Unraveling the functional divergence of membrane-bound pyrophosphatases

Inorganic pyrophosphatases (PPases) are enzymes that hydrolyze pyrophosphate (PPi)which is produced as a byproduct in many important growth related processes e.g. in the biosynthesis of DNA, proteins and lipids. PPases can be either soluble or membranebound. Membrane-bound PPases (mPPases) are ion transporters that couple the energy released during PPi hydrolysis to Na+ or H+ transport. When I started the project, only three Na+-transporting mPPases were known to exist. In this study, I aimed to confirm if Na+-transport is a common function of mPPases. Furthermore, the amino acid residues responsible for determining the transporter specificity were unknown. I constructed a phylogenetic tree for mPPases and selected the representative bacterial and archaeal mPPases to be investigated. I expressed different prokaryotic mPPases in Escherichia coli, isolated these as inverted membrane vesicles and characterized their functions. In the first project I identified four new Na+-PPases, two K+-dependent H+-PPases and one K+-independent mPPase. The residues determining the transporter specificity were identified by site-directed mutagenesis. I showed that the conserved glutamate residues are important for specificity, though are not the only residues that influence it. This research clarified the ion transport specificities throughout the mPPase phylogenetic tree, and revealed that Na+ transport is a widespread function of mPPases. In addition, it became clear that the transporter specificity can be predicted from the amino acid sequence in combination with a phylogenetic analysis. In the second project, I identified a novel class of mPPases, which is capable of transporting both Na+ and H+ ions and is mainly found in bacteria of the human gastrointestinal tract. The physiological role of these novel enzymes may be to help the bacteria survive in the demanding conditions of the host. In the third project, I characterized the Chlorobium limicola Na+-PPase and found that this and related mPPases are able to transport H+ ions at subphysiological Na+ concentrations. In addition, the H+-transport activity was shown to be a common function of all studied Na+-PPases at low Na+ concentrations. I observed that mutating gate-lysine to asparagine eliminated the H+ but not the Na+ ion transport function, indicating the important role of the residue in the transport of H+. In the fourth project, I characterized the unknown and evolutionary divergent mPPase clade of the phylogenetic tree. The enzymes belonging to this clade are able to transport H+ ions and, based on their sequence, were expected to be K+- and Na+-independent. The sequences of membrane-bound PPase are usually highly conserved, but the enzymes belonging to this clade are more divergent and usually contain 100−150 extra amino acid residues compared to other known mPPases. Despite the vast sequence differences, these mPPases have the full set of important residues and, surprisingly, are regulated by Na+ and K+ ions. These enzymes are mainly of bacterial origin.

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.

Partial purification of tightly bound mitochondrial hexokinase from maize (Zea mays L.) root membranes

In mammals, hexokinase (HK) is strategically located at the outer membrane of mitochondria bound to the porin protein. The mitochondrial HK is a crucial modulator of apoptosis and reactive oxygen species generation. In plants, these properties related to HK are unknown. In order to better understand the physiological role of non-cytosolic hexokinase (NC-HK) in plants, we developed a purification strategy here described. Crude extract of 400 g of maize roots (230 mg protein) contained a specific activity of 0.042 µmol G6P min-1 mg PTN-1. After solubilization with detergent two fractions were obtained by DEAE column chromatography, NC-HK 1 (specific activity = 3.6 µmol G6P min-1 mg PTN-1 and protein recovered = 0.7 mg) and NC-HK 2. A major purification (yield = 500-fold) was obtained after passage of NC-HK 1 through the hydrophobic phenyl-Sepharose column. The total amount of protein and activity recovered were 0.04 and 18%, respectively. The NC-HK 1 binds to the hydrophobic phenyl-Sepharose matrix, as observed for rat brain HK. Mild chymotrypsin digestion did not affect adsorption of NC-HK 1 to the hydrophobic column as it does for rat HK I. In contrast to mammal mitochondrial HK, glucose-6-phosphate, clotrimazole or thiopental did not dissociate NC-HK from maize (Zea mays) or rice (Oryza sativa) mitochondrial membranes. These data show that the interaction between maize or rice NC-HK to mitochondria differs from that reported in mammals, where the mitochondrial enzyme can be displaced by modulators or pharmacological agents known to interfere with the enzyme binding properties with the mitochondrial porin protein.

Modelling Cutting States in Rough Turning of 34CrNiMo6 Steel

Rough turning is an important form of manufacturing cylinder-symmetric parts. Thus far, increasing the level of automation in rough turning has included process monitoring methods or adaptive turning control methods that aim to keep the process conditions constant. However, in order to improve process safety, quality and efficiency, an adaptive turning control should be transformed into an intelligent machining system optimizing cutting values to match process conditions or to actively seek to improve process conditions. In this study, primary and secondary chatter and chip formation are studied to understand how to measure the effect of these phenomena to the process conditions and how to avoid undesired cutting conditions. The concept of cutting state is used to address the combination of these phenomena and the current use of the power capacity of the lathe. The measures to the phenomena are not developed based on physical measures, but instead, the severity of the measures is modelled against expert opinion. Based on the concept of cutting state, an expert system style fuzzy control system capable of optimizing the cutting process was created. Important aspects of the system include the capability to adapt to several cutting phenomena appearing at once, even if the said phenomena would potentially require conflicting control action.

The Streptococcus mutans GlnR protein exhibits an increased affinity for the glnRA operon promoter when bound to GlnK

The control of nitrogen metabolism in pathogenic Gram-positive bacteria has been studied in a variety of species and is involved with the expression of virulence factors. To date, no data have been reported regarding nitrogen metabolism in the odontopathogenic species Streptococcus mutans. GlnR, which controls nitrogen assimilation in the related bacterial species, Bacillus subtilis, was assessed in S. mutans for its DNA and protein binding activity. Electrophoretic mobility shift assay of the S. mutans GlnR protein indicated that GlnR binds to promoter regions of the glnRA and amtB-glnK operons. Cross-linking and pull-down assays demonstrated that GlnR interacts with GlnK, a signal transduction protein that coordinates the regulation of nitrogen metabolism. Upon formation of this stable complex, GlnK enhances the affinity of GlnR for the glnRA operon promoter. These results support an involvement of GlnR in transcriptional regulation of nitrogen metabolism-related genes and indicate that GlnK relays information regarding ammonium availability to GlnR.

Specific alterations in plasma proteins during depressed, manic, and euthymic states of bipolar disorder

Bipolar disorder (BD) is a common psychiatric mood disorder affecting more than 1-2% of the general population of different European countries. Unfortunately, there is no objective laboratory-based test to aid BD diagnosis or monitor its progression, and little is known about the molecular basis of BD. Here, we performed a comparative proteomic study to identify differentially expressed plasma proteins in various BD mood states (depressed BD, manic BD, and euthymic BD) relative to healthy controls. A total of 10 euthymic BD, 20 depressed BD, 15 manic BD, and 20 demographically matched healthy control subjects were recruited. Seven high-abundance proteins were immunodepleted in plasma samples from the 4 experimental groups, which were then subjected to proteome-wide expression profiling by two-dimensional electrophoresis and matrix-assisted laser desorption/ionization-time-of-flight/time-of-flight tandem mass spectrometry. Proteomic results were validated by immunoblotting and bioinformatically analyzed using MetaCore. From a total of 32 proteins identified with 1.5-fold changes in expression compared with healthy controls, 16 proteins were perturbed in BD independent of mood state, while 16 proteins were specifically associated with particular BD mood states. Two mood-independent differential proteins, apolipoprotein (Apo) A1 and Apo L1, suggest that BD pathophysiology may be associated with early perturbations in lipid metabolism. Moreover, down-regulation of one mood-dependent protein, carbonic anhydrase 1 (CA-1), suggests it may be involved in the pathophysiology of depressive episodes in BD. Thus, BD pathophysiology may be associated with early perturbations in lipid metabolism that are independent of mood state, while CA-1 may be involved in the pathophysiology of depressive episodes.

Collective redundancies in the State of California of the United States and in the Republic of Finland. Procedures and Provisions

Video games industry has recently bonded California and Finland in a new way and where the employers are recruiting they also need to be aware of the provisions and procedures related to terminations. In general, collective dismissals are on a relatively high level both in Finland and in California. In California, collective redundancies are regulated under the WARN law. The WARN obligates employers with 75 or more employees to give a 60-day notice prior to a mass lay off and some other similar events. Employers with less than 75 employees are free to administer the terminations without the WARN notice period. Generally, the California at-will presumption allows employment relationship to be terminated any day with or without reason and without notice period if conditions of collective agreements or employment contract do not limit this right. Termination cannot anyhow be in violation of the anti-discrimination law. In Finland the termination related provisions are part of the Employment Contracts Act and the Act on Co-operation within Undertakings. Collective redundancies are allowed under financial and production related grounds. Small employers with less than 20 employees follow the termination provisions of the Employment Contracts Act and are obligated to inform the employee to be terminated on the details of the termination itself and also the services of the Employment and Economic Development Office. Employers with 20 or more employees are to initiate co-operation procedure under the Act on Co-operation within Undertakings when reducing personnel. The co- operation negotiations are to inform employees on the employer’s plans and financial situation as well as to involve them in the decision making regarding the terminations. The employer’s duty to inform the employees of the services of Employment and Economic Development Office needs to be fulfilled also in terminations under the co-operation procedure. Discrimination is prohibited in Finland in terminations of employment. As an alternative for terminations, employees can for example be transferred to another position or be temporarily laid off. Employer’s duties related to search of alternatives for layoff are broader in Finland than in California. The recent development of the labor laws in Finland and in California suggests that the labor law is not static in either one of these environments but changes can be expected as the needs of the business life so require.

Screening of iron-enriched fungus from natural environment and evaluation of organically bound iron bioavailability in rats

Iron is an essential element for nearly all living organisms, and its deficiency is the most common form of malnutrition in the world. The organic forms of trace elements are considered more bioavailable than the inorganic forms. Although Saccharomyces cerevisiae can enrich metal elements and convert inorganic iron to organic species, its tolerability and transforming capacity are limited. The aim of this study was to screen higher biomass and other iron-enriched fungi strains besides Saccharomyces cerevisiae from the natural environment. A PDA medium containing 800 μg/mL iron was used for initial screening. Fifty strains that tolerated high iron concentration were isolated from the natural environment, and only one strain, No.BY1109, grew well at Fe (II) concentration of 10,000μg/ml. According to morphological characterization, 18S rDNA sequence analysis, and biophysical and biochemical characterization, the strain No.BY1109 was identified as Rhodotorula. The iron content of No.BY1109 (10 mg Fe/g dry cell) was determined using atomic absorption spectrometry. The results of distribution of iron in the cells showed that iron ion was mainly chelated in the cell walls and vacuoles. The bioavailability in rats confirmed that strain No.BY1109 had higher absorption efficiency than that of ferrous sulfate after single dose oral administration. The present study introduces new iron supplements, and it is a basis for finding new iron supplements from natural environment.

Cross Listing of a Finnish Company on an Exchange in the United States of America

Finnish companies cross listing in the United States is an exceptional phenomenon. This study examines the cross listing decision, cross listing choice and cross listing process with associated challenges and critical factors. The aim is to create an in-depth understanding of the cross listing process and the required financial information. Based on that, the aim is to establish the process phases with the challenges and the critical factors that ought to be considered be- fore establishing the process plus re-evaluated and further considered at points in time during the process. The empirical part of this study is conducted as a qualitative study. The research data was collected through the adoption of two approaches, which are the interview approach and the textual data approach. The interviews were conducted with Finnish practitioners in the field of accounting and finance. The textual data was from publicly available publications of this phenomenon by the two BIG5 accounting companies worldwide. The results of this study demonstrate the benefits of cross listing in the U.S. are the better growth opportunities, the reduction of cost of capital and the production of higher quality financial information. In the decision making process companies should assess whether the benefits exceed the increased costs, the pressure for performance, the uncertainty of market recognition and the requirements of management. The exchange listing is seen as the most favourable cross listing choice for Finnish companies. The establishment of the processes for producing reliable, transparent and timely financial information was seen as both highly critical and very challenging. The critical success factors relating to the cross listing phases are the assessment and planning as well as the right mix of experiences and expertise. The timing plays important role in the process. The results mainly corroborate the literature concerning cross listing decision and choice. This study contributes to the literature on the cross listing process offering a useful model for the phases of the cross listing process.

Nanoclustering augmentation : a novel mechanism of Ras activation in cancer

Proteins of the Ras family are central regulators of crucial cellular processes, such as proliferation, differentiation and apoptosis. Their importance is emphasized in cancer, in which the isoforms H-ras, N-ras and K-ras are misregulated by mutations in approximately 20 – 30 % of cases. Thus, they represent major cancer oncogenes and one of the most important targets for cancer drug development. Ras proteins are small GTPases, which cycle between the GTP-bound active and GDP-bound inactive state. Despite the tremendous research conducted in the last three decades, many fundamental properties of Ras proteins remain poorly understood. For instance, although new concepts have recently emerged, the understanding of Ras behavior in its native environment, the membrane, is still largely missing. On the membrane Ras organizes into nanoscale clusters, also called nanoclusters. They differ between isoforms, but also between activation states of Ras. It is considered that nanoclusters represent the basic Ras signaling units. Recently, it was demonstrated that on the membrane Ras adopts distinct conformations, the so-called orientations, which are dependent on the Ras activations state. The membrane-orientation of H-ras is stabilized by the helix α4 and the C-terminal hypervariable region (hvr). The novel switch III region was proposed to be involved in mediating the change between different H-ras orientations. When the regions involved in this mechanism are mutated, H-ras activity is changed by an unknown mechanism. This thesis has explained the connection between the change of Ras orientation on the membrane and Ras activity. We demonstrated that H-ras orientation mutants exhibit altered diffusion properties on the membrane, which reflect the changes in their nanoclustering. The altered nanoclustering consequently rules the activity of the mutants. Moreover, we demonstrated that specific cancer-related mutations, affecting the switch III region of different Ras isoforms, exhibit increased nanoclustering, which consequently leads to stronger Ras signaling and tumorigenicity. Thus, we have discovered nanoclustering increase as a novel mechanism of Ras activity modulation in cancer. The molecular architecture of complexes formed on the membrane upon Ras activation is another poorly understood property of Ras. The following work has provided novel details on the regulation of Ras nanoclustering by a known H-ras-GTP nanoclustering stabilizer galectin-1 (Gal-1). Our study demonstrated that Gal-1 is not able to bind Ras directly, as it was previously proposed. Instead, its effect on H-ras-GTP nanoclustering is indirect, through binding of the effector proteins. Collectively, our findings represent valuable novel insights in the behavior of Ras, which will help the future research to eventually develop new strategies to successfully target Ras in cancer.