Phylogenetic Analysis of Avidins and Expression of Novel Avidins from Lactrodectus hesperus and Hoeflea phototrophica

Avidins (Avds) are homotetrameric or homodimeric glycoproteins with typically less than 130 amino acid residues per monomer. They form a highly stable, non-covalent complex with biotin (vitamin H) with Kd = 10-15 M (for chicken Avd). The best-studied Avds are the chicken Avd from Gallus gallus and streptavidin from Streptomyces avidinii, although other Avd studies have also included Avds from various origins, e.g., from frogs, fishes, mushrooms and from many different bacteria. Several engineered Avds have been reported as well, e.g., dual-chain Avds (dcAvds) and single-chain Avds (scAvds), circular permutants with up to four simultaneously modifiable ligand-binding sites. These engineered Avds along with the many native Avds have potential to be used in various nanobiotechnological applications. In this study, we made a structure-based alignment representing all currently available sequences of Avds and studied the evolutionary relationship of Avds using phylogenetic analysis. First, we created an initial multiple sequence alignment of Avds using 42 closely related sequences, guided by the known Avd crystal structures. Next, we searched for non-redundant Avd sequences from various online databases, including National Centre for Biotechnology Information and the Universal Protein Resource; the identified sequences were added to the initial alignment to expand it to a final alignment of 242 Avd sequences. The MEGA software package was used to create distance matrices and a phylogenetic tree. Bootstrap reproducibility of the tree was poor at multiple nodes and may reflect on several possible issues with the data: the sequence length compared is relatively short and, whereas some positions are highly conserved and functional, others can vary without impinging on the structure or the function, so there are few informative sites; it may be that periods of rapid duplication have led to paralogs and that the differences among them are within the error limit of the data; and there may be other yet unknown reasons. Principle component analysis applied to alternative distance data did segregate the major groups, and success is likely due to the multivariate consideration of all the information. Furthermore, based on our extensive alignment and phylogenetic analysis, we expressed two novel Avds, lacavidin from Lactrodectus Hesperus, a western black widow spider, and hoefavidin from Hoeflea phototrophica, an aerobic marine bacterium, the ultimate aim being to determine their X-ray structures. These Avds were selected because of their unique sequences: lacavidin has an N-terminal Avd-like domain but a long C-terminal overhang, whereas hoefavidin was thought to be a dimeric Avd. Both these Avds could be used as novel scaffolds in biotechnological applications.

Tarjoustoiminnankehittäminen projektiliiketoiminnassa - tiedonhallinta ja työkalut

Työn tavoitteena on tehdä pohjatutkimus tarjoustoiminnan kehittämiseksi Larox Oyj:ssä. Työssä hahmotetaan haastatteluiden avulla tämänhetkiset ongelma-alueet tarjoustoiminnassa ja tiedonhallinnassa. Nykyisin suurimpina kehityshaasteina ovat rutiinityön manuaalinen hallinta, tiedon hankala saatavuus ja selkeiden yhteisten pelisääntöjen puuttuminen tarjoustoiminnassa. Näihin haasteisiin pyritään löytämään ratkaisuvaihtoehtoja. Työ sisältää teoriaosan, jossa käydään läpi projektin ominaispiirteitä, tarjoustoiminnan osuutta projektiliiketoiminnassa, elinkaarenaikaisen tiedonhallinnan keinoja sekä massaräätälöinnin toimintaperiaatteita. Tarjoustoimintaa pyritään kehittämään käsitellyn teorian, benchmark-vierailuilta saatujen ideoiden sekä haastatteluissa tulleiden toiveiden pohjalta. Tuloksena saadaan kehitysideat pitkäjänteiseen kehitystyöhön sekä nopeasti toteutettaviin toimenpiteisiin. Keskeinen kehitysidea on tarjouskonfiguraattorin kehitystyön aloittaminen. Sen avulla pyritään vähentämään tarjousinsinöörien työtaakkaa. Silloin tarjousinsinööreille jää aikaa toteuttaa osaamistaan haastavampien ja suurempien tarjouksien tekemisessä. Tuloksena on saatu neliportainen kehityspolku, jota kulkemalla päästään kohti hahmotettua tavoitetilaa. Työn tuloksia käytetään hyväksi aloitettaessa konfiguraattorin kehitys Laroxilla sekä kehitettäessä koko tarjoustoimintaa ja elinkaarenaikaista tiedonhallintaa yrityksessä.

Flow phenomena, heat and mass transfer in microchannel reactors

The studies of flow phenomena, heat and mass transfer in microchannel reactors are beneficial to estimate and evaluate the ability of microchannel reactors to be operated for a given process reaction such as Fischer-Tropsch synthesis. The flow phenomena, for example, the flow regimes and flow patterns in microchannel reactors for both single phase and multiphase flow are affected by the configuration of the flow channel. The reviews of the previous works about the analysis of related parameters that affect the flow phenomena are shown in this report. In order to predict the phenomena of Fischer-Tropsch synthesis in microchannel reactors, the 3-dimensional computational fluid dynamic simulation with commercial software package FLUENT was done to study the flow phenomena and heat transfer for gas phase Fischer-Tropsch products flow in rectangular microchannel with hydraulic diameter 500 ¿m and length 15 cm. Numerical solution with slip boundary condition was used in the simulation and the flowphenomena and heat transfer were determined.

Stock flow through a drum screen

Tässä diplomityössä haluttiin mallintaa kuidutusrummun toimintaa Fluent virtausmallinusohjelman avulla. Aikaisempi tieto ja kehitystyö on perustunut kokemukseen ja käytännön kokeisiin. Kehitystyön alkuaikoina on suoritettu muutamia laskelmia koskien rummun tuottoa mutta sen jälkeen ei toimintaa ole laskennallisesti kuvattu. Työn ensimmäinen osa käsittelee yleisesti keräyspaperin käsittelyyn liittyviä laitteita ja menetelmiä. Toimintaperiaatteita on kuvattu yleisellä tasolla ja FibreFlow® rumpu on sitten käsitelty muita laitteita tarkemmin. Työn toinen osa sisältää sitten laboratoriotestit paikallisilta tahteilta hankittujen näytteiden viskositeettien ja tiheyksien määrittämiseksi. Kokeet suoritettiin Kemiantekniikan osastolla Brookfield viskoosimetrillä. Joitain alustavia laskentoja tuotosta suoritettiin aikaisempien tietojen perusteella. Rumpua kun on valmistettu vuodesta 1976, on tietoa kertynyt runsaasti vuosien mittaan. Laskelmia varten valittiin mallinnettavaksi alueeksi vain yksittäinen reikä sihdistä jolle laskettiin massavirta. Käytetyt laadut olivat OCC ja DIP. Myös eri rumpukoot otettiin jossain määrin huomioon.

Terveydenhuollon toimintaverkoston kehittäminen

Työn tavoitteena oli selvittää, jäsentää ja kartoittaa terveydenhuollon toiminta-verkoston yhteistyön nykytilaa sekä hahmotella uutta toimintamallia. Työ toteutettiin teemahaastatteluna Pohjois-Savon sairaanhoitopiirin alueella. Kyselylomakkeilta ja haastatteluista saatuja tietoja on analysoitu SPSS for Windows –analysointi- ja tiedonhallintaohjelmistolla. Käsitys toimintaverkoston nykytilasta saatiin yhdistämällä tilastollisesti merkitsevät tulokset, haastattelutiedot sekä haastattelutietojen pohjalta piirretyt riippuvuuskuvat. Aiheen teoriatarkastelun ja analyysitulosten pohjalta on hahmoteltu uutta terveydenhuollon toimintaverkoston toimintamallia, jossa keskeiseksi tekijäksi nousee toimijoiden yhdessä tuottama lisäarvo hoitoketjun asiakkaalle. Erilaiset kitkatekijät ja potilaan tilaa kohentamattomat odotusajat on mahdollista poistaa mallin avulla. Tieto- ja viestintätekniikan rooli toimintaa tukevana työkaluna edesauttaa tiedon liikkumista eri toimijoiden integroitujen tietojärjestelmien välillä. Työssä esitellään myös työkaluja helpottamaan käytännön toimenpiteitä uuden toimintamallin käyttöönottamisessa.

Kysynnän ennustaminen sekä informaatiovirtojen integrointi tuotannonohjaukseen arvoketjun tehostamiseksi

Tässä työssä on tarkasteltu kokoonpano-osien valmistajan näkökulmasta eri keinoja tehostaa tilaus-toimitusketjua sekä mahdollisuuksia parantaa samalla omaa tuotannonohjausta ja suunnittelua. Kysynnän heilahteluihin on pystyttävä varautumaan koko ketjun tasolla, jotta suurilta piiskavaikutuksilta voitaisiin välttyä sekä taattaisiin koko ketjun tehokas toiminta. Piiskavaikutus korostuu erityisesti ketjun alapäässä toimivaan yritykseen. Yritykset eivät kilpaile enää pelkästään keskenään. Kilpailu tapahtuu yhä enemmän ja enemmän myös kokonaisten arvoketjujen välillä. Arvoketjujen toimivuuden pohjana on tehokas informaationvaihto sekä yhteistyö informaation tehokkaaseen hyödyntämiseen. Käytännön tasolla arvoketjun logistista tehokkuutta voidaan lisätä informaation vaihdon lisäämisellä siirtymällä sähköisen tiedon siirtoon (EDI). Tuotannonsuunnittelun tehostamiseksi ja varastoihin sidottujen pääomien vapauttamiseksi on siirrytty toimittajan hallinnoiman varastoinnin (VMI) käyttöön. Kysynnän ennustamisella pyritään tasaamaan kysynnän heilahteluja sekä helpottamaan resurssien varaamista ja raaka-aineiden tilauksia. Näillä toimilla on pystytty tehostamaan tilausten käsittelyä sekä tuotannonohjausta. Lisäksi läpinäkyvyyden lisääntyminen on sitouttanut kahden arvoketjussa peräkkäin toimivan yrityksen toimintaa.

Quantitative proteomics in the characterization of T helper lymphocyte differentiation

The term proteome is used to define the complete set of proteins expressed in cells or tissues of an organism at a certain timepoint. Respectively, proteomics is used to describe the methods, which are used to study such proteomes. These methods include chromatographic and electrophoretic techniques for protein or peptide fractionation, mass spectrometry for their identification, and use of computational methods to assist the complicated data analysis. A primary aim in this Ph.D. thesis was to set-up, optimize, and develop proteomics methods for analysing proteins extracted from T-helper (Th) lymphocytes. First, high-throughput LC-MS/MS and ICAT labeling methods were set-up and optimized for analysing the microsomal fraction proteins extracted from Th lymphocytes. Later, iTRAQ method was optimized to study cytokine regulated protein expression in the nuclei of Th lymphocytes. High-throughput LC-MS/MS analyses, like ICAT and iTRAQ, produce large quantities of data and robust software and data analysis pipelines are needed. Therefore, different software programs used for analysing such data were evaluated. Moreover, a pre-filtering algorithm was developed to classify good-quality and bad-quality spectra prior to the database searches. Th-lymphocytes can differentiate into Th1 or Th2 cells based on surrounding antigens, co-stimulatory molecules, and cytokines. Both subsets have individual cytokine secretion profiles and specific functions. Th1 cells participate in the cellular immunity against intracellular pathogens, while Th2 cells have important role in the humoral immunity against extracellular parasites. An abnormal response of Th1 and Th2 cells and imbalance between the subsets are charasteristic of several diseases. Th1 specific reactions and cytokines have been detected in autoimmune diseases, while Th2 specific response and cytokine profile is common in allergy and asthma. In this Ph. D. thesis mass spectrometry-based proteomics was used to study the effects of Th1 and Th2 promoting cytokines IL-12 and IL-4 on the proteome of Th lymphocytes. Characterization of microsomal fraction proteome extracted from IL-12 treated lymphobasts and IL-4 stimulated cord blood CD4+ cells resulted in finding of cytokine regulated proteins. Galectin-1 and CD7 were down-regulated in IL-12 treated cells, while IL-4 stimulation decreased the expression of STAT1, MXA, GIMAP1, and GIMAP4. Interestingly, the transcription of both GIMAP genes was up-regulated in Th1 polarized cells and down-regulated in Th2 promoting conditions.

Yhteisvikaparametrien määritys

Tässä kandidaatintyössä selvitetään yhteisvikaparametrien määritysprosessia todennäköisyysperustaista riskianalyysia varten Teollisuuden Voiman Olkiluodossa käytössä olevien Olkiluoto-1 ja Olkiluoto-2 ydinvoimalaitosyksiköiden osalta. Kandidaatintyön tavoitteena on selvittää yhteisvikaparametrien määrittämisen yleiset työvaiheet ja tutkia alkuperäisen selvityksen jälkeen käytettäväksi tulleen ICDE-yhteisvika-aineiston soveltamismahdollisuudet Olkiluodon laitosyksiköihin.

Real-Time Simulation of Mobile and Industrial Machines Using the Multibody Simulation Approach

This thesis introduces a real-time simulation environment based on the multibody simulation approach. The environment consists of components that are used in conventional product development, including computer aided drawing, visualization, dynamic simulation and finite element software architecture, data transfer and haptics. These components are combined to perform as a coupled system on one platform. The environment is used to simulate mobile and industrial machines at different stages of a product life time. Consequently, the demands of the simulated scenarios vary. In this thesis, a real-time simulation environment based on the multibody approach is used to study a reel mechanism of a paper machine and a gantry crane. These case systems are used to demonstrate the usability of the real-time simulation environment for fault detection purposes and in the context of a training simulator. In order to describe the dynamical performance of a mobile or industrial machine, the nonlinear equations of motion must be defined. In this thesis, the dynamical behaviour of machines is modelled using the multibody simulation approach. A multibody system may consist of rigid and flexible bodies which are joined using kinematic joint constraints while force components are used to describe the actuators. The strength of multibody dynamics relies upon its ability to describe nonlinearities arising from wearing of the components, friction, large rotations or contact forces in a systematic manner. For this reason, the interfaces between subsystems such as mechanics, hydraulics and control systems of the mechatronic machine can be defined and analyzed in a straightforward manner.

Aging based maintenance and reinvestment scheduling of electric distribution

The maintenance of electric distribution network is a topical question for distribution system operators because of increasing significance of failure costs. In this dissertation the maintenance practices of the distribution system operators are analyzed and a theory for scheduling maintenance activities and reinvestment of distribution components is created. The scheduling is based on the deterioration of components and the increasing failure rates due to aging. The dynamic programming algorithm is used as a solving method to maintenance problem which is caused by the increasing failure rates of the network. The other impacts of network maintenance like environmental and regulation reasons are not included to the scope of this thesis. Further the tree trimming of the corridors and the major disturbance of the network are not included to the problem optimized in this thesis. For optimizing, four dynamic programming models are presented and the models are tested. Programming is made in VBA-language to the computer. For testing two different kinds of test networks are used. Because electric distribution system operators want to operate with bigger component groups, optimal timing for component groups is also analyzed. A maintenance software package is created to apply the presented theories in practice. An overview of the program is presented.

Acceleration of Solar Energetic Particles in coronal shocks through self-generated turbulence

The acceleration of solar energetic particles (SEPs) by flares and coronal mass ejections (CMEs) has been a major topic of research for the solar-terrestrial physics and geophysics communities for decades. This thesis discusses theories describing first-order Fermi acceleration of SEPs through repeated crossings at a CME-driven shock. We propose that particle trapping occurs through self-generated Alfvén waves, leading to a turbulent trapping region in front of the shock. Decelerating coronal shocks are shown to be capable of efficient SEP acceleration, provided seed particle injection is sufficient. Quasi-parallel shocks are found to inject thermal particles with good efficiency. The roles of minimum injection velocities, cross-field diffusion, downstream scattering efficiency and cross-shock potential are investigated in detail, with downstream isotropisation timescales having a major effect on injection efficiency. Accelerated spectra of heavier elements up to iron are found to exhibit significantly harder spectra than protons. Accelerated spectra cut-off energies are found to scale proportional to (Q/A)^1.5, which is explained through analysis of the spectral shape of amplified Alfvénic turbulence. Acceleration times to different threshold energies are found to be non-linear, indicating that self-consistent time-dependent simulations are required in order to expose the full extent of acceleration dynamics. The well-established quasilinear theory (QLT) of particle scattering is investigated by comparing QLT scattering coefficients with those found via full-orbit simulations. QLT is found to overemphasise resonance conditions. This finding supports the simplifications implemented in the presented coronal shock acceleration (CSA) simulation software. The CSA software package is used to simulate a range of acceleration scenarios. The results are found to be in agreement with well-established particle acceleration theory. At the same time, new spatial and temporal dynamics of particle population trapping and wave evolution are revealed.

Reasoning over knowledge-based generation of situations in context spaces to reduce food waste

With the ever-growing amount of connected sensors (IoT), making sense of sensed data becomes even more important. Pervasive computing is a key enabler for sustainable solutions, prominent examples are smart energy systems and decision support systems. A key feature of pervasive systems is situation awareness which allows a system to thoroughly understand its environment. It is based on external interpretation of data and thus relies on expert knowledge. Due to the distinct nature of situations in different domains and applications, the development of situation aware applications remains a complex process. This thesis is concerned with a general framework for situation awareness which simplifies the development of applications. It is based on the Situation Theory Ontology to provide a foundation for situation modelling which allows knowledge reuse. Concepts of the Situation Theory are mapped to the Context Space Theory which is used for situation reasoning. Situation Spaces in the Context Space are automatically generated with the defined knowledge. For the acquisition of sensor data, the IoT standards O-MI/O-DF are integrated into the framework. These allow a peer-to-peer data exchange between data publisher and the proposed framework and thus a platform independent subscription to sensed data. The framework is then applied for a use case to reduce food waste. The use case validates the applicability of the framework and furthermore serves as a showcase for a pervasive system contributing to the sustainability goals. Leading institutions, e.g. the United Nations, stress the need for a more resource efficient society and acknowledge the capability of ICT systems. The use case scenario is based on a smart neighbourhood in which the system recommends the most efficient use of food items through situation awareness to reduce food waste at consumption stage.