A reação "click" na síntese de 1,2,3-triazóis: aspectos químicos e aplicações

The Copper-catalyzed azide-alkyne cycloaddition (CuAAC), often referred to as "click" reaction, has become a very popular reaction in the last years. It affords exclusively 1,4-disubstituted 1,2,3-triazoles and has been widely used to connect readily accessible building blocks containing various functional groups. The great success of this reaction is based on the fact that it is general, virtually quantitative and very robuste. The scope of this copper-catalyzed synthesis is extraordinary and the reaction has found numerous applications in many research fields, including biological chemistry and materials science. In this review, the main chemical aspects and applications of the "click" reaction in the synthesis of 1,2,3-triazoles are presented.

Parallel-Operating Three-Phase Voltage Source Inverters – Circulating CurrentModeling, Analysis and Mitigation

The maximum realizable power throughput of power electronic converters may be limited or constrained by technical or economical considerations. One solution to this problemis to connect several power converter units in parallel. The parallel connection can be used to increase the current carrying capacity of the overall system beyond the ratings of individual power converter units. Thus, it is possible to use several lower-power converter units, produced in large quantities, as building blocks to construct high-power converters in a modular manner. High-power converters realized by using parallel connection are needed for example in multimegawatt wind power generation systems. Parallel connection of power converter units is also required in emerging applications such as photovoltaic and fuel cell power conversion. The parallel operation of power converter units is not, however, problem free. This is because parallel-operating units are subject to overcurrent stresses, which are caused by unequal load current sharing or currents that flow between the units. Commonly, the term ’circulatingcurrent’ is used to describe both the unequal load current sharing and the currents flowing between the units. Circulating currents, again, are caused by component tolerances and asynchronous operation of the parallel units. Parallel-operating units are also subject to stresses caused by unequal thermal stress distribution. Both of these problemscan, nevertheless, be handled with a proper circulating current control. To design an effective circulating current control system, we need information about circulating current dynamics. The dynamics of the circulating currents can be investigated by developing appropriate mathematical models. In this dissertation, circulating current models aredeveloped for two different types of parallel two-level three-phase inverter configurations. Themodels, which are developed for an arbitrary number of parallel units, provide a framework for analyzing circulating current generation mechanisms and developing circulating current control systems. In addition to developing circulating current models, modulation of parallel inverters is considered. It is illustrated that depending on the parallel inverter configuration and the modulation method applied, common-mode circulating currents may be excited as a consequence of the differential-mode circulating current control. To prevent the common-mode circulating currents that are caused by the modulation, a dual modulator method is introduced. The dual modulator basically consists of two independently operating modulators, the outputs of which eventually constitute the switching commands of the inverter. The two independently operating modulators are referred to as primary and secondary modulators. In its intended usage, the same voltage vector is fed to the primary modulators of each parallel unit, and the inputs of the secondary modulators are obtained from the circulating current controllers. To ensure that voltage commands obtained from the circulating current controllers are realizable, it must be guaranteed that the inverter is not driven into saturation by the primary modulator. The inverter saturation can be prevented by limiting the inputs of the primary and secondary modulators. Because of this, also a limitation algorithm is proposed. The operation of both the proposed dual modulator and the limitation algorithm is verified experimentally.

Cuticular and Suberin Polymers of Edible Plants. Analysis by Gas Chromatographic-Mass Spectrometric and Solid State Spectroscopic Methods

Cutin and suberin are structural and protective polymers of plant surfaces. The epidermal cells of the aerial parts of plants are covered with an extracellular cuticular layer, which consists of polyester cutin, highly resistant cutan, cuticular waxes and polysaccharides which link the layer to the epidermal cells. A similar protective layer is formed by a polyaromatic-polyaliphatic biopolymer suberin, which is present particularly in the cell walls of the phellem layer of periderm of the underground parts of plants (e.g. roots and tubers) and the bark of trees. In addition, suberization is also a major factor in wound healing and wound periderm formation regardless of the plants’ tissue. Knowledge of the composition and functions of cuticular and suberin polymers is important for understanding the physiological properties for the plants and for nutritional quality when these plants are consumed as foods. The aims of the practical work were to assess the chemical composition of cuticular polymers of several northern berries and seeds and suberin of two varieties of potatoes. Cutin and suberin were studied as isolated polymers and further after depolymerization as soluble monomers and solid residues. Chemical and enzymatic depolymerization techniques were compared and a new chemical depolymerization method was developed. Gas chromatographic analysis with mass spectrometric detection (GC-MS) was used to assess the monomer compositions. Polymer investigations were conducted with solid state carbon-13 cross polarization magic angle spinning nuclear magnetic resonance spectroscopy (13C CP-MAS NMR), Fourier transform infrared spectroscopy (FTIR) and microscopic analysis. Furthermore, the development of suberin over one year of post-harvest storage was investigated and the cuticular layers from berries grown in the North and South of Finland were compared. The results show that the amounts of isolated cuticular layers and cutin monomers, as well as monomeric compositions vary greatly between the berries. The monomer composition of seeds was found to differ from the corresponding berry peel monomers. The berry cutin monomers were composed mostly of long-chain aliphatic ω-hydroxy acids, with various mid-chain functionalities (double-bonds, epoxy, hydroxy and keto groups). Substituted α,ω-diacids predominated over ω-hydroxy acids in potato suberin monomers and slight differences were found between the varieties. The newly-developed closed tube chemical method was found to be suitable for cutin and suberin analysis and preferred over the solvent-consuming and laborious reflux method. Enzymatic hydrolysis with cutinase was less effective than chemical methanolysis and showed specificity towards α,ω-diacid bonds. According to ₁₃C CP-MAS NMR and FTIR, the depolymerization residues contained significant amounts of aromatic structures, polysaccharides and possible cutan-type aliphatic moieties. Cultivation location seems to have effect on cuticular composition. The materials studied contained significant amounts of different types of biopolymers that could be utilized for several purposes with or without further processing. The importance of the so-called waste material from industrial processes of berries and potatoes as a source of either dietary fiber or specialty chemicals should be further investigated in detail. The evident impact of cuticular and suberin polymers, among other fiber components, on human health should be investigated in clinical trials. These by-product materials may be used as value-added fiber fractions in the food industry and as raw materials for specialty chemicals such as lubricants and emulsifiers, or as building blocks for novel polymers.

Exploration and Design of Power-Efficient Networked Many-Core Systems

Multiprocessing is a promising solution to meet the requirements of near future applications. To get full benefit from parallel processing, a manycore system needs efficient, on-chip communication architecture. Networkon- Chip (NoC) is a general purpose communication concept that offers highthroughput, reduced power consumption, and keeps complexity in check by a regular composition of basic building blocks. This thesis presents power efficient communication approaches for networked many-core systems. We address a range of issues being important for designing power-efficient manycore systems at two different levels: the network-level and the router-level. From the network-level point of view, exploiting state-of-the-art concepts such as Globally Asynchronous Locally Synchronous (GALS), Voltage/ Frequency Island (VFI), and 3D Networks-on-Chip approaches may be a solution to the excessive power consumption demanded by today’s and future many-core systems. To this end, a low-cost 3D NoC architecture, based on high-speed GALS-based vertical channels, is proposed to mitigate high peak temperatures, power densities, and area footprints of vertical interconnects in 3D ICs. To further exploit the beneficial feature of a negligible inter-layer distance of 3D ICs, we propose a novel hybridization scheme for inter-layer communication. In addition, an efficient adaptive routing algorithm is presented which enables congestion-aware and reliable communication for the hybridized NoC architecture. An integrated monitoring and management platform on top of this architecture is also developed in order to implement more scalable power optimization techniques. From the router-level perspective, four design styles for implementing power-efficient reconfigurable interfaces in VFI-based NoC systems are proposed. To enhance the utilization of virtual channel buffers and to manage their power consumption, a partial virtual channel sharing method for NoC routers is devised and implemented. Extensive experiments with synthetic and real benchmarks show significant power savings and mitigated hotspots with similar performance compared to latest NoC architectures. The thesis concludes that careful codesigned elements from different network levels enable considerable power savings for many-core systems.

A feature-based object-oriented expert system to model and support product design

In this paper a computer program to model and support product design is presented. The product is represented through a hierarchical structure that allows the user to navigate across the product’s components, and it aims at facilitating each step of the detail design process. A graphical interface was also developed, which shows visually to the user the contents of the product structure. Features are used as building blocks for the parts that compose the product, and object-oriented methodology was used as a means to implement the product structure. Finally, an expert system was also implemented, whose knowledge base rules help the user design a product that meets design and manufacturing requirements.

Very High Energy Gamma-Rays emitting BL LAC's Population Study

Context: BL Lacs are the most numerous extragalactic objects which are detected in Very High Energy (VHE) gamma-rays band. They are a subclass of blazars. Large flux variability amplitude, sometimes happens in very short time scale, is a common characteristic of them. Significant optical polarization is another main characteristics of BL Lacs. BL Lacs' spectra have a continuous and featureless Spectral Energy Distribution (SED) which have two peaks. Among 1442 BL Lacs in the Roma-BZB catalogue, only 51 are detected in VHE gamma-rays band. BL Lacs are most numerous (more than 50% of 514 objects) objects among the sources that are detected above 10 GeV by FERMI-LAT. Therefore, many BL Lacs are expected to be discovered in VHE gamma-rays band. However, due to the limitation on current and near future technology of Imaging Air Cherenkov Telescope, astronomers are forced to predict whether an object emits VHE gamma-rays or not. Some VHE gamma-ray prediction methods are already introduced but still are not confirmed. Cross band correlations are the building blocks of introducing VHE gamma-rays prediction method. Aims: We will attempt to investigate cross band correlations between flux energy density, luminosity and spectral index of the sample. Also, we will check whether recently discovered MAGIC J2001+435 is a typical BL Lac. Methods: We select a sample of 42 TeV BL Lacs and collect 20 of their properties within five energy bands from literature and Tuorla blazar monitoring program database. All of the data are synchronized to be comparable to each other. Finally, we choose 55 pair of datasets for cross band correlations finding and investigating whether there is any correlation between each pair. For MAGIC J2001+435 we analyze the publicly available SWIFT-XRT data, and use the still unpublished VHE gamma-rays data from MAGIC collaboration. The results are compared to the other sources of the sample. Results: Low state luminosity of multiple detected VHE gamma-rays is strongly correlated luminosities in all other bands. However, the high state does not show such strong correlations. VHE gamma-rays single detected sources have similar behaviour to the low state of multiple detected ones. Finally, MAGIC J2001+435 is a typical TeV BL Lac. However, for some of the properties this source is located at the edge of the whole sample (e.g. in terms of X-rays flux). Keywords: BL Lac(s), Population study, Correlations finding, Multi wavelengths analysis, VHE gamma-rays, gamma-rays, X-rays, Optical, Radio

Chemical derivatization of galactoglucomannan for functional materials

In the framework of the biorefinery concept researchers aspire to optimize the utilization of plant materials, such as agricultural wastes and wood. For most of the known processes, the first steps in the valorisation of biomass are the extraction and purification of the individual components. The obtained raw products by means of a controlled separation can consecutively be modified to result in biofuels or biogas for energy production, but also in value-added products such as additives and important building blocks for the chemical and material industries. Considerable efforts are undertaken in order to substitute the use of oil-based starting materials or at least minimize their processing for the production of everyday goods. Wood is one of the raw materials, which have gained large attention in the last decades and its composition has been studied in detail. Nowadays, the extraction of water-soluble hemicelluloses from wood is well known and so for example xylan can be obtained from hardwoods and O-acetyl galactoglucomannans (GGMs) from softwoods. The aim of this work was to develop water-soluble amphiphilic materials of GGM and to assess their potential use as additives. Furthermore, GGM was also applied as a crosslinker in the synthesis of functional hydrogels for the removal of toxic metals and metalloid ions from aqueous solutions. The distinguished products were obtained by several chemical approaches and analysed by nuclear magnetic resonance spectroscopy (NMR), Fourier transform infrared spectroscopy (FTIR), size exclusion chromatography (SEC), thermal gravimetric analysis (TGA), scanning electron microscope SEM, among others. Bio-based surfactants were produced by applying GGM and different fatty acids as starting materials. On one hand, GGM-grafted-fatty acids were prepared by esterification and on the other hand, well-defined GGM-block-fatty acid derivatives were obtained by linking amino-functional fatty acids to the reducing end of GGM. The reaction conditions for the syntheses were optimized and the resultant amphiphilic GGM derivatives were evaluated concerning their ability to reduce the surface tension of water as surfactants. Furthermore, the block-structured derivatives were tested in respect to their applicability as additives for the surface modification of cellulosic materials. Besides the GGM surfactants with a bio-based hydrophilic and a bio-based hydrophobic part, also GGM block-structured derivatives with a synthetic hydrophobic tail, consisting of a polydimethylsiloxane chain, were prepared and assessed for the hydrophobization of surface of nanofibrillated cellulose films. In order to generate GGM block-structured derivatives containing a synthetic tail with distinguished physical and chemical properties, as well as a tailored chain length, a controlled polymerization method was used. Therefore, firstly an initiator group was introduced at the reducing end of the GGM and consecutively single electron transfer-living radical polymerization (SET-LRP) was performed by applying three different monomers in individual reactions. For the accomplishment of the synthesis and the analysis of the products, challenges related to the solubility of the reactants had to be overcome. Overall, a synthesis route for the production of GGM block-copolymers bearing different synthetic polymer chains was developed and several derivatives were obtained. Moreover, GGM with different molar masses were, after modification, used as a crosslinker in the synthesis of functional hydrogels. Hereby, a cationic monomer was used during the free radical polymerization and the resultant hydrogels were successfully tested for the removal of chromium and arsenic ions from aqueous solutions. The hydrogel synthesis was tailored and materials with distinguished physical properties, such as the swelling rate, were obtained after purification. The results generated in this work underline the potential of bio-based products and the urge to continue carrying out research in order to be able to use more green chemicals for the manufacturing of biorenewable and biodegradable daily products.

Distribution network design and optimization

The objective of this thesis is to examine distribution network designs and modeling practices and create a framework to identify best possible distribution network structure for the case company. The main research question therefore is: How to optimize case company’s distribution network in terms of customer needs and costs? Theory chapters introduce the basic building blocks of the distribution network design and needed calculation methods and models. Framework for the distribution network projects was created based on the theory and the case study was carried out by following the defined framework. Distribution network calculations were based on the company’s sales plan for the years 2014 - 2020. Main conclusions and recommendations were that the new Asian business strategy requires high investments in logistics and the first step is to open new satellite DC in China as soon as possible to support sales and second possible step is to open regional DC in Asia within 2 - 4 years.

JNK regulates dendrite and spine architecture in the central nervous system influencing spatial learning and motor tasks

JNK1 is a MAP-kinase that has proven a significant player in the central nervous system. It regulates brain development and the maintenance of dendrites and axons. Several novel phosphorylation targets of JNK1 were identified in a screen performed in the Coffey lab. These proteins were mainly involved in the regulation of neuronal cytoskeleton, influencing the dynamics and stability of microtubules and actin. These structural proteins form the dynamic backbone for the elaborate architecture of the dendritic tree of a neuron. The initiation and branching of the dendrites requires a dynamic interplay between the cytoskeletal building blocks. Both microtubules and actin are decorated by associated proteins which regulate their dynamics. The dendrite-specific, high molecular weight microtubule associated protein 2 (MAP2) is an abundant protein in the brain, the binding of which stabilizes microtubules and influences their bundling. Its expression in non-neuronal cells induces the formation of neurite-like processes from the cell body, and its function is highly regulated by phosphorylation. JNK1 was shown to phosphorylate the proline-rich domain of MAP2 in vivo in a previous study performed in the group. Here we verify three threonine residues (T1619, T1622 and T1625) as JNK1 targets, the phosphorylation of which increases the binding of MAP2 to microtubules. This binding stabilizes the microtubules and increases process formation in non-neuronal cells. Phosphorylation-site mutants were engineered in the lab. The non-phosphorylatable mutant of MAP2 (MAP2- T1619A, T1622A, T1625A) in these residues fails to bind microtubules, while the pseudo-phosphorylated form, MAP2- T1619D, T1622D, Thr1625D, efficiently binds and induces process formation even without the presence of active JNK1. Ectopic expression of the MAP2- T1619D, T1622D, Thr1625D in vivo in mouse brain led to a striking increase in the branching of cortical layer 2/3 (L2/3) pyramidal neurons, compared to MAP2-WT. The dendritic complexity defines the receptive field of a neuron and dictates the output to the postsynaptic cells. Previous studies in the group indicated altered dendrite architecture of the pyramidal neurons in the Jnk1-/- mouse motor cortex. Here, we used Lucifer Yellow loading and Sholl analysis of neurons in order to study the dendritic branching in more detail. We report a striking, opposing effect in the absence of Jnk1 in the cortical layers 2/3 and 5 of the primary motor cortex. The basal dendrites of pyramidal neurons close to the pial surface at L2/3 show a reduced complexity. In contrast, the L5 neurons, which receive massive input from the L2/3 neurons, show greatly increased branching. Another novel substrate identified for JNK1 was MARCKSL1, a protein that regulates actin dynamics. It is highly expressed in neurons, but also in various cancer tissues. Three phosphorylation target residues for JNK1 were identified, and it was demonstrated that their phosphorylation reduces actin turnover and retards migration of these cells. Actin is the main cytoskeletal component in dendritic spines, the site of most excitatory synapses in pyramidal neurons. The density and gross morphology of the Lucifer Yellow filled dendrites were characterized and we show reduced density and altered morphology of spines in the motor cortex and in the hippocampal area CA3. The dynamic dendritic spines are widely considered to function as the cellular correlate during learning. We used a Morris water maze to test spatial memory. Here, the wild-type mice outperformed the knock-out mice during the acquisition phase of the experiment indicating impaired special memory. The L5 pyramidal neurons of the motor cortex project to the spinal cord and regulate the movement of distinct muscle groups. Thus the altered dendrite morphology in the motor cortex was expected to have an effect on the input-output balance in the signaling from the cortex to the lower motor circuits. A battery of behavioral tests were conducted for the wild-type and Jnk1-/- mice, and the knock-outs performed poorly compared to wild-type mice in tests assessing balance and fine motor movements. This study expands our knowledge of JNK1 as an important regulator of the dendritic fields of neurons and their manifestations in behavior.

Pressurized hot water flow-through extraction of birch wood

Effective processes to fractionate the main compounds in biomass, such as wood, are a prerequisite for an effective biorefinery. Water is environmentally friendly and widely used in industry, which makes it a potential solvent also for forest biomass. At elevated temperatures over 100 °C, water can readily hydrolyse and dissolve hemicelluloses from biomass. In this work, birch sawdust was extracted using pressurized hot water (PHWE) flow-through systems. The hypothesis of the work was that it is possible to obtain polymeric, water-soluble hemicelluloses from birch sawdust using flow-through PHW extractions at both laboratory and large scale. Different extraction temperatures in the range 140–200 °C were evaluated to see the effect of temperature to the xylan yield. The yields and extracted hemicelluloses were analysed to obtain sugar ratios, the amount of acetyl groups, furfurals and the xylan yields. Higher extraction temperatures increased the xylan yield, but decreased the molar mass of the dissolved xylan. As the extraction temperature increased, more acetic acid was released from the hemicelluloses, thus further decreasing the pH of the extract. There were only trace amounts of furfurals present after the extractions, indicating that the treatment was mild enough not to degrade the sugars further. The sawdust extraction density was increased by packing more sawdust in the laboratory scale extraction vessel. The aim was to obtain extracts with higher concentration than in typical extraction densities. The extraction times and water flow rates were kept constant during these extractions. The higher sawdust packing degree decreased the water use in the extractions and the extracts had higher hemicellulose concentrations than extractions with lower sawdust degrees of packing. The molar masses of the hemicelluloses were similar in higher packing degrees and in the degrees of packing that were used in typical PHWE flow-through extractions. The structure of extracted sawdust was investigated using small angle-(SAXS) and wide angle (WAXS) x-ray scattering. The cell wall topography of birch sawdust and extracted sawdust was compared using x-ray tomography. The results showed that the structure of the cell walls of extracted birch sawdust was preserved but the cell walls were thinner after the extractions. Larger pores were opened inside the fibres and cellulose microfibrils were more tightly packed after the extraction. Acetate buffers were used to control the pH of the extracts during the extractions. The pH control prevented excessive xylan hydrolysis and increased the molar masses of the extracted xylans. The yields of buffered extractions were lower than for plain water extractions at 160–170 °C, but at 180 °C yields were similar to those from plain water and pH buffers. The pH can thus be controlled during extraction with acetate buffer to obtain xylan with higher molar mass than those obtainable using plain water. Birch sawdust was extracted both in the laboratory and pilot scale. The performance of the PHWE flow-through system was evaluated in the laboratory and the pilot scale using vessels with the same shape but different volumes, with the same relative water flow through the sawdust bed, and in the same extraction temperature. Pre-steaming improved the extraction efficiency and the water flow through the sawdust bed. The extracted birch sawdust and the extracted xylan were similar in both laboratory and pilot scale. The PHWE system was successfully scaled up by a factor of 6000 from the laboratory to pilot scale and extractions performed equally well in both scales. The results show that a flow-through system can be further scaled up and used to extract water-soluble xylans from birch sawdust. Extracted xylans can be concentrated, purified, and then used in e.g. films and barriers, or as building blocks for novel material applications.

Brand Identity of an Ecological Oriented SME

Tämän eksploratiivisen tutkimuksen tarkoituksena on tutkia yrittäjän persoonallisuuden roolia ekologisesti suuntautuneen brändin identiteetin ja assosiaatioiden rakentamisessa. Tutkimus on tehty yrittäjän näkökulmasta, jonka kontekstina ovat pienet ja keskisuuret yritykset. Tämä tutkimus pyrkii laajentamaan ja saamaan ymmärrystä keskeisistä käsitteistä, ja samalla edistämään PK-yrityksiin liittyvää kirjallisuutta. Tämän lisäksi tutkimus tarkastelee mitä assosiaatioita ekologisesti suuntautunut brändi korostaa identiteetissään. Tutkimus suoritettiin tapaustutkimuksena. Laadullista primääridataa kerättiin teemahaastattelemalla yrittäjää, havainnoimalla yhtä case-yrityksen messuosastoa, sekä keräämällä yrittäjän persoonallisuusattribuutteja. Jotta tutkimus saavuttaisi myös datan triangulaation, sekundääristä dataa kerättiin vahvistamaan aiempaa tutkimusta. Yhtenä sekundäärilähteenä toimivat kaksi artikkelia, jotka auttoivat vahvistamaan aiemmin esiin nostetut yrittäjän persoonallisuusattribuutit. Persoonallisuusattribuutteja verrattiin case-yrityksen brändin identiteettiin, jotta yrittäjän persoonallisuuden rooli brändin identiteetin rakentamisessa saataisiin selville. Tulokset osoittivat yhteyden brändin identiteetin ja yrittäjän persoonallisuuden välillä ekologisesti suuntautuneessa case-yrityksessä. Tulokset paljastivat myös joitakin yleisiä assosiaatioita joita luodaan ja vahvistetaan brändin identiteetin eri osa-alueiden avulla.

Synthesis of Short Oligonucleotides on a Soluble Support by the Phosphoramidite Method

In the last decades, the chemical synthesis of short oligonucleotides has become an important aspect of study due to the discovery of new functions for nucleic acids such as antisense oligonucleotides (ASOs), aptamers, DNAzymes, microRNA (miRNA) and small interfering RNA (siRNA). The applications in modern therapies and fundamental medicine on the treatment of different cancer diseases, viral infections and genetic disorders has established the necessity to develop scalable methods for their cheaper and easier industrial manufacture. While small scale solid-phase oligonucleotide synthesis is the method of choice in the field, various challenges still remain associated with the production of short DNA and RNA-oligomers in very large quantities. On the other hand, solution phase synthesis of oligonucleotides offers a more predictable scaling-up of the synthesis and is amenable to standard industrial manufacture techniques. In the present thesis, various protocols for the synthesis of short DNA and RNA oligomers have been studied on a peracetylated and methylated β-cyclodextrin, and also on a pentaerythritol-derived support. On using the peracetylated and methylated β-cyclodextrin soluble supports, the coupling cycle was simplified by replacement of the typical 5′-O-(4,4′-dimethoxytrityl) protecting group with an acid-labile acetal-protected 5′-O-(1-methoxy-1-methylethyl) group, which upon acid-catalyzed methanolysis released easily removable volatile products. For this reason monomeric building blocks 5′-O-(1-methoxy-1-methylethyl) 3′-(2-cyano-ethyl-N,N-diisopropylphosphoramidite) were synthesized. Alternatively, on using the precipitative pentaerythritol support, novel 2´-O-(2-cyanoethyl)-5´-O-(1-methoxy-1-methylethyl) protected phosphoramidite building blocks for RNA synthesis have been prepared and their applicability by the synthesis of a pentamer was demonstrated. Similarly, a method for the preparation of short RNAs from commercially available 5´-O-(4,4´-dimethoxytrityl)-2´-O-(tert-butyldimethyl-silyl)ribonucleoside 3´-(2-cyanoethyl-N,N-diisopropylphosphoramidite) building blocks has been developed

Bio and chemocatalysis for stereo and regioselective one-pot reaction applications

The development of cost efficient, selective and sustainable chemical processes for production of chiral building blocks is of great importance in synthetic and industrial organic chemistry. One way to reach these objectives is to carry out several reactions steps in one vessel at one time. Furthermore, when this kind of one-pot multi step reactions are catalyzed by heterogeneous chemo- and bio-catalysts, which can be separated from the reaction products by filtration, practical access to chiral small molecules for further utilization can be obtained. The initial reactions studied in this thesis are the two step dynamic kinetic resolution of rac-2-hydroxy-1-indanone and the regioselective hydrogenation of 1,2-indanedione. These reactions are then combined in a new heterogeneously catalyzed one-pot reaction sequence enabling simple recovery of the catalysts by filtration, facilitating simple reaction product isolation. Conclusively, the readily available 1,2-indanedione is by the presented one-pot sequence, utilizing heterogeneous enzyme and transition metal based catalysts, transferred with high regio- and stereoselectivity to a useful chiral vicinal hydroxyl ketone structure. Additional and complementary investigation of homogeneous half-sandwich ruthenium complexes for catalyzing the epimerization of chiral secondary alcohols of five natural products containing additional non-functionalized stereocenters was conducted. In principle, this kind of epimerization reactions of single stereocenters could be utilized for converting inexpensive starting materials, containing other stereogenic centers, into diastereomeric mixtures from which more valuable compounds can be isolated by traditional isolation techniques.

From protein structure to function with bioinformatics

It has long been known that amino acids are the building blocks for proteins and govern their folding into specific three-dimensional structures. However, the details of this process are still unknown and represent one of the main problems in structural bioinformatics, which is a highly active research area with the focus on the prediction of three-dimensional structure and its relationship to protein function. The protein structure prediction procedure encompasses several different steps from searches and analyses of sequences and structures, through sequence alignment to the creation of the structural model. Careful evaluation and analysis ultimately results in a hypothetical structure, which can be used to study biological phenomena in, for example, research at the molecular level, biotechnology and especially in drug discovery and development. In this thesis, the structures of five proteins were modeled with templatebased methods, which use proteins with known structures (templates) to model related or structurally similar proteins. The resulting models were an important asset for the interpretation and explanation of biological phenomena, such as amino acids and interaction networks that are essential for the function and/or ligand specificity of the studied proteins. The five proteins represent different case studies with their own challenges like varying template availability, which resulted in a different structure prediction process. This thesis presents the techniques and considerations, which should be taken into account in the modeling procedure to overcome limitations and produce a hypothetical and reliable three-dimensional structure. As each project shows, the reliability is highly dependent on the extensive incorporation of experimental data or known literature and, although experimental verification of in silico results is always desirable to increase the reliability, the presented projects show that also the experimental studies can greatly benefit from structural models. With the help of in silico studies, the experiments can be targeted and precisely designed, thereby saving both money and time. As the programs used in structural bioinformatics are constantly improved and the range of templates increases through structural genomics efforts, the mutual benefits between in silico and experimental studies become even more prominent. Hence, reliable models for protein three-dimensional structures achieved through careful planning and thoughtful executions are, and will continue to be, valuable and indispensable sources for structural information to be combined with functional data.

Life without Phd? – Phd Oxygen Sensor Proteins in Hypoxic Carcinoma Cell Survival

The microenvironment within the tumor plays a central role in cellular signaling. Rapidly proliferating cancer cells need building blocks for structures as well as nutrients and oxygen for energy production. In normal tissue, the vasculature effectively transports oxygen, nutrient and waste products, and maintains physiological pH. Within a tumor however, the vasculature is rarely sufficient for the needs of tumor cells. This causes the tumor to suffer from lack of oxygen (hypoxia) and nutrients as well as acidification, as the glycolytic end product lactate is accumulated. Cancer cells harbor mutations enabling survival in the rough microenvironment. One of the best characterized mutations is the inactivation of the von Hippel-Lindau protein (pVHL) in clear cell renal cell carcinoma (ccRCC). Inactivation causes constitutive activation of hypoxia-inducible factor HIF which is an important survival factor regulating glycolysis, neovascularization and apoptosis. HIFs are normally regulated by HIF prolyl hydroxylases (PHDs), which in the presence of oxygen target HIF α-subunit to ubiquitination by pVHL and degradation by proteasomes. In my thesis work, I studied the role of PHDs in the survival of carcinoma cells in hypoxia. My work revealed an essential role of PHD1 and PHD3 in cell cycle regulation through two cyclin-dependent kinase inhibitors (CKIs) p21 and p27. Depletion of PHD1 or PHD3 caused a cell cycle arrest and subjected the carcinoma cells to stress and impaired the survival.