Functional studies on bacterial nucleotide-regulated inorganic pyrophosphatases

CBS domains are ~60 amino acid tandemly repeated regulatory modules forming a widely distributed domain superfamily. Found in thousands of proteins from all kingdoms of life, CBS domains have adopted a variety of functions during evolution, one of which is regulation of enzyme activity through binding of adenylate-containing compounds in a hydrophobic cavity. Mutations in human CBS domain-containing proteins cause hereditary diseases. Inorganic pyrophosphatases (PPases) are ubiquitous enzymes, which pull pyrophosphate (PPi) producing reactions forward by hydrolyzing PPi into phosphate. Of the two nonhomologous soluble PPases, dimeric family II PPases, belonging to the DHH family of phosphoesterases, require a transition metal and magnesium for maximal activity. A quarter of the almost 500 family II PPases, found in bacteria and archaea, contain a 120-250 amino acid N-terminal insertion, comprised of two CBS domains separated in sequence by a DRTGG domain. These enzymes are thus named CBS-PPases. The function of the DRTGG domain in proteins is unknown. The aim of this PhD thesis was to elucidate the structural and functional differences of CBS-PPases in comparison to family II PPases lacking the regulatory insert. To this end, we expressed, purified and characterized the CBS-PPases from Clostridium perfringens (cpCBS-PPase) and Moorella thermoacetica (mtCBS-PPase), the latter lacking a DRTGG domain. Both enzymes are homodimers in solution and display maximal activity against PPi in the presence of Co2+ and Mg2+. Uniquely, the DRTGG domain was found to enable tripolyphosphate hydrolysis at rates similar to that of PPi. Additionally, we found that AMP and ADP inhibit, while ATP and AP4A activate CBSPPases, thus enabling regulation in response to changes in cellular energy status. We then observed substrate- and nucleotide-induced conformational transitions in mtCBS-PPase and found that the enzyme exists in two differentially active conformations, interconverted through substrate binding and resulting in a 2.5-fold enzyme activation. AMP binding was shown to produce an alternate conformation, which is reached through a different pathway than the substrate-induced conformation. We solved the structure of the regulatory insert from cpCBS-PPase in complex with AMP and AP4A and proposed that conformational changes in the loops connecting the catalytic and regulatory domains enable activity regulation. We examined the effects of mutations in the CBS domains of mtCBS-PPase on catalytic activity, as well as, nucleotide binding and inhibition.

Composition of Hawthorn (Crataegus spp.) Fruits and Leaves and emblic Leafflower (Phyllanthus emblica) Fruits

Hawthorn (Crataegus sp.) is widely distributed in the northern hemisphere (Asia, Europe and North America). It has been used as a medicinal material and food for hundreds of years both in Europe and in China. Clinical investigations and other research suggest that extracts of hawthorn fruits and leaves have multiple health effects including hypolipidaemic, anti-atherosclerotic, hypotensive, cardioprotective and blood vessel relaxing activities. Hawthorn fruit extracts have also displayed antioxidant and radical scavenging activities. Emblic leafflower fruit (Phyllanthus emblica) is widely used in Chinese and Indian traditional medicine. It has been found to have anti-cancer, hypoglycaemic and hypolipidaemic activities as well as cardioprotective effects and antioxidant activity. The fruit is currently used as a functional food targeted at obese people in China. Phenolic compounds, procyanidins (PCs), flavonols and C-glycosyl flavones in hawthorn and hydrolysable tannins in emblic leafflower fruits are considered among the major bioactive compounds in these berries. Moreover, hawthorn and emblic leafflower fruits are rich in vitamin C, triterpenoids, fruit acids, sugar alcohols and some other components with beneficial effects on the health of human beings. The aim of the thesis work was to characterise the major phenolic compounds in hawthorn fruits and leaves and emblic leafflower fruits as well as other components contributing to the nutritional profile and sensory properties of hawthorn fruits. Differences in the content and compositional profile of the major phenolic compounds, sugars, acids and sugar alcohols within various origins and species of hawthorn were also investigated. Acids, sugars and sugar alcohols in the fruits of different origins/cultivars belonging to three species (C. pinnatifida, C. brettschneideri and C. scabrifolia) of hawthorn were analysed by gas chromatography (GC-FID) and mass spectrometry (Publication I). Citric acid, quinic acid, malic acid, fructose, glucose, sorbitol and myo-inositol were found in all the subspecies. Sucrose was present only in C. scabrifolia and three cultivars of C. pinnatifida var. major. Forty-two phenolic compounds were identified/tentatively identified in fruits of C. pinnatifida var. major by polyamide column chromatography combined with high-performance liquid chromatograph-electrospray ionisation mass spectrometry (HPLC-ESI-MS) (Publication II). Ideain, chlorogenic acid, procyanidin (PC) B2, (-)-epicatechin, hyperoside and isoquercitrin were the major phenolic components identified. In addition, 35 phenolic compounds were tentatively identified based on UV and mass spectra. Eleven major phenolic compounds (hyperoside, isoquercitrin, chlorogenic acid, ideain, (-)-epicatechin, two PC dimers, three PC trimers and a PC dimer-hexoside) were quantified in the fruits of 22 cultivars/origins of three species of Chinese hawthorn by HPLC-ESI-MS with single ion recording function (SIR) (Publication III). The fruits of the hawthorn cultivars/origins investigated fell into two groups, one rich in sugars and flavonols, the other rich in acids and procyanidins. Based on the compositional features, different biological activities and sensory properties may be expected between cultivars/origins of the two groups. The results suggest that the contents of phenolic compounds, acids, sugars and sugar alcohols may be used as chemotaxonomic information distinguishing the hawthorn species from each other. Phenolic compounds in fruits and leaves of C. grayana and their changes during fruit ripening/harvesting were investigated using HPLC-UV-ESI-MS (Publication IV). (-)-Epicatechin, PC B2 and C1, hyperoside and a quercetin-pentoside were the major phenolic compounds in both fruits and leaves. Three C-glycosyl flavones (a luteolin-C-hexoside, a methyl luteolin-C-hexoside and an apigenin-C-hexoside) were present in leaves in abundance, but only at trace levels in fruits. Ideain and 5-O-caffeoylquinic acid were found in fruits only. Additionally, eleven phenolic compounds were identified/tentatively identified in both leaves and fruits (three B-type PC trimers, two B-type PC tetramers, a quercetin-rhamnosylhexoside, a quercetin-pentoside, a methoxykaempferol-methylpentosylhexoside, a quercetin-hexoside acetate, a methoxykaempferol-pentoside, chlorogenic acid and an unknown hydroxycinnamic acid derivative). The total content of phenolic compounds reached the highest level by the end of August in fruits and by the end of September in leaves. The compositional profiles of phenolic compounds in fruits and leaves of C. grayana were different from those of C. pinnatifida, C. brettschneideri, C. scabrifolia, C. pinnatifida. var. major, C. monogyna, C. laevigata and C. pentagyna. Phenolic compounds in emblic leafflower fruits were characterised by Sephadex LH-20 column chromatography combined with HPLC-ESI-MS (Publication V). A mucic acid gallate, three isomers of mucic acid lactone gallate, a galloylglucose, gallic acid, a digalloylglucose, putranjivain A, a galloyl-HHDP-glucose, elaeocarpusin and chebulagic acid represented the major phenolic compounds in fruits of emblic leafflower. In conclusion, results of this study significantly increase the current knowledge on the key bioactive and nutritional components of hawthorn and emblic leafflower fruits. These results provide important information for research on the mechanism responsible for the health benefits of these fruits.

Distributed Energy Production in the North-West Region of Russia

The energy system of Russia is the world's fourth largest measured by installed power. The largest are that of the the United States of America, China and Japan. After 1990, the electricity consumption decreased as a result of the Russian industry crisis. The vivid economic growth during the latest few years explains the new increase in the demand for energy resources within the State. In 2005 the consumption of electricity achieved the maximum level of 1990 and continues to growth. In the 1980's, the renewal of power facilities was already very slow and practically stopped in the 1990's. At present, the energy system can be very much characterized as outdated, inefficient and uneconomic because of the old equipment, non-effective structure and large losses in the transmission lines. The aim of Russia's energy reform, which was started in 2001, is to achieve a market based energy policy by 2011. This would thus remove the significantly state-controlled monopoly in Russia's energy policy. The reform will stimulateto decrease losses, improve the energy system and employ energy-saving technologies. The Russian energy system today is still based on the use of fossil fuels, and it almost totally ignores the efficient use of renewable sources such as wind, solar, small hydro and biomass, despite of their significant resources in Russia. The main target of this project is to consider opportunities to apply renewable energy production in the North-West Federal Region of Russia to partly solve the above mentioned problems in the energy system.

Protection of publicly distributed software components

The nature of client-server architecture implies that some modules are delivered to customers. These publicly distributed commercial software components are under risk, because users (and simultaneously potential malefactors) have physical access to some components of the distributed system. The problem becomes even worse if interpreted programming languages are used for creation of client side modules. The language Java, which was designed to be compiled into platform independent byte-code is not an exception and runs the additional risk. Along with advantages like verifying the code before execution (to ensure that program does not produce some illegal operations)Java has some disadvantages. On a stage of byte-code a java program still contains comments, line numbers and some other instructions, which can be used for reverse-engineering. This Master's thesis focuses on protection of Java code based client-server applications. I present a mixture of methods to protect software from tortious acts. Then I shall realize all the theoretical assumptions in a practice and examine their efficiency in examples of Java code. One of the criteria's to evaluate the system is that my product is used for specialized area of interactive television.

Global Distributed Delivery Model for Internet Service Provider

Globaalin talouden rakenteet muuttuvat jatkuvasti. Yritykset toimivat kansainvälisillä markkinoilla aiempaa enemmän. Tuotannon lisäämiseksi monet yritykset ovat ulkoistaneet tuotteidensa tuki- ja ylläpitotoiminnot halvan työvoiman maihin. Yritykset voivat tällöin keskittää toimintansa ydinosamiseensa. Vapautuneita resursseja voidaan käyttää yrityksen sisäisessä tuotekehityksessä ja panostaa seuraavan sukupolven tuotteiden ja teknologioiden kehittämiseen. Diplomityö esittelee Globaalisti hajautetun toimitusmallin Internet-palveluntarjoajalle jossa tuotteiden tuki- ja ylläpito on ulkoistettu Intiaan. Teoriaosassa esitellään erilaisia toimitusmalleja ja keskitytään erityisesti hajautettuun toimitusmalliin. Tämän lisäksi luetellaan valintakriteerejä joilla voidaan arvioida projektin soveltuvuutta ulkoistettavaksi sekä esitellään mahdollisuuksia ja uhkia jotka sisältyvät globaaliin ulkoistusprosessiin. Käytäntöosassa esitellään globaali palvelun toimittamisprosessi joka on kehitetty Internet-palveluntarjoajan tarpeisiin.

Data-parallel computation in parallel and distributed environments

The past few decades have seen a considerable increase in the number of parallel and distributed systems. With the development of more complex applications, the need for more powerful systems has emerged and various parallel and distributed environments have been designed and implemented. Each of the environments, including hardware and software, has unique strengths and weaknesses. There is no single parallel environment that can be identified as the best environment for all applications with respect to hardware and software properties. The main goal of this thesis is to provide a novel way of performing data-parallel computation in parallel and distributed environments by utilizing the best characteristics of difference aspects of parallel computing. For the purpose of this thesis, three aspects of parallel computing were identified and studied. First, three parallel environments (shared memory, distributed memory, and a network of workstations) are evaluated to quantify theirsuitability for different parallel applications. Due to the parallel and distributed nature of the environments, networks connecting the processors in these environments were investigated with respect to their performance characteristics. Second, scheduling algorithms are studied in order to make them more efficient and effective. A concept of application-specific information scheduling is introduced. The application- specific information is data about the workload extractedfrom an application, which is provided to a scheduling algorithm. Three scheduling algorithms are enhanced to utilize the application-specific information to further refine their scheduling properties. A more accurate description of the workload is especially important in cases where the workunits are heterogeneous and the parallel environment is heterogeneous and/or non-dedicated. The results obtained show that the additional information regarding the workload has a positive impact on the performance of applications. Third, a programming paradigm for networks of symmetric multiprocessor (SMP) workstations is introduced. The MPIT programming paradigm incorporates the Message Passing Interface (MPI) with threads to provide a methodology to write parallel applications that efficiently utilize the available resources and minimize the overhead. The MPIT allows for communication and computation to overlap by deploying a dedicated thread for communication. Furthermore, the programming paradigm implements an application-specific scheduling algorithm. The scheduling algorithm is executed by the communication thread. Thus, the scheduling does not affect the execution of the parallel application. Performance results achieved from the MPIT show that considerable improvements over conventional MPI applications are achieved.

Improving distributed simulation in a workstation environment

Technological development brings more and more complex systems to the consumer markets. The time required for bringing a new product to market is crucial for the competitive edge of a company. Simulation is used as a tool to model these products and their operation before actual live systems are built. The complexity of these systems can easily require large amounts of memory and computing power. Distributed simulation can be used to meet these demands. Distributed simulation has its problems. Diworse, a distributed simulation environment, was used in this study to analyze the different factors that affect the time required for the simulation of a system. Examples of these factors are the simulation algorithm, communication protocols, partitioning of the problem, distributionof the problem, capabilities of the computing and communications equipment and the external load. Offices offer vast amounts of unused capabilities in the formof idle workstations. The use of this computing power for distributed simulation requires the simulation to adapt to a changing load situation. This requires all or part of the simulation work to be removed from a workstation when the owner wishes to use the workstation again. If load balancing is not performed, the simulation suffers from the workstation's reduced performance, which also hampers the owner's work. Operation of load balancing in Diworse is studied and it is shown to perform better than no load balancing, as well as which different approaches for load balancing are discussed.

The role of trust and its evolution in distributed teams in a multinational organisation

Tutkimuksen päätavoitteena on ollut selvittää miten kansallinen ja organisaatiokulttuuri, niihin liittyvät normit ja arvot edesauttavat tai vaikeuttavat luottamuksen kehittymistä monikulttuurisissa tiimeissä maailmanlaajuisessa organisaatiossa. Tutkimuksen avulla haluttiin myös selvittää miten luottamus kehittyy hajautetuissa monikansallisissa tiimeissä WorldCom Internationalissa. Empiirinen tutkimusmenetelmä perustuu kvalitatiivisiin teemahaastatteluihin, jotka tehtiin WorldComin työntekijöille. Tutkimuksessa havaittiin, ettei yhteisten sosiaalisten normien merkitys luottamuksen syntymiselle ole niin merkittävä, koska WorldComin yhtenäiset toimintatavat sekä hallitseva amerikkalaisen emoyhtiön "kotikulttuuri" muodostavat yhtenäiset toimintalinjat tiimeissä. Tietokonevälitteisen kommunikoinnin jatkuva käyttö on edesauttanut työntekijöiden ns. sosiaalisen älyn kehittymistä, sillä henkilökohtaisen tapaamisen puuttuminen kehittää vastaavasti taitoja aistia ja tulkita sähköpostien tai puhelinneuvotteluiden aikana välittyviä vastapuolen "näkymättömiä" vihjeitä.

CORBA-pohjaisen hajautetun palvelun dynaaminen konfiguroinnin hallinta

Internetin välityksellä tarjottavien palveluiden kasvaneet käyttäjämäärät ovat lisänneet hajautettujen palveluiden määrää. Hajautusta tarvitaan täyttämään palveluiden kasvaneet suorituskykyvaatimukset. Hajautetut palvelut asettavat uusia vaatimuksia palvelujen hallinnan toteuttamiselle. Hallintajärjestelmien on myös mukauduttava palvelujen hajautettuun luonteeseen ja oltava joustavia palveluissa tapahtuvien muutosten ja ongelmien varalta. Tässä työssä esitellään aluksi CORBA-teknologiaa ja sen tarjoamia valmiita palveluita. Palvelunhallinnasta esitellään yleiset periaatteet ja hallinnan tehtävät. Työn käytännön osuudessa tutustutaan Finder-projektissa suunniteltuun hajautettuun hakemistopalveluun. Tarkemmin osuudessa keskitytään esittelemään suunnitellut menetelmät palvelun komponenttien hallintaan CORBA-ympäristössä.

Implementation of CORBA interface in a wireless device

CORBA (Common Object Request Broker Architecture) on laajalle levinnyt ja teollisuudessa yleisesti käytetty hajautetun tietojenkäsittelyn arkkitehtuuri. CORBA skaalautuu eri kokoisiin tarpeisiin ja sitä voidaan hyödynntää myös sulautetuissa langattomissa laitteissa. Oleellista sulautetussa ympäristössä on rakentaa rajapinnat kevytrakenteisiksi, pysyviksi ja helposti laajennettaviksi ilman että yhteensopivuus aikaisempiin rajapintoihin olisi vaarassa. Langattomissa laitteissa resurssit, kuten muistin määrä ja prosessointiteho, ovat hyvin rajalliset, joten rajapinta tulee suunnitella ja toteuttaa optimaalisesti. Palveluiden tulee ottaa huomioon myös langattomuuden rajoitukset, kuten hitaat tiedonsiirtonopeudet ja tiedonsiirron yhteydettömän luonteen. Työssä suunniteltiin ja toteutettiin CORBA-rajapinta GSM-päätelaitteeseen, jonka on todettu täyttävän sille asetetut tavoitteet. Rajapinta tarjoaa kaikki yleisimmät GSM-terminaalin ominaisuudet ja on laajennettavissa tulevia tuotteita ja verkkotekniikoita varten. Laajennettavuutta saavutetaan esimerkiksi kuvaamalla terminaalin ominaisuudet yleisellä kuvauskielellä, kuten XML:lla (Extensible Markup Language).

Building distributed high availability system

Today’s commercial web sites are under heavy user load and they are expected to be operational and available at all times. Distributed system architectures have been developed to provide a scalable and failure tolerant high availability platform for these web based services. The focus on this thesis was to specify and implement resilient and scalable locally distributed high availability system architecture for a web based service. Theory part concentrates on the fundamental characteristics of distributed systems and presents common scalable high availability server architectures that are used in web based services. In the practical part of the thesis the implemented new system architecture is explained. Practical part also includes two different test cases that were done to test the system's performance capacity.

Development a distributed simulation environment on a cluster of workstations

Simulation has traditionally been used for analyzing the behavior of complex real world problems. Even though only some features of the problems are considered, simulation time tends to become quite high even for common simulation problems. Parallel and distributed simulation is a viable technique for accelerating the simulations. The success of parallel simulation depends heavily on the combination of the simulation application, algorithm and message population in the simulation is sufficient, no additional delay is caused by this environment. In this thesis a conservative, parallel simulation algorithm is applied to the simulation of a cellular network application in a distributed workstation environment. This thesis presents a distributed simulation environment, Diworse, which is based on the use of networked workstations. The distributed environment is considered especially hard for conservative simulation algorithms due to the high cost of communication. In this thesis, however, the distributed environment is shown to be a viable alternative if the amount of communication is kept reasonable. Novel ideas of multiple message simulation and channel reduction enable efficient use of this environment for the simulation of a cellular network application. The distribution of the simulation is based on a modification of the well known Chandy-Misra deadlock avoidance algorithm with null messages. The basic Chandy Misra algorithm is modified by using the null message cancellation and multiple message simulation techniques. The modifications reduce the amount of null messages and the time required for their execution, thus reducing the simulation time required. The null message cancellation technique reduces the processing time of null messages as the arriving null message cancels other non processed null messages. The multiple message simulation forms groups of messages as it simulates several messages before it releases the new created messages. If the message population in the simulation is suffiecient, no additional delay is caused by this operation A new technique for considering the simulation application is also presented. The performance is improved by establishing a neighborhood for the simulation elements. The neighborhood concept is based on a channel reduction technique, where the properties of the application exclusively determine which connections are necessary when a certain accuracy for simulation results is required. Distributed simulation is also analyzed in order to find out the effect of the different elements in the implemented simulation environment. This analysis is performed by using critical path analysis. Critical path analysis allows determination of a lower bound for the simulation time. In this thesis critical times are computed for sequential and parallel traces. The analysis based on sequential traces reveals the parallel properties of the application whereas the analysis based on parallel traces reveals the properties of the environment and the distribution.

Integrating distributed generation and Smart Grids into single-family house

This study examines Smart Grids and distributed generation, which is connected to a single-family house. The distributed generation comprises small wind power plant and solar panels. The study is done from the consumer point of view and it is divided into two parts. The first part presents the theoretical part and the second part presents the research part. The theoretical part consists of the definition of distributed generation, wind power, solar energy and Smart Grids. The study examines what the Smart Grids will enable. New technology concerning Smart Grids is also examined. The research part introduces wind and sun conditions from two countries. The countries are Finland and Germany. According to the wind and sun conditions of these two countries, the annual electricity production from wind power plant and solar panels will be calculated. The costs of generating electricity from wind and solar energy are calculated from the results of annual electricity productions. The study will also deal with feed-in tariffs, which are supporting systems for renewable energy resources. It is examined in the study, if it is cost-effective for the consumers to use the produced electricity by themselves or sell it to the grid. Finally, figures for both countries are formed. The figures include the calculated cost of generating electricity from wind power plant and solar panels, retail and wholesale prices and feed-in tariffs. In Finland, it is not cost-effective to sell the produced electricity to the grid, before there are support systems. In Germany, it is cost-effective to sell the produced electricity from solar panels to the grid because of feed-in tariffs. On the other hand, in Germany it is cost-effective to produce electricity from wind to own use because the retail price is higher than the produced electricity from wind.

Sustainable Waste-to-Energy Production: Performance Evaluation of Distributed Generation fuelled by Landfill Gas

The environmental impact of landfill is a growing concern in waste management practices. Thus, assessing the effectiveness of the solutions implemented to alter the issue is of importance. The objectives of the study were to provide an insight of landfill advantages, and to consolidate landfill gas importance among others alternative fuels. Finally, a case study examining the performances of energy production from a land disposal at Ylivieska was carried out to ascertain the viability of waste to energy project. Both qualitative and quantitative methods were applied. The study was conducted in two parts; the first was the review of literatures focused on landfill gas developments. Specific considerations were the conception of mechanism governing the variability of gas production and the investigation of mathematical models often used in landfill gas modeling. Furthermore, the analysis of two main distributed generation technologies used to generate energy from landfill was carried out. The review of literature revealed a high influence of waste segregation and high level of moisture content for waste stabilization process. It was found that the enhancement in accuracy for forecasting gas rate generation can be done with both mathematical modeling and field test measurements. The result of the case study mainly indicated the close dependence of the power output with the landfill gas quality and the fuel inlet pressure.