Responses of soil respiration and barley growth to modified supply of oxygen in the soil

Selostus: Maan hengityksen ja ohran kasvun reagointi hapensaannin muutoksiin maassa

Selvityksiä reaktiokalorimetrin soveltuvuudesta hydrometallurgiaan

Tämän työn tavoitteena oli reaktiokalorimetrin käyttöönotto sekä sen käyttökelpoisuuden selvittäminen hydrometallurgisten sovellusten ja erityisesti sinkkisulfidin liuotuksen tutkimiseen. Työn kirjallisuusosassa on käsitelty yleisellä tasolla kalorimetrian ja reaktiokalorimetrian teoriaa, termodynamiikkaa sekä sinkkirikasteen liuotuksen kemiaa. Lisäksi työssä esitellään erilaisten kalorimetrien ja termoanalyyttisten mittauslaitteiden toimintaperiaatteita. Työn kokeellisessa osassa selvitettiin reaktiokalorimetrin mittaustulosten tarkkuutta vesi- kokeiden avulla. Laitteistolla määritettiin myös reaktiolämmöt sinkkisulfidin liukenemisreaktiolle sekä elohopeasuolan saostusreaktiolle. Lisäksi tutkittiin sekoitusnopeuden, lämpötilan ja kiintoainepitoisuuden vaikutusta mittaustuloksiin. Reaktiokalorimetrillä suoritettujen kokeiden perusteella havaittiin, että reaktiolämpöjen absoluuttisten arvojen määrittäminen laitteistolla on käytännössä vaikeaa. Koska reaktiokalorimetrillä pystytään määrittämään vain mittauksen aikana tapahtunut kokonaislämpömuutos, vaikuttavat mahdolliset faasimuutokset ja reaktorin lämpöhäviöt mittaustuloksiin. Näiden tekijöiden vaikutus on pyrittävä eliminoimaan tai niiden vaikutus on tunnettava tarkkaan, jos laitteella halutaan saada luotettavia reaktiolämpömittaustuloksia. Laitteiston mittaustarkkuus huononee huomattavasti, kun reaktorin lämpötila nousee yli 60 °C:een. Laitteistolla mitatut reaktiolämmöt poikkeavat huomattavasti vastaavista kirjallisuuden arvoista. Vedelle määritetyt ominaislämpökapasiteetit poikkeavat kirjallisuuden arvoista enintään 5 alle 90 °C:een lämpötilassa.

Performance and Methodological Aspects in Positron Emission Tomography

Performance standards for Positron emission tomography (PET) were developed to be able to compare systems from different generations and manufacturers. This resulted in the NEMA methodology in North America and the IEC in Europe. In practices, the NEMA NU 2- 2001 is the method of choice today. These standardized methods allow assessment of the physical performance of new commercial dedicated PET/CT tomographs. The point spread in image formation is one of the factors that blur the image. The phenomenon is often called the partial volume effect. Several methods for correcting for partial volume are under research but no real agreement exists on how to solve it. The influence of the effect varies in different clinical settings and it is likely that new methods are needed to solve this problem. Most of the clinical PET work is done in the field of oncology. The whole body PET combined with a CT is the standard investigation today in oncology. Despite the progress in PET imaging technique visualization, especially quantification of small lesions is a challenge. In addition to partial volume, the movement of the object is a significant source of error. The main causes of movement are respiratory and cardiac motions. Most of the new commercial scanners are in addition to cardiac gating, also capable of respiratory gating and this technique has been used in patients with cancer of the thoracic region and patients being studied for the planning of radiation therapy. For routine cardiac applications such as assessment of viability and perfusion only cardiac gating has been used. However, the new targets such as plaque or molecular imaging of new therapies require better control of the cardiac motion also caused by respiratory motion. To overcome these problems in cardiac work, a dual gating approach has been proposed. In this study we investigated the physical performance of a new whole body PET/CT scanner with NEMA standard, compared methods for partial volume correction in PET studies of the brain and developed and tested a new robust method for dual cardiac-respiratory gated PET with phantom, animal and human data. Results from performance measurements showed the feasibility of the new scanner design in 2D and 3D whole body studies. Partial volume was corrected, but there is no best method among those tested as the correction also depends on the radiotracer and its distribution. New methods need to be developed for proper correction. The dual gating algorithm generated is shown to handle dual-gated data, preserving quantification and clearly eliminating the majority of contraction and respiration movement

Cyanobacteria from the Baltic Sea and Finnish lakes as an energy source and modulators of bioenergetic pathways

Cyanobacteria are a diverse group of oxygenic photosynthetic bacteria that inhabit in a wide range of environments. They are versatile and multifaceted organisms with great possibilities for different biotechnological applications. For example, cyanobacteria produce molecular hydrogen (H2), which is one of the most important alternatives for clean and sustainable energy. Apart from being beneficial, cyanobacteria also possess harmful characteristics and may become a source of threat to human health and other living organisms, as they are able to form surface blooms that are producing a variety of toxic or bioactive compounds. The University of Helsinki Culture Collection (UHCC) maintains around 1,000 cyanobacterial strains representing a large number of genera and species isolated from the Baltic Sea and Finnish lakes. The culture collection covers different life forms such as unicellular and filamentous, N2-fixing and non-N2-fixing strains, and planktonic and benthic cyanobacteria. In this thesis, the UHCC has been screened to identify potential strains for sustainable biohydrogen production and also for strains that produce compounds modifying the bioenergetic pathways of other cyanobacteria or terrestrial plants. Among the 400 cyanobacterial strains screened so far, ten were identified as high H2-producing strains. The enzyme systems involved in H2 metabolism of cyanobacteria were analyzed using the Southern hybridization approach. This revealed the presence of the enzyme nitrogenase in all strains tested, while none of them are likely to have contained alternative nitrogenases. All the strains tested, except for two Calothrix strains, XSPORK 36C and XSPORK 11A, were suggested to contain both uptake and bidirectional hydrogenases. Moreover, 55 methanol extracts of various cyanobacterial strains were screened to identify potent bioactive compounds affecting the photosynthetic apparatus of the model cyanobacterium, Synechocystis PCC 6803. The extract from Nostoc XPORK 14A was the only one that modified the photosynthetic machinery and dark respiration. The compound responsible for this effect was identified, purified, and named M22. M22 demonstrated a dual-action mechanism: production of reactive oxygen species (ROS) under illumination and an unknown mechanism that also prevailed in the dark. During summer, the Baltic Sea is occupied by toxic blooms of Nodularia spumigena (hereafter referred to as N. spumigena), which produces a hepatotoxin called nodularin. Long-term exposure of the terrestrial plant spinach to nodularin was studied. Such treatment resulted in inhibition of growth and chlorosis of the leaves. Moreover, the activity and amount of mitochondrial electron transfer complexes increased in the leaves exposed to nodularin-containing extract, indicating upregulation of respiratory reactions, whereas no marked changes were detected in the structure or function of the photosynthetic machinery. Nodularin-exposed plants suffered from oxidative stress, evidenced by oxidative modifications of various proteins. Plants initiated strategies to combat the stress by increasing the levels of alpha-tocopherol, mitochondrial alternative oxidase (AOX), and mitochondrial ascorbate peroxidase (mAPX).

Dynaamisen lämmönsiirtomallin kehittäminen

Dynaamisia simulointimalleja tarvitaan, jotta voidaan tarkastella järjestelmän käyttäytymistä ajan funktiona. Simulointimallilla voidaan simuloida järjestelmän lähtö erilaisilla herätteillä. Mallin avulla saadaan myös tarkempi käsitys järjestelmästä ja sen osa-alueista, koska simulointimallista voidaan tarkastella sellaisia asioita, jotka voivat olla oikeasta järjestelmästä vaikeasti mitattavia. Tässä työssä kehitetään LUT Energian hyötysuhdemittapaikan keskikokoista kalorimetriä approksimoiva dynaaminen lämmönsiirtomalli käyttäen Matlab® Simulink -ohjelmistoa. Kehitetyn lämmönsiirtomallin tarkkuutta arvioidaan todellisella järjestelmällä tehdyillä mittauksilla. Työssä käytetään karkeita approksimaatioita, jotka tulee korvata tarkemmilla matemaattisilla malleilla jatkokehitystä varten. Työssä kehitetty dynaaminen lämmönsiirtomalli approksimoi todellisen järjestelmän vastetta lämmitysvaiheessa keskimääräisenvirheen ±0,19 °C tarkkuudella.

Motoneuronitautiin liittyvä hengitysvajaus: hengitystoiminnan ja energia-aineenvaihdunnan mittaaminen

Tavoitteet: Tämän tutkimussarjan tavoitteena oli tutkia hengitystoiminnan sekä energia-aineen¬vaihdunnan muutoksia motoneuronitautia (amyotrofinen lateraaliskleroosi, ALS) sairastavilla potilailla. Erityisenä mielenkiinnon kohteena olivat kotihoitoon soveltuvan hengityslaitteen vai¬kutus elinajan ennusteeseen sekä hengitysvajauksen etenemistä kuvaavien keuhkotoimintakokei¬den arviointi ALS-potilailla, epäsuoran kalorimetrian mittaustarkkuus ja perusaineenvaihdunnan (PAV) suuruus kajoavaa hengityslaitetta käyttävillä ALS-potilailla. Aineisto ja menetelmät: Kajoamattoman hengityslaitteen käytön ja iän vaikutusta elinajan en¬nusteeseen arvioitiin 84:llä ja hengitystoiminnan muutoksia 42 ALS-potilaalla. Epäsuoran kalo¬rimetrian mittaustarkkuutta kajoamatonta hengityslaitetta käytettäessä arvioitiin hereillä olevilla 12 vapaaehtoisella mieshenkilöllä. PAV:n suuruutta arvioitiin viidellä kajoavaa hengityslaitetta käyttävällä ALS-potilaalla. Osatöistä kaksi ensimmäistä olivat luonteeltaan havainnoivia (retros¬pektiivisiä) ja kaksi viimeistä seurantatutkimuksia (prospektiivisia). Tulokset: Alle 65-vuotiailla ALS-potilailla ei havaittu eroa elinajan ennusteessa kajoamaton¬ta hengityslaitetta käyttävien ja käyttämättömien potilaiden välillä. Sen sijaan yli 65-vuotiail¬la ALS-potilailla elinajan ennuste piteni merkittävästi kajoamatonta hengityslaitetta käyttävillä potilailla (elinaika diagnoosin jälkeen 22 vs. 8 kk, Hazard Ratio = 0.25, 95 % luottamusväli 0.11 – 0.55, p <0.001). ALS-potilailla, joilla kajoamaton hengityslaite katsottiin tarpeelliseksi kuuden kuukauden kuluessa diagnoosihetkestä, hengitystiheys osoittautui diagnoosihetkellä mer-kittävästi kiihtyneeksi (21/min) ja rintakehän liike merkittävästi alentuneeksi (2.9 cm) verrattuna ALS-potilaisiin, joille kajoamaton hengityslaite katsottiin tarpeelliseksi myöhemmin (16/min ja 4.0 cm). Kajoamattoman hengityslaitehoidon aikana keskimääräinen mitattu PAV vapaaehtoisilla miehillä oli 1858 kcal/vrk kun PAV ilman hengityslaitetta oli 1852 kcal/vrk, p = 0.8. Kajoavaa hengityslaitehoitoa käyttävien viiden ALS-potilaan keskimääräinen PAV vastaavalla mittausase¬telmalla mitattaessa oli 1130 kcal/vrk, kun vastaava PAV laskettuna viidellä eri laskentakaavalla oli 1700 kcal/vrk, p < 0.001. Johtopäätökset: Yli 65-vuotiailla ALS-potilailla, jotka eivät sopeutuneet kajoamattomaan hen¬gityslaitehoitoon, oli nelinkertainen riski menehtyä aiemmin kuin kajoamattomaan hengityslai¬tehoitoon sopeutuneilla ALS-potilailla. Hengitystiheys osoittautui merkittävästi kiihtyneeksi ja rintakehän liike alentuneeksi ALS-potilailla, joille kajoamaton hengityslaitehoito katsottiin ai¬heelliseksi kuuden kuukauden kuluessa diagnoosihetkestä. Kajoamattoman hengityslaitehoidon aikana mitattu PAV ei poikennut mitatusta PAV:sta itsenäisen hengityksen aikana. Näin ollen epäsuoraa kalorimetriamenetelmää voidaan käyttää luotettavasti PAV:n määrittämiseen käytet¬täessä samanaikaisesti kotihoitoon soveltuvaa hengityslaitehoitoa. Elämää ylläpitävää kajoavaa hengityslaitehoitoa käyttävien ALS-potilaiden PAV oli merkittävästi hidastunut laskennallisella menetelmällä arvioituun PAV verrattuna.

The Role of Oxidative Stress in Environmental Responses of Fennoscandian Animals

All aerobic organisms have to deal with the toxicity of oxygen. Oxygen enables more efficient energy production compared to anaerobic respiration or fermentation, but at the same time reactive oxygen species (ROS) are being formed. ROS can also be produced by external factors such as UV-radiation and contamination. ROS can cause damage to biomolecules such as DNA, lipids and proteins and organisms try to keep the damage as small as possible by repairing biomolecules and metabolizing ROS. All ROS are not harmful, because they are used as signaling molecules. To cope against ROS organism have an antioxidant (AOX) system which consists both enzymatic and non-enzymatic AOX defense. Some AOX are produced by the organism itself and some are gained via diet. In this thesis I studied environmentally caused changes in the redox regulation of different wild vertebrate animals to gain knowledge on the temporal, spatial and pollution-derived-effects on the AOX systems. As study species I used barn swallow, ringed seal and the Baltic salmon. For the barn swallow the main interest was the seasonal fluctuation in the redox regulation and its connection to migration and breeding. The more contaminated ringed seals of the Baltic Sea were compared to seals from cleaner Svalbard to investigate whether they suffered from contaminant induced oxidative stress. The regional and temporal variation in redox regulation and regional variation in mRNA and protein expressions of Baltic salmon were studied to gain knowledge if the salmon from different areas are equally stressed. As a comparative aspect the redox responses of these different species were investigated to see which parts of the AOX system are substantial in which species. Certain parts of AOX system were connected to breeding and others to migration in barn swallows, there was also differences in biotransformation between birds caught from Africa and Finland. The Baltic ringed seal did not differ much from the seals from Svalbard, despite the difference in contaminant load. A possible explanation to this could be the enhanced AOX mechanisms against dive-associated oxidative stress in diving air-breathing animals, which also helps to cope with ROS derived from other sourses. The Baltic salmon from Gulf of Finland (GoF) showed higher activities in their AOX defense enzymes and more oxidative damage than fish from other areas. Also on mRNA and proteomic level, stress related metabolic changes were most profound in in the fish from GoF. Mainly my findings on species related differences followed the pattern of mammals showing highest activities and least damage and birds showing lower activities and most damage, fish being intermediate. In general, the glutathione recycling-related enzymes and the ratio of oxidized and reduced glutathione seemed to be the most affected parameters in all of the species.

Possibility Of Controlling The Atmosphere Inside A Package Using Microperforation

This work focuses on the study of the determination on the possibilities of controlling the required moisture within the inside of film sealed packages. The task is based on the challenges faced by fresh food producers in actualizing a longer product shelf-life coupled with the growing complex desires coming from consumers in the aspect of quality. One way to realize this is by proper evaluation on the use of the flexible plastic films through permeation measurements on the required amount of moisture penetrating through the plastic film with the application of microperforation. A packaging material requires proper interaction on moisture transmission, between the product and the outside environment. The plastic film material that stands between, fresh fruits, vegetables and the outside environment could have appropriate respiration rates through possible micro holes. This work simulates similar process with the aid of water vapor transmission rate (WVTR) experiment using anhydrous CaCl2 as the desiccant, in studying the WVTR values of various perforated film materials at different conditions of storage (standard, fridge, and tropical conditions). However, the results showed absorption rates of water vapor at various conditions in grams of H2O/m2/24h.

Modification of commercial poly-lactide for extrusion coated food packaging applications

Poly-L-lactide (PLLA) is a widely used sustainable and biodegradable alternative to replace synthetic non-degradable plastic materials in the packaging industry. Conversely, its processing properties are not always optimal, e.g. insufficient melt strength at higher temperatures (necessary in extrusion coating processes). This thesis reports on research to improve properties of commercial PLLA grade (3051D from NatureWorks), to satisfy and extend end-use applications, such as food packaging by blending with modified PLLA. Adjustment of the processability by chain branching of commercial poly-L-lactide initiated by peroxide was evaluated. Several well-defined branched structures with four arms (sPLLA) were synthesized using pentaerythritol as a tetra-functional initiator. Finally, several block copolymers consisting of polyethylene glycol and PLLA (i.e. PEGLA) were produced to obtain a well extruded material with improved heat sealing properties. Reactive extrusion of poly-L-lactide was carried out in the presence of 0.1, 0.3 and 0.5 wt% of various peroxides [tert-butyl-peroxybenzoate (TBPB), 2,5-dimethyl-2,5-(tert-butylperoxy)-hexane (Lupersol 101; LOL1) and benzoyl peroxide (BPO)] at 190C. The peroxide-treated PLLAs showed increased complex viscosity and storage modulus at lower frequencies, indicating the formation of branched/cross linked architectures. The material property changes were dependent on the peroxide, and the used peroxide concentration. Gel fraction analysis showed that the peroxides, afforded different gel contents, and especially 0.5 wt% peroxide, produced both an extremely high molar mass, and a cross linked structure, not perhaps well suited for e.g. further use in a blending step. The thermal behavior was somewhat unexpected as the materials prepared with 0.5 wt% peroxide showed the highest ability for crystallization and cold crystallization, despite substantial cross linking. The peroxide-modified PLLA, i.e. PLLA melt extruded with 0.3 wt% of TBPB and LOL1 and 0.5 wt% BPO was added to linear PLLA in ratios of 5, 15 and 30 wt%. All blends showed increased zero shear viscosity, elastic nature (storage modulus) and shear sensitivity. All blends remained amorphous, though the ability of annealing was improved slightly. Extrusion coating on paperboard was conducted with PLLA, and peroxide-modified PLLA blends (90:10). All blends were processable, but only PLLA with 0.3 wt% of LOL1 afforded a smooth high quality surface with improved line speed. Adhesion levels between fiber and plastic, as well as heat seal performance were marginally reduced compared with pure 3051D. The water vapor transmission measurements (WVTR) of the blends containing LOL1 showed acceptable levels, only slightly lower than for comparable PLLA 3051D. A series of four-arm star-shaped poly-L-lactide (sPLLA) with different branch length was synthesized by ring opening polymerization (ROP) of L-lactide using pentaerythritol as initiator and stannous octoate as catalyst. The star-shaped polymers were further blended with its linear resin and studied for their melt flow and thermal properties. Blends containing 30 wt% of sPLLA with low molecular weight (30 wt%; Mwtotal: 2500 g mol-1 and 15000 g mol-1) showed lower zero shear viscosity and significantly increased shear thinning, while at the same time slightly increased crystallization of the blend. However, the amount of crystallization increased significantly with the higher molecular weight sPLLA, therefore the star-shaped structure may play a role as nucleating agent. PLLA-polyethylene glycol–PLLA triblock copolymers (PEGLA) with different PLLA block length were synthesized and their applicability as blends with linear PLLA (3051D NatureWorks) was investigated with the intention of improving heat-seal and adhesion properties of extrusion-coated paperboard. PLLA-PEG-PLLA was obtained by ring opening polymerization (ROP) of L-lactide using PEG (molecular weight 6000 g mol-1) as an initiator, and stannous octoate as catalyst. The structures of the PEGLAs were characterized by proton nuclear magnetic resonance spectroscopy (1H-NMR). The melt flow and thermal properties of all PEGLAs and their blends were evaluated using dynamic rheology, and differential scanning calorimeter (DSC). All blends containing 30 wt% of PEGLAs showed slightly higher zero shear viscosity, higher shear thinning and increased melt elasticity (based on tan delta). Nevertheless, no significant changes in thermal properties were distinguished. High molecular weight PEGLAs were used in extrusion coating line with 3051D without problems.

Uncertainty of Efficiency Measurements in Electric Drives

The two central goals of this master's thesis are to serve as a guidebook on the determination of uncertainty in efficiency measurements and to investigate sources of uncertainty in efficiency measurements in the field of electric drives by a literature review, mathematical modeling and experimental means. The influence of individual sources of uncertainty on the total instrumental uncertainty is investigated with the help of mathematical models derived for a balance and a direct air cooled calorimeter. The losses of a frequency converter and an induction motor are measured with the input-output method and a balance calorimeter at 50 and 100 % loads. A software linking features of Matlab and Excel is created to process measurement data, calculate uncertainties and to calculate and visualize results. The uncertainties are combined with both the worst case and the realistic perturbation method and distributions of uncertainty by source are shown based on experimental results. A comparison of the calculated uncertainties suggests that the balance calorimeter determines losses more accurately than the input-output method with a relative RPM uncertainty of 1.46 % compared to 3.78 - 12.74 % respectively with 95 % level of confidence at the 93 % induction motor efficiency or higher. As some principles in uncertainty analysis are open to interpretation the views and decisions of the analyst can have noticeable influence on the uncertainty in the measurement result.

Monooxygenase Diversity and Oxygen Activation within Polyketide Antibiotic Biosynthesis

Molecular oxygen (O2) is a key component in cellular respiration and aerobic life. Through the redox potential of O2, the amount of free energy available to organisms that utilize it is greatly increased. Yet, due to the nature of the O2 electron configuration, it is non-reactive to most organic molecules in the ground state. For O2 to react with most organic compounds it must be activated. By activating O2, oxygenases can catalyze reactions involving oxygen incorporation into organic compounds. The oxygen activation mechanisms employed by many oxygenases to have been studied, and they often include transition metals and selected organic compounds. Despite the diversity of mechanisms for O2 activation explored in this thesis, all of the monooxygenases studied in the experimental part activate O2 through a transient carbanion intermediate. One of these enzymes is the small cofactorless monooxygenase SnoaB. Cofactorless monooxygenases are unusual oxygenases that require neither transition metals nor cofactors to activate oxygen. Based on our biochemical characterization and the crystal structure of this enzyme, the mechanism most likely employed by SnoaB relies on a carbanion intermediate to activate oxygen, which is consistent with the proposed substrate-assisted mechanism for this family of enzymes. From the studies conducted on the two-component system AlnT and AlnH, both the functions of the NADH-dependent flavin reductase, AlnH, and the reduced flavin dependent monooxygenase, AlnT, were confirmed. The unusual regiochemistry proposed for AlnT was also confirmed on the basis of the structure of a reaction product. The mechanism of AlnT, as with other flavin-dependent monooxygenases, is likely to involve a caged radical pair consisting of a superoxide anion and a neutral flavin radical formed from an initial carbanion intermediate. In the studies concerning the engineering of the S-adenosyl-L-methionine (SAM) dependent 4-O-methylase DnrK and the homologous atypical 10-hydroxylase RdmB, our data suggest that an initial decarboxylation of the substrate is catalyzed by both of these enzymes, which results in the generation of a carbanion intermediate. This intermediate is not essential for the 4-O-methylation reaction, but it is important for the 10-hydroxylation reaction, since it enables substrate-assisted activation of molecular oxygen involving a single electron transfer to O2 from a carbanion intermediate. The only role for SAM in the hydroxylation reaction is likely to be stabilization of the carbanion through the positive charge of the cofactor. Based on the DnrK variant crystal structure and the characterizations of several DnrK variants, the insertion of a single amino acid in DnrK (S297) is sufficient for gaining a hydroxylation function, which is likely caused by carbanion stabilization through active site solvent restriction. Despite large differences in the three-dimensional structures of the oxygenases and the potential for multiple oxygen activation mechanisms, all the enzymes in my studies rely on carbanion intermediates to activate oxygen from either flavins or their substrates. This thesis provides interesting examples of divergent evolution and the prevalence of carbanion intermediates within polyketide biosynthesis. This mechanism appears to be recurrent in aromatic polyketide biosynthesis and may reflect the acidic nature of these compounds, propensity towards hydrogen bonding and their ability to delocalize π-electrons.