Sorocarpy is the aggregation of unicellular organisms to form multicellular fruiting bodies (sorocarps). This thesis is about the two best-known groups of sorocarpic amoebae, Dictyostelids and Acrasids. Paper I describes assembly and analysis of a multigene dataset to identify the root of the dictyostelid tree. Phylogenetic analyses of 213 genes (conserved in all sequenced dictyostelid genomes and an outgroup) place the root between Groups 1+2 and 3+4 (now: Cavenderiaceae + Acytosteliaceae and Raperosteliaceae + Dictyosteliaceae). Resolution of the dictyostelid root made it possible to proceed with a major taxonomic revision of the group. Paper II focuses on the taxonomic revision of Dictyostelia based on molecular phylogeny and SSU ribosomal RNA sequence signatures. The two major divisions were treated at the rank of order as Acytosteliales ord. nov. and Dictyosteliales. The two major clades within each of these orders were given the rank of family. Twelve genera were recognized. This is the first revision of a major protist taxon using molecular signatures and offers guidelines for taxonomic revision of protist groups where morphology is insufficient. Paper III presents the mitochondrial genome (mtDNA) of Acrasis kona. Over a quarter of the genome consists of novel open reading frames, while 16 genes present in the mtDNA of its relative, Naegleria gruberi, are missing. We identified many of these genes in the A. kona nuclear DNA, and used phylogenetic analyses to show that most of these genes arose by transfer from mtDNA. Paper IV presents the nuclear genome of A. kona, the second genome sequence of a free-living excavate. The 44 Mb genome has 15,868 open reading frames of which 4,987 are novel. A surprising number of genes are most similar to homologs in distant relatives, suggesting acquisition by horizontal gene transfer (HGT). Most HGT candidates are expressed and many constitute multi-gene families and/or have acquired introns and membrane targeting sequences. Strong HGT candidates include some genes essential to development and signaling in Dictyostelia. Flagellar motility and meiosis genes are also present and conserved, suggesting cryptic flagellar and sexual stages.

Conjugated polymers have been found useful in a wide range of applications such as sensors, electrochemical transistors, solar cells, and printed electronics due to their mechanical, optical and electronic properties. An amazing research field has grown during the last three decades since the discovery of conducting polymers in 1976. Since the materials can be made from solutions, different processing methods such as spin coating and vapor phase polymerization can be used to coat a huge variety of substrates. The choice of method depends mainly on monomer solubility and kind of substrate to be coated. During the synthesis the polymers can be chemically modified to tailor their functionalities. Due to this variability in materials and the processability, electronics can be achieved on unconventional substrates such as flexible plastic foils and cell culturing dishes. As a contrast to inorganic, usually metallic materials, conducting polymers are built up from organic compounds in a molecular structure with soft mechanical properties that have shown to be a benefit in combination with biology, ranging from interactions with cells to interactions with advanced biological species such as tissues. This combination of research fields and the possible applications are merged within the field of organic bioelectronics. The primary purpose of this thesis is to give a background to organic electronics in general and how electrochemical devices can be processed and developed for biological applications in particular. An organic electronic surface switch is introduced to control cell adhesion and proliferation as well as an electrochemical transistor to spatially tune the cell adhesion along an electrochemical gradient. To mimic a more natural cell environment a three dimensional fiber substrate was used to design an electronically active matrix to promote nerve cell adhesion and communication. By combining standard microfabrication techniques and conjugated polymers desired patterns of electroactive polymer were created to enable active regulation of cell populations and their extracellular environment at high spatial resolution. Finally, a brief look into future challenges will also be presented.

Amyloid diseases are caused by protein misfolding and aggregation. To date there are 27 known proteins causing amyloid disorders involving brain and peripheral protein deposition. The proteins involved in this mechanism do not share sequence homology, but the amyloid fibrils share biophysical properties and possibly a common pathogenic mechanism. Amyloid deposits are known to be involved in a broad range of neurodegenerative diseases, such as Alzheimer’s disease and Creutzfeldt-Jakob disease, as well as in non-neuropathic diseases, such as senile systemic amyloidosis and type II diabetes. During the last decade the fruit fly, Drosophila melanogaster (Drosophila), have increasingly been used as a model for neurodegenerative disease, such as Alzheimer’s disease, Huntington’s disease, amyotrophic lateral sclerosis, and familial amyloidotic polyneuropathy. The advantages of using the Drosophila model are the well-defined genetic characteristics, the quantity, short life span, simplicity in genetic manipulation and the powerful binary UAS-Gal4 transgenic system. The UAS-Gal4 system allows for rapid generation of individual strains in which expression of a specific gene of interest can be directed to different tissues or cell types. The system allows the target gene to be activated in different cell- and tissue-types by altering the activator-expressing lines. This thesis has been focused on modeling amyloid diseases in Drosophila. This has been performed by: Creating new model systems of senile systemic amyloidosis and familial amyloidotic polyneuropathy in Drosophila Developing a new staining protocol for detection of amyloid in Drosophila Initiate a compound screen of Alzheimer’s disease modeled in Drosophila

Zinc Oxide (ZnO), a II-VI wurtzite semiconductor, has been drawing enormous research interest for decades as an electronic material for numerous applications. It has a wide and direct band gap of 3.37eV and a large exciton binding energy of 60 meV that leads to intense free exciton (FX) emission at room temperature. As a result, ZnO is currently considered among the key materials for UV light emitting devices with tailored dimensionality and solid state white lighting. Full exploration of ZnO in various applications requires detailed knowledge of its fundamental and materialrelated properties, which remains incomplete. The research work summarized in this thesis addresses a selection of open issues on optical properties of ZnO based on (but not limited to) detailed time-resolved photoluminescence (PL) and magneto-optical studies of various excitonic transitions as specified below. Papers 1 and 2 analyze recombination dynamics of FX and donor bound excitons (DX) in bulk and tetrapod ZnO with the aim to evaluate contributions of radiative and nonradiative carrier recombination processes in the total carrier lifetime. We show that changes in relative contributions of these processes in “bulk” and near-surface areas are responsible for bi-exponential exciton decays typically observed in these materials. The radiative FX lifetime is found to be relatively long, i.e. >1 ns at 77 K and >14 ns at room temperature. In the case of DX, the radiative lifetime depends on exciton localization. Radiative recombination is concluded to dominate the exciton dynamics in “bulk regions” of high-quality materials. It leads to appearance of a slow component in the decays of no-phonon (NP) FX and DX lines, which also determines the dynamics of the longitudinal optical (LO) phonon-assisted and two-electronsatellite DX transitions. On the other hand, the fast component of the exciton decays is argued to be a result of surface recombination. Paper 3 evaluates exciton-phonon coupling in bulk and tetrapod ZnO. It is found that, in contrast to bulk ZnO, the NP FX emission in ZnO tetrapods is weak as compared with the LO phonon assisted transitions. We show that the observed high intensity of the FX-1LO emission does not reflect enhanced exciton-phonon coupling in nanostructured ZnO. Instead, it is a result of stronger suppression of the NP FX emission in faceted regions of the tetrapods as revealed from spatially resolved cathodoluminescence (CL) studies. This is attributed to enhanced re-absorption due to multiple internal reflections, which become especially pronounced in the vicinity of the FX resonance. Effects of exciton-photon coupling on light propagation through the ZnO media are studied in Papers 4 and 5. By employing the time-of-flight spectroscopy, in Paper 4 we demonstrate that the group velocity of laser pulses propagating through bulk ZnO can be slowed down to as low as 2044 km/s when photon energies approach the optical absorption edge of the material. The magnitude of this decrease can be manipulated by changing light polarization. In Paper 5 we show that the observed slow-down is caused by the formation of free exciton-polaritons and is determined by their dispersion. On the other hand, contributions of DX polaritons become important only in the proximity to their corresponding resonances. Excitonic effects can also be utilized to investigate fundamental properties and defect formation in ZnO. In Paper 6, we employ DX to study magneto-optical properties of the B valence band (B-VB) states as well as dynamics of inter-VB energy relaxation. We show that PL decays of the emissions involving the B-VB holes are faster than that of their counterparts involving the A-VB holes, which is interpreted as being due to energy relaxation of the holes assisted by acoustic phonons. Values of effective Landé g factors for the B-VB holes are also accurately determined. In paper 7, we uncover the origin of a new class of bound exciton lines detected within the nearband-edge region. Based on their magnetic behavior we show that these lines do not stem from DXs bound to either ionized or neutral donors but instead arise from an exciton bound to an isoelectronic center with a hole-attractive local potential. In Paper 8, DX emissions are used to monitor energy upconversion in bulk and nanorod ZnO. Based on excitation power dependent PL measurements performed with different energies of excitation photons, the physical processes responsible for the upconversion are assigned to two-photon-absorption (TPA) via virtual states and twostep TPA (TS-TPA) via real states. In the former case the observed threshold energy for the TPA process is larger than half of that for one-photon absorption across the bandgap, which can be explained by the different selection rules between the involved optical transitions. It is also concluded that the TS-TPA process occurs via a defect/impurity with an energy level lying within 1.14-1.56 eV from one of the band edges, likely a zinc vacancy.

Semiconductor spintronics is one of the most interesting research fields that exploits both charge and spin properties for future photonics and electronic devices. Among many challenges of using spin in semiconductors, efficient generation of electron spin polarization at room temperature (RT) remains difficult. Recently, a new approach using defect-mediated spin filtering effect, employing <img src="http://www.diva-portal.org/cgi-bin/mimetex.cgi?Ga_%7Bi%7D%5E2%5E+%20" />-interstitial defects in Ga(In)NAs alloys, has been shown to turn the material into an efficient spin-polarized source capable of generating &gt;40% conduction electron spin polarization at RT without an application of external fields. In order to fully explore the defectengineered spin functionalities, a better understanding and control of the spin filtering effects is required. This thesis work thus aims to advance our understanding, in terms of both physical and material insights, of the recently discovered spin filtering defects in Ga(In)NAs alloys. We have focused on the important issues of optimization and applications of the spin filtering effects. To improve spin filtering efficiency, important material and defect parameters must be addressed. Therefore, in Papers I–III formation of the <img src="http://www.diva-portal.org/cgi-bin/mimetex.cgi?Ga_%7Bi%7D%5E2%5E+%20" /> defects in Ga(In)NAs alloys has been examined under different growth and post-growth treatment conditions, as well as in different structures. We found that the <img src="http://www.diva-portal.org/cgi-bin/mimetex.cgi?Ga_%7Bi%7D%5E2%5E+%20" /> defects were the dominant and important nonradiative recombination centers in Ga(In)NAs epilayers and GaNAs/GaAs multiple quantum wells, independent of growth conditions and post-growth annealing. However, by varying growth and post-growth conditions, up to four configurations of the <img src="http://www.diva-portal.org/cgi-bin/mimetex.cgi?Ga_%7Bi%7D%5E2%5E+%20" /> defects, exhibiting different hyperfine  interaction (HFI) strengths between defect electron and nuclear (e-n) spins, have been found. This difference was attributed to different interstitial sites and/or complexes of <img src="http://www.diva-portal.org/cgi-bin/mimetex.cgi?Ga_%7Bi%7D%5E2%5E+%20" /> . Further studiesfocused on the effect of post-growth hydrogen (H) irradiation on the spin filtering effect. Beside the roles of H passivation of N resulting in bandgap reopening of the alloys, H treatment was shown to lead to complete quenching of the spin filtering effect, accompanied by strong suppression in the concentrations of the <img src="http://www.diva-portal.org/cgi-bin/mimetex.cgi?Ga_%7Bi%7D%5E2%5E+%20" /> defects. We concluded that the observed effect was due to the passivation of the <img src="http://www.diva-portal.org/cgi-bin/mimetex.cgi?Ga_%7Bi%7D%5E2%5E+%20" /> defects by H, most probably due to the formation of H-<img src="http://www.diva-portal.org/cgi-bin/mimetex.cgi?Ga_%7Bi%7D%5E2%5E+%20" /> complexes. Optimizing spin filtering efficiency also requires detailed knowledge of spin interactions at the defect centers. This issue was addressed in Papers IV and V. From both experimental and theoretical studies, we were able to conclude that the HFI between e-n spins at the <img src="http://www.diva-portal.org/cgi-bin/mimetex.cgi?Ga_%7Bi%7D%5E2%5E+%20" /> defects led to e-n spin mixing, which degraded spin filtering efficiency at zero field.  Moreover, we have identified the microscopic origin of electron spin relaxation (T1) at the defect centers, that is, hyperfine-induced e-n spin cross-relaxation. Our finding thus provided a guideline to improve spin filtering efficiency by selectively incorporating the <img src="http://www.diva-portal.org/cgi-bin/mimetex.cgi?Ga_%7Bi%7D%5E2%5E+%20" /> defects with weak HFI by optimizing growth and post-growth treatment conditions, or by searching for new spin filtering defect centers containing zero nuclear spin. The implementation of the defect-engineered spin filtering effect has been addressed in Papers VI–VIII. First, we experimentally demonstrated for the first time at RT an efficient electron spin amplifier employing the <img src="http://www.diva-portal.org/cgi-bin/mimetex.cgi?Ga_%7Bi%7D%5E2%5E+%20" /> defects in Ga(In)NAs alloys, capable of amplifying a weak spin signal up to 27 times with a high cut-off frequency of 1 GHz. We further showed that the defectmediated spin amplification effect could turn the GaNAs alloy into an efficient RT optical spin detector. This enabled us to reliably conduct in-depth spin injection studies across a semiconductor heterointerface at RT. We found a strong reduction of electron spin polarization after optical spin injection from a GaAs layer into an adjacent GaNAs layer. This observation was attributed to severe spin loss across the heterointerface due to structural inversion asymmetry and probably also interfacial point defects. Finally, we went beyond the generation of strongly polarized electron spins. In Paper IX we focused on an interesting aspect of using strongly polarized electron spins to induce strong nuclear spin polarization at RT, relevant to solid-state quantum computation using a defect nuclear spin of long spin memory as a quantum bit (qubit). By combining the spin filtering effect and the HFI, we obtained a sizeable nuclear spin polarization of ~15% at RT that could be sensed by conduction electrons. This demonstrated the feasibility of controlling defect nuclear spins via conduction electrons even at RT, the first case ever being demonstrated in a semiconductor.

Semiconductor quantum dots (QDs) are a promising building block of future spin-functional devices for applications in spintronics and quantum information processing. Essential to the realization of such devices is our ability to create a desired spin orientation of charge carriers (electrons and holes), typically via injection of spin polarized carriers from other parts of the QD structures. In this thesis, the optical orientation technique has been used to characterize spin generation, relaxation and detection in self-assembled single and multi-QD structures in the InAs/GaAs system prepared by modern molecular beam epitaxy technique. Optical generation of spin-oriented carriers in the wetting layer (WL) and GaAs barrier was carried  out via circularly polarized excitation of uncorrelated electron-hole pairs from band-to-band transitions or via resonant excitation of correlated electron-hole pairs, i.e. excitons. It was shown that the generation and injection of uncorrelated electron-hole pairs is advantageous for spin-preserving injection into the QDs. The lower spin injection efficiency of excitons was attributed to an enhanced spin relaxation caused by the mutual electron-hole Coulomb exchange interaction. This correlation affects the spin injection efficiency up to elevated temperatures of around 150 K. Optical orientation at the energy of the WL light-hole (lh) exciton (XL) is accompanied by simultaneous excitation from the heavy-hole (hh) valence band at high ~k-vectors. Quantum interference of the two excitation pathways in the spectral vicinity of the XL energy resulted in occurrence of an asymmetric absorption peak, a Fano resonance. Complete quenching of spin generation efficiency at the resonance was observed and attributed to enhanced spin scattering between the hh and lh valence bands in conjunction with the Coulomb exchange interaction in the XL. This mechanism remains effective up to temperatures exceeding 100 K. In longitudinal magnetic fields up to 2 T, the spin detection efficiency in the QD ensemble was observed to increase by a factor of up to 2.5 in the investigated structures. This is due to the suppression of two spin depolarization mechanisms of the QD electron: the hyperfine interaction with the randomly oriented nuclear spins and the anisotropic exchange interaction with the hole. At higher magnetic fields, when these spin depolarization processes are quenched, only anisotropic QD structures (such as double QDs, aligned along a specific crystallographic axis) still exhibit a rather strong field dependence of the QD electron spin polarization under non-resonant excitation. Here, an increased spin relaxation in the spin injector, i.e. the WL or GaAs barrier, is suggested to lead to more efficient thermalization of the spins to the lower Zeeman-split spin state before capture to the QD. Finally, the influence of elevated temperatures on the spin properties of the QD structures was studied. The temperature dependence of dynamic nuclear polarization (DNP) of the host lattice atoms in the QDs and its effect on the QD electron spin relaxation and dephasing were investigated for temperatures up to 85 K. An increase in DNP efficiency with temperature was found, accompanied by a decrease in the extent of spin dephasing. Both effects are attributed to an accelerating electron spin relaxation, suggested to be due to phonon-assisted electronnuclear spin flip-flops driven by the hyperfine interaction. At even higher temperatures, reaching up to room temperature, a surprising, sharp rise in the QD polarization degree has been found. Experiments in a transverse magnetic field showed a rather constant QD spin lifetime, which could be governed by the spin dephasing time T*2. The observed rising in QD spin polarization degree could be likely attributed to a combined effect of shortening of trion lifetime and increasing spin injection efficiency from the WL. The latter may be caused by thermal activation of non-radiative carrier relaxation channels.

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Rivning av dammar ökar globalt och fortsatta ökningar kan förväntas i framtiden. Trots det så är det fortfarande svårt att veta vilka effekter det kommer att få. Det gör det mycket viktigt att förstå hur organismer reagerar på borttagandet av en damm samt vilka faktorer som kontrollerar deras reaktion. Andra studier har visat på varierande resultat så syftet med den här studien att jämföra förändringar i total abundans, EPT, biodiversitet samt jämnhet (evenness) hos makroevertebrater i Nianån före och efter en dammutrivning, samt jämföra med ett kontrollvattendrag där ingen åtgärd gjorts. Provtagning skedde i tre lokaler som delades in i sex transekter vardera. Vid varje transekt mättes vattenhastighet, djup, substrattäckning och vid tre av transekterna samlades bentisk fauna in med sparkprover. Proverna nycklades till familjenivå och data analyserades. Resultatet visar inga signifikanta skillnader hos makroevertebrater gällande total abundans, EPT täthet, biodiversitet eller jämnhet före och efter att dammen revs, stora variationer i makroevertebrats index. Den fysisk livsmiljön såg förändringar före och efter avlägsnandet av dammen men förändringar hos makroevertebrater kan förväntas ske efter en längre tid.  Studier som denna är viktiga för att få ökad kunskap om effekterna av dammutrivningar på makroevertebrater och bidra som kunskapsunderlag vid förlag till avlägsnande av dammar. / Removal of dams in regulated rivers to restore natural flow regimes is increasing globally, and further increases can be expected in the future. Even so, it is difficult to quantify the biotic and abiotic effects of dam removal. That makes it very important to understand how organisms react to the removal of a dam and the factors that control their reaction. Previous  studies have yielded varying results, so the purpose of this study is to: 1) compare changes in total abundance, Ephemeroptera, Plecoptera, and Tricoptera (EPT), biodiversity and evenness of macrovertebrates in River Nianån, Sweden, before and after a dam removal, and 2) to compare it with a control stream where no action has been taken. Sampling took place at three locations each in the treatment and control streams, each divided into six transects. At each transect, water velocity, depth and substrate coverage were measured; in three of the transects, benthic fauna was collected by standardized kick samplimg. Macroinvertebrates were keyed to the family level and the data where analyzed. The result shows no significant differences in macroinvertebrates regarding total abundance, EPT density, biodiversity or evenness before and after the dam removal, high variability in macroinvertebrate indices. Physical habitat was found to differ before and after dam removal, however, so changes in macroinvertebrate indices might be expected over longer time scales. Studies like this are important for gaining increased knowledge of the effects of dam removal on macrovertebrates and as a basis for knowledge when considering a dam removal.

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