For the vast majority of proteins no experimental information about the three-dimensional structure is known, but only its sequence. Therefore, the easiest way to obtain some understanding of the structure and function of these proteins is by relating them to well studied proteins. This can be done by searching for homologous proteins. It is easy to identify a homologous sequence if the sequence identity is above 30%. However, if the sequence identity drops below 30% then more sophisticated methods have to be used. These methods often use evolutionary information about the sequences, which makes it possible to identify homologous sequences with a low sequence identity. In order to build a three--dimensional model from the sequence based on a protein structure the two sequences have to be aligned. Here the aligned residues serve as a first approximation of the structure. This thesis focuses on the development of fold recognition and alignment methods based on evolutionary information. The use of evolutionary information for both query and target proteins was shown to improve both recognition and alignments. In a benchmark of profile--profile methods it was shown that the probabilistic methods were best, although the difference between several of the methods was quite small once optimal gap-penalties were used. An artificial neural network based alignment method ProfNet was shown to be at least as good as the best profile--profile method, and by adding information from a self-organising map and predicted secondary structure we were able to further improve ProfNet.

The Heck reaction is one of the most appreciated methods for carbon-carbon bond formation. Due to its mildness and ability to be tuned by additives, it often leaves few alternative competitive reactions. It has also proven easy to develop the reaction conditions in an environmentally benign direction. Through the introduction of palladium chelating groups in olefinic precursors for the Heck reaction, it has been possible to direct the substitution in the following Heck arylation in favor of the terminal position with good regioselectivity. In this thesis, the concept has been utilized to produce a small array of drug-like compounds at useful yields under fast microwave-enhanced conditions utilizing the thermostable Herrmanns palladacycle. During the last decade, this, together with other palladacycles has become commonly employed as precatalyst for the Heck reaction. However, there have been conflicting opinions regarding the mechanisms governing its catalytic effect. A PdII-PdIV catalytic cycle has been suggested to be operative, in contrast to the classical Pd0-PdII cycle. In order to clarify the presence of such a mechanism, a set of Heck reactions was performed with the advent of different palladium precatalysts (classical and palladacycles), which revealed that the regiochemicαal substitution pattern is highly conserved, regardless of which precatalyst was employed, and thus, the same mechanism seems to be operative. This is also supported by data from ESI-MS investigations where all the reactions investigated gave rise to the same set of oxidative addition complexes. A crafted route to 3-aryl-1,2-cyclohexandiones has been developed in which 1,2-cyclohexandione is produced is situ from 2,3-epoxycyclohexanone, followed by Heck arylation. A diverse array of aryl bromides encompassing electron-rich, electron-poor, neutral and sterically hindered repressentatives has been successfully utilized to produce the corresponding products at useful yields.The intramolecular Heck reaction offers a route to quaternary carbonic centersand is being increasingly exploited in synthetic endeavors. However, the use of electron-rich olefinic precursors is only reported in a few cases. The implementation of one capto-dative and five electron-rich olefins has therefore been successfully subjected to Heck reaction conditions rendering the corresponding spiro compounds.

Membrane proteins are of broad interest since they constitute a large fraction of the proteome in all organisms, up to 20-30%. They play a crucial role in many cellular processes mediating information flow and molecular transport across otherwise nearly impermeable membranes. Traditional three-dimensional structural analyses of membrane proteins are difficult to perform, which makes studies of other structural aspects important. The topology of an α-helical membrane protein is a two-dimensional description of how the protein is embedded in the membrane and gives valuable information on both structure and function. This thesis is focused on predicting the topology of α-helical membrane proteins and on assessing and improving the prediction accuracy. Reliability scores have been derived for a number of prediction methods, and have been integrated into the widely used TMHMM predictor. The reliability score makes it possible to estimate the trustworthiness of a prediction. Mapping the full topology of a membrane protein experimentally is time-consuming and cannot be done on a genome-wide scale. However, determination of the location of one part of a membrane protein relative to the membrane is feasible. We have analyzed the impact of incorporating such experimental information a priori into TMHMM predictions and show that the accuracy increases significantly. We further show that the C-terminal location of a membrane protein (inside or outside) is the optimal information to use as a constraint in the predictions. By combining experimental techniques for determining the C-terminal location of membrane proteins with topology predictions, we have produced reliable topology models for the majority of all membrane proteins in the model organisms E. coli and S. cerevisiae. The results were further expanded to ~15,000 homologous proteins in 38 fully sequenced eukaryotic genomes. This large set of reliable topology models should be useful, in particular as the structural data for eukaryotic membrane proteins is very limited.

This thesis is focused on the synthesis and structural determination of a series of quasicrystal approximants in the RE13Zn~58 (RE = Ce, Pr, Nd, Sm, Gd, Tb, Dy, Ho, Er, Tm, Yb and Lu), Ce13Cd~58 and RECd6 (RE = Tb, Ho, Er, Tm and Lu) systems. Structural studies were performed by single crystal X-ray diffraction methods. The RECd6 phases are 1/1 cubic approximants to the stable icosahedral quasicrystals. The structure of quasicrystals cannot be solved by conventional crystallography due to the lack of periodicity in three-dimensional space. On the other hand, quasicrystal approximants exhibit long-range order, which makes their structural determination possible by standard methods. Since they are believed to display the same local arrangement as the quasicrystals, the structures of the quasicrystal approximants play a key role in understanding quasicrystals. The RE13Zn~58 and Ce13Cd~58 quasicrystal approximants show measurable compositional variations coupled to subtle structural differences. The crystal structures are generally rather more complex than previously reported, and exhibit a number of different ordering and disordering modes.

The synthesis, structural characterisation and the properties of the Zintl hydrides AeE2H2 and AeAlSiH (Ae = Ba, Ca, Sr; E = Al, Ga, In, Si, Zn) are reported. The first hydride in this class of compounds is SrAl2H2 which was discovered under an experiment by Gingl, who hydrogenated SrAl2 at various temperatures. (Gingl et al, Journal of Alloys and Compounds 306 (2000) 127-132). The intention was to form alanates, e.g. AlH4-, by terminating the three dimensional four connected aluminium network in SrAl2. The new hydride, SrAl2H2, has a partially conserved aluminium network. The three dimensional anionic network in SrAl2 is reduced to two dimensions in the hydride, with aluminium bonded to both aluminium and hydrogen. This type of bonding configuration has not been observed before. The hydrogenation of SrAl2 is straight forward, 190 oC and 50 bar, compared to the difficult synthesis of alanates and alane, AlH3. The latter synthesises uses aluminium in its zero oxidation state in contrast to the synthesis of SrAl2H2 from SrAl2. (In the SrAl2-precursor aluminium is reduced by the electropositive metal to -I.) Thus, the discovery shows a different route to alanates by using precursors with aluminium in a reduced state. If SrAl2H2 is further hydrogenated at 250 oC the two dimensional network breaks and Sr2AlH7 forms. We wanted to investigate if SrAl2H2 was a singularity or if other similar compounds exist. We wanted to study how hydrogenation of precursors similar to the aluminide result in 1) new routes to compounds with high hydrogen content, as alanates, 2) to investigate how the E-H bond is affected as function of the network composition among different ternary hydrides, in particular BaAlxSi2-xHx, and choice of active metal. BaGa2H2 and SrGa2H2, two hydrides isostructural with SrAl2H2, were synthesized from its precursors BaGa2 and SrGa2. In addition three ternary hydrides BaAlSiH, CaAlSiH and SrAlSiH were manufactured from their related AeAlSi precursors. All powders were characterized by neutron and x-ray diffraction methods. An increased stability towards water/moisture compared to ordinary saline hydrides was noticed, especially for the ternary hydrides. Heat stability was measured with DSC (differential scanning calorimetry). The hydrides BaGa2H2 and SrGa2H2 decompose around 300 oC at 1 atm. This is similar to isostructural SrAl2H2. The ternary hydrides BaAlSiH and SrAlSiH decompose at 600 oC, at 1 atm, which is the highest noticed temperature for compounds with Al-H bonds. Inelastic neutron scattering experiments showed that these hydrides Al-H and Sr-H bonds are really weak, even weaker then the Al-H interactions in alanates and alanes. These hydrides are probably stabilized be their lattices. The electric properties among the ternary hydrides were measured with IR-spectroscopy (diffuse reflectance). The ternary hydrides, AeAlSiH, are indirect semi conductors. BaGa2H2 and SrGa2H2 are conductors. The ternary hydrides, AeAlxSi2-xHx, may have adjustable band gaps, which we were not able to determine. This work is leading into a new research area within the field of metal hydrides.

This thesis is focussing on the crystallographic challenges and what knowledge we can gain from studying the different open-framework germanates. Five new open-framework germanates have been synthesized and the structures have been determined by single crystal X-ray diffraction. A thorough description is made of the different problems raised with the different compounds, whether it is choice of crystal system in SU-61, twinning and possible ordering in SU-46, superstructure and variation in elemental content in SU-57, template disorder in JLG-5 or framework disorder in SU-44. Open-framework germanates are often built from one type of cluster, such as the Ge7 [Ge7X19], Ge8 [Ge8X20], Ge9 [Ge9Xn, n =25-26] and Ge10 [Ge10X28], (X =O, OH, F) clusters. The structures built by clusters containing different kinds of polyhedra are discussed, with a focus on the 4-coordinated Ge7 clusters, the larger cluster aggregate found in SU-8 and SU-44 and the structures built by the Ge10 clusters.

In this thesis, a synthesis concept has been developed, which uses nitrogen-rich liquid phases for sintering of Ca-α-sialon ceramics. First, keeping the Si/Al ratios constant, the effects of N/O ratio on the properties and microstructure were investigated through a liquid phase sintering process. Second, nitrogen-rich Ca-α-sialon ceramics, with nominal compositions: CaxSi12-2xAl2xN16, x < 2.0, was synthesized and characterized. Third, mechanical and thermal properties of nitrogen-rich Ca-α-sialons were investigated in terms of high temperature deformation resistance,reaction mechanism, phase stability and oxidation resistance, and further correlated to their phase assemblage and microstructure observation. It has been found that increasing the N/O and Ca/Al ratio simultaneously in the materials could result in development of a microstructure with well shaped, high-aspect-ratio Ca-α-sialon grains, and an improvement in both toughness and hardness. For the nitrogen-rich Ca-α-sialon, mono-phasic α-sialon ceramics were obtained for 0.51 ≤ x ≤ 1.32. The obtained Ca-α-sialon ceramics with elongated-grain microstructures show a combination of high hardness and high fracture toughness. Compared with the oxygen-rich Ca-α-sialons, the nitrogen-rich Ca-α-sialons exhibited approximately 150 oC higher deformation onset temperatures and decent properties even after the deformation. The α-sialon phase was first observed at 1400 oC, however the phase pure Ca-α-sialon ceramics couldn’t be obtained until 1800 oC. The nitrogen-rich Ca-α-sialons were thermal stable, no phase transformation observed in the temperatures range1400-1600 oC. In general, mixed α/β-sialon showed better oxidation resistance than pure α-sialon in the low temperature range (1250-1325 oC), while α-sialons with compositions located at α/β-sialon border-line showed significant weight gains over the entire temperature range (1250-1400 oC).

Insulin as well as glucagon are important hormones in maintaining glucose homeostasis and regulating the metabolism in the body. Insulin receptors (IR) are transmembrane receptors that promote a signal transduction when activated by insulin. This can for example cause an increased influx of glucose into the cell performed by so called glucose transporters (GLUTs). These membrane proteins facilitate the transport of glucose from the blood into the cells, so the cell always has a constant supply of energy. Peroxisome proliferator-activated receptors (PPAR) are nuclear fatty acid receptors. They are activated by lipids and regulate fatty acid transcription. PPARδ/β is located in skeletal muscle and can promote fatty acid catabolism as well as cause a switch in fuel preference from glucose to fatty acids. It has been suggested that ligands for PPARδ could act as insulin sensitizers. The PPARγ coactivator-1α can increase mitochondrial content in skeletal muscle if over expressed. The same is true for endurance exercise. Hormones released from adipose tissue can cause hyperphagia and obesity if over- or under expressed. They can also work in the opposite way by decreasing appetite with weight loss as an effect. Impaired signalling or dysfunctional receptor can cause insulin resistance, obesity and diabetes. Lipolysis occurs in adipose tissues and is conducted by three enzymes, namely adipose triglyceride lipase (ATGL), hormone-sensitive lipase (HSL) and monoglyceride lipase (MGL). There are some factors that can increase lipolysis such as caffeine, a low glycemic index, high protein intake and training. The enzyme PEPCK is involved in the gluconeogensis in the liver and kidney cortex, and also in the glyceroneogenesis in the liver, as well as in brown and white adipose tissue. When overexpressed in skeletal muscle the enzyme increases the muscle activity. The overexpression of the enzyme did promote the β-oxidation as energy source for the muscles during exercise, instead of muscle glycogen as fuel. The processes of protein synthesis and breakdown are together called protein turnover. Muscle grows when synthesis is greater than breakdown, and withers if breakdown exceeds the level of synthesis. Acute effects of training is catabolic, but long time exercise causes however an increased protein synthesis. Leucine, an essential amino acid, has an important role in the initiation phase of translation. Glutamine is probably important in the regulation of muscle protein synthesis and breakdown. Together with glutamate, aspartate and asparagine, these are responsible for the amino acid metabolism that occurs in the muscles. Protein synthesis reaches its maximum in the recovery phase after intense training.

I skolan använder sig lärare av skriftliga prov som ett av underlagen vid betygssättning, men det finns dåliga och bra prov. Ett bra prov utvärderar det som avses. Kan det vara så att betyg på skriftliga prov i dagens skola grundas på annat än vad som avses i betygskriterierna? För att granska detta gjordes en kvalitativ samstämmighetsanalys av autentiska prov och betygskriterier gällande organisk kemi, kemi b på gymnasiet. Till detta användes Blooms reviderade taxonomi. Undersökningen ämnade visa om skriftliga prov i var konstruerade på sådant vis att eleverna tilläts visa på kvalitéer som motsvarar Väl Godkänt (VG) och Mycket Väl Godkänt (MVG). En kompletterande enkätundersökning genomfördes med avsikten att ta reda på ifall lärarna använder sig av skriftliga prov för att bedöma VG och MVG. De skriftliga proven i vår undersökning och betygskriterierna för VG och MVG visar mycket dålig samstämmighet. De skriftliga proven betonar en lägre kognitiv nivå än betygskriterierna. Samtidigt visar enkätundersökningen att de skriftliga proven endast är en av flera underlag vid betygssättning.

Johan Afzelius held the chair in chemistry at Uppsala University 1784-1820. His predecessor was the reputable Torbern Bergman, one of Afzelius’ students the famous Jacob Berzelius. The published scientific production of Afzelius is very limited. Afzelius has been described as with no interest of chemistry, reluctant to scientific innovations and as an opponent to the new "antiflogistic" chemistry. Also, he is believed to have given Jacob Berzelius hard times when Berzelius studied in Uppsala. The study suggests that the judgement of Johan Afzelius should be revised. It appears that the above description of Afzelius is to be regarded as an artefact. So, Afzelius, besides being devoted to mineralogy, was keen at chemistry, interested in scientific innovations, and from 1799 on no opponent to the new chemistry.