The Significance of Hydrogen Bonding Interactions in the Cleavage of RNA

RNA is essential for all living organisms. It has important roles in protein synthesis, controlling gene expression as well as catalyzing biological reactions. Chemically RNA is a very stable molecule, although in biological systems many agents catalyze the cleavage of RNA, such as naturally occurring enzymes and ribozymes. Much effort has been put in the last decades in developing highly active artificial ribonucleases since such molecules could have potential in the therapeutic field and provide tools for molecular biology. Several potential catalysts have emerged, but usually detailed cleavage mechanism remains unresolved. This thesis is aimed at clarifying mechanistic details of the cleavage and isomerization of RNA by using simpler nucleoside models of RNA. The topics in the experimental part cover three different studies, one concerning the mechanism of catalysis by large ribozymes, one dealing with the reactivity of modified and unmodified RNA oligonucleotides and one showing an efficient catalysis of the cleavage and isomerization of an RNA phosphodiester bond by a dinuclear metal ion complex. A review of the literature concerning stabilization of the phosphorane intermediate of the hydrolysis and isomerization of RNA phosphodiester bond is first presented. The results obtained in the experimental work followed by mechanistic interpretations are introduced in the second part of the thesis. Especially the significance of hydrogen bonding interactions is discussed.

Initial development and gas exchange of Talisia subalbens (Mart.) Radlk. under different shading conditions

Ecophysiological studies under semi-controlled conditions in nurseries and greenhouses are essential to enable the use of native species to recover degraded areas and for commercial planting. Talisia subalbens (Mart) Radlk, 'cascudo', is a native fruiting species of the Cerrado on the verge of extinction. The ecophysiological performance of this species was evaluated in nursery conditions under different levels of shading (full sunshine, 30%, 50% and 70%). Initial growth, biomass allocation, gas exchange and chlorophyll content of the plants were analyzed. Full sunshine cultivated plants showed a higher accumulation of total, shoot, and root dry biomass. There was no significant difference in the root/shoot ratio among the treatments. Seedlings cultivated under full sunshine and 30% shading showed higher values for height, basal diameter, and leaf area. Differences in stomata conductance and photosynthesis rate were not observed among the different shading levels. Plants cultivated under 70% of shading had higher contents of chlorophyll a, b, and total. During the initial phase with higher levels of radiation were fundamental for the development of T. subalbens seedlings.

GAS EXCHANGE IN YOUNG PLANTS OF Tabebuia aurea(Bignoniaceae Juss.) SUBJECTED TO FLOODING STRESS1

ABSTRACT The Paratudo (Tabebuia aurea) is a species occurring in the Pantanal of Miranda, Mato Grosso do Sul, Brazil, an area characterized by seasonal flooding. To evaluate the tolerance of this plant to flooding, plants aged four months were grown in flooded soil and in non-flooded soil (control group). Stomatal conductance, transpiration and CO2 assimilation were measured during the stress (48 days) and recovery (11 days) period, totalling 59 days. The values of stomatal conductance of the control group and stressed plants at the beginning of the flooded were 0.33 mol m-2s-1 and reached 0.02 mol m-2 s-1 (46th day) at the end of this event. For the transpiration parameter, the initial rate was 3.1 mol m s-1, and the final rate reached 0.2 or 0.3 mol m-2 s-1 (47/48 th day). The initial photosynthesis rate was 8.9 mmol m-2s-1 and oscillated after the sixth day, and the rate reached zero on the 48th day. When the photosynthesis rate reached zero, the potted plants were dried, and the rate was analyzed (11th day). The following values were obtained for dried plants: stomatal conductance = 0.26 mol m-2 s-1, transpiration rate = 2.5 mol m-2 s-1 and photosynthesis rate = 7.8 mmol m-2 s-1. Flooded soil reduced photosynthesis and stomatal conductance, leading to the hypertrophy of the lenticels. These parameters recovered and after this period, and plants exhibited tolerance to flooding stress by reducing their physiological activities.

Information exchange and disruption risk in multimodal maritime supply chains

Supply chains are becoming increasingly dependent on information ex-change in today’s world, and any disruption can cause severe repercus-sions to the flow of materials in the chain. The speed, accuracy and amount of information are key factors. The aim in this thesis is to address a gap in the research by focusing on information exchange and the risks related to it in a multimodal wood supply chain operating between the Baltic States and Finland. The study involved interviewing people engaged in logistics management in the supply chain in question. The main risk the interviewees identified arose from the sea logistics system, which held a lot of different kinds of information. The threat of breakdown in the Internet connection was also found to hinder the operations significantly. A vulnerability analysis was carried out in order to identify the main actors and channels of infor-mation flow in the supply chain. The analysis revealed that the most important and therefore most vulnerable information-exchange channels were those linking the terminal superintendent, the operative managers and the mill managers. The study gives a holistic picture of the investigated supply chain. Information-exchange-related risks varied greatly. One of the most frequently mentioned was the risk of information inaccuracy, which was usually due to the fact that those in charge of the various functions did not fully understand the consequences for the entire chain.

Synthesis of percarboxylic acids in microreactor

Percarboxylic acids are commonly used as disinfection and bleaching agents in textile, paper, and fine chemical industries. All of these applications are based on the oxidative potential of these compounds. In spite of high interest in these chemicals, they are unstable and explosive chemicals, which increase the risk of synthesis processes and transportation. Therefore, the safety criteria in the production process should be considered. Microreactors represent a technology that efficiently utilizes safety advantages resulting from small scale. Therefore, microreactor technology was used in the synthesis of peracetic acid and performic acid. These percarboxylic acids were produced at different temperatures, residence times and catalyst i.e. sulfuric acid concentrations. Both synthesis reactions seemed to be rather fast because with performic acid equilibrium was reached in 4 min at 313 K and with peracetic acid in 10 min at 343 K. In addition, the experimental results were used to study the kinetics of the formation of performic acid and peracetic acid. The advantages of the microreactors in this study were the efficient temperature control even in very exothermic reaction and good mixing due to the short diffusion distances. Therefore, reaction rates were determined with high accuracy. Three different models were considered in order to estimate the kinetic parameters such as reaction rate constants and activation energies. From these three models, the laminar flow model with radial velocity distribution gave most precise parameters. However, sulfuric acid creates many drawbacks in this synthesis process. Therefore, a ´´greener´´ way to use heterogeneous catalyst in the synthesis of performic acid in microreactor was studied. The cation exchange resin, Dowex 50 Wx8, presented very high activity and a long life time in this reaction. In the presence of this catalyst, the equilibrium was reached in 120 second at 313 K which indicates a rather fast reaction. In addition, the safety advantages of microreactors were investigated in this study. Four different conventional methods were used. Production of peracetic acid was used as a test case, and the safety of one conventional batch process was compared with an on-site continuous microprocess. It was found that the conventional methods for the analysis of process safety might not be reliable and adequate for radically novel technology, such as microreactors. This is understandable because the conventional methods are partly based on experience, which is very limited in connection with totally novel technology. Therefore, one checklist-based method was developed to study the safety of intensified and novel processes at the early stage of process development. The checklist was formulated using the concept of layers of protection for a chemical process. The traditional and three intensified processes of hydrogen peroxide synthesis were selected as test cases. With these real cases, it was shown that several positive and negative effects on safety can be detected in process intensification. The general claim that safety is always improved by process intensification was questioned.

Simulation and optimization of IGCC technique for power generation and hydrogen production by using lignite Thar coal and cotton stalk

The purpose of this study was to simulate and to optimize integrated gasification for combine cycle (IGCC) for power generation and hydrogen (H2) production by using low grade Thar lignite coal and cotton stalk. Lignite coal is abundant of moisture and ash content, the idea of addition of cotton stalk is to increase the mass of combustible material per mass of feed use for the process, to reduce the consumption of coal and to increase the cotton stalk efficiently for IGCC process. Aspen plus software is used to simulate the process with different mass ratios of coal to cotton stalk and for optimization: process efficiencies, net power generation and H2 production etc. are considered while environmental hazard emissions are optimized to acceptance level. With the addition of cotton stalk in feed, process efficiencies started to decline along with the net power production. But for H2 production, it gave positive result at start but after 40% cotton stalk addition, H2 production also started to decline. It also affects negatively on environmental hazard emissions and mass of emissions/ net power production increases linearly with the addition of cotton stalk in feed mixture. In summation with the addition of cotton stalk, overall affects seemed to negative. But the effect is more negative after 40% cotton stalk addition so it is concluded that to get maximum process efficiencies and high production less amount of cotton stalk addition in feed is preferable and the maximum level of addition is estimated to 40%. Gasification temperature should keep lower around 1140 °C and prefer technique for studied feed in IGCC is fluidized bed (ash in dry form) rather than ash slagging gasifier

Influence of vinasse application in hydraulic conductivity of three soils

The potassium ion, present in great amount in the vinasse because it is a monovalent cation, has the characteristic of promoting the dispersion of clay particles, in the same way as the sodium, causing a reduction in the pore space of the soil and, in its turn, reducing its permeability. To evaluate this effect of reduction by application of vinasse to the soil, an experiment was conducted for three different soils, with the objective of evaluating the effect of the application of different doses of vinasse on hydraulic conductivity of saturated soil and verifying its possible chemical changes of these soils. For that, it was used PVC columns (in a scheme of constant head permeameter to obtain the values of hydraulic conductivity of saturated soil), filled with three soils - Dark Red Latosol (DRL), Purple Latosol (PL) and Eutrophic Red Nitossol (ERN) - , in which were applied four doses of vinasse (0, 150, 300 and 450m³ ha-1), distributed in a completely randomized design with a 3x4 factorial scheme with three replications. The results evidenced that only the Dark Red Latosol (DRL) showed a reduction in the values of hydraulic conductivity of saturated soil, and in front of the application of vinasse, up to 300m³ ha-1, it was observed an increase in the concentrations of potassium, calcium and cation exchange capacity (CEC) ions.

Hydrogen production from cassava processing wastewater in an anaerobic fixed bed reactor with bamboo as a support material

Attempting to associate waste treatment to the production of clean and renewable energy, this research sought to evaluate the biological production of hydrogen using wastewater from the cassava starch treatment industry, generated during the processes of extraction and purification of starch. This experiment was carried out in a continuous anaerobic reactor with a working volume of 3L, with bamboo stems as the support medium. The system was operated at a temperature of 36°C, an initial pH of 6.0 and under variations of organic load. The highest rate of hydrogen production, of 1.1 L.d-1.L-1, was obtained with application of an organic loading rate of 35 g.L-1.d-1, in terms of total sugar content and hydraulic retention time of 3h, with a prevalence of butyric and acetic acids as final products of the fermentation process. Low C/N ratios contributed to the excessive growth of the biomass, causing a reduction of up to 35% in hydrogen production, low percentages of H2 and high concentrations of CO2in the biogas.

Optimization of hydrogen plant efficiency

The purpose of this master’s thesis was to study ways to increase the operating cost-efficiency of the hydrogen production process by optimizing the process parameters while, at the same time, maintaining plant reliability and safety. The literature part reviewed other hydrogen production and purification processes as well as raw material alternatives for hydrogen production. The experimental part of the master’s thesis was conducted at Solvay Chemicals Finland Oy’s hydrogen plant in spring 2012. It was performed by changing the process parameters, first, one by one, aiming for a more efficient process with clean product gas and lower natural gas consumption. The values of the process parameters were tested based on the information from the literature, process simulation and experiences of previous similar processes. The studied parameters were reformer outlet temperature, shift converter inlet temperature and steam/carbon ratio. The results show that the optimal process conditions are a lower steam/carbon ratio and reformer outlet temperature than the current values of 3.0 and 798 °C. An increase/decrease in the shift conversion inlet temperature does not affect natural gas consumption, but it has an effect on minimizing the process steam overload.

Spin-Dynamics in Cold Gases of 87Rb and Atomic Hydrogen. The spins they are a-changin’

In this thesis the dynamics of cold gaseous atoms is studied. Two different atomic species and two different experimental techniques have been used. In the first part of the thesis experiments with Bose-Einstein condensates of Rb-87 are presented. In these experiments the methods of laser cooling and magnetic trapping of atoms were utilized. An atom chip was used as the experimental technique for implementation of magnetic trapping. The atom chip is a small integrated instrument allowing accurate and detailed manipulation of the atoms. The experiments with Rb-87 probed the behaviour of a falling beam of atoms outcoupled from the Bose-Einstein condensate by electromagnetic field induced spin flips. In the experiments a correspondence between the phases of the outcoupling radio frequency field and the falling beam of atoms was found. In the second part of the thesis experiments of spin dynamics in cold atomic hydrogen gas are discussed. The experiments with atomic hydrogen are conducted in a cryostat using a dilution refrigerator as the cooling method. These experiments concentrated on explaining and quantifying modulations in the electron spin resonance spectra of doubly polarized atomic hydrogen. The modifications to the previous experimental setup are described and the observation of electron spin waves is presented. The observed spin wave modes were caused by the identical spin rotation effect. These modes have a strong dependence on the spatial profile of the polarizing magnetic field. We also demonstrated confinement of these modes in regions of strong magnetic field and manipulated their spatial distribution by changing the position of the field maximum.

Adsorption of hydrogen sulfide by modified cellulose nano/microcrystals

Hydrogen sulfide is toxic and hazardous pollutant. It has been under great interest for past few years because of all the time tighten environmental regulations and increased interest of mining. Hydrogen sulfide gas originates from mining and wastewater treatment systems have caused death in two cases. It also causes acid rains and corrosion for wastewater pipelines. The aim of this master thesis was to study if chemically modified cellulose nanocrystals could be used as adsorbents to purify hydrogen sulfide out from water and what are the adsorption capacities of these adsorbents. The effects of pH and backgrounds on adsorption capacities of different adsorbents are tested. In theoretical section hydrogen sulfide, its properties and different purification methods are presented. Also analytical detection methods for hydrogen sulfide are presented. Cellulose nano/microcrystals, properties, application and different modification methods are discussed and finally theory of adsorption and modeling of adsorption is shortly discussed. In experimental section different cellulose nanocrystals based adsorbents are prepared and tested at different hydrogen sulfide concentrations and in different conditions. Result of experimental section was that the highest adsorption capacity at one component adsorption had wet MFC/CaCO3. At different pH the adsorption capacities of adsorbents changed quite dramatically. Also change of hydrogen sulfide solution background did have effect on adsorption capacities. Although, when tested adsorbents’ adsorption capacities are compared to those find in literatures, it seems that more development of MFC based adsorbents is needed.

Electroactive ion exchange membranes based on conducting polymers

Ion exchange membranes are indispensable for the separation of ionic species. They can discriminate between anions and cations depending on the type of fixed ionic group present in the membrane. These conventional ion exchange membranes (CIX) have exceptional ionic conductivity, which is advantageous in various electromembrane separation processes such as electrodialysis, electrodeionisation and electrochemical ion exchange. The main disadvantage of CIX membranes is their high electrical resistance owing to the fact that the membranes are electronically non conductive. An alternative can be electroactive ion exchange membranes, which are ionically and electronically conducting. Polypyrrole (PPy) is a type of electroactive ion exchange material as well as a commonly known conducting polymer. When PPy membranes are repeatedly reduced and oxidised, ions are pumped through the membrane. The main aim of this thesis was to develop electroactive cation transport membranes based on PPy for the selective transport of divalent cations. Membranes developed composed of PPy films deposited on commercially available support materials. To carry out this study, cation exchange membranes based on PPy doped with immobile anions were prepared. Two types of dopant anions known to interact with divalent metal ions were considered, namely 4-sulphonic calix[6]arene (C6S) and carboxylated multiwalled carbon nanotubes (CNT). The transport of ions across membranes containing PPy doped with polystyrene sulphonate (PSS) and PPy doped with para-toluene sulphonate (pTS) was also studied in order to understand the nature of ion transport and permeability across PPy(CNT) and PPy(C6S) membranes. In the course of these studies, membrane characterisation was performed using electrochemical quartz crystal microbalance (EQCM) and scanning electron microscopy (SEM). Permeability of the membranes towards divalent cations was explored using a two compartment transport cell. EQCM results demonstrated that the ion exchange behaviour of polypyrrole is dependent on a number of factors including the type of dopant anion present, the type of ions present in the surrounding medium, the scan rate used during the experiment and the previous history of the polymer film. The morphology of PPy films was found to change when the dopant anion was varied and even when the thickness of the film was altered in some cases. In nearly all cases the permeability of the membranes towards metal ions followed the order K+ > Ca2+ > Mn2+. The one exception was PPy(C6S), for which the permeability followed the order Ca2+ ≥ K+ > Mn2+ > Co2+ > Cr3+. The above permeability sequences show a strong dependence on the size of the metal ions with metal ions having the smallest hydrated radii exhibiting the highest flux. Another factor that affected the permeability towards metal ions was the thickness of the PPy films. Films with the least thickness showed higher metal ion fluxes. Electrochemical control over ion transport across PPy(CNT) membrane was obtained when films composed of the latter were deposited on track-etched Nucleopore® membranes as support material. In contrast, the flux of ions across the same film was concentration gradient dependent when the polymer was deposited on polyvinylidene difluoride membranes as support material. However, electrochemical control over metal ion transport was achieved with a bilayer type of PPy film consisting of PPy(pTS)/PPy(CNT), irrespective of the type of support material. In the course of studying macroscopic charge balance during transport experiments performed using a two compartment transport cell, it was observed that PPy films were non-permselective. A clear correlation between the change in pH in the receiving solution and the ions transported across the membrane was observed. A decrease in solution pH was detected when the polymer membrane acted primarily as an anion exchanger, while an increase in pH occurred when it functioned as a cation exchanger. When there was an approximately equal flux of anions and cations across the polymer membrane, the pH in the receiving solution was in the range 6 - 8. These observations suggest that macroscopic charge balance during the transport of cations and anions across polypyrrole membranes was maintained by introduction of anions (OH-) and cations (H+) produced via electrolysis of water.

Development of an environmentally friendly method of starch oxidation by hydrogen peroxide and a complex water-soluble Iron catalyst

Oxidized starch is a key component in the paper industry, where it is used as both surfacing sizer and filler. Large quantities are annually used for this purpose; however, the methods for the oxidation are not environmentally friendly. In our research, we have studied the possibility to replace the harmful oxidation agents, such as hypochlorite or iodates and transition metal catalysts, with a more environmentally friendly oxidant, hydrogen peroxide (H2O2), and a special metal complex catalyst (FePcS), of which only a small amount is needed. The work comprised batch and semi-batch studies by H2O2, ultrasound studies of starch particles, determination of low-molecular by-products and determination of the decomposition kinetics of H2O2 in the presence of starch and the catalyst. This resulted in a waste-free oxidation method, which only produces water and oxygen as side products. The starch oxidation was studied in both semi-batch and batch modes in respective to the oxidant (H2O2) addition. The semi-batch mode proved to yield a sufficient degree of substitution (COOH groups) for industrial purposes. Treatment of starch granules by ultrasound was found to improve the reactivity of starch. The kinetic results were found out to have a rather complex pattern – several oxidation phases were observed, apparently due to the fact that the oxidation reaction in the beginning only took place on the surface, whereas after a prolonged reaction time, partial degradation of the solid starch granules allowed further reaction in the interior parts. Batch-mode experiments enabled a more detailed study of the mechanisms of starch in the presence of H2O2 and the catalyst, but yielded less oxidized starch due to rapid decomposition of H2O2 due to its high concentrations. The effect of the solid-liquid (S/L) ratio in the reaction system was studied in batch experiments. These studies revealed that the presence of the catalyst and the starch enhance the H2O2 decomposition.