diminished and delayed in Δspt3 and Δmed3 deletion strains. The refolding of heat-denatured secretory protein CPY to a transport-competent conformation was retarded, and a heat-denatured reporter enzyme failed to be effectively reactivated in the cytoplasm of the deletion strains.

Individualized immunosuppression after renal transplantation in childhood

Pediatric renal transplantation (TX) has evolved greatly during the past few decades, and today TX is considered the standard care for children with end-stage renal disease. In Finland, 191 children had received renal transplants by October 2007, and 42% of them have already reached adulthood. Improvements in treatment of end-stage renal disease, surgical techniques, intensive care medicine, and in immunosuppressive therapy have paved the way to the current highly successful outcomes of pediatric transplantation. In children, the transplanted graft should last for decades, and normal growth and development should be guaranteed. These objectives set considerable requirements in optimizing and fine-tuning the post-operative therapy. Careful optimization of immunosuppressive therapy is crucial in protecting the graft against rejection, but also in protecting the patient against adverse effects of the medication. In the present study, the results of a retrospective investigation into individualized dosing of immunosuppresive medication, based on pharmacokinetic profiles, therapeutic drug monitoring, graft function and histology studies, and glucocorticoid biological activity determinations, are reported. Subgroups of a total of 178 patients, who received renal transplants in 1988 2006 were included in the study. The mean age at TX was 6.5 years, and approximately 26% of the patients were <2 years of age. The most common diagnosis leading to renal TX was congenital nephrosis of the Finnish type (NPHS1). Pediatric patients in Finland receive standard triple immunosuppression consisting of cyclosporine A (CsA), methylprednisolone (MP) and azathioprine (AZA) after renal TX. Optimal dosing of these agents is important to prevent rejections and preserve graft function in one hand, and to avoid the potentially serious adverse effects on the other hand. CsA has a narrow therapeutic window and individually variable pharmacokinetics. Therapeutic monitoring of CsA is, therefore, mandatory. Traditionally, CsA monitoring has been based on pre-dose trough levels (C0), but recent pharmacokinetic and clinical studies have revealed that the immunosuppressive effect may be related to diurnal CsA exposure and blood CsA concentration 0-4 hours after dosing. The two-hour post-dose concentration (C2) has proved a reliable surrogate marker of CsA exposure. Individual starting doses of CsA were analyzed in 65 patients. A recommended dose based on a pre-TX pharmacokinetic study was calculated for each patient by the pre-TX protocol. The predicted dose was clearly higher in the youngest children than in the older ones (22.9±10.4 and 10.5±5.1 mg/kg/d in patients <2 and >8 years of age, respectively). The actually administered oral doses of CsA were collected for three weeks after TX and compared to the pharmacokinetically predicted dose. After the TX, dosing of CsA was adjusted according to clinical parameters and blood CsA trough concentration. The pharmacokinetically predicted dose and patient age were the two significant parameters explaining post-TX doses of CsA. Accordingly, young children received significantly higher oral doses of CsA than the older ones. The correlation to the actually administered doses after TX was best in those patients, who had a predicted dose clearly higher or lower (> ±25%) than the average in their age-group. Due to the great individual variation in pharmacokinetics standardized dosing of CsA (based on body mass or surface area) may not be adequate. Pre-Tx profiles are helpful in determining suitable initial CsA doses. CsA monitoring based on trough and C2 concentrations was analyzed in 47 patients, who received renal transplants in 2001 2006. C0, C2 and experienced acute rejections were collected during the post-TX hospitalization, and also three months after TX when the first protocol core biopsy was obtained. The patients who remained rejection free had slightly higher C2 concentrations, especially very early after TX. However, after the first two weeks also the trough level was higher in the rejection-free patients than in those with acute rejections. Three months after TX the trough level was higher in patients with normal histology than in those with rejection changes in the routine biopsy. Monitoring of both the trough level and C2 may thus be warranted to guarantee sufficient peak concentration and baseline immunosuppression on one hand and to avoid over-exposure on the other hand. Controlling of rejection in the early months after transplantation is crucial as it may contribute to the development of long-term allograft nephropathy. Recently, it has become evident that immunoactivation fulfilling the histological criteria of acute rejection is possible in a well functioning graft with no clinical sings or laboratory perturbations. The influence of treatment of subclinical rejection, diagnosed in 3-month protocol biopsy, to graft function and histology 18 months after TX was analyzed in 22 patients and compared to 35 historical control patients. The incidence of subclinical rejection at three months was 43%, and the patients received a standard rejection treatment (a course of increased MP) and/or increased baseline immunosuppression, depending on the severity of rejection and graft function. Glomerular filtration rate (GFR) at 18 months was significantly better in the patients who were screened and treated for subclinical rejection in comparison to the historical patients (86.7±22.5 vs. 67.9±31.9 ml/min/1.73m2, respectively). The improvement was most remarkable in the youngest (<2 years) age group (94.1±11.0 vs. 67.9±26.8 ml/min/1.73m2). Histological findings of chronic allograft nephropathy were also more common in the historical patients in the 18-month protocol biopsy. All pediatric renal TX patients receive MP as a part of the baseline immunosuppression. Although the maintenance dose of MP is very low in the majority of the patients, the well-known steroid-related adverse affects are not uncommon. It has been shown in a previous study in Finnish pediatric TX patients that steroid exposure, measured as area under concentration-time curve (AUC), rather than the dose correlates with the adverse effects. In the present study, MP AUC was measured in sixteen stable maintenance patients, and a correlation with excess weight gain during 12 months after TX as well as with height deficit was found. A novel bioassay measuring the activation of glucocorticoid receptor dependent transcription cascade was also employed to assess the biological effect of MP. Glucocorticoid bioactivity was found to be related to the adverse effects, although the relationship was not as apparent as that with serum MP concentration. The findings in this study support individualized monitoring and adjustment of immunosuppression based on pharmacokinetics, graft function and histology. Pharmacokinetic profiles are helpful in estimating drug exposure and thus identifying the patients who might be at risk for excessive or insufficient immunosuppression. Individualized doses and monitoring of blood concentrations should definitely be employed with CsA, but possibly also with steroids. As an alternative to complete steroid withdrawal, individualized dosing based on drug exposure monitoring might help in avoiding the adverse effects. Early screening and treatment of subclinical immunoactivation is beneficial as it improves the prospects of good long-term graft function.

Pathophysiology of Congenital Nephrotic Syndrome of the Finnish type

Congenital nephrotic syndrome of the Finnish type (NPHS1) is an autosomal recessive disease which is highly enriched in the Finnish population. It is caused by mutations in the NPHS1 gene encoding for nephrin, which is a major component of the glomerular filtration barrier in the kidney. Patients with NPHS1 have heavy proteinuria and nephrotic syndrome (NS) from birth and develop renal fibrosis in early childhood. Renal transplantation (TX) is the only curative treatment for NPHS1. These patients form the largest group of pediatric kidney transplant children in our country. The NPHS1 kidneys are removed in infancy and they serve as an excellent human material for studies of the pathophysiology of proteinuric kidney diseases. Sustained proteinuria is a major factor leading to end-stage renal failure and understanding this process is crucial for nephrology. In this study we investigated the glomerular and tubulointerstitial changes that occur in the NPHS1 kidneys during infancy as well as the expression of nephrin in non-renal tissues. We also studied the pathology and management of recurrent proteinuria in kidney grafts transplanted to NPHS1 children. Severe renal lesions evolved in patients with NPHS1 during the first months of life. Glomerular sclerosis developed through progressive mesangial sclerosis, and capillary obliteration was an early consequence of this process. Shrinkage of the glomerular tuft was common, whereas occlusion of tubular opening or protrusion of the glomerular tuft into subepithelial space or through the Bowman's capsule were not detected. Few inflammatory cells were detected in the mesangial area. The glomerular epithelial cells (podocytes) showed severe ultrastructural changes and hypertrophy. Podocyte proliferation and apoptosis were rare, but moderate amounts of podocytes were detached and ended up in the urine. The results showed that endocapillary lesions not extracapillary lesions, as generally believed were important for the sclerotic process in the NPHS1 glomeruli. In the tubulointerstitium, severe lesions developed in NPHS1 kidneys during infancy. Despite heavy proteinuria, tubular epithelial cells (TECs) did not show transition into myofibroblasts. The most abundant chemokines in NPHS1 tissue were neutrophil activating protein-2 (NAP-2), macrophage inhibiting factor (MIF), and monocyte chemoattractant protein-1 (MCP-1). Interstitial inflammation and fibrosis were first detected in the paraglomerular areas and the most abundant inflammatory cells were monocytes/macrophages. Arteries and arterioles showed intimal hypertrophy, but the pericapillary microvasculature remained quite normal. However, excessive oxidative stress was evident in NPHS1 kidneys. The results indicated that TECs were relatively resistant to the heavy tubular protein load. Nephrin was at first thought to be podocyte specific, but some studies especially in experimental animals have suggested that nephrin might also be expressed in non-renal tissues such as pancreas and central nervous system. The knowledge of nephrin biology is important for the evaluation of nephrin related diseases. In our study, no significant amounts of nephrin protein or mRNA were detected in non-renal tissues of man and pig as studied by immunohistochemistry and in situ hybridization. The phenotype analysis of NPHS1 children, who totally lack nephrin, revealed no marked impairment in the neurological, testicular, or pancreatic function speaking against the idea that nephrin would play an important functional role outside the kidney. The NPHS1 kidneys do not express nephrin and antibodies against this major glomerular filter protein have been observed in NPHS1 children after renal TX most likely as an immune reaction against a novel antigen. These antibodies have been associated with the development of recurrent NS in the kidney graft of NPHS1 patients. In our study, a third of the NPHS1 patients homozygous for Fin-Major mutation developed recurrent NS in the transplanted graft. Re-transplantations were performed to patients who lost their graft due to recurrent NS and heavy proteinuria immediately developed in all cases. While 73% of the patients had detectable serum anti-nephrin antibodies, the kidney biopsy findings were minimal. Introduction of plasma exchange (PE) to the treatment of recurrent nephroses increased the remission rate from 54% to 89%. If remission was achieved, recurrent NS did not significantly deteriorate the long term graft function. In conclusion, the results show that the lack of nephrin in podocyte slit diaphragm in NPHS1 kidneys induces progressive mesangial expansion and glomerular capillary obliteration and inflicts interstitial fibrosis, inflammation, and oxidative stress with surprisingly little involvement of the TECs in this process. Nephrin appears to have no clinical significance outside the kidney. Development of antibodies against nephrin seems to be a major cause of recurrent NS in kidney grafts of NPHS1 patients and combined use of PE and cyclophosphamide markedly improved remission rates.

Si, CdTe and CdZnTe radiation detectors for imaging applications

The structure and operation of CdTe, CdZnTe and Si pixel detectors based on crystalline semiconductors, bump bonding and CMOS technology and developed mainly at Oy Simage Ltd. And Oy Ajat Ltd., Finland for X- and gamma ray imaging are presented. This detector technology evolved from the development of Si strip detectors at the Finnish Research Institute for High Energy Physics (SEFT) which later merged with other physics research units to form the Helsinki Institute of Physics (HIP). General issues of X-ray imaging such as the benefits of the method of direct conversion of X-rays to signal charge in comparison to the indirect method and the pros and cons of photon counting vs. charge integration are discussed. A novel design of Si and CdTe pixel detectors and the analysis of their imaging performance in terms of SNR, MTF, DQE and dynamic range are presented in detail. The analysis shows that directly converting crystalline semiconductor pixel detectors operated in the charge integration mode can be used in X-ray imaging very close to the theoretical performance limits in terms of efficiency and resolution. Examples of the application of the developed imaging technology to dental intra oral and panoramic and to real time X-ray imaging are given. A CdTe photon counting gamma imager is introduced. A physical model to calculate the photo peak efficiency of photon counting CdTe pixel detectors is developed and described in detail. Simulation results indicates that the charge sharing phenomenon due to diffusion of signal charge carriers limits the pixel size of photon counting detectors to about 250 μm. Radiation hardness issues related to gamma and X-ray imaging detectors are discussed.

Measuring the Cosmic Microwave Background : Topics along the analysis pipeline

The first quarter of the 20th century witnessed a rebirth of cosmology, study of our Universe, as a field of scientific research with testable theoretical predictions. The amount of available cosmological data grew slowly from a few galaxy redshift measurements, rotation curves and local light element abundances into the first detection of the cos- mic microwave background (CMB) in 1965. By the turn of the century the amount of data exploded incorporating fields of new, exciting cosmological observables such as lensing, Lyman alpha forests, type Ia supernovae, baryon acoustic oscillations and Sunyaev-Zeldovich regions to name a few. -- CMB, the ubiquitous afterglow of the Big Bang, carries with it a wealth of cosmological information. Unfortunately, that information, delicate intensity variations, turned out hard to extract from the overall temperature. Since the first detection, it took nearly 30 years before first evidence of fluctuations on the microwave background were presented. At present, high precision cosmology is solidly based on precise measurements of the CMB anisotropy making it possible to pinpoint cosmological parameters to one-in-a-hundred level precision. The progress has made it possible to build and test models of the Universe that differ in the way the cosmos evolved some fraction of the first second since the Big Bang. -- This thesis is concerned with the high precision CMB observations. It presents three selected topics along a CMB experiment analysis pipeline. Map-making and residual noise estimation are studied using an approach called destriping. The studied approximate methods are invaluable for the large datasets of any modern CMB experiment and will undoubtedly become even more so when the next generation of experiments reach the operational stage. -- We begin with a brief overview of cosmological observations and describe the general relativistic perturbation theory. Next we discuss the map-making problem of a CMB experiment and the characterization of residual noise present in the maps. In the end, the use of modern cosmological data is presented in the study of an extended cosmological model, the correlated isocurvature fluctuations. Current available data is shown to indicate that future experiments are certainly needed to provide more information on these extra degrees of freedom. Any solid evidence of the isocurvature modes would have a considerable impact due to their power in model selection.

Simulations of dimensionally reduced effective theories of high temperature QCD

Quantum chromodynamics (QCD) is the theory describing interaction between quarks and gluons. At low temperatures, quarks are confined forming hadrons, e.g. protons and neutrons. However, at extremely high temperatures the hadrons break apart and the matter transforms into plasma of individual quarks and gluons. In this theses the quark gluon plasma (QGP) phase of QCD is studied using lattice techniques in the framework of dimensionally reduced effective theories EQCD and MQCD. Two quantities are in particular interest: the pressure (or grand potential) and the quark number susceptibility. At high temperatures the pressure admits a generalised coupling constant expansion, where some coefficients are non-perturbative. We determine the first such contribution of order g^6 by performing lattice simulations in MQCD. This requires high precision lattice calculations, which we perform with different number of colors N_c to obtain N_c-dependence on the coefficient. The quark number susceptibility is studied by performing lattice simulations in EQCD. We measure both flavor singlet (diagonal) and non-singlet (off-diagonal) quark number susceptibilities. The finite chemical potential results are optained using analytic continuation. The diagonal susceptibility approaches the perturbative result above 20T_c$, but below that temperature we observe significant deviations. The results agree well with 4d lattice data down to temperatures 2T_c.

Agoralla : avauksia ympäristöasiantuntijoiden vuorovaikutusprosesseista

Ympäristöasiantuntijoiden vuorovaikutusta on tutkittu agoralla (antiikin tori). Se on julkinen tila, jossa markkinat, politiikka, tiede ja yhteiskunta kohtaavat. Tutkimus kuuluu yhteiskuntatieteellisen ympäristötutkimuksen alaan, mutta siinä hyödynnetään myös tulevaisuudentutkimusta. Työn motivaationa on ollut tekijän monitieteinen koulutustausta: yhteiskuntatieteilijä ja luonnontieteilijä. Miten ja miksi vuorovaikutus eri asiantuntijoiden välillä on haasteellista ja merkityksellistä esimerkiksi metsän biodiversiteetin vähenemisen ehkäisemiseksi. Keskeisiä käsitteitä ovat asiantuntijuus, vuorovaikutus, tiedon luotettavuusja kontekstisidonnaisuus, Väitöskirja koostuu neljästä eri asiantuntijuustarinasta. Ensimmäinen (luku 2) perustuu haastatteluihin suomalaisten ja saksalaisten bio- ja yhteiskuntatietelijöiden käsityksistä luonnosta ja ympäristöstä. Tutkimusongelmana on luonnontieteilijöiden ja yhteiskuntatieteilijöiden Suomessa ja Saksassa ”kulttuurierot” luonnon ja ympäristön käsitteellistämisessä. Johtopäätöksenä on, että aistittu luonto, ympäröivä ympäristö sekä ihmisen muokkaama elinympäristö eivät tunne selkeitä tiede- eikä maanrajoja. Tämä luku toimii ponnahduslautana konstruktioiden taakse vuorovaikutuksen haasteisiin. Kirjan toinen tarina (luku 3) perustuu haastatteluihin suomalaisten metsän biodiversiteettiasiantuntijoiden vuorovaikutuksesta. Tutkimusongelman lähtökohtana on metsän biodiversiteetin väheneminen ja tästä seuraavat polittisetkin vuorovaikutustilanteet. Miten konteksti vaikuttaa eri asiantuntijoiden vuorovaikutukseen ja mitä tästä seuraa? Analyysin päätulos on implisiittisen, vahvasti kontekstisidonnaisen asiantuntijatiedon hyödyntämisen tarve ja voimavara metsän biodiversiteetin vähenemisen ennaltaehkäisemiksi. Kolmas tarina asiantuntijuudesta (luku 4) perustuu Etelä-Suomen metsien suojelutoimikunnassa (Metso) tehtyihin havainnointeihin. Tutkija on näin ollut itse eräänlaisella torilla havainnoijana. Tutkimusongelmana on ”ohipuhuminen”, tiedon luotettavuus ja implisiittien tiedon hyväksyttävyys. Johtopäätöksenä on asiantuntijuuden vahva kontekstisidonnaisuus hetkeen ja paikkaan ja yhteisen kielen (vrt. transdisiplinaarisuus) löytyminen yhteisen tavoitteen saavuttamiseksi. Merkittäviä välineitä vuorovaikutuksen onnistumiseen ovat esimerkiksi yhteinen vahva tavoitetila, interkatio, joka koskee läsnä olevia ihmisiä ei instituutioita sekä fasilitaattorin vahva rooli tulkkina ja välittäjänä. Neljäs tarina (luku 5) vie agoran konkretiaan. Tässä luvussa on kehitetty eläytymiskävely- menetelmää, jossa fasilitaattori (tutkija) johdattaa Espoon keskuksessa hallinnon, politiikan, asukkaiden ja konsultin edustajat aistimaan ja tulkitsemaan alueen sosiaalista tilaa, toiminnallisuutta ja elämyksellisyyttä. Ongelmana on aistimaailman asiantuntemuksen hyödyntämättömyys yhdyskuntasuunnittelun välineenä mm. asiantuntijoiden vuorovaikutuksen välineenä. Menetelmäkehitys on aluillaan, mutta jo tässä tapauksessa käy ilmi, että jaettu tila, jaetut aistikokemukset konkreettisella kävelyllä avaavaat vuorovaikutuksen uusiin ulottuvuuksiin, jossa implisiittiselle asiantuntemukselle annetaan sijansa vuorovaikutuksessa ja tätä kautta voidaan vaikuttaa myös tehtäviin päätöksiin, toimenpiteisiin. Johtopäätöksissä (luku 6) korostuu implisiittisen asiantuntijuuden merkitys. Onnistunut vuorovaikutteinen toiminta eri asiantuntijoiden kesken esimerkiksi erilaisia ympäristöongelmia –ja ilmiöitä ratkottaessa ja pohdittaessa vaatii vuorovaikutusosaamista. Tutkimuksen lopuksi suositellaan esimerkiksi ennakkoluulottomia avauksia agoralla. Asiantuntijuus ei ole yksi ja vain asiaatuntevuus on mahdollista. Agora on jatkuvassa liikkeessä ja juuri siinä piilee voimavara tulevaisuuden haasteisiin erilaisilla rajapinnoilla. Avainsanat: asiantuntijuus, vuorovaikutus, tieto, konteksti, agora

Contesting Forests and Power : Dispute, Violence and Negotiations

"Contesting Forests and Power; Dispute, Violence and Negotiations in Central Java" is an ethnographic analysis of an ongoing forest land dispute and its negotiations in an upland forest village in the district of Wonosobo, Central Java. Rather than focusing only on the village site, this ethnography of global connections explores the inequalities of power in different negotiation arenas and how these power relations have had an effect on the dispute and efforts made to settle it. Today, national and transnational connections have an effect on how land disputes develop. This study argues that different cosmological and cultural orientations influence how the dispute and its negotiations have evolved. It draws its theoretical framework from legal and political anthropology by looking at the position of law in society, exploring state formation processes and issues of power. The dispute over state forest land is about a struggle over sovereignty which involves violence on the parts of different parties who maintain that they have a legitimate right to the state forest land. This anthropological study argues that this dispute and its negotiations reflect the plurality of laws in Java and Indonesia in a complex way. It shows that this dispute over forests and land in Java has deep historical roots that were revealed as the conflict emerged. Understanding land disputes in Java is important because of the enormous potential for conflicts over land and other natural resources throughout Indonesia. After the fall of President Suharto in 1998, disputes over access to state forest land emerged as a problem all over upland Java. As the New Order came to an end, forest cover on state forest lands in the Wonosobo district was largely destroyed. Disputes over access to land and forests took another turn after the decentralization effort in 1999, suggesting that decentralization does not necessarily contribute to the protection of forests. The dispute examined here is not unique, but, rather, this study attempts to shed light on forest-related conflicts all around upland Indonesia and on the ways in which differential power relations are reflected in these conflicts and the negotiation processes meant to resolve them.

Kansallisen konsensuskulttuurin jäljillä : Globalisaatioajan Suomi Helsingin Sanomissa

The dissertation analyzes Finnish consensual culture in public discussion and journalism in Helsingin Sanomat (HS). The consensual Finnish political culture has evolved and persisted over a long period of time and it has been affected by historical circumstances as well as the dynamics of political and journalistic structures and actors. A historical chronology is drawn in the study regarding the nature and development of consensus culture in 20th century Finland. This political culture is traced by looking at public discussion on globalization at the turn of the millennium. Globalization as a concept has been contested and various societal actors have given different meanings to it. This research looks at how the globalization discussion in HS during the years 1992-2004 constructs consensus. Helsingin Sanomat (and its predecessor Päivälehti) has been an important actor in Finnish journalism and the public sphere almost since its founding 120 years ago. The history of the paper is tightly connected to Finland s general political history and history of the public sphere. Moreover, the paper s connections to the societal elite have always been close. The central question in this research was to see how the globalization discussion in HS evolved in relation to consensus as well as legitimate controversies. As a result it is stated that the globalization question has clearly divided the Finnish societal actors. The most powerful societal elites (government, most civil servants, corporate sector) had a profile of being pro globalization. They communicated their globalization strategy as a national, unified way of thinking. Other elites which have been losing their influence (the president, labor union, part of members of parliament), as well as civil society actors tried to bring forward conflicting views in relation to globalization. The paper did give some room to these elements, but on the other hand it also tried to keep up the consensual discussion culture especially in the editorial section. In line with its traditions Helsingin Sanomat strived to create national unity. At the same time it did not give adequate attention to the changes brought about by globalization to the positions and roles of various elites and civil society actors. In this discussion HS seemed more like a medium of the state than as a critical and independent actor. Journalism has an important role in upholding and also reviving the Finnish political culture and public discussion. From this point of view it is problematic if the area of so called legitimate controversy in broad societal questions like globalization becomes very limited. As the Finnish elites are small and there is no considerable competition between them, journalism should actively bring up controversial issues. This task becomes complicated, however, if the elite circles are closed up and no initiatives come from their ranks. Political decision making as well as democracy can suffer, if issues are not brought to the public agenda.

Women and Marital Breakdown in South India : Reconstructing Homes, Bonds and Persons

Women and Marital Breakdown in South India: Reconstructing Homes, Bonds and Persons is an ethnographic analysis of the situation of divorced and separated women and their families in the South Indian city of Bangalore. The study is based on 16 months of anthropological fieldwork, i.e., participant observation and life history interviews among 50 divorced and separated women from different socio-religious backgrounds in their homes, in the women s organisations and in the Family Court. The study follows the divorced and separated women from their natal homes to their affinal homes through homelessness and legal battles to their reconstructed natal, affinal or single homes in order to find out what it means to be a person within hierarchical gender and kinship relations in South India. Marital breakdown impacts on kin relations and discloses the existing gender relations and power structure through its consequences. It makes the transformability of relational personhood as well as the transformability of relational society and culture visible. Although the study reveals the painful history of women s ill-treatment in marriage, family and kinship systems, it also demonstrates the women s rejection of the domination; and shows their ability to re-negotiate and promote changes not only to their own positions but to the whole hierarchical system as well. The study explores the divorced and separated women s manifold dilemmas, complicated legal battles, and endless arrangements when they have to struggle with the very practical problems of supporting themselves financially, finding and making a new home for themselves, and re-arranging relationships with their kin and friends. As marital breakdown fundamentally transforms the women s relational field, it forces them to recreate substitutive relations in a flexible way and, simultaneously, to re-construct themselves and their lives without a ready or positive cultural or behavioural template. This process reveals the agency of the divorced and separated women as well as shedding light on issues of gender and the cultural construction of the person in South India. This topical study explores the previously neglected subject of marital breakdown in India and shows the new meaning of kinship in South India.