Novel Proteins Involved in Dynamics of The Photosynthetic Apparatus

During the past few years, a considerable number of research articles have been published relating to the structure and function of the major photosynthetic protein complexes, photosystem (PS) I, PSII, cytochrome (Cyt) b6f, and adenosine triphosphate (ATP) synthase. Sequencing of the Arabidopsis thaliana (Arabidopsis) genome together with several high-quality proteomics studies has, however, revealed that the thylakoid membrane network of plant chloroplasts still contains a number of functionally unknown proteins. These proteins may have a role as auxiliary proteins guiding the assembly, maintenance, and turnover of the thylakoid protein complexes, or they may be as yet unknown subunits of the photosynthetic complexes. Novel subunits are most likely to be found in the NAD(P)H dehydrogenase (NDH) complex, the structure and function of which have remained obscure in the absence of detailed crystallographic data, thus making this thylakoid protein complex a particularly interesting target of investigation. In this thesis, several novel thylakoid-associated proteins were identified by proteomics-based methods. The major goal of characterization of the stroma thylakoid associated polysome-nascent chain complexes was to determine the proteins that guide the dynamic life cycle of PSII. In addition, a large protein complex of ≥ 1,000 kDa, residing in the stroma thylakoid, was characterized in greater depth and it was found to be a supercomplex composed of the PSI and NDH complexes. A set of newly identified proteins from Arabidopsis thylakoids was subjected to detailed characterization using the reverse genetics approach and extensive biochemical and biophysical analysis. The role of the novel proteins, either as auxiliary proteins or subunits of the photosynthetic protein complexes, was revealed. Two novel thylakoid lumen proteins, TLP18.3 and AtCYP38, function as auxiliary proteins assisting specific steps of the assembly/repair of PSII. The role of the 10-kDa thylakoid lumen protein PsbR is related to the optimization of oxygen evolution of PSII by assisting the assembly of the PsbP protein. Two integral thylakoid membrane proteins, NDH45 and NDH48, are novel subunits of the chloroplast NDH complex. Finally, the thylakoid lumen immunophilin AtCYP20-2 is suggested to interact with the NDH complex, instead of PSII as was hypothesized earlier.

Development of Russian Ports in The Gulf of Finland

Russia has been one of the fastest developing economic areas in the world. Based on the GDP, the Russian economy grew evenly since the crisis in 1998 up till 2008. The growth in the gross domestic product has annually been some 5–10%. In 2007, the growth reached 8.1%, which is the highest figure after the 10% growth in 2000. Due to the growth of the economy and wage levels, purchasing power and consumption have been strongly increasing. The growing consumption has especially increased the imports of durables, such as passenger cars, domestic appliances and electronics. The Russian ports and infrastructure have not been able to satisfy the growing needs of exports and imports, which is why quite a large share of Russian foreign trade is going through third countries as transit transports. Finnish ports play a major role in transit transports to and from Russia. About 15% of the total value of Russian imports was transported through Finland in 2008. The economic recession that started in autumn 2008 and continues to date has had an impact on the economic development of Russia. The export income has decreased, mainly due to the reduced world market prices of energy products (oil and gas) and raw minerals. Investments have been postponed, getting credit is more difficult than before, and the ruble has weakened in relation to the euro and the dollar. The imports are decreasing remarkably, and are not forecast to reach the 2008 volumes even in 2012. The economic crisis is reflected in Finland's transit traffic. The volume of goods transported through Finland to and from Russia has decreased almost in the same proportion as the imports of goods to Russia. The biggest risk threatening the development of the Russian economy over long term is its dependence on export income from oil, gas, metals, minerals and forest products, as well as the trends of the world market prices of these products. Nevertheless, it is expected that the GDP of Russia will start to grow again in the forthcoming years due to the increased demand for energy products and raw minerals in the world. At the same time, it is obvious that the world market prices of these products will go up with the increasing demand. The increased income from exports will lead to a growth of imports, especially those of consumer goods, as the living standard of Russian citizens rises. The forecasts produced by the Russian Government concerning the economic development of Russia up till 2030 also indicate a shift in exported goods from raw materials to processed products, which together with energy products will become the main export goods of Russia. As a consequence, Russia may need export routes through third countries, which can be seen as an opportunity for increased transit transports through the ports of Finland. The ports competing with the ports of Finland for Russian foreign trade traffic are the Russian Baltic Sea ports and the ports of the Baltic countries. The strongest competitors are the Baltic Sea ports handling containers. On the Russian Baltic Sea, these ports include Saint Petersburg, Kaliningrad and, in the near future, the ports of Ust-Luga and possibly Vyborg. There are plans to develop Ust-Luga and Vyborg as modern container ports, which would become serious competitors to the Finnish ports. Russia is aiming to redirect as large a share as possible of foreign trade traffic to its own ports. The ports of Russia and the infrastructure associated with them are under constant development. On the other hand, the logistic capacity of Russia is not able to satisfy the continually growing needs of the Russian foreign trade. The capacity problem is emphasized by a structural incompatibility between the exports and imports in the Russian foreign trade. Russian exports can only use a small part of the containers brought in with imports. Problems are also caused by the difficult ice conditions and narrow waterways leading to the ports. It is predicted that Finland will maintain its position as a transit route for the Russian foreign trade, at least in the near future. The Russian foreign trade is increasing, and Russia will not be able to develop its ports in proportion with the increasing foreign trade. With the development of port capacity, cargo flows through the ports of Russia will grow. Structural changes in transit traffic are already visible. Firms are more and more relocating their production to Russia, for example as regards the assembly of cars and warehousing services. Simultaneously, an increasing part of transit cargoes are sent directly to Russia without unloading and reloading in Finland. New product groups have nevertheless been transported through Finland (textile products and tools), replacing the lost cargos. The global recession that started in autumn 2008 has influenced the volume of Russian imports and, consequently, the transit volumes of Finland, but the recession is not expected to be of long duration, and will thus only have a short-term impact on transit volumes. The Finnish infrastructure and services offered by the logistic chain should also be ready to react to the changes in imported product groups as well as to the change in Russian export products in the future. If the development plans of the Russian economy are realized, export products will be more refined, and the share of energy and raw material products will decrease. The other notable factor to be taken into consideration is the extremely fast-changing business environment in Russia. Operators in the logistic chain should be flexible enough to adapt to all kinds of changes to capitalise on business opportunities offered by the Russian foreign trade for the companies and for the transit volumes of Finnish ports, also in the future.

Formation of polyelectrolyte multilayers and polyelectrolyte complexes in dual polymer treatment of papermaking pulp

The goal of this study was to find a new approach to modify chemically the properties of paper by improving fiber quality. This Master’s thesis includes the multiple polymer treatment in general and themeasurement methods with which the formation of multilayers and complexes can be noticed. The treatment by an oppositely charged dual polymer system is a good approach to increase paper strength. In this work, starch, a cationic polymer, and carboxymethyl cellulose (CMC), an anionic polymer, were used step-by-step to improve paper strength. The adsorption of cationic starch and CMC on cellulose fibers were analyzed via polyelectrolyte titration. The results showed that paper strength was enhanced slightly with a layer-by-layer assembly of the polymers. However, if the washing stage, which was required for layer-by-layer assembly, was eliminated, the starch/CMC complex was deposited on fibers more efficiently, and the paper strength was improved more significantly.

Algorithmic Solutions for Combinatorial Problems in Resource Management of Manufacturing Environments

This thesis studies the use of heuristic algorithms in a number of combinatorial problems that occur in various resource constrained environments. Such problems occur, for example, in manufacturing, where a restricted number of resources (tools, machines, feeder slots) are needed to perform some operations. Many of these problems turn out to be computationally intractable, and heuristic algorithms are used to provide efficient, yet sub-optimal solutions. The main goal of the present study is to build upon existing methods to create new heuristics that provide improved solutions for some of these problems. All of these problems occur in practice, and one of the motivations of our study was the request for improvements from industrial sources. We approach three different resource constrained problems. The first is the tool switching and loading problem, and occurs especially in the assembly of printed circuit boards. This problem has to be solved when an efficient, yet small primary storage is used to access resources (tools) from a less efficient (but unlimited) secondary storage area. We study various forms of the problem and provide improved heuristics for its solution. Second, the nozzle assignment problem is concerned with selecting a suitable set of vacuum nozzles for the arms of a robotic assembly machine. It turns out that this is a specialized formulation of the MINMAX resource allocation formulation of the apportionment problem and it can be solved efficiently and optimally. We construct an exact algorithm specialized for the nozzle selection and provide a proof of its optimality. Third, the problem of feeder assignment and component tape construction occurs when electronic components are inserted and certain component types cause tape movement delays that can significantly impact the efficiency of printed circuit board assembly. Here, careful selection of component slots in the feeder improves the tape movement speed. We provide a formal proof that this problem is of the same complexity as the turnpike problem (a well studied geometric optimization problem), and provide a heuristic algorithm for this problem.

The calcium-modulated proteins, S100A1 and S100B, as potential regulators of the dynamics of type III intermediate filaments

The Ca2+-modulated, dimeric proteins of the EF-hand (helix-loop-helix) type, S100A1 and S100B, that have been shown to inhibit microtubule (MT) protein assembly and to promote MT disassembly, interact with the type III intermediate filament (IF) subunits, desmin and glial fibrillary acidic protein (GFAP), with a stoichiometry of 2 mol of IF subunit/mol of S100A1 or S100B dimer and an affinity of 0.5-1.0 µM in the presence of a few micromolar concentrations of Ca2+. Binding of S100A1 and S100B results in inhibition of desmin and GFAP assemblies into IFs and stimulation of the disassembly of preformed desmin and GFAP IFs. S100A1 and S100B interact with a stretch of residues in the N-terminal (head) domain of desmin and GFAP, thereby blocking the head-to-tail process of IF elongation. The C-terminal extension of S100A1 (and, likely, S100B) represents a critical part of the site that recognizes desmin and GFAP. S100B is localized to IFs within cells, suggesting that it might have a role in remodeling IFs upon elevation of cytosolic Ca2+ concentration by avoiding excess IF assembly and/or promoting IF disassembly in vivo. S100A1, that is not localized to IFs, might also play a role in the regulation of IF dynamics by binding to and sequestering unassembled IF subunits. Together, these observations suggest that S100A1 and S100B may be regarded as Ca2+-dependent regulators of the state of assembly of two important elements of the cytoskeleton, IFs and MTs, and, potentially, of MT- and IF-based activities.

Expression of anti-Z-DNA single chain antibody variable fragment on the filamentous phage surface

We describe the expression of an anti-Z-DNA single chain variable region antibody fragment (scFv) on a filamentous phage surface. Four vectors for phage display were constructed. Two of them are able to display multiple copies of the antibody fragment, and the others can be used to make monovalent libraries. The vectors use different promoter/leader sequences to direct the expression of the fused proteins. All were able to promote the assembly of fusion virion particles. In this paper we also show the affinity selection (biopanning) of those phage-antibodies based on the capacity of their products to recognize the antigen. We used biotinylated Z-DNA and the selection was performed in a solution phase fashion. The data presented here indicate that these vectors can be further used to construct anti-nucleic acid antibody fragment libraries that can be used to study the basis of nucleic acid-protein interaction and its role in autoimmunity mechanisms.

Sphingosine-1-phosphate-evoked invasion of follicular thyroid cancer cells : evidence for the involvement of HIF-Iα, MMP2 and MMP9

Sphingolipids are widely expressed molecules, which traditionally were considered to have majorly structural properties. Nowadays, however, they are implicated in a wide range of different biological processes. The bioactive lipid sphingosine 1-phosphate (S1P) has emerged during the past decade as one of the most studied molecules due to its proliferative and pro-migratory abilities both during normal physiology and in the pathology of a subset of different diseases. Migration and invasion of cancer cells require changes in cell behavior and modulation of the tissue microenvironment. Tumor aggressiveness is markedly enhanced by hypoxia, in which hypoxia inducible transcription factors 1-2α (HIF-1-2α) are activated to promote metabolism, proliferation and migration. Invasion requires degradation of the extracellular matrix (ECM) achieved by several degrading and remodeling enzymes. Matrix metalloproteinases (MMPs) are broadly expressed and well accepted as proteolytic enzymes with essential roles both in normal physiology and in pathology. Previously, S1P was shown to strongly evoke migration of follicular ML-1 thyroid cancer cells. The objective of this study was to further investigate and understand the mechanisms behind this regulation. In the first project it was demonstrated that S1P enhances the expression and activity of HIF-1α. S1P enhanced the expression of HIF-1α by increasing its synthesis and stability. The S1P-increased HIF-1α was mediated via S1P3, Gi/0, PI3K, PKCβI, ERK1/2, mTOR and translation factors p70S6K and eIF4E. Finally, it was shown that HIF-1α mediated S1P-induced migration. The ECM is constituted of a complex and coordinated assembly of many types of proteins. In order to be able to invade, cells need to break down the ECM, therefore several key players in this event were investigated in the second project. S1P increased the secretion and activity of MMP2 and MMP9 via S1P-receptor 1 and 3 and that these MMPs participated in the S1P-facilitated invasion of ML-1 cells. In this interplay, calpains and Rac1 were involved, both of which are crucial players in migration and invasion. The prognosis for some types of thyroid cancer is relatively good. However, there are forms of thyroid cancers, for which there are no treatments or the current available treatments are inefficient. Thus, new medical interventions are urgently needed. In the third project the significance of the S1P-receptor modulating drug FTY720, which is currently used for the treatment of multiple sclerosis (MS), was studied. The effect of FTY720 was tested on several thyroid cancer cell lines, and it inhibited the proliferation and invasion of all cancer cell lines tested. In ML-1 cells, FTY720 attenuated invasion by blocking signaling intermediates important for migration and invasion of the cells. Moreover, FTY720 inhibited the proliferation of ML-1 cells by increasing the expression of p21 and p27, hence, inducing cell arrest in G1 phase of the cell cycle. Thus, it can be suggested that FTY720 could be used in the treatment of thyroid cancer.

Characterisation of Cladonia rangiferina transcriptome and genome, and the effects of dehydration and rehydration on its gene expression

Lichens are symbiotic organisms, which consist of the fungal partner and the photosynthetic partner, which can be either an alga or a cyanobacterium. In some lichen species the symbiosis is tripartite, where the relationship includes both an alga and a cyanobacterium alongside the primary symbiont, fungus. The lichen symbiosis is an evolutionarily old adaptation to life on land and many extant fungal species have evolved from lichenised ancestors. Lichens inhabit a wide range of habitats and are capable of living in harsh environments and on nutrient poor substrates, such as bare rocks, often enduring frequent cycles of drying and wetting. Most lichen species are desiccation tolerant, and they can survive long periods of dehydration, but can rapidly resume photosynthesis upon rehydration. The molecular mechanisms behind lichen desiccation tolerance are still largely uncharacterised and little information is available for any lichen species at the genomic or transcriptomic level. The emergence of the high-throughput next generation sequencing (NGS) technologies and the subsequent decrease in the cost of sequencing new genomes and transcriptomes has enabled non-model organism research on the whole genome level. In this doctoral work the transcriptome and genome of the grey reindeer lichen, Cladonia rangiferina, were sequenced, de novo assembled and characterised using NGS and traditional expressed sequence tag (EST) technologies. RNA extraction methods were optimised to improve the yield and quality of RNA extracted from lichen tissue. The effects of rehydration and desiccation on C. rangiferina gene expression on whole transcriptome level were studied and the most differentially expressed genes were identified. The secondary metabolites present in C. rangiferina decreased the quality – integrity, optical characteristics and utility for sensitive molecular biological applications – of the extracted RNA requiring an optimised RNA extraction method for isolating sufficient quantities of high-quality RNA from lichen tissue in a time- and cost-efficient manner. The de novo assembly of the transcriptome of C. rangiferina was used to produce a set of contiguous unigene sequences that were used to investigate the biological functions and pathways active in a hydrated lichen thallus. The de novo assembly of the genome yielded an assembly containing mostly genes derived from the fungal partner. The assembly was of sufficient quality, in size similar to other lichen-forming fungal genomes and included most of the core eukaryotic genes. Differences in gene expression were detected in all studied stages of desiccation and rehydration, but the largest changes occurred during the early stages of rehydration. The most differentially expressed genes did not have any annotations, making them potentially lichen-specific genes, but several genes known to participate in environmental stress tolerance in other organisms were also identified as differentially expressed.

The design, synthesis and characterization of new building blocks for the preparation of molecule-based magnetic materials /

Two new families of building blocks have been prepared and fully characterized and their coordination chemistry exploited for the preparation of molecule-based magnetic materials. The first class of compounds were prepared by exploiting the chemistry of 3,3'-diamino-2,2'-bipyridine together with 2-pyridine carbonyl chloride or 2-pyridine aldehyde. Two new ligands, 2,2'-bipyridine-3,3'-[2-pyridinecarboxamide] (Li, 2.3) and N'-6/s(2-pyridylmethyl) [2,2'bipyridine]-3,3'-diimine (L2, 2.7), were prepared and characterized. For ligand L4, two copper(II) coordination compounds were isolated with stoichiometrics [Cu2(Li)(hfac)2] (2.4) and [Cu(Li)Cl2] (2.5). The molecular structures of both complexes were determined by X-ray crystallography. In both complexes the ligand is in the dianionic form and coordinates the divalent Cu(II) ions via one amido and two pyridine nitrogen donor atoms. In (2.4), the coordination geometry around both Cu11 ions is best described as distorted trigonal bipyramidal where the remaining two coordination sites are satisfied by hfac counterions. In (2.5), both Cu(II) ions adopt a (4+1) distorted square pyramidal geometry. One copper forms a longer apical bond to an adjacent carbonyl oxygen atom, whereas the second copper is chelated to a neighboring Cu-Cl chloride ion to afford chloride bridged linear [Cu2(Li)Cl2]2 tetramers that run along the c-axis of the unit cell. The magnetic susceptibility data for (2.4) reveal the occurrence of weak antiferromagnetic interactions between the copper(II) ions. In contrast, variable temperature magnetic susceptibility measurements for (2.5) reveal more complex magnetic properties with the presence of ferromagnetic exchange between the central dimeric pair of copper atoms and weak antiferromagnetic exchange between the outer pairs of copper atoms. The Schiff-base bis-imine ligand (L2, 2.7) was found to be highly reactive; single crystals grown from dry methanol afforded compound (2.14) for which two methanol molecules had added across the imine double bond. The susceptibility of this ligand to nucleophilic attack at its imine functionality assisted via chelation to Lewis acidic metal ions adds an interesting dimension to its coordination chemistry. In this respect, a Co(II) quaterpyridine-type complex was prepared via a one-pot transformation of ligand L2 in the presence of a Lewis acidic metal salt. The rearranged complex was characterized by X-ray crystallography and a reaction mechanism for its formation has been proposed. Three additional rearranged complexes (2.13), (2.17) and (2.19) were also isolated when ligand (L2, 2.7) was reacted with transition metal ions. The molecular structures of all three complexes have been determined by X-ray crystallography. The second class of compounds that are reported in this thesis, are the two diacetyl pyridine derivatives, 4-pyridyl-2,6-diacetylpyridine (5.5) and 2,2'-6,6'-tetraacetyl-4,4'-bipyridine (5.15). Both of these compounds have been designed as intermediates for the metal templated assembly of a Schiff-base N3O2 macrocycle. From compound (5.15), a covalently tethered dimeric Mn(II) macrocyclic compound of general formula {[Mn^C^XJCl-FkO^Cl-lO.SFbO (5.16) was prepared and characterized. The X-ray analysis of (5.16) reveals that the two manganese ions assume a pentagonal-bipyramidal geometry with the macrocycle occupying the pentagonal plane and the axial positions being filled by a halide ion and a H2O molecule. Magnetic susceptibility data reveal the occurrence of antiferromagnetic interactions between covalently tethered Mn(II)-Mn(II) dimeric units. Following this methodology a Co(II) analogue (5.17) has also been prepared which is isostructural with (5.16).

Annual report of the Commissioners for the Queen Victoria Niagara Falls Park of the Province of Ontario, 1887.

Description based on: 16th ed. (1901).

Annual report of the Commissioners for the Queen Victoria Niagara Falls Park of the Province of Ontario, 1888.

Description based on: 16th ed. (1901).

Annual report of the Commissioners for the Queen Victoria Niagara Falls Park of the Province of Ontario, 1889.

Description based on: 16th ed. (1901).

Annual report of the Commissioners for the Queen Victoria Niagara Falls Park of the Province of Ontario.

Description based on: 16th ed. (1901).

Annual report of the Commissioners for the Queen Victoria Niagara Falls Park of the Province of Ontario, 1892.

Description based on: 16th ed. (1901).

Annual report of the Commissioners for the Queen Victoria Niagara Falls Park of the Province of Ontario, 1893.

Description based on: 16th ed. (1901).