Prediction of 3D structure and ligand-binding properties : ABC transporters and flavodiiron proteins from Synechocystis sp. strain PCC 6803

Cyanobacteria are unicellular, non-nitrogen-fixing prokaryotes, which perform photosynthesis similarly as higher plants. The cyanobacterium Synechocystis sp. strain PCC 6803 is used as a model organism in photosynthesis research. My research described herein aims at understanding the function of the photosynthetic machinery and how it responds to changes in the environment. Detailed knowledge of the regulation of photosynthesis in cyanobacteria can be utilized for biotechnological purposes, for example in the harnessing of solar energy for biofuel production. In photosynthesis, iron participates in electron transfer. Here, we focused on iron transport in Synechocystis sp. strain PCC 6803 and particularly on the environmental regulation of the genes encoding the FutA2BC ferric iron transporter, which belongs to the ABC transporter family. A homology model built for the ATP-binding subunit FutC indicates that it has a functional ATPbinding site as well as conserved interactions with the channel-forming subunit FutB in the transporter complex. Polyamines are important for the cell proliferation, differentiation and apoptosis in prokaryotic and eukaryotic cells. In plants, polyamines have special roles in stress response and in plant survival. The polyamine metabolism in cyanobacteria in response to environmental stress is of interest in research on stress tolerance of higher plants. In this thesis, the potd gene encoding an polyamine transporter subunit from Synechocystis sp. strain PCC 6803 was characterized for the first time. A homology model built for PotD protein indicated that it has capability of binding polyamines, with the preference for spermidine. Furthermore, in order to investigate the structural features of the substrate specificity, polyamines were docked into the binding site. Spermidine was positioned very similarly in Synechocystis PotD as in the template structure and had most favorable interactions of the docked polyamines. Based on the homology model, experimental work was conducted, which confirmed the binding preference. Flavodiiron proteins (Flv) are enzymes, which protect the cell against toxicity of oxygen and/or nitric oxide by reduction. In this thesis, we present a novel type of photoprotection mechanism in cyanobacteria by the heterodimer of Flv2/Flv4. The constructed homology model of Flv2/Flv4 suggests a functional heterodimer capable of rapid electron transfer. The unknown protein sll0218, encoded by the flv2-flv4 operon, is assumed to facilitate the interaction of the Flv2/Flv4 heterodimer and energy transfer between the phycobilisome and PSII. Flv2/Flv4 provides an alternative electron transfer pathway and functions as an electron sink in PSII electron transfer.

Growth, crown structure and seed production of birch seedlings, grafts and micropropagated plants

Summary

Vegetation succession and diversity on Teuravuoma experimental drainage area in northern Finland

Tiivistelmä: Kasvillisuuden sukkessio ja monimuotoisuus Teuravuoman koeojitusalueella Pohjois-Suomessa

Slits in container wall improve root structure and stem straightness of outplanted Scots pine seedlings

Abstract

The structure and development of Russia's food retail sector from the point of view of Finnish food industry

Tämän diplomityön tavoitteena on selvittää Venäjän ruoan vähittäiskaupan rakenne ja sen tuleva kehitys. Tällä hetkellä se on yksi maailman nopeimmin kasvavista markkinoista. Kasvun syynä on korkea öljyn hinta, jokaon kumuloitunut ihmisten palkkoihin. Kuitenkin vaikka tulot kasvavat, ruokaan käytetty osuus tuloista on pysynyt suhteellisen vakaana. Kulutus on siis siirtymässä laadukkaampiin ja arvokkaampiin tuotteisiin Modernien kauppojen osuus markkinoista on vielä pieni, koska Venäjän vähittäiskauppasektori on yhä hajaantunut perinteisiin kauppaformaatteihin kuten kioskeihin, toreille ja pieniin ruokakauppoihin. Kauppaketjut ovat kuitenkin tulossa merkittävämmiksi. Suurin markkina-alue vähittäiskauppiaille on Moskova, mutta tällä hetkellä ketjut laajentavat toimintojaan nopeasti myös muille Venäjän alueille. Parhaat kasvunäkymät ovat alueilla, vaikka Moskovan markkinat eivät olekaan kyllästyneet. Tärkein kasvua rajoittava tekijä Moskovassa on rakennustonttien ja kiinteistöjen saatavuus. Vähittäiskauppamarkkinat lähestyvät kyllästymispistettä, josta seuraa markkinoiden konsolidaatio. Tämä prosessi on jo alkanut, mutta kovin paljon yritysostoja ei ole vielätehty. Toistaiseksi kauppaketjut ovat tyytyneet muodostamaan alliansseja. Ketjut pyrkivät parantamaan asemaansa hintaneuvotteluissa muodostamalla osto-alliansseja, luomalla omia brändejä ja käyttämällä alueellista laajentumista lyömäaseena. Jotta ruoan tuottaja pääsisi myös alueellisille markkinoille, on sen ehkä suostuttava myymään tuotteitaan edullisempaan hintaan. Tavarantoimittajat ovat vahvassa asemassa silloin, kun heillä on toimiva jakeluverkko, kyky JIT-toimituksiin,kunnollinen dokumentaatiokäytäntö, vahva brändi ja edullinen hinta. Ns. listausmaksun suuruus voi määrittää tuottajan tuotteilleen saaman hyllytilan koon.

Value added logistical support service: logistics cost structure and performance in the new concept. Part 3

The aim of this study is to present an Activity-Based Costing spreadsheet tool for analyzing the logistics costs. The tool can be used both by customer-companies and logistics service providers. The study discusses the influence of different activity models on costs. Additionally this paper discusses about the logistical performance across the total supply chain This study is carried out using ananalytical research approach and literature material has been used for supplementing the concerned research approach. Cost structure analysis was based on the theory of activity-based management. This study was outlined to spare part logistics in machine-shop industry. The outlines of logistics services and logisticalperformance discussed in this report are based on the new logistics business concept (LMS-concept), which has been presented earlier in the Valssi-project. Oneof the aims of this study is to increase awareness of different activity modelson logistics costs. The report paints an overall picture about the business environment and requirements for the new logistics concept.

The Sottunga-Jurmo shear zone : structure and deformation history of a crustal-scale ductile shear zone in SW Finland

The aim of this study is to gain a better understanding of the structure and the deformation history of a NW-SE trending regional, crustal-scale shear structure in the Åland archipelago, SW Finland, called the Sottunga-Jurmo shear zone (SJSZ). Approaches involving e.g. structural geology, geochronology, geochemistry and metamorphic petrology were utilised in order to reconstruct the overall deformation history of the study area. The study therefore describes several features of the shear zone including structures, kinematics and lithologies within the study area, the ages of the different deformation phases (ductile to brittle) within the shear zone, as well as some geothermobarometric results. The results indicate that the SJSZ outlines a major crustal discontinuity between the extensively migmatized rocks NE of the shear zone and the unmigmatised, amphibolite facies rocks SW of the zone. The main SJSZ shows overall dextral lateral kinematics with a SW-side up vertical component and deformation partitioning into pure shear and simple shear dominated deformation styles that was intensified toward later stages of the deformation history. The deformation partitioning resulted in complex folding and refolding against the SW margin of the SJSZ, including conical and sheath folds, and in a formation of several minor strike-slip shear zones both parallel and conjugate to the main SJSZ in order to accommodate the regional transpressive stresses. Different deformation phases within the study area were dated by SIMS (zircon U-Pb), ID-TIMS (titanite U-Pb) and 40Ar/39Ar (pseudotachylyte wholerock) methods. The first deformation phase within the ca. 1.88 Ga rocks of the study area is dated at ca. 1.85 Ga, and the shear zone was reactivated twice within the ductile regime (at ca. 1.83 Ga and 1.79 Ga), during which the strain was successively increasingly partitioned into the main SJSZ and the minor shear zones. The age determinations suggest that the orogenic processes within the study area did not occur in a temporal continuum; instead, the metamorphic zircon rims and titanites show distinct, 10-20 Ma long breaks in deformation between phases of active deformation. The results of this study further imply slow cooling of the rocks through 600-700ºC so that at 1.79 Ga, 2 the temperature was still at least 600ºC. The highest recorded metamorphic pressures are 6.4-7.1 kbar. At the late stages or soon after the last ductile phase (ca. 1.79 Ga), relatively high-T mylonites and ultramylonites were formed, witnessing extreme deformation partitioning and high strain rates. After the rocks reached lower amphibolite facies to amphibolite-greenschist facies transitional conditions (ca. 500-550ºC), they cooled rapidly, probably due to crustal uplift and exhumation. The shear zone was reactivated at least once within the semi-brittle to brittle regime between ca. 1.79 Ga and 1.58 Ga, as evidenced by cataclasites and pseudotachylytes. In summary, the results of this study suggest that the Sottunga-Jurmo shear zone (and the South Finland shear zone) defines a major crustal discontinuity, and played a central role in accommodating the regional stresses during and after the Svecofennian orogeny.

Nuclear magnetic resonance investigation of structure and dynamics of some electrolyte solutions

Electrolyte solutions are of importance in a wide range of scientific contexts and as such have attracted considerable theoretical and experimental effort over many years. Nuclear Magnetic resonance provides a precise and versatile tool for investigation of electrolyte solutions, both in water and in organic solvents. Many structural and dynamic properties can be obtained through NMR experiments. The solution of aluminum chloride in water was studied. Different concentrations were taken for investigation. Independence of maximum line shift from concentration and acidity was shown. Six-coordinated structure of solvation shell was confirmed by experiments on 'H and 27A1 nuclei. Diffusion coefficients were studied. The solution of nickel chloride in methanol was studied. Lines, corresponding to coordinated and bulk methanol were found. Four-, five- and six-coordinated structures were found in different temperatures. The line for coordinated -OD group of deuterated methanol was observed on 2H spectrum for the first time. Partial deuteration of CH3 group was detected. Inability to observe coordinated -OH group was explained.

Contract manufacturing networks structure and supply chain management

The usual objectives that companies have for subcontracting are studied in this thesis. The case company’s objectives for contract manufacturing now and in the future are identified. The main objective of the thesis is to create a focused model for the structure and supply chain management in the contract manufacturing network. This model is made for case company’s certain profit center. The different possibilities and their advantages and disadvantages for the structure and supply chain management are examined trough a theoretical review of literature. The possibilities found are then examined from the case company’s point of view. The case company point of view is established based on the opinions of the case company’s representatives. The outcome of the thesis is that the star shaped structure with supply chain management centralized to case company would be the best choice for the case company to manage the contract manufacture network.