The human protein kinase superfamily consists of over 500 members that individually control specific aspects of cell behavior and collectively control the complete range of cellular processes. That such a large group of proteins is able to uniquely diversify and establish individual identities while retaining common enzymatic function and significant sequence/structural conservation is remarkable. The means by which this is achieved is poorly understood, and we have begun to examine the issue by performing a comparative analysis of the catalytic domain of protein kinases. A novel approach for protein structural alignment has revealed a high degree of similarity found across the kinase superfamily, with variability confined largely to a single region thought to be involved in substrate binding. The similarity detected is not limited to amino acids, but includes a group of conserved water molecules that play important structural roles in stabilizing critical residues and the fold of the kinase domain. The development of a novel technique for identifying kinase substrates on a large scale directly from cell lysate has revealed that substrate specificity is not what discriminates the closely related p38α and β mitogen-activated protein kinases. Instead cellular localization appears to be their distinguishing characteristic, at least during myoblast differentiation. Together these results highlight the extent of conservation, as well as the minimal variability, that is found in the catalytic domain of all protein kinase superfamily members, and that while distantly related kinases may be distinguished by substrate specificity, closely related kinases are likely to be distinguished by other factors. Although these results focus on representative members of the kinase superfamily, they give insight as to how all protein kinases likely diversified and established unique non-redundant identities. In addition, the novel techniques developed and presented here for structural alignment and substrate discovery offer new tools for studying molecular biology and cell signaling.

This thesis focuses on the analysis of the role of adhesion between substrate and cell and factors of Quorum sensing on the migration of Dictyostelium amoeba. Tools to automate the recordings of videomicroscopy and image analysis have been developed to work with very large samples of cells and toquantify cell migration. A microfluidic device for cell detachment in hydrodynamic flow combined witha motorized stage has allowed a statistical study of adhesion but also the dynamics of detachment. The analysis of the migration of Dictyostelium in non nutritive medium highlights the role of density on celldifferentiation and migration capacity. We observe the presence of a maximum speed of migration after6 hours of starvation. We show that the adhesion to glass is twice as low in deprivation buffer as inthe nutrient medium. The experiences of migration in growth medium revealed the presence of a factorof detection of density secreted by the cells and regulating their random migration. The diffusion coefficient, the persistence of the movement and morphology of cells vary depending on the concentrationof this factor. This factor does not affect cell adhesion but only the dynamics of detachment. Finally, the testing protocol developed allowed us to make a comparative study of migration by varying otherparameters such as surface or the chemical composition of experimental medium. This work concludesby outlining the possible role of adhesion to the migration of Dictyostelium in nutrient medium.

Caspases are important players in programmed cell death. Normal activities of caspases are critical for the cell life cycle and dysfunction of caspases may lead to the development of cancer and neurodegenerative diseases. They have become a popular target for drug design against abnormal cell death. In this study, the recognition of P5 position in substrates by caspase-3, -6 and -7 has been investigated by kinetics, modeling and crystallography. Crystal structures of caspase-3 and -7 in complexes with substrate analog inhibitor Ac-LDESD-CHO have been determined at resolutions of 1.61 and 2.45 Å, respectively, while a model of caspase-6/LDESD is constructed. Enzymatic study and structural analysis have revealed that Caspase-3 and -6 recognize P5 in pentapeptides, while caspase-7 lacks P5-binding residues. D-arginine dehydrogenase catalyzes the flavin-dependent oxidative deamination of D-amino acids to the corresponding imino acids and ammonia. The X-ray crystal structures of DADH and its complexes with several imino acids were determined at 1.03-1.30 Å resolution. The DADH crystal structure comprises a product-free conformation and a product-bound conformation. A flexible loop near the active site forms an “active site lid” and may play an essential role in substrate recognition. The DADH Glu87 forms an ionic interaction with the side chain of iminoarginine, suggesting its importance for DADH preference of positively charged D-amino acids. Comparison of the kinetic data of DADH activity on different D-amino acids and the crystal structures demonstrated that this enzyme is characterized by relatively broad substrate specificity, being able to oxidize positively charged and large hydrophobic D-amino acids bound within a flask-like cavity. Understanding biology at the system level has gained much more attention recently due to the rapid development in genome sequencing and high-throughput measurements. Current simulation methods include deterministic method and stochastic method. Both have their own advantages and disadvantages. Our group has developed a deterministic-stochastic crossover algorithm for simulating biochemical networks. Simulation studies have been performed on biological systems like auto-regulatory gene network and glycolysis system. The new system retains the high efficiency of deterministic method while still reflects the random fluctuations at lower concentration.

Treatment wetlands been showed efficient for reducing pollutant in waste water. In Lajeado – RS, Brazil the landfill has poor leachate water treatment. It is necessary to supplement the treatment plant because they need to reduce BOD, COD and nitrate of the water going to recipient. A subsurface flow wetland (SSF) can be a good choice.  In order to be able to design an efficient SSF it is important to understand how the grain sizes of a substrate affect the reducing of pollutants in waste water. This study focus on two substrate, sand with grain size of 0 - 3 mm and gravel with the grain size of 10 - 20 mm. To see the grain size reduces BOD, COD and nitrate best, the experiment used eight pilot scales SSF for leachate water treatment, four filled with sand and four filled with gravel. Two different flows, four with batch and four used continuous flow; two of each was planted with Thypa angustifolia L. Samples were taken from each wetland every week during a four week period. The results showed that the wetlands with the fine- grained substrate; sand gave the better reduction of BOD, COD and TKN (total kjeldahl kväve). It also showed great reduction in color. Important to notice in this study is the lack of time; more samples are required to be able to establish a pattern.

The focus of this thesis is on the optimization and fabrication of p-i-n amorphous silicon (a-Si:H) solar cells both on glass and transparent plastic substrates. These solar cells are specifically fabricated on transparent substrates to facilitate the integration of thin film batteries with these solar cells. To comply with plastic substrates, different silicon layers are optimized at the low processing temperature of 135 C. In the first part of the optimization process, the structural, electronic, and optical properties of boron- and phosphorous-doped, hydrogenated nanocrystalline silicon (nc-Si:H) thin films deposited by plasma-enhanced chemical vapor deposition (PECVD) at the substrate temperature of 135 C are elaborated. Additionally, in this part, the deposition of protocrystalline silicon (pc-Si) films on glass substrates are investigated. In the device integration and fabrication part of this thesis, the optimization process is continued by fabricating single junction devices with different hydrogen dilution ratios for the cell absorber layer. The optimum device performance is achieved with an absorber layer right at the transition from amorphous to microcrystalline silicon. To further improve the performance of the fabricated solar cells, amorphous silicon carbide buffer layers are introduced between the nc-Si p-layer and the undoped pc-Si absorber layer. Single junction p-p'-i-n solar cells are fabricated and characterized both on glass and plastic substrates. Our measurements show conversion efficiencies of 7.0% and 6.07% for the cells fabricated on glass and plastic substrates, respectively. In the last part of this research, the light trapping enhancement in amorphous silicon solar cells using Distributed Bragg Reflectors (DBRs) are experimentally demonstrated. Reflectance characteristics of DBR test structures, consisting of amorphous silicon (a-Si) / amorphous silicon nitride (SiN) film stacks are analysed and compared with those of conventional ZnO/Al back reflectors. DBR optical measurements show that the average total reflectance over the wavelength region of 600-800 nm is improved by 28% for DBR back structures. Accordingly, single junction amorphous silicon solar cells with DBR and Al back reflectors are fabricated both on glass and plastic substrates. Our results show that the short-circuit current density and consequently the conversion efficiency is enhanced by 10% for the cells fabricated on textured transparent conductive oxide substrates. In addition, these DBR back structures are designed and employed to improve the efficiency of semi-transparent solar cells. In this application, the optimized DBR structures are designed to be optically transparent for the part of the visible range and highly reflective for the red and infra-red part of the spectrum. Using these DBR structures, the efficiency of the optimum semi-transparent solar cell is enhanced by 5%.

The thick shelled river mussel (Unio crassus) has a fragmented distribution in southern Sweden. It is a threatened and protected species. In both the Swedish red list and the IUCN Red List of Threatened Species Unio crassus is classified as Endangered (EN). Causes for this classification are for instance differentiated bottom substrate and deterioration in water quality. In this study, habitat preferences of Unio crassus were investigated to assist in future restoration work. The environmental parameters that were used to characterize the habitat in sites with or without Unio crassus were water depth, bottom substrate, water velocity, slope, and shading. In this thesis I focused in bottom substrate and water velocity. Sites with Unio crassus had finer bottom substrate and lower water velocity than sites without (t>2.54, p<0.05, t-test). Most of the sites with Unio crassus had a bottom substrate with a size <4 mm and a water velocity around 0.3-0.5 m/s. These two variables were correlated with each other. When the water velocity was higher, the bottom substrate was coarser. These results are in line with other studies, showing that if the bottom substrate is either too coarse or too fine, it could impact Unio crassus. Too coarse bottom substrate probably results in difficulty in burrowing and too fine most likely results in interfering with respiration and feeding. Earlier studies indicate that the water velocity can have a greater impact on unionids than bottom substrate. Because of the correlation between bottom substrate and water velocity it is not easy to disentangle the importance of each factor.

The thick shelled river mussel (Unio crassus) has a fragmented distribution in southern Sweden. It is a threatened and protected species. In both the Swedish red list and the IUCN Red List of Threatened Species Unio crassus is classified as Endangered (EN). Causes for this classification are for instance differentiated bottom substrate and deterioration in water quality. In this study, habitat preferences of Unio crassus were investigated to assist in future restoration work. The environmental parameters that were used to characterize the habitat in sites with or without Unio crassus were water depth, bottom substrate, water velocity, slope, and shading. In this thesis I focused in bottom substrate and water velocity. Sites with Unio crassus had finer bottom substrate and lower water velocity than sites without (t>2.54, p<0.05, t-test). Most of the sites with Unio crassus had a bottom substrate with a size <4 mm and a water velocity around 0.3-0.5 m/s. These two variables were correlated with each other. When the water velocity was higher, the bottom substrate was coarser. These results are in line with other studies, showing that if the bottom substrate is either too coarse or too fine, it could impact Unio crassus. Too coarse bottom substrate probably results in difficulty in burrowing and too fine most likely results in interfering with respiration and feeding. Earlier studies indicate that the water velocity can have a greater impact on unionids than bottom substrate. Because of the correlation between bottom substrate and water velocity it is not easy to disentangle the importance of each factor.

Verrucariaceae are a family including mostly lichenized species (Verrucariales, Ascomycota). Its current generic classification, which mainly relies on three morphological characters (spore septation, thallus structure, and hymenial algae), has never been subjected to molecular data. Because these characters were suspected to be homoplastic, the monophyly of the genera as currently delimited based on morphology need to be assessed. A three-gene phylogenetic analysis was carried out using three methods (Maximum Parsimony, Maximum Likelihood, and a Bayesian approach) on 83 taxa, selected from 15 genera in Verrucariaceae. Ancestral state reconstructions were undertaken for four characters (spore septation, thallus structure, hymenial algae, and upper cortex structure). The results confirmed that most of the genera were not monophyletic, and that the most recent common ancestor of Verrucariaceae was most likely crustose, lacking hymenial algae, and with simple spores and a pseudocortex. The use of symplesiomorphic traits to define Verrucaria, the largest and type genus for the Verrucariaceae, as well as the non monophyly of the genera Polyblastia, Staurothele and Thelidium, explain most of the discrepancies between the current classification and a classification using monophyly as a grouping criterion. In order to accommodate newly inferred monophyletic groups, existing genera were re-delimited and three new genera were proposed. Recent broad-scale phylogenetic analyses have shown that Verrucariales was sister to Chaetothyriales, an order first known as including mostly saprophytes and opportunistic animal and human parasites. Investigations of fungal communities colonizing rocks in extreme environments have shown that some slow-growing melanized fungi inhabiting bare rock surfaces belonged to the Chaetothyriales. Multigene phylogenetic analyses were carried out using Maximum Likelihood and a Bayesian approach in order to confirm the affiliation of 25 of these rock isolates. Ancestral state reconstructions were then undertaken on two different datasets to look at the evolutionary history of lichenization within Pezizomycotina, and the rock-inhabiting habit within Eurotiomycetes. Results suggest that the ancestor of the lineage including Verrucariales and Chaetothyriales was likely to be an extremotolerant non-lichenized, rock-inhabiting fungus. Virulence factors of opportunistic parasites within Chaetothyriales, such as melanization and meristematic growth, might have primary been adaptations for life in extreme habitats. / Dissertation

In this research that we design in the polymer structure containing the core monomer into benzene ring structure for appied on the flexible substrate and the optoelectronic components .Three novel bisphenol monomers have been synthesised successfully and converted to a series of poly(arylene ether)s by nucleophilic displacement reaction with Bis(4-fluorophenyl) sulfone, then we called them:P1, P2 and P3.We can see from the material structure that the steric hindrance of the group connected to the side of the main chain (M2) is larger than the group in the main chain(M1,M3),and the steric hindrance of the longer length of main chain (M3) is smaller than the shorter one(M1) in the polymerization Thermal analysis physics studies with these polymers confirmed by Thermogravimetric analyzer(TGA) and differential scanning calorimetry (DSC).It is indicated that Td5% of these polymers were 476¢XC~577¢XC in TGA and Tg of these polymers were 264¢XC~290¢XC in DSC. Besides, these polymers were not observed apparent crystallizing point, so we consider that they are not crystallized easily. The transmission spectra of thin film in the visible light region were up to 87%~93%. In drop shape analysis system, the contact angles of them are 85¢X~87¢X, show that they have good hyrophobicity.By above material properties of these polymers, they have high thermal stabilities, high optical transparency and good hydrophobicity.

Soil and groundwater at many existing and former industrial areas and disposal sites is contaminated by halogenated organic compounds that were released into the environment. Halogenated organic compounds are heavier than water. When they are released into the subsurface, they tend to adsorb onto the soils and cause the appearance of DNAPL (dense-non-aqueous phase liquid) pool. Among those halogenated organic compounds, trichloroethylene (TCE), a human carcinogen, is one of the commonly observed contaminants in groundwater. Thus, TCE was used as the target compound in this study. The objective of this study was to develop the emulsified carbon-releasing substrate and apply it as the filling material in the permeable reactive barrier to remediate TCE-contaminated groundwater. In this study, the developed emulsified carbon-releasing substrate contained soybean oil, lactate, biodegradable surfactant (Simple GreenTM and lecithin), and nutrients. Results of emulsion test show that up to 90% of the emulsified carbon-releasing substrate was distributed effectively in the soil pores. The emulsified carbon-releasing substrate was able to provide carbon for the enhancement of in situ anaerobic biodegradation for a long period of time. A pilot-scale study was operated at a TCE-contaminated site located in southern Taiwan. Emulsified carbon-releasing substrate emulsion was pressure-injected into the remediation wells. A total of 120 L of emulsified carbon-releasing substrate was injected into the test site. Based on the groundwater analytical results, dissolved oxygen, oxidation-reduction potential, and sulfate concentrations decreased after injection. However, the anaerobic degradation byproduct, acetic acid, increased after injection. Results also show that the total viable bacteria increased in the upgradient injection (remediation) well. Decrease in TCE concentration (dropped to below 0.01 mg/L) was also observed after substrate injection, and TCE degradation byproducts, cis-1,2-dichloroethene (cDCE) and vinyl chloride (VC) were also observed. Result of microbial analyses show that various TCE-degrading bacteria exist in the groundwater samples including Ralstonia sp., Clostridium sp., Uncultured Burkholderiales bacterium, Hydrogenophaga sp., Acidovorax sp., Zoogloea sp., Hydrocarboniphaga sp., Uncultured Curvibacter sp., Pseudomonas sp., Comamonas sp., Aquabacterium sp., and Variovorax strains. This reveals that the anaerobic dechlorination of TCE is a feasible technology at this site. Slug test result show that only a slight variation in soil permeability of the injection well was observed. This indicates that the substrate injection would not cause clogging of the soil pores. Results from the cost analysis show that the total cost for the test site remediation was approximately USD13,442 per year. This indicates that the developed system has the potential to be developed into an environmentally, economically, and naturally acceptable remedial technology. Knowledge obtained from this study will aid in designing a carbon-released substrate biobarrier system for site remediation.