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.

Effects of feed processing on the apparent ileal digestibility of amino acids in pig diets containing wheat bran or wheat middlings

Selostus: Prosessoinnin vaikutus vehnän sivutuotteita sisältävien rehuseosten aminohappojen ohutsuolisulavuuteen sioilla

Dietary preferences of weaned piglets offered diets containing organic acids

Selostus: Orgaanisten happojen vaikutus porsasrehun maittavuuteen

Calculation of Activity Coefficients of Uni-Univalent Electrolytes by Equations Containing No Adjustable Parameters in Aqueous Solutions at 298.15 K

Normally either the Güntelberg or Davies equation is used to predict activity coefficients of electrolytes in dilute solutions when no better equation is available. The validity of these equations and, additionally, of the parameter-free equations used in the Bates-Guggenheim convention and in the Pitzerformalism for activity coefficients were tested with experimentally determined activity coefficients of HCl, HBr, HI, LiCl, NaCl, KCl, RbCl, CsCl, NH4Cl, LiBr,NaBr and KBr in aqueous solutions at 298.15 K. The experimental activity coefficients of these electrolytes can be usually reproduced within experimental errorby means of a two-parameter equation of the Hückel type. The best Hückel equations were also determined for all electrolytes considered. The data used in the calculations of this study cover almost all reliable galvanic cell results available in the literature for the electrolytes considered. The results of the calculations reveal that the parameter-free activity coefficient equations can only beused for very dilute electrolyte solutions in thermodynamic studies.

Calculation of Activity Coefficients of Electrolytes of Other Charge Types than 1-1 by Equations Containing No Adjustable Parameters in Aqueous Solutions at 25 0C

Normally either the Güntelberg or Davies equation is used to predict activity coefficients of electrolytes in dilute solutions when no betterequation is available. The validity of these equations and, additionally, of the parameter-free equation used in the Bates-Guggenheim convention for activity coefficients were tested with experimentally determined activity coefficients of LaCl3, CaCl2, SrCl2 and BaCl2 in aqueous solutions at 298.15 K. The experimentalactivity coefficients of these electrolytes can be usually reproduced within experimental error by means of a two-parameter equation of the Hückel type. The best Hückel equations were also determined for all electrolytes considered. The data used in the calculations of this study cover almost all reliable galvanic cell results available in the literature for the electrolytes considered. The results of the calculations reveal that the parameter-free activity coefficient equations can only be used for very dilute electrolyte solutions in thermodynamic studies

Unsaturated Polyester Coatings containing Biocides

Vesistöissä laivojen pintaan tarttuvat eliöt ovat sekä taloudellinen että kosmeettinen ongelma. Kontrolloimattoman eliöiden kiinnittymisen seurauksena aiheutuu kitkaa, joka puolestaan hidastaa laivan nopeutta ja aiheuttaa polttoaineen kulutuksen kasvua. Tavallisesti eliöiden kiinnittymistä ehkäistään kiinnittymisenestomaalien avulla. Niiden toiminta perustuu biosidien liukenemiseen, jolloin veden ja pinnoitteen väliselle rajapinnalle muodostuu korkea biosidipitoisuus, joka estää eliöiden kiinnittymistä pinnalle. Maailmanlaajuinen orgaanisten tinayhdisteiden käyttökielto kiinnittymisen-estomaaleissa tulee voimaan vuoden 2003 alusta. Tällä hetkellä 70 % maailman laivastoista on suojattu orgaanista tinayhdistettä sisältävällä kiinnittymisenestomaalilla. Nyt onkin kasvava tarve kehittää uusia ympäristöystävällisempiä kiinnittymisenesto-pinnoitteita. Todennäköisesti tinayhdisteet tullaan korvaamaan synteettisillä orgaanisilla yhdisteillä käytettyinä yhdessä kuparin kanssa. Työn tarkoituksena oli valmistaa ympäristöystävällisempi tyydyttämätön polyesteripinnoite, joka itsessään ehkäisisi eliöiden kiinnittymistä. Kirjallisuusosassa tutustuttiin markkinoilla oleviin biosideihin, niiden myrkyllisyyteen ja vaikutuksiin ympäristölle sekä muuttuvaan lainsäädäntöön. Työssä tarkasteltiin myös tällä hetkellä markkinoilla olevia pinnoitteita ja niiden toimintamekanismeja sekä myrkyttömiä vaihtoehtopinnoitteita kiinnittymisenestoon. Kokeellinen osa koostui kahdesta osasta. Ensimmäisessä osassa tutkittiin biosidien sopivuutta käytettäväksi yhdessä tyydyttymättömän polyesterin kanssa. Yhteensopivuutta määritettiin applikaatiotesteillä ja pinnoitteen käyttäytymisen perusteella. Toinen vaihe oli selvittää pinnoitteen tehokkuus leväntarttumista vastaan. Tyydyttymätön polyesteri gel coat kiinnittymisenesto-ominaisuuksilla valmistettiin dispergoimalla biosideja tyydyttymättömään polyesterigeeliin. Yhteensopivuustestien tulosten perusteella huomattiin, ettei biosidien lisääminen geeliin vaikuta mainittavasti applikaatio-ominaisuuksien huononemiseen. Brookfield viskositeetin stabiilisuus jopa paranee ja yksi työssä käytetyistä biosideista parantaa pinnoitteen säänkestoominaisuuksia. Tässä työssä ei pystytty määrittämään eri biosidien välisiä eroja tehokkuudessa levää vastaan.

CFD simulation of complex phenomena containing suspensions and flow throughporous media

There is an increasing reliance on computers to solve complex engineering problems. This is because computers, in addition to supporting the development and implementation of adequate and clear models, can especially minimize the financial support required. The ability of computers to perform complex calculations at high speed has enabled the creation of highly complex systems to model real-world phenomena. The complexity of the fluid dynamics problem makes it difficult or impossible to solve equations of an object in a flow exactly. Approximate solutions can be obtained by construction and measurement of prototypes placed in a flow, or by use of a numerical simulation. Since usage of prototypes can be prohibitively time-consuming and expensive, many have turned to simulations to provide insight during the engineering process. In this case the simulation setup and parameters can be altered much more easily than one could with a real-world experiment. The objective of this research work is to develop numerical models for different suspensions (fiber suspensions, blood flow through microvessels and branching geometries, and magnetic fluids), and also fluid flow through porous media. The models will have merit as a scientific tool and will also have practical application in industries. Most of the numerical simulations were done by the commercial software, Fluent, and user defined functions were added to apply a multiscale method and magnetic field. The results from simulation of fiber suspension can elucidate the physics behind the break up of a fiber floc, opening the possibility for developing a meaningful numerical model of the fiber flow. The simulation of blood movement from an arteriole through a venule via a capillary showed that the model based on VOF can successfully predict the deformation and flow of RBCs in an arteriole. Furthermore, the result corresponds to the experimental observation illustrates that the RBC is deformed during the movement. The concluding remarks presented, provide a correct methodology and a mathematical and numerical framework for the simulation of blood flows in branching. Analysis of ferrofluids simulations indicate that the magnetic Soret effect can be even higher than the conventional one and its strength depends on the strength of magnetic field, confirmed experimentally by Völker and Odenbach. It was also shown that when a magnetic field is perpendicular to the temperature gradient, there will be additional increase in the heat transfer compared to the cases where the magnetic field is parallel to the temperature gradient. In addition, the statistical evaluation (Taguchi technique) on magnetic fluids showed that the temperature and initial concentration of the magnetic phase exert the maximum and minimum contribution to the thermodiffusion, respectively. In the simulation of flow through porous media, dimensionless pressure drop was studied at different Reynolds numbers, based on pore permeability and interstitial fluid velocity. The obtained results agreed well with the correlation of Macdonald et al. (1979) for the range of actual flow Reynolds studied. Furthermore, calculated results for the dispersion coefficients in the cylinder geometry were found to be in agreement with those of Seymour and Callaghan.

Tautomerism and Fragmentation of Biologically Active Hetero Atom (O, N)-Containing Acyclic and Cyclic Compounds Under Electron Ionization

In this thesis a total of 86 compounds containing the hetero atoms oxygen and nitrogen were studied under electron ionization mass spectrometry (EIMS). These compounds are biologically active and were synthesized by various research groups. The main attention of this study was paid on the fragmentations related to different tautomeric forms of 2- phenacylpyridines, 2-phenacylquinolines, 8-aryl-3,4-dioxo-2H,8H-6,7-dihydroimidazo- [2,1-c][1,2,4]triazines and aryl- and benzyl-substituted 2,3-dihydroimidazo[1,2-a]pyrimidine-5,7-(1H,6H)-diones. Also regio/stereospecific effects on fragmentations of pyrrolo- and isoindoloquinazolinones and naphthoxazine, naphthpyrrolo-oxazinone and naphthoxazino-benzoxazine derivatives were screened. Results were compared with NMR data, when available. The first part of thesis consists of theory and literature review of different types of tautomerism and fragmentation mechanisms in EIMS. The effects of tautomerism in biological systems are also briefly reviewed. In the second part of the thesis the own results of the author, based on six publications,are discussed. For 2-phenacylpyridines and 2-phenacylquinolines the correlation of different Hammett substituent constants to the relative abundances (RA) or total ion currents (% TIC) of selected ions were investigated. Although it was not possible to assign most of the ions formed unambiguously to the different tautomers, the linear fits of their RAs and % TICs can be related to changing contributions of different tautomeric forms. For dioxoimidazotriazines and imidazopyrimidinediones the effects of substituents were rather weak. The fragmentations were also found useful for obtaining structural information. Some stereoisomeric pairs of pyrrolo- and isoindoloquinazolines and regiomeric pairs of naphtoxazine derivatives showed clear differences in thir mass spectra. Some mechanisms are suggested for their fragmentations.

Utilization of retention chemicals in non-wood containing furnishes

The usage of the non-wood pulps in furnishes for various paper grades is the real alternative for substitution of wood fibres in the papermaking. This is especially important now, when the prices for wood are increasing and forest resources are depleting in many regions of our planet. However, there are several problems associated with utilization of such pulps. In terms of the papermaking process one of the main problems is the poor dewatering of the non-wood pulps. This problem can be partially solved by means of retention aids. In the literature part were described technological features of the non-wood pulps as the raw materials for paper production. Moreover, overviews of the retention chemicals and methods for retention measurement were done; special attention was paid to the mechanisms of retention and drainage. Finally, factors affecting on the drainage and retention of non-wood pulps were considered holistically. Particular emphasis was put on the possibility of enzyme treatment for drainage improvement. It was stated that retention aids can significantly improve dewatering of non-wood pulps. In the experimental part the goal was to investigate influence of various microparticle retention aids on the drainage, retention and formation of furnish containing wheat straw pulp, obtained by novel pulping process (Formico™Fib). The parallel test were performed with reference furnish containing only wood pulps. It was found that Bentonite-CPAM retention aid can significantly improve drainage and retention; however formation seems be suffer from such additives. It was stated that performance of the Silica-Starch retention aid significantly depends on the starch dosing sequence and wet-end conditions; this system have shown better formation than other tested retention aids. Silica-CPAM retention aid have provided comparable results in retention and drainage with Bentonite-CPAM, while Silica-starch did not improve dewatering and yielded in lowest filler retention among other aids. Ultimately, optimal dosages for the tested retention chemicals have been suggested.

The history of Lapland : containing a geographical description, and a natural history of that country; with an account of the inhabitants, their original, religion, customs, habits, marriages, conjurations, employments, &c. Written by John Scheffer, ... Translated from the last edition in Latin, and illustrated with many curious copper-cutts. To which are added, the travels of the King of Sweden's mathematicians into Lapland: the history of Livonia, and the wars there: also a journey into Lapland, Finland, &c. Written by Dr. Olof Rudbeck in the year 1701

Added engraved title page: The history of Lapland.

Corrosion behaviour of boiler tube materials during combustion of fuels containing Zn and Pb

Många förbränningsanläggningar som bränner utmanande bränslen såsom restfraktioner och avfall råkar ut för problem med ökad korrosion på överhettare och/eller vattenväggar pga. komponenter i bränslena som är korrosiva. För att minimera problemen i avfallseldade pannor hålls ångparametrarna på en relativt låg nivå, vilket drastiskt minskar energiproduktionen. Beläggningarna i avfallseldade pannor består till största delen av element som är förknippade med högtemperaturkorrosion: Cl, S, alkalimetaller, främst K och Na, och tungmetaller som Pb och Zn, och det finns också indikationer av Br-förekomst. Det låga ångtrycket i avfallseldade pannor påverkar också stålrörens temperatur i pannväggarna i eldstaden. I dagens läge hålls temperaturen normalt vid 300-400 °C. Alkalikloridorsakad (KCl, NaCl) högtemperaturkorrosion har inte rapporterats vara relevant vid såpass låga temperaturer, men närvaro av Zn- och Pb-komponenter i beläggningarna har påvisats förorsaka ökad korrosion redan vid 300-400 °C. Vid förbränning kan Zn och Pb reagera med S och Cl och bilda klorider och sulfater i rökgaserna. Dessa tungmetallföreningar är speciellt problematiska pga. de bildar lågsmältande saltblandningar. Dessa lågsmältande gasformiga eller fasta föreningar följer rökgasen och kan sedan fastna eller kondensera på kallare ytor på pannväggar eller överhettare för att sedan bilda aggressiva beläggningar. Tungmetallrika (Pb, Zn) klorider och sulfater ökar risken för korrosion, och effekten förstärks ytterligare vid närvaro av smälta. Motivet med den här studien var att få en bättre insikt i högtemperaturkorrosion förorsakad av Zn och Pb, samt att undersöka och prediktera beteendet och motståndskraften hos några stålkvaliteter som används i överhettare och pannväggar i tungmetallrika förhållanden och höga materialtemperaturer. Omfattande laboratorie-, småskale- och fullskaletest utfördes. Resultaten kan direkt utnyttjas i praktiska applikationer, t.ex. vid materialval, eller vid utveckling av korrosionsmotverkande verktyg för att hitta initierande faktorer och förstå deras effekt på högtemperaturkorrosion.

Unusual bismuth-containing surface layers of III-V compound semiconductors

The understanding and engineering of bismuth (Bi) containing semiconductor surfaces are signi cant in the development of novel semiconductor materials for electronic and optoelectronic devices such as high-e ciency solar cells, lasers and light emitting diodes. For example, a Bi surface layer can be used as a surfactant which oats on a III-V compound-semiconductor surface during the epitaxial growth of IIIV lms. This Bi surfactant layer improves the lm-growth conditions if compared to the growth without the Bi layer. Therefore, detailed knowledge of the properties of the Bi/III-V surfaces is needed. In this thesis, well-de ned surface layers containing Bi have been produced on various III-V semiconductor substrates. The properties of these Bi-induced surfaces have been measured by low-energy electron di raction (LEED), scanning-tunneling microscopy and spectroscopy (STM), and synchrotron-radiation photoelectron spectroscopy. The experimental results have been compared with theoretically calculated results to resolve the atomic structures of the studied surfaces. The main ndings of this research concern the determination of the properties of an unusual Bi-containing (2×1) surface structure, the discovery and characterization of a uniform pattern of Bi nanolines, and the optimization of the preparation conditions for this Bi-nanoline pattern.

Treatment of NI-containing acidic mine waters with calcite side-stones

Acid mine drainage (AMD) presents a serious problem for the environment for the massive formation of acidic leachates containing heavy metals. The present work deals with the AMD treatment using neutralizing limestone side-products. The conventional methods for prevention, mitigating and control of AMD formation are described. The experimental testing of Nordkalk Oy calcite-containing side-stones for acid neutralizing and removal of nickel from solutions presents the research objective. The batch experiments in acid neutralizing with subsequent metal content analysis were carried out. The results showed the dependence of pH on the dose of neutralizing material and the exposure time. The nickel removal, unlike iron, within the pH range from 1.2 to 6.0 appeared to be inadequate. The further research on nickel co-precipitation with iron and aluminium may appear to be necessary together with testing of alkalinity strengthening materials.

Regioselective modification of galactose-containing polysaccharides in aqueous media

Biorefining is defined as sustainable conversion of biomass into marketable products and energy. Forests cover almost one third of earth’s land area, and account for approximately 40% of the total annual biomass production. In forest biorefining, the wood components are, in addition to the traditional paper and board products, converted into chemicals and biofuels. The major components in wood are cellulose, hemicelluloses, and lignin. The main hemicellulose in softwoods, which are of interest especially for the Nordic forest industry, is O-acetyl galactoglucomannan (GGM). GGM can be isolated in industrial scale from the waste waters of the mechanical pulping process, but is not yet today industrially utilized. In order to attain desired properties of GGM for specific end-uses, chemical and enzymatic modifications can be performed. Regioselective modifications of GGM, and other galactose-containing polysaccharides were done by oxidations, and by combining oxidations with subsequent derivatizations of the formed carbonyl or carboxyl groups. Two different pathways were investigated: activation of the C-6 positions in different sugar units by TEMPO-mediated oxidation, and activation of C-6 position in only galactose-units by oxidation catalyzed by the enzyme galactose oxidase. The activated sites were further selectively derivatized; TEMPO-oxidized GGM by a carbodiimide-mediated reaction forming amides, and GO-oxidized GGM by indium-mediated allylation introducing double or triple bonds to the molecule. In order to better understand the reaction, and to develop a MALDI-TOF-MS method for characterization of regioselectively allylated GGM, α-D-galactopyranoside and raffinose were used as model compounds. All reactions were done in aqueous media. To investigate the applicability of the modified polysaccharides for, e.g., cellulose surface functionalization, their sorption onto pulp fibres was studied. Carboxylation affects the sorption tendency significantly; a higher degree of oxidation leads to lower sorption. By controlling the degree of oxidation of the polysaccharides and the ionic strength of the sorption media, high degrees of sorption of carboxylated polysaccharides onto cellulose could, however, be obtained. Anionic polysaccharides were used as templates during laccase-catalyzed polymerization of aniline, offering a green, chemo-enzymatic route for synthesis of conducting polyaniline (PANI) composite materials. Different polysaccharide templates, such as, native GGM, TEMPO-oxidized GGM, naturally anionic κ-carrageenan, and nanofibrillated cellulose produced by TEMPO-oxidation, were assessed. The conductivity of the synthesized polysaccharide/PANI biocomposites varies depending on the polysaccharide template; κ-CGN, the anionic polysaccharide with the lowest pKa value, produces the polysaccharide/PANI biocomposites with the highest conductivity. The presented derivatization, sorption, and polymerization procedures open new application windows for polysaccharides, such as spruce GGM. The modified polysaccharides and the conducting biocomposites produced provide potential applications in biosensors, electronic devices, and tissue engineering.