Artificial Ribonucleases: Oligonucleotides Conjugated with Metal Ion Chelates of Azacrowns

Ribonucleic acid (RNA) has many biological roles in cells: it takes part in coding, decoding, regulating and expressing of the genes as well as has the capacity to work as a catalyst in numerous biological reactions. These qualities make RNA an interesting object of various studies. Development of useful tools with which to investigate RNA is a prerequisite for more advanced research in the field. One of such tools may be the artificial ribonucleases, which are oligonucleotide conjugates that sequence-selectively cleave complementary RNA targets. This thesis is aimed at developing new efficient metal-ion-based artificial ribonucleases. On one hand, to solve the challenges related to solid-supported synthesis of metal-ion-binding conjugates of oligonucleotides, and on the other hand, to quantify their ability to cleave various oligoribonucleotide targets in a pre-designed sequence selective manner. In this study several artificial ribonucleases based on cleaving capability of metal ion chelated azacrown moiety were designed and synthesized successfully. The most efficient ribonucleases were the ones with two azacrowns close to the 3´- end of the oligonucleotide strand. Different transition metal ions were introduced into the azacrown moiety and among them, the Zn2+ ion was found to be better than Cu2+ and Ni2+ ions.

An account of a copy from the 15th century of a map of the world engraved on metal, which is preserved in cardinal Stephan Borgia's museum at Velletri

Erip.: Ymer 1891.

Welding of additively manufactured stainless steel parts: Comparative study between sheet metal and selective laser melted parts

Additive manufacturing is a fast growing manufacturing technology capable of producing complex objects without the need for conventional manufacturing process planning. During the process the work piece is built by adding material one layer at a time according to a digital 3D CAD model. At first additive manufacturing was mainly used to make prototypes but the development of the technology has made it possible to also make final products. Welding is the most common joining method for metallic materials. As the maximum part size of additive manufacturing is often limited, it may sometimes be required to join two or more additively manufactured parts together. However there has been almost no research on the welding of additively manufactured parts so far, which means that there has been very little information available on the possible differences compared to the welding of sheet metal parts. The aim of this study was to compare the weld joint properties of additively manufactured parts to those of sheet metal parts. The welding process that was used was TIG welding and the test material was 316L austenitic stainless steel. Weld joint properties were studied by making tensile, bend and hardness tests and by studying the weld microstructures with a microscope. Results show that there are certain characteristics in the welds of additively manufactured parts. The building direction of the test pieces has some impact on the mechanical properties of the weld. Nevertheless all the welds exhibited higher yield strength than the sheet metal welds but at the same time elongation at break was lower. It was concluded that TIG welding is a feasible process for welding additively manufactured parts.

Nitric oxide, cholesterol oxides and endothelium-dependent vasodilation in plasma of patients with essential hypertension

The objective of the present study was to identify disturbances of nitric oxide radical (·NO) metabolism and the formation of cholesterol oxidation products in human essential hypertension. The concentrations of·NO derivatives (nitrite, nitrate, S-nitrosothiols and nitrotyrosine), water and lipid-soluble antioxidants and cholesterol oxides were measured in plasma of 11 patients with mild essential hypertension (H: 57.8 ± 9.7 years; blood pressure, 148.3 ± 24.8/90.8 ± 10.2 mmHg) and in 11 healthy subjects (N: 48.4 ± 7.0 years; blood pressure, 119.4 ± 9.4/75.0 ± 8.0 mmHg).Nitrite, nitrate and S-nitrosothiols were measured by chemiluminescence and nitrotyrosine was determined by ELISA. Antioxidants were determined by reverse-phase HPLC and cholesterol oxides by gas chromatography. Hypertensive patients had reduced endothelium-dependent vasodilation in response to reactive hyperemia (H: 9.3 and N: 15.1% increase of diameter 90 s after hyperemia), and lower levels of ascorbate (H: 29.2 ± 26.0, N: 54.2 ± 24.9 µM), urate (H: 108.5 ± 18.9, N: 156.4 ± 26.3 µM), ß-carotene (H: 1.1 ± 0.8, N: 2.5 ± 1.2 nmol/mg cholesterol), and lycopene (H: 0.4 ± 0.2, N: 0.7 ± 0.2 nmol/mg cholesterol), in plasma, compared to normotensive subjects. The content of 7-ketocholesterol, 5alpha-cholestane-3ß,5,6ß-triol and 5,6alpha-epoxy-5alpha-cholestan-3alpha-ol in LDL, and the concentration of endothelin-1 (H: 0.9 ± 0.2, N: 0.7 ± 0.1 ng/ml) in plasma were increased in hypertensive patients. No differences were found for ·NO derivatives between groups. These data suggest that an increase in cholesterol oxidation is associated with endothelium dysfunction in essential hypertension and oxidative stress, although ·NO metabolite levels in plasma are not modified in the presence of elevated cholesterol oxides.

Metal additive manufacturing of internal flow channels with powder bed fusion processes

This thesis studies the advantages, disadvantages and possibilities of additive manufacturing in making components with internal flow channels. These include hydraulic components, components with cooling channels and heat exchangers. Processes studied in this work are selective laser sintering and selective laser melting of metallic materials. The basic principles of processes and parameters involved in the process are presented and different possibilities of internal channel manufacturing and flow improvement are introduced

Emission, kinetic and magnetic phenomena in rare-earth and transition metal doped ZnSe single crystals

In this work emission, optical, electrical and magnetic properties of the d- and f- elements doped zinc selenide crystals were investigated within a wide temperature range. Doping was performed in various technological processes: during the growth by chemical vapor transport method; by thermal diffusion from the Bi or Zn melt. Concentration of the doping impurity in the crystals was controlled by amount of the dopant in the source material or by its concentration in the doping media. Special interest in the work was paid to the influence of the different concentrations of Cr and Yb impurities on ZnSe crystals’ properties, correlations between observed effects and similarities with the Ni, Mn and Gd dopants are analysed. Possibility of formation of the excitons bound to the doping d-ions was shown. In contrast to this, it was observed that f-elements do not bound excitons, but prevent formation of excitons bound to some uncontrolled impurities. A mechanism of Cr doping impurity interaction with background impurities and zinc selenide structural defects was proposed based on experimental data. An assumption about resonant energy transfer between double charged chromium ions and complexes based on crystals’ vacancy defects was made. A correlation between emission and magnetic properties of the d- ions doped samples was established. Based on this correlation a mechanism explaining the concentration quench of the emission was proposed. It was found that f-ions bind electrically active shallow and deep donor and acceptor states of background impurity to electrically neutral complexes. This may be observed as “purification” of ZnSe crystals by doping with the rare-earth elements, resulting i tendency of the properties of f-ion doped crystals to the properties of intrinsic crystals, but with smaller concentration of uncontrolled native and impurity defects. A possible interpretation of this effect was proposed. It was shown that selenium substituting impurities decrease efficiency of the Yb doping. Based on this experimental results an attempt to determine ytterbium ion surroundings in the crystal lattice was made. It was shown that co-doping of zinc selenide crystals with the d- and f- ions leads to the combination of the impurities influence on the material’s properties. On the basis of obtained data an interaction mechanism of the d- and f-elements co-dopants was proposed. Guided by the model of the ytterbium ion incorporation in the selenide sublattice of the ZnSe crystals, an assumption about stabilization of single charged chromium ions in the zinc sublattice crystal nodes, by means of formation of the local charge compensating clusters, was made.

Predictors of restenosis after percutaneous coronary intervention using bare-metal stents: a comparison between patients with and without dysglycemia

The objective of this study was to identify intravascular ultrasound (IVUS), angiographic and metabolic parameters related to restenosis in patients with dysglycemia. Seventy consecutive patients (77 lesions) selected according to inclusion and exclusion criteria were evaluated by the oral glucose tolerance test and the determination of insulinemia after a successful percutaneous coronary intervention (PCI) with a bare-metal stent. The degree of insulin resistance was calculated by the homeostasis model assessment of insulin resistance (HOMA-IR). Six-month IVUS and angiogram follow-up were performed. Thirty-nine patients (55.7%) had dysglycemia. The restenosis rate in the dysglycemic group was 37.2 vs 23.5% in the euglycemic group (P = 0.299). The predictors of restenosis using bivariate analysis were reference vessel diameter (RVD): £2.93 mm (RR = 0.54; 95%CI = 0.05-0.78; P = 0.048), stent area (SA): <8.91 mm² (RR = 0.66; 95%CI = 0.24-0.85; P = 0.006), stent volume (SV): <119.75 mm³ (RR = 0.74; 95%CI = 0.38-0.89; P = 0.0005), HOMA-IR: >2.063 (RR = 0.44; 95%CI = 0.14-0.64; P = 0.027), and fasting plasma glucose (FPG): ≤108.8 mg/dL (RR = 0.53; 95%CI = 0.13-0.75; P = 0.046). SV was an independent predictor of restenosis by multivariable analysis. Dysglycemia is a common clinical condition in patients submitted to PCI. The degree of insulin resistance, FPG, RVD, SA, and SV were correlated with restenosis. SV was inversely correlated with an independent predictor of restenosis in patients treated with a bare-metal stent.

Weldability of powder bed fusion fabricated stainless steel 316L sheets to cold rolled sheet metal

Weldability of powder bed fusion (PBF) fabricated components has come to discussion in past two years due to resent developments in the PBF technology and limited size of the machines used in the fabrication process. This study concentrated on effects of energy input of welding on mechanical properties and microstructural features of welds between PBF fabricated stainless steel 316L sheets and cold rolled sheet metal of same composition by the means of destructive testing and microscopic analysis. Optical fiber diameter, laser power and welding speed were varied during the experiments that were executed following one variable at a time (OVAT) method. One of the problems of welded PBF fabricated components has been lower elongations at break comparing to conventionally manufactured components. Decreasing energy input of the laser keyhole welding decreased elongations at break of the welded specimens. Ultimate tensile strengths were not affected significantly by the energy input of the welding, but fracturing of the specimens welded using high energy input occurred from the weld metal. Fracturing of the lower energy input welds occurred from the PBF fabricated base metal. Energy input was found to be critical factor for mechanical properties of the welds. Multioriented grain growth and formation of neck at fusion zone boundary on the cold rolled side of the weld was detected and suspected to be result from weld pool flows caused by differences in molten weld pool behaviour between the PBF fabricated and cold rolled sides of the welds.

The role of metal ions in selective and sustainable processes

Sustainability and recycling are core values in today’s industrial operations. New materials, products and processes need to be designed in such a way as to consume fewer of the diminishing resources we have available and to put as little strain on the environment as possible. An integral part of this is cleaning and recycling. New processes are to be designed to improve the efficiency in this aspect. Wastewater, including municipal wastewaters, is treated in several steps including chemical and mechanical cleaning of waters. Well-cleaned water can be recycled and reused. Clean water for everyone is one of the greatest challenges we are facing today. Ferric sulphate, made by oxidation from ferrous sulphate, is used in water purification. The oxidation of ferrous sulphate, FeSO4, to ferric sulphate in acidic aqueous solutions of H2SO4 over finely dispersed active carbon particles was studied in a vigorously stirred batch reactor. Molecular oxygen was used as the oxidation agent and several catalysts were screened: active carbon, active carbon impregnated with Pt, Rh, Pd and Ru. Both active carbon and noble metal-active carbon catalysts enhanced the oxidation rate considerably. The order of the noble metals according to the effect was: Pt >> Rh > Pd, Ru. By the use of catalysts, the production capacities of existing oxidation units can be considerably increased. Good coagulants have a high charge on a long polymer chain effectively capturing dirty particles of the opposite charge. Analysis of the reaction product indicated that it is possible to obtain polymeric iron-based products with good coagulation properties. Systematic kinetic experiments were carried out at the temperature and pressure ranges of 60B100°C and 4B10 bar, respectively. The results revealed that both non-catalytic and catalytic oxidation of Fe2+ to Fe3+ take place simultaneously. The experimental data were fitted to rate equations, which were based on a plausible reaction mechanism: adsorption of dissolved oxygen on active carbon, electron transfer from Fe2+ ions to adsorbed oxygen and formation of surface hydroxyls. A comparison of the Fe2+ concentrations predicted by the kinetic model with the experimentally observed concentrations indicated that the mechanistic rate equations were able to describe the intrinsic oxidation kinetics of Fe2+ over active carbon and active carbon-noble metal catalysts. Engineering aspects were closely considered and effort was directed to utilizing existing equipment in the production of the new coagulant. Ferrous sulphate can be catalytically oxidized to produce a novel long-chained polymeric iron-based flocculent in an easy and affordable way in existing facilities. The results can be used for modelling the reactors and for scale-up. Ferric iron (Fe3+) was successfully applied for the dissolution of sphalerite. Sphalerite contains indium, gallium and germanium, among others, and the application can promote their recovery. The understanding of the reduction process of ferric to ferrous iron can be used to develop further the understanding of the dissolution mechanisms and oxidation of ferrous sulphate. Indium, gallium and germanium face an ever-increasing demand in the electronics industry, among others. The supply is, however, very limited. The fact that most part of the material is obtained through secondary production means that real production quota depends on the primary material production. This also sets the pricing. The primary production material is in most cases zinc and aluminium. Recycling of scrap material and the utilization of industrial waste, containing indium, gallium and geranium, is a necessity without real options. As a part of this study plausible methods for the recovery of indium, gallium and germanium have been studied. The results were encouraging and provided information about the precipitation of these valuables from highly acidic solutions. Indium and gallium were separated from acidic sulphuric acid solutions by precipitation with basic sulphates such as alunite or they were precipitated as basic sulphates of their own as galliunite and indiunite. Germanium may precipitate as a basic sulphate of a mixed composition. The precipitation is rapid and the selectivity is good. When the solutions contain both indium and gallium then the results show that gallium should be separated before indium to achieve a better selectivity. Germanium was separated from highly acidic sulphuric acid solutions containing other metals as well by precipitating with tannic acid. This is a highly selective method. According to the study other commonly found metals in the solution do not affect germanium precipitation. The reduction of ferric iron to ferrous, the precipitation of indium, gallium and germanium, and the dissolution of the raw materials are strongly depending on temperature and pH. The temperature and pH effect were studied and which contributed to the understanding and design of the different process steps. Increased temperature and reduced pH improve the reduction rate. Finally, the gained understanding in the studied areas can be employed to develop better industrial processes not only on a large scale but also increasingly on a smaller scale. The small amounts of indium, gallium and germanium may favour smaller and more locally bound recovery.

Metal-Ion-Binding Oligonucleotides: High-Affinity Probes for Nucleic Acid Sequences

Small non-coding RNAs have numerous biological functions in cell and are divided into different classes such as: microRNA, snoRNA, snRNA and siRNA. MicroRNA (miRNA) is the most studied non-coding RNA to date and is found in plants, animals and some viruses. miRNA with short sequences is involved in suppressing translation of target genes by binding to their mRNA post-transcriptionally and silencing it. Their function besides silencing of the viral gene, can be oncogenic and therefore the cause of cancer. Hence, their roles are highlighted in human diseases, which increases the interest in using them as biomarkers and drug targets. One of the major problems to overcome is recognition of miRNA. Owing to a stable hairpin structure, chain invasion by conventional Watson-Crick base-pairing is difficult. One way to enhance the hybridization is exploitation of metal-ion mediated base-pairing, i. e. oligonucleotide probes that tightly bind a metal ions and are able to form a coordinative bonds between modified and natural nucleobases. This kind of metallo basepairs containing short modified oligonucleotides can also be useful for recognition of other RNA sequences containing hairpin-like structural motives, such as the TAR sequence of HIV. In addition, metal-ion-binding oligonucleotides will undoubtedly find applications in DNA-based nanotechnology. In this study, the 3,5-dimethylpyrazol-1-yl substituted purine derivatives were successfully incorporated within oligonucleotides, into either a terminal or non-terminal position. Among all of the modified oligonucleotides studied, a 2-(3,5-dimethylpyrazol-1-yl)-6-oxopurine base containing oligonucleotide was observed to bind most efficiently to their unmodified complementary sequences in the presence of both Cu2+ or Zn2+. The oligonucleotide incorporating 2,6-bis(3,5-dimethylpyrazol-1-yl)purine base also markedly increased the stability of duplexes in the presence of Cu2+ without losing the selectivity.

Hydrogen Sensor Application of Anodic Titanium Oxide Nanostructures

Hydrogen (H2) fuel cells have been considered a promising renewable energy source. The recent growth of H2 economy has required highly sensitive, micro-sized and cost-effective H2 sensor for monitoring concentrations and alerting to leakages due to the flammability and explosiveness of H2 Titanium dioxide (TiO2) made by electrochemical anodic oxidation has shown great potential as a H2 sensing material. The aim of this thesis is to develop highly sensitive H2 sensor using anodized TiO2. The sensor enables mass production and integration with microelectronics by preparing the oxide layer on suitable substrate. Morphology, elemental composition, crystal phase, electrical properties and H2 sensing properties of TiO2 nanostructures prepared on Ti foil, Si and SiO2/Si substrates were characterized. Initially, vertically oriented TiO2 nanotubes as the sensing material were obtained by anodizing Ti foil. The morphological properties of tubes could be tailored by varying the applied voltages of the anodization. The transparent oxide layer creates an interference color phenomena with white light illumination on the oxide surface. This coloration effect can be used to predict the morphological properties of the TiO2 nanostructures. The crystal phase transition from amorphous to anatase or rutile, or the mixture of anatase and rutile was observed with varying heat treatment temperatures. However, the H2 sensing properties of TiO2 nanotubes at room temperature were insufficient. H2 sensors using TiO2 nanostructures formed on Si and SiO2/Si substrates were demonstrated. In both cases, a Ti layer deposited on the substrates by a DC magnetron sputtering method was successfully anodized. A mesoporous TiO2 layer obtained on Si by anodization in an aqueous electrolyte at 5°C showed diode behavior, which was influenced by the work function difference of Pt metal electrodes and the oxide layer. The sensor enabled the detection of H2 (20-1000 ppm) at low operating temperatures (50–140°C) in ambient air. A Pd decorated tubular TiO2 layer was prepared on metal electrodes patterned SiO2/Si wafer by anodization in an organic electrolyte at 5°C. The sensor showed significantly enhanced H2 sensing properties, and detected hydrogen in the range of a few ppm with fast response/recovery time. The metal electrodes placed under the oxide layer also enhanced the mechanical tolerance of the sensor. The concept of TiO2 nanostructures on alternative substrates could be a prospect for microelectronic applications and mass production of gas sensors. The gas sensor properties can be further improved by modifying material morphologies and decorating it with catalytic materials.

Recognition of nucleic acids by metal ion complexes

Metal-ion-mediated base-pairing of nucleic acids has attracted considerable attention during the past decade, since it offers means to expand the genetic code by artificial base-pairs, to create predesigned molecular architecture by metal-ion-mediated inter- or intra-strand cross-links, or to convert double stranded DNA to a nano-scale wire. Such applications largely depend on the presence of a modified nucleobase in both strands engaged in the duplex formation. Hybridization of metal-ion-binding oligonucleotide analogs with natural nucleic acid sequences has received much less attention in spite of obvious applications. While the natural oligonucleotides hybridize with high selectivity, their affinity for complementary sequences is inadequate for a number of applications. In the case of DNA, for example, more than 10 consecutive Watson-Crick base pairs are required for a stable duplex at room temperature, making targeting of sequences shorter than this challenging. For example, many types of cancer exhibit distinctive profiles of oncogenic miRNA, the diagnostics of which is, however, difficult owing to the presence of only short single stranded loop structures. Metallo-oligonucleotides, with their superior affinity towards their natural complements, would offer a way to overcome the low stability of short duplexes. In this study a number of metal-ion-binding surrogate nucleosides were prepared and their interaction with nucleoside 5´-monophosphates (NMPs) has been investigated by 1H NMR spectroscopy. To find metal ion complexes that could discriminate between natural nucleobases upon double helix formation, glycol nucleic acid (GNA) sequences carrying a PdII ion with vacant coordination sites at a predetermined position were synthesized and their affinity to complementary as well as mismatched counterparts quantified by UV-melting measurements.

Sample preparation and heavy metal determination by atomic spectrometry /

Microwave digestions of mercury in Standards Reference Material (SRM) coal samples with nitric acid and hydrogen peroxide in quartz vessels were compared with Teflon® vessel digestion by using flow injection cold vapor atomic absorption spectrometry. Teflon® vessels gave poor reproducibiUty and tended to deliver high values, while the digestion results from quartz vessel show good agreement with certificate values and better standard deviations. Trace level elements (Ag, Ba, Cd, Cr, Co, Cu, Fe, Mg, Mn, Mo, Pb, Sn, Ti, V and Zn) in used oil and residual oil samples were determined by inductively coupled plasma-optical emission spectrometry. Different microwave digestion programs were developed for each sample and most of the results are in good agreement with certified values. The disagreement with values for Ag was due to the precipitation of Ag in sample; while Sn, V and Zn values had good recoveries from the spike test, which suggests that these certified values might need to be reconsidered. Gold, silver, copper, cadmium, cobalt, nickel and zinc were determined by continuous hydride generation inductively coupled plasma-optical emission spectrometry. The performance of two sample introduction systems: MSIS™ and gas-liquid separator were compared. Under the respective optimum conditions, MSIS^"^ showed better sensitivity and lower detection limits for Ag, Cd, Cu, Co and similar values for Au, Ni and Zn to those for the gas-liquid separator.

A fast atom bombardment mass spectrometry study of tris (3, 6-dioxaheptyl) amine-alkali metal halide complexes and hydrogen bonded complexes

The objective of this thesis was to demonstrate the potential of fast atom bombardment mass spectrometry (FABMS) as a probe of condensed phase systems and its possible uses for the study of hydrogen bonding. FABMS was used to study three different systems. The first study was aimed at investigating the selectivity of the ligand tris(3,6-dioxaheptyl) amine (tdoha) for the alkali metal cations. FABMS results correlated well with infrared and nmr data. Systems where a crown ether competed with tdoha for a given alkali metal cation were also investigated by fast atom bombardment. The results were found to correlate with the cation affinity of tdoha and the ability of the crown ether to bind the cation. In the second and third studies, H-bonded systems were investigated. The imidazole-electron donor complexes were investigated and FABMS results showed the expected H-bond strength of the respective complexes. The effects of concentration, liquid matrix, water content, deuterium exchange, and pre-ionization of the complex were also investigated. In the third system investigated, the abundance of the diphenyl sulfone-ammonium salt complexes (presumably H-bonded) in the FABMS spectrum were found to correlate with qualitative considerations such as steric hindrance and strength of ion pairs.