A Análise de Acoplamentos Estatísticos é uma técnica computacional capaz de identificar resíduos importantes para a estrutura e função de proteínas em uma família por meio da quantificação de conservação posicional, correlação entre posições e identificação de grupos de resíduos correlacionados entre si. Neste trabalho, a análise de acoplamentos estatísticos foi implementada e aplicada ao estudo das proteínas tirosina fosfatases. Em conjunto com as proteínas tirosina quinases (PTKs), que adicionam um grupo fosforil a um resíduo de tirosina em uma proteína, as proteínas tirosina fosfatases (PTPs), que o removem, são responsáveis por diversos processos de sinalização celular. Elas são um caso de evolução convergente, onde um subgrupo (as proteínas tirosina fosfatases de baixo peso molecular) não apresenta homologia às chamadas PTPs \"clássicas\", capazes de defosforilar apenas resíduos de tirosina, e às fosfatases de especifidicade dupla, capazes de defosforilar também resíduos de serina e treonina, além de substratos não-protéicos. Em comum, as três subfamílias apresentam apenas o motivo CX5R, característico para todas as PTPs. Através do estudo das três subfamílias utilizando a análise de acoplamentos estatísticos, foi possível obter uma descrição detalhada de suas características conservadas e correlacionadas, relacionando-as ao conhecimento acumulado sobre proteínas tirosina fosfatases e a questões em aberto como a regulação por dimerização, a especificidade e mutações relacionadas a patologias. Foi possível também apresentar um método capaz de distinguir proteínas tirosina fosfatases de baixo peso molecular das arsenato redutases, derivadas das primeiras por evolução divergente. Adicionalmente, a técnica foi aplicada ao estudo das hexoquinases, às superóxido dismutases e às peroxidases. A tese descreve também estudos desenvolvidos pelo autor na área de cristalografia de proteínas a determinação das estruturas da Transtirretina humana em complexo com genisteína, da holo-Hexoquinase PI de S. cerevisae, do complexo IL-22/IL-22R1 e da Laminarinase de R. marinus. / The statistical coupling analysis is a computational technique which can identify important residues for the structure and function of proteins in a family by quantifying positional conservation, correlation between positions and identifying groups of self-correlating residues. Its implementation in this research group was applied to the study of the protein tyrosine phosphatases. Together with the protein tyrosine kinases (PTKs), which add a phosphoryl group to a tyrosine residue in proteins, the protein tyrosine phosphatases (PTPs), which remove it, are responsible for a variety of cell signaling processes. They are a case of convergent evolution, since one subgroup (the low molecular weight protein tyrosine phosphatases) are not homologous to the classical phosphatases, which can only dephosphorilate tyrosine residues, and the dual-specificity phosphatases, which can also dephosphorilate serine and threonine residues, and also non-proteinaceous substrates. All three sub-families have, in common, the CX5R motif, a characteristic of all PTPs. By applying the statistical coupling analysis to the study of the three sub-families, it was possible to obtain a detailed depiction of their conserved and correlated characteristics, relating them to the accumulated knowledge on protein tyrosine phosphatases and open questions such as protein regulation by dimerization, specificity and disease-related mutations. It was also possible to present a method to distinguish between low molecular weight phosphatases and arsenate reductases, which are derived by the former by divergent evolution. In addition, the technique was applied to the study of hexokinases, superoxide dismutases and peroxidases. The thesis also describe studies developed by the author in the field of protein crystallography the structure determination of human transthyretin in complex with genistein, holo-hexokinase PI from S. cerevisae, the IL-22/IL-22R1 complex and the laminarinase from R. marinus.

Abstract Lime precipitation has been used for the treatment of mine water for decades; however, the impact of precipitation conditions is not adequately known. In this thesis, four aspects related to the removal of sulphate from mine water by lime precipitation are considered: the effect of magnesium on lime precipitation, the utilisation of by-products in lime precipitation, enhancement of lime precipitation, and utilisation of the precipitate. Sulphate removal in the presence of magnesium at the commonly used lime precipitation treatment pH of 9.6 was found unefficient as magnesium was keeping the sulphate soluble in the form of magnesium sulphate. At higher treatment pH of 11.5, magnesium that was naturally present in the mine water was shown to precipitate as magnesium hydroxide, which could serve as seed crystals for gypsum or co-precipitate sulphate thus enhancing sulphate removal. Quicklime manufacturing generates by-products that, currently, have few applications. The by-products examined in this study were successfully applied for mine water neutralization replacing commercial lime products. These by-products were found to remove sulphate equally well from the mine water. However, differences between by-products were observed in the consumption, and produced sludge quantities and qualities. An enhanced lime precipitation method is the precipitation as ettringite, which was used to reduce the sulphate content in mine water to less than the value set as the drinking water guideline in Finland. Furthermore, the formed precipitate was found to remove arsenate from the model solution. / Tiivistelmä Vaikka kalkkisaostusta on käytetty kaivosten vesienkäsittelyyn useiden vuosikymmenten ajan, tieto olosuhteiden vaikutuksesta käsittelyn tehokkuuteen sulfaatin poiston osalta on puutteellista. Tämä väitöskirja käsittelee sulfaatinpoistoa kaivosvesistä kalkkisaostuksen avulla neljällä eri osa-alueella: magnesiumin vaikutus kalkkisaostukseen, kalkinpolton sivutuotteiden hyödyntäminen kalkkisaostuksessa, kalkkisaostuksen tehostaminen ja muodostuvan saostuman hyödyntäminen. Magnesiumin todettiin kokeellisesti ja laskennallisesti haittaavan sulfaatin poistoa kaivosvedestä kalkkisaostuksessa yleisesti käytetyssä pH:ssa 9.6 pitämällä sulfaattia liukoisessa muodossa magnesiumsulfaattina. Korkeammassa pH:ssa 11.5 puolestaan kaivosveden luontaisesti sisältämän magnesiumin havaittiin kokeellisesti ja laskennallisesti saostuvan magnesiumhydroksidina, joka voi toimia siemenkiteinä kipsille tai kerasaostaa sulfaattia ja siten tehostaa sulfaatin poistoa. Kalkinpolton sivutuotteina muodostuu jakeita, joille ei tällä hetkellä ole juurikaan käyttökohteita. Tässä työssä käytettiin kalkinpolton sivutuotteita korvaamaan kaupallista kalkkia kaivosveden neutraloinnissa. Sivutuotteet poistivat sulfaattia yhtä tehokkaasti kuin kaupalliset kalkkituotteet. Sivutuotteiden välillä havaittiin eroja niiden kulutuksessa sekä muodostuvan lietteen määrässä ja laadussa. Saostuksella ettringiittinä, joka on tehostettu versio perinteisestä kalkkisaostuksesta, saavutettiin sulfaattipitoisuuden lasku alle Suomessa juomavedelle käytetyn suositusarvon. Lisäksi havaittiin muodostuneen ettringiittisaostuman olevan potentiaalinen materiaali arsenaatin poistoon vedestä.

A Análise de Acoplamentos Estatísticos é uma técnica computacional capaz de identificar resíduos importantes para a estrutura e função de proteínas em uma família por meio da quantificação de conservação posicional, correlação entre posições e identificação de grupos de resíduos correlacionados entre si. Neste trabalho, a análise de acoplamentos estatísticos foi implementada e aplicada ao estudo das proteínas tirosina fosfatases. Em conjunto com as proteínas tirosina quinases (PTKs), que adicionam um grupo fosforil a um resíduo de tirosina em uma proteína, as proteínas tirosina fosfatases (PTPs), que o removem, são responsáveis por diversos processos de sinalização celular. Elas são um caso de evolução convergente, onde um subgrupo (as proteínas tirosina fosfatases de baixo peso molecular) não apresenta homologia às chamadas PTPs \"clássicas\", capazes de defosforilar apenas resíduos de tirosina, e às fosfatases de especifidicade dupla, capazes de defosforilar também resíduos de serina e treonina, além de substratos não-protéicos. Em comum, as três subfamílias apresentam apenas o motivo CX5R, característico para todas as PTPs. Através do estudo das três subfamílias utilizando a análise de acoplamentos estatísticos, foi possível obter uma descrição detalhada de suas características conservadas e correlacionadas, relacionando-as ao conhecimento acumulado sobre proteínas tirosina fosfatases e a questões em aberto como a regulação por dimerização, a especificidade e mutações relacionadas a patologias. Foi possível também apresentar um método capaz de distinguir proteínas tirosina fosfatases de baixo peso molecular das arsenato redutases, derivadas das primeiras por evolução divergente. Adicionalmente, a técnica foi aplicada ao estudo das hexoquinases, às superóxido dismutases e às peroxidases. A tese descreve também estudos desenvolvidos pelo autor na área de cristalografia de proteínas a determinação das estruturas da Transtirretina humana em complexo com genisteína, da holo-Hexoquinase PI de S. cerevisae, do complexo IL-22/IL-22R1 e da Laminarinase de R. marinus. / The statistical coupling analysis is a computational technique which can identify important residues for the structure and function of proteins in a family by quantifying positional conservation, correlation between positions and identifying groups of self-correlating residues. Its implementation in this research group was applied to the study of the protein tyrosine phosphatases. Together with the protein tyrosine kinases (PTKs), which add a phosphoryl group to a tyrosine residue in proteins, the protein tyrosine phosphatases (PTPs), which remove it, are responsible for a variety of cell signaling processes. They are a case of convergent evolution, since one subgroup (the low molecular weight protein tyrosine phosphatases) are not homologous to the classical phosphatases, which can only dephosphorilate tyrosine residues, and the dual-specificity phosphatases, which can also dephosphorilate serine and threonine residues, and also non-proteinaceous substrates. All three sub-families have, in common, the CX5R motif, a characteristic of all PTPs. By applying the statistical coupling analysis to the study of the three sub-families, it was possible to obtain a detailed depiction of their conserved and correlated characteristics, relating them to the accumulated knowledge on protein tyrosine phosphatases and open questions such as protein regulation by dimerization, specificity and disease-related mutations. It was also possible to present a method to distinguish between low molecular weight phosphatases and arsenate reductases, which are derived by the former by divergent evolution. In addition, the technique was applied to the study of hexokinases, superoxide dismutases and peroxidases. The thesis also describe studies developed by the author in the field of protein crystallography the structure determination of human transthyretin in complex with genistein, holo-hexokinase PI from S. cerevisae, the IL-22/IL-22R1 complex and the laminarinase from R. marinus.

L’attività di ricerca ha previsto il confronto fra due siti inquinati da metalli pesanti e due siti controllo naturali. Contrariamente ai parametri chimico-fisici e ai contenuti in metallo dei suoli, le analisi vegetazionali non hanno evidenziato differenze significative tra i siti. E’ stata necessaria la messa a punto strumentale di tecniche ICP-OES, ED(P)XRF per la calibrazione empirica di un XRF portatile, per le osservazioni puntiformi in situ di suoli e flora ed è stata modificata la metodica ufficiale per le stime della biodisponibilità dei metalli pesanti nei suoli inquinati. 6 specie comuni ai 4 siti sono state valutate per i loro TF e BAF. Viene confermata la specie-specificità del TF e del BAF per il quale è stato elaborato un inedito algoritmo per un corretto confronto tra le specie. Tra le sei specie, Silene Alba ha i migliori TF e BAF. Successivamente, sono state valutate alcune caratteristiche del Pennisetum clandestinum, candidato per la fitodepurazione: tollera le concentrazioni di arseniato tipiche dei suoli inquinati, l’arseniato è un inibitore competitivo del trasporto del fosfato, possiede un’elevata velocità di assorbimento dell’arseniato che accumula nella radice, ma non lo trasloca nella frazione epigea, parte dell’As(V) viene ridotto ad As(III) che viene efflusso dalla radice / The research has provided a comparison between two heavy metals polluted sites and two natural control sites. Unlike physical-chemical parameters and metal content in the soils, vegetation analysis showed no significant differences between sites. The development and optimization of instrumental techniques ICP-OES and ED(P)XRF was necessary to calibrate empirically a portable XRF for soil and flora point observations in situ and the official method for estimation of bioavailability of heavy metals in polluted soil was changed. Six species, common to the four sites, were evaluated for their TF and BAF. Were confirmed the TF and the BAF species-specificity for which it was developed a novel algorithm to obtain a correct comparison among species. Among the six species, Silene Alba has the best TF and BAF. In the second stage, some characteristics of Pennisetum clandestinum, candidate for the phytoremediation, were assessed: it tolerates arsenate concentrations typical of polluted soil, arsenate is a competitive inhibitor of phosphate transport, it has a high uptake rate of arsenic that accumulates in the root, but it doesn’t move in the aboveground fraction and part of As(V) is reduced to As(III), which is efflux from roots.

Förorenad mark är ett problem som kan hota ekologiska värden samt skada människors hälsa. Det finns flera åtgärder för föroreningar både ex-situ och in-situ. På senare tid har användningen av nollvärt järn som in-situ åtgärd studerats, men har inte använts tidigare i Sverige. Denna studie innefattar ett pilotförök i fält där en in-situ injektering av nollvärt järn i nanostorlek (nZVI) i Hjältevad, Eksjö kommun. Där bedrev dåvarande Televerket en impregneringsanläggning för telefonstolpar där de använde koppar, krom och arsenik (CCA) som efter ett läckage i en lagringstank förorenade grundvattnet på platsen.  Innan denna studie visade skak och kolonnförsök att tillsats av nZVI till jordprover från Hjältevad minskade koncentrationen av både total arsenik och arsenit med över 90 %. Syftet med pilotförsöket var att undersöka hur långt nZVI skulle spridas i akvifären och om arsenikhalten och grundvattenkemin påverkades på samma sätt av nZVI injekteringen som i labbförsöken.  Dynamiska grundvattenprovtagningar utfördes innan behandlingen för att kunna karakterisera grundvattnet i försöksytan. I ett inledande försök uppskattades spridningen av en 5 g/L nZVI slurry med tillsatt 0,75 g/L polyakrylsyra som injekterades med direct push teknologi. Spridningen av en nZVI injektering undersöktes genom mätning av elektrisk konduktivitet samt genom att observera färgen på grundvattnet. En spridning av nZVI mellan 0,6 och 1,5 m observerades och influensradien ökade med djupet i försöksytan samt visar på större vertikal utbredning vid grundare djup. Preferentiellt flöde kunde ses och överlappande injekteringspunkter behövs för en heltäckande utbredning. Pilotförsöket omfattade fem injekteringspunkter som borrades med 2 m avstånd vid källtermen. Sex nya grundvattenrör installerades uppströms och nedströms injektionspunkterna. Vattenprover togs under 4 månader där grundvattenkemiska parametrar som pH, EH, total As, trevärd As, och Fe koncentrationer mättes. Arsenikhalten låg runt 1700 µg/L innan behandlingen och har inte minskat 4 månader efter injektering av nZVI. I grundvattenrören närmast injekteringspunkterna fanns en tendens till ökad totalhalt och andel arsenit. Möjliga orsaker diskuteras och en hypotes är att lägre temperatur i akvifären jämfört med labbförsök förklarar lägre reaktivitet för nZVI. / Soil contamination poses ecological risks and enhances risks for human exposure to chemical in many areas of the world. Various ex-situ and in-situ soil remediation strategies have therefore been developed. The in-situ use of zero-valent iron sorbents is a relatively new strategy that has not yet been used in the field in Sweden. The current study involves a pilot study of an in-situ inejction of nano-scale zerovalent iron (nZVI) in a contaminated site in Hjältevad, Eksjö municipality. The former Swedish State-owned telephone compmnay operated a plant where telegraph poles were impregnated with chromated copper arsenate (CCA) that leaked into the groundwater following a tank rupture.   Batch and column tests done prior to the current study in the lab showed that addition of nZVI to sediment sampled from the aquifer reduced the dissolved concentrations of total arsenic as well as arsenite with more than 90 %. The aim of this pilot test was therefore firstly to investigate to investigate whether the same reduction could be obtained in the field.  Dynamic groundwater sampling was carried out before the pilot test to characterize hydrology and chemistry of the aquifer. A 5 g/L nZVI slurry was injected using direct push technology initially in one injection well to investigate spread of nZVI by measuring electrical conductivity and observing the color of the groundwater. The measured electrical conductivity and color observation showed a spread of nZVI between 0.6 and 1.5 m. The radius of influence increased with depth in the test zone and shows greater vertical spread at shallower depths. Preferential flow could be seen and overlapping injection points are thus needed for a complete coverage of the source zone. Five injection well were then drilled into the source zone at a distance of 2 m. New groundwater wells were installed downstream from the source zone where samples were taken over a period of 4 months in which chemical parameters such as pH, EH, total As, trivalent As, and Fe concentrations were measured. Arsenic concentrations were 1700 µg/L before the treatment and this concentration as well as other measured groundwater paramters did not decrease significantly during the 4 months monitoring period. In the groundwater wells closest to the injection points, the concentration of total and trivalent arsenic increased significantly. Possibly reasons are discussed and it is hypothesized that the lower aquifer temperature in the field comapred to the lab experiments may explain the lower nZVI reactivity.