No description available.

No description available.

No description available.

No description available.

Tetrahydrofolate-mediated one-carbon metabolism is required for the biosynthesis of many central metabolites, including some amino acids, nucleobases, and nucleotides, and hence dysfunction of one-carbon metabolism is associated with many human diseases and disorders. The mitochondrial glycine decarboxylase complex (GDC) is an important component of one-carbon metabolism, generating 5,10-methylene-tetrahydrofolate (5,10-CH2-H??4folate) from glycine. Previous work has shown that the genes encoding the unique sub-units of the Saccharomyces cerevisiae GDC (GCV1, GCV2 and GCV3) are regulated in response to changes in the levels of cytosolic 5,10-CH2-H??4folate (Piper et al., 2000). Given the centrality of 5,10-CH2-H??4folate to many aspects of metabolism, it was hypothesised that other genes may be regulated by the same mechanism. Using microarray analysis of S. cerevisiae under a number of conditions that affect 5,10-CH2-H??4folate levels, the ??one-carbon regulon??, a group of genes that were co-regulated with the GCV genes was identified. The one-carbon regulon corresponds closely to genes whose promoters are bound by the purine biosynthesis regulator Bas1p, but not all one-carbon regulon members are significantly purine regulated. Genetic approaches demonstrated that the one-carbon unit response and the purine response are distinct, though both depend on the presence of Bas1p. This demonstrated that the close metabolic connections of one-carbon and purine metabolism are reflected in over-lapping, but separable regulatory mechanisms. The identity of the sensor of one-carbon unit depletion remains unknown, but in the course of investigation of the candidate regulator Caf17p, it was demonstrated that Caf17p is in fact involved in Fe/S cluster protein maturation. Examination of the effects of Caf17p depletion revealed that Caf17p is required for the function and maturation of the related mitochondrial Fe/S proteins aconitase and homoaconitase, as well as the function of, but not de novo iron incorporation into, the mitochondrial radical-SAM Fe/S protein biotin synthase. Because other Fe/S proteins were unaffected, Caf17p appears to be a specialised Fe/S maturation factor. The presence of a putative H4folate binding site indicates that Caf17p may constitute a metabolic link between one-carbon and iron metabolism.

Tetrahydrofolate-mediated one-carbon metabolism is required for the biosynthesis of many central metabolites, including some amino acids, nucleobases, and nucleotides, and hence dysfunction of one-carbon metabolism is associated with many human diseases and disorders. The mitochondrial glycine decarboxylase complex (GDC) is an important component of one-carbon metabolism, generating 5,10-methylene-tetrahydrofolate (5,10-CH2-H??4folate) from glycine. Previous work has shown that the genes encoding the unique sub-units of the Saccharomyces cerevisiae GDC (GCV1, GCV2 and GCV3) are regulated in response to changes in the levels of cytosolic 5,10-CH2-H??4folate (Piper et al., 2000). Given the centrality of 5,10-CH2-H??4folate to many aspects of metabolism, it was hypothesised that other genes may be regulated by the same mechanism. Using microarray analysis of S. cerevisiae under a number of conditions that affect 5,10-CH2-H??4folate levels, the ??one-carbon regulon??, a group of genes that were co-regulated with the GCV genes was identified. The one-carbon regulon corresponds closely to genes whose promoters are bound by the purine biosynthesis regulator Bas1p, but not all one-carbon regulon members are significantly purine regulated. Genetic approaches demonstrated that the one-carbon unit response and the purine response are distinct, though both depend on the presence of Bas1p. This demonstrated that the close metabolic connections of one-carbon and purine metabolism are reflected in over-lapping, but separable regulatory mechanisms. The identity of the sensor of one-carbon unit depletion remains unknown, but in the course of investigation of the candidate regulator Caf17p, it was demonstrated that Caf17p is in fact involved in Fe/S cluster protein maturation. Examination of the effects of Caf17p depletion revealed that Caf17p is required for the function and maturation of the related mitochondrial Fe/S proteins aconitase and homoaconitase, as well as the function of, but not de novo iron incorporation into, the mitochondrial radical-SAM Fe/S protein biotin synthase. Because other Fe/S proteins were unaffected, Caf17p appears to be a specialised Fe/S maturation factor. The presence of a putative H4folate binding site indicates that Caf17p may constitute a metabolic link between one-carbon and iron metabolism.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniversitet, 2005. / Härtill 6 uppsatser.

<p> A levitation apparatus has been constructed for investigating the behaviour of liquid iron drops containing sulphur, whilst suspended in a moving gas stream.</p> <p> To further this investigation, a source of iron-sulphur alloys, in form and size suitable for levitation, was required. Four methods for the preparation of the desired alloys were suggested, and each was experimentally examined in sequence.</p> <p> The first 2 methods involved the quenching of a liquid solution of sulphur in iron, to give a solid alloy. The well-known behaviour of sulphur, to segregate on solidification, was observed, and the non-uniformity of the resulting alloys could not be tolerated. The third method involved preparing a large number of individual iron-sulphur samples by allowing drops of iron to fall and quench on particles of sulphur or iron sulphide. The repeatability of the method was found to be unsatisfactory. In the final attempt a levitated liquid drop of iron was equilibrated in a gas mixture of hydrogen-hydrogen sulphide. This method was considered more successful than the earlier three, and has the advantage that the prepared alloy drop is levitated and at the desired temperature.</p> / Thesis / Master of Engineering (MEngr)

Jusqu’à 40% des protéines sont connues pour fixer des métaux, ces hétéroatomes jouant un rôle capital dans la régulation, la catalyse ou le maintien de la structure de ces protéines. Ces métalloprotéines sont ubiquitaires et d’une importance primordiale dans les trois domaines du vivant. Cependant, les méthodes actuelles dédiées à l’identification des membres de cette grande famille dans les protéomes bactériens sont soit inadaptées pour des approches à grande échelle, soit présentent des performances relativement limitées en l’absence d’une structure tridimensionnelle résolue. Dans ce contexte, différents outils d’analyse de séquence ont été testés, en recherchant des descripteurs de ces protéines (e.g. motifs, domaines conservés, empreintes phylogénétiques). Pour pallier le relatif manque de sensibilité de ceux-ci, de nouveaux descripteurs ont été construits, dédiés spécifiquement à l’identification des protéines à centre fer-soufre : (i) des profils de co-conservation des ligands du métal et (ii) des profile-HMMs adaptés à la détection d’homologues distants. Les pouvoirs prédictifs respectifs de ces catégories de descripteurs ont été évalués sur un jeu de protéines fer-soufre expertisé, en les considérant soit séparément soit en combinaison. L’ensemble de ces descripteurs a finalement été intégré dans un modèle linéaire généralisé en utilisant la technique d’elastic-net. Le modèle prédictif obtenu a été évalué sur le protéome complet d’Escherichia coli, sur lequel il atteint une précision de 89% et une sensibilité de 83%. Enfin, il a été appliqué à environ 300 protéomes pour explorer différentes relations biologiques comme l’abondance relative des protéines Fe-S et la tolérance à l’oxygène des organismes auxquelles elles appartiennent. / Up to 40% of all proteins are known to bind metals, the intrinsic metal atoms providing catalytic, regulatory and/or structural roles critical to their functions. These metalloproteins are ubiquitous and of major importance within the three domains of life. However, current methods dedicated to identifying members of this large family within bacterial proteomes are either not suitable for large-scale approach or are of relatively limited performance when no 3D structural template is available. Within this context, different sequence analysis tools relying on different category of protein descriptors (e.g. patterns, conserved domains, phylogenetic prints) were assessed. To overcome their relative lack of sensibility, new descriptors, specific towards iron-sulfur proteins identification were built: (i) co-conservation profiles of the metal ligands and (ii) tailored profile-HMMs for remote homologs detection. Their respective predictive power towards the identification of a manually curated iron-sulfur proteins dataset were assessed, either separately or in combination. All relevant descriptors were finally gathered into a generalized linear model by using the elastic-net method. The predictive model has been evaluated on Escherichia coli whole proteome resulting in a precision of 89% and a recall of 83%. Eventually, it has been applied to 300 proteomes allowing investigating different biological relationships, such as iron-sulfur proteins relative abundances and the oxygen dependency of bacterial organisms.

Thesis (MScEng)--Stellenbosch University, 2011. / ENGLISH ABSTRACT: In a first stage atmospheric leach at the Lonmin Marikana base metals refinery, nickel-copper-iron-sulphur Peirce Smith converter matte is leached in recycled electrolyte from the electrowinning section. The electrolyte contains sulphuric acid, copper and nickel sulphates, and a small amount of iron sulphate. The converter matte contains mostly nickel, copper and sulphur (typically 48 %, 28 % and 23 %, respectively), but also minor amounts (<5 %) iron and cobalt. The matte also contains platinum group elements (PGEs) and other precious metals totalling 0.2 – 0.7 % (platinum, palladium, iridium, rhodium, ruthenium, osmium and some gold). The predominant mineral phases are heazlewoodite, chalcocite and a nickel-copper alloy phase, as well as some entrained slag and spinel minerals. The purpose of the first stage leach is to extract nickel, while simultaneously precipitating copper and PGEs contained in the recycled electrolyte. Nickel, cobalt and iron are leached by acid and oxygen. Copper is precipitated by a redox reaction in which copper ions oxidise nickel from the matte. The purpose of this study was to determine the effects of key variables on the performance of the first stage leach (specifically on the removal of PGEs and copper from solution and the overall extraction of nickel) and to improve fundamental understanding of these effects. Batch leaching tests were carried out to investigate the effects of the following factors: availability of oxygen, initial acid concentration, initial copper concentration, iron endpoint (iron content of the matte), solids/liquid ratio and stirring rate. Liquid samples were analysed with Atomic Absorption Spectroscopy (AA) to determine leaching kinetics. Characterisation of solid samples from leach tests by quantitative X-Ray diffraction (XRD) and scanning electron microscopy with an energy dispersive system (SEM-EDS) helped to improve understanding of the leaching mechanism. The oxidative leaching mechanism entails an initial period in which the alloy phase is leached by acid and oxygen, while copper reacts with the nickel-copper-alloy and heazlewoodite phases (which react galvanically with each other) to form a chalcocite precipitate. In a second reaction period, heazlewoodite was transformed to millerite by acid leaching and the particle structure became more porous. The rate of copper precipitation and nickel extraction were faster during the second reaction period than the first reaction period. Some copper leaching occurred once the leachable nickel (60 – 70 %) had been dissolved, provided that the solution was strongly acidic (pH < 2). The non-oxidative leaching mechanism entails a galvanic interaction, between the nickel-copper-alloy and heazlewoodite phases, in which nickel is leached from both phases and copper is precipitated as chalcocite. Leaching by acid was negligible in most non-oxidative tests. An initial fast period of copper precipitation was followed by a second slower period. The decrease in reaction rate can probably be linked to the decreasing availability of the nickel-copper-alloy phase. During non-oxidative leaching, the particle structure remained mostly intact. Copper precipitation kinetics under non-oxidative conditions was found to be slower than under oxidative conditions. The faster copper precipitation kinetics under oxidative conditions is most likely caused by an increase in porosity and reaction area as nickel is leached from the matte by acid and oxygen. The initial acid concentration, solids/liquid ratio and Fe-endpoint were the most important factors determining reaction kinetics under oxidative conditions. Low initial acid concentrations (37 g/L) and a high solids/liquid ratio improved the extent of copper precipitation. Nickel extraction was enhanced by low solids/liquid ratios and high initial acid concentrations (74 g/L). Nickel extraction was significantly less (56 % less in one instance) when leaching high iron mattes (5.7 % Fe) rather than low iron mattes (< 1 % Fe). Copper precipitation was initially faster when leaching a high iron matte, but slower nickel leaching from high iron mattes led to an excess of available acid, which resulted in copper being leached. The results suggest that high iron mattes will lead to poor copper and PGE precipitation in the first stage leach and also to lower nickel extractions. Consequently, Peirce Smith converting at the plant must be carefully controlled to avoid high iron mattes. Under non-oxidative conditions, the solids/liquid ratio and Fe-endpoint were the most important factors. The rate of copper precipitation was faster when a high iron matte was leached, so that a higher percentage copper was precipitated and more nickel was extracted from the matte. / AFRIKAANSE OPSOMMING: As ‘n eerste stap in die Lonmin Marikana basis-metale veredelingsaanleg word nikkel-koper-yster-swawel Peirce-Smith-converter-mat geloog in elektroliet wat hersirkuleer word vanaf die aanleg se koper-elektroplaterings-afdeling. Die loging word by atmosferiese druk uitgevoer. Die elektroliet bevat swawelsuur, koper- en nikkel-sulfate en ‘n klein hoeveelheid ystersulfaat. Die mat bevat hoofsaaklik nikkel, koper en swawel (tipies 48 %, 28 % en 23 %), maar ook klein hoeveelhede (< 5 %) yster en kobalt. Verder maak Platinum Groep Elemente (PGE’s) en ander waardevolle metale (platinum, palladium, iridium, rhodium, ruthenium, osmium en goud) 0.2 % tot 0.7 % van die massa van die mat uit. In terme van minerale bestaan die materiaal hoofsaaklik uit heazlewoodite, chalcocite en ‘n nikkel-koper allooi fase, asook slak en spinel minerale, wat tydens Peirce-Smith-converting weens meesleuring in die mat rapporteer. Die doel van die eerste stadium loog is om nikkel op te los, terwyl koper en PGE’s wat in die elektroliet voorkom presipiteer moet word. Nikkel, kobalt en koper word geloog in reaksies met suurstof en swawelsuur. Koper word presipiteer deur middel van ‘n redoks reaksie waarin koper-ione nikkel in die mat oksideer. Die doel van hierdie studie was om die effekte van sleutelveranderlikes op die proses te bepaal (spesifiek hoe nikkel-loging en koper presipitasie affekteer word) en om fundamentele begrip van die veranderlikes en hul effekte te verkry. Lot loogtoetse is uitgevoer op ‘n laboratorium-skaal en die effekte van die volgende faktore is ondersoek: beskibaarheid van suurstof, begin suurkonsentrasie, yster eindpunt (die ysterinhoud van die mat), vastestof/vloeistof verhouding en die roertempo. Vloeistof monsters geneem tydens loogtoetse is geanaliseer met behulp van Atoom Absorpsie Spektroskopie (AA) om kinetika te bepaal. Vastestof monsters is ook geneem tydens loogtoetse en kwantitatiewe X-straal diffraksie (XRD), asook skanderings-elektron-mikroskopie met ‘n energie dispersie sisteem (SEM-EDS) is gebruik om die materiaal te karakteriseer en die logingsmeganisme te verduidelik. Die oksidatiewe logingsmeganisme behels ‘n aanvanklike periode waartydens die allooi fase geloog word deur suur en suurstof, terwyl koper presipiteer om chalcocite te vorm as gevolg van ‘n reaksie waarin galvanise interaksie tussen die nikkel-koperallooi en heazlewoodite fases ‘n belangrike rol speel. In ‘n tweede reaksie periode is heazlewoodite geloog deur suur om millerite te vorm. Tydens hierdie tweede fase het die partikel struktuur meer porieus geword. Die tempo van koper presipitasie en nikkel loging was vinniger tydens die tweede reaksie periode as tydens die eerste. Koper is geloog indien die oplossing baie suur was (pH < 2) en die loogbare nikkel (60 – 70 %) reeds opgelos het. Die nie-oksidatiewe logingsmeganisme behels galvaniese interaksie tussen die nikkel-koper-allooi en heazlewoodite fases, wat lei tot koper presipitasie as chalcocite. Loging deur swawelsuur was onbeduidend. ‘n Aanvanklike vinnige periode van koper presipitasie tydens nie-oksidatiewe toetse is gevolg deur ‘n tweede stadiger periode. Die afname in reaksietempo kan waarskynlik verklaar word deur die afnemende beskikbaarheid van die nikkel-koper-allooi fase. Tydens nieoksidatiewe loging het die partikel struktuur redelik onveranderd gebly. Koper presipitasie kinetika in nie-oksidatiewe toetse was stadiger as in oksidatiewe toetse. Die belangrikste faktore wat kinetika in oksidatiewe toetse beïnvloed het was die suurkonsentrasie, vastestof/vloeistof verhouding en die yster-eindpunt. Lae beginsuurkonsentrasies (37 g/L) en ‘n hoë vastestof/vloeistof verhouding het gelei daartoe dat meer koper uit die elektroliet herwin is. Nikkel ekstraksie was hoër indien die vastestof/vloeistof verhouding laag was en die begin suurkonsentrasie hoog (74 g/L). Nikkel ekstraksie was beduidend laer (56 % laer in een geval) wanneer hoë-yster mat (5.7 % Fe) geloog is, eerder as lae yster mat (< 1 % Fe). Wanneer ‘n hoë yster mat geloog is, was koper presipitasie aanvanklik vinniger, maar weens stadige nikkel-ekstraksie-tempos was ‘n oormaat van suur beskikbaar sodat koper uiteindelik geloog is. PGE presipitasie is ook nadelig beïnvloed wanneer koper geloog is en veral tydens toetse met hoë yster mat. Die mees belangrike faktore wat nie-oksidatiewe loging beïnvloed het was die vastestof/vloeistof verhouding en die yster-eindpunt. Die tempo van koper presipitasie was vinniger in toetse met ‘n hoë yster mat, sodat ‘n hoër persentasie koper presipiteer het en meer nikkel opgelos het wanneer ‘n hoë yster mat geloog is.