| 1. |
- Allard, Bert, 1945-, et al.
(författare)
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Metal Exchangeability in the REE-Enriched Biogenic Mn Oxide Birnessite from Ytterby, Sweden
- 2023
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Ingår i: Minerals. - : MDPI. - 2075-163X. ; 13:8
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Tidskriftsartikel (refereegranskat)abstract
- A black substance exuding from fractures was observed in 2012 in Ytterby mine, Sweden, and identified in 2017 as birnessite with the composition Mx[Mn(III,IV)](2)O-4 center dot(H2O)n. M is usually calcium and sodium, with x around 0.5. The Ytterby birnessite is unique, with M being calcium, magnesium, and also rare earth elements (REEs) constituting up to 2% of the total metal content. The biogenic origin of the birnessite was established in 2018. Analysis of the microbial processes leading to the birnessite formation and the REE enrichment has continued since then. The process is fast and dynamic, as indicated by the depletion of manganese and of REE and other metals in the fracture water during the passage over the precipitation zone in the mine tunnel. Studies of the exchangeability of metals in the structure are the main objective of the present program. Exposure to solutions of sodium, calcium, lanthanum, and iron led to exchanges and altered distribution of the metals in the birnessite, however, generating phases with almost identical structures after the exchanges, and no new mineral phases were detected. Exchangeability was more efficient for trivalent elements (REE) over divalent (calcium) and monovalent (sodium) elements of a similar size (ionic radii 90-100 pm).
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| 2. |
- Allard, Bert, et al.
(författare)
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On the formation and metal exchangeability of the rare earth element enriched birnessite from the Ytterby mine, Sweden
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- A porous black substance exuding from fractures in an underground tunnel leading to the shaft of the Ytterby mine, Sweden, was observed in 2012 and characterized as a secondary manganese (Mn) oxide in 2015. The oxide was identified in 2017 as a birnessite variety, Mx[Mn(III,IV)]2O4∙(H2O)n where M usually is Ca, Na and x is around 0.5, but the Ytterby birnessite appears to be unique with M being Ca, Mg but also yttrium and rare earth elements (YREE), constituting up to 2% of the metal content. The biogenic origin of the Ytterby birnessite was established in 2018. Studies of the formation of this unique birnessite phase has progressed during 2018-19 with detailed studies of the hydrochemistry of the fracture water as well of the exchangeability of the metals M in the structure: Na, Ca, Fe and La representing the YREE. Exposure to solutions of Na, Ca, Fe, and La, respectively (1 M) led to exchanges and altered distribution of the metals constituting M, with a preference of YREE (trivalent) over Ca (divalent) over Na (monovalent), all of similar ionic radii, as well as higher affinity for YREE over Fe(III), being smaller. Fe(III) did not replace Mn(III) in the structure, despite the fact that their radii are almost identical. No discrete new Fe phase was indicated, and the structure of the birnessite phase was almost identical after exchanges of M, as indicated from XRD. The formation of birnessite in the fracture opening on the tunnel wall appears to be a fast and dynamic process, as indicated by a significant depletion of Mn as well as of YREE in the fracture water during the passage over the precipitation zone, from top to bottom.
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| 3. |
- Carén, Helena, 1979, et al.
(författare)
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A cluster of genes located in 1p36 are down-regulated in neuroblastomas with poor prognosis, but not due to CpG island methylation.
- 2005
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Ingår i: Molecular cancer. - : Springer Science and Business Media LLC. - 1476-4598. ; 4:1
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: A common feature of neuroblastoma tumours are partial deletions of the short arm of chromosome 1 (1p-deletions). This is indicative of a neuroblastoma tumour suppressor gene being located in the region. Several groups including our have been studying candidate neuroblastoma genes in the region, but no gene/genes have yet been found that fulfil the criteria for being a neuroblastoma tumour suppressor. Since frequent mutations have not been detected, we have now analyzed the expression and promoter CpG island methylation status of the genes UBE4B, KIF1B, PGD, APITD1, DFFA and PEX14 in the 1p36.22 region in order to find an explanation for a possible down-regulation of this region. RESULTS: The current study shows that gene transcripts in high stage neuroblastoma tumours are significantly down-regulated compared to those in low stage tumours in the 1p36.22 region. CpG island methylation does not seem to be the mechanism of down-regulation for most of the genes tested, since no methylation was detected in the fragments analyzed. One exception is the CpG island of APITD1. Methylation of this gene is also seen in blood from control individuals and is therefore not believed to participate in tumour development. CONCLUSION: The genes UBE4B, KIF1B, PGD, APITD1, DFFA and PEX14 are down-regulated in high stage NB tumours, a feature that can not be explained by CpG island methylation.
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| 4. |
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| 5. |
- Giménez-Gómez, Pablo, 1984-, et al.
(författare)
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Distance-based paper analytical device for the determination of dissolved inorganic carbon concentration in freshwater
- 2023
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Ingår i: Sensors and actuators. B, Chemical. - : Elsevier BV. - 0925-4005 .- 1873-3077. ; 385
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Tidskriftsartikel (refereegranskat)abstract
- Dissolved inorganic carbon (DIC) levels in freshwaters play a key role in the equilibrium of the carbon cycle between the atmosphere, water and living beings. Standard classical methods for DIC determination generally involve bulky and expensive equipment used in centralized laboratories, resulting in time-consuming processes that do not allow for adequate monitoring in the field. In order to address this challenge, we have developed a distance-based paper analytical device (PAD) for on-site determination of DIC in water. The portable, cost-effective and easy-to-use device was based on the miniaturization and integration of a classical acid-base colorimetric titration on a paper channel, enabling an accurate determination of DIC in less than 20 min. The length of the blue colored line in the detection channel after being filled with the sample was related to the DIC concentration in the sample. The reagent solution used to modify the titration channel was optimized so that DIC concentrations in the range 50–1000 mg L−1 could be measured. The long-term stability of the paper-based device was also evaluated, demonstrating a working stability for more than 70 days after their fabrication, an important characteristic for in-the-field analysis. Finally, the PAD was validated with different water samples, i.e. tap water, commercial bottled drinking water and water samples from a mine, with excellent agreement between the results obtained from the PAD and the standard method. This demonstrates the high potential of the proposed paper analytical device to quantify DIC in situ by minimally-trained personnel without the need for peripheral equipment, which represents an important advance compared to the current limited analysis systems.
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| 6. |
- Huld, Sigrid, et al.
(författare)
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Chemical Gardens Mimic Electron Paramagnetic Resonance Spectra and Morphology of Biogenic Mn Oxides
- 2023
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Ingår i: Astrobiology. - : Mary Ann Liebert. - 1531-1074 .- 1557-8070. ; 23:1, s. 24-32
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Tidskriftsartikel (refereegranskat)abstract
- Manganese (Mn) oxides are ubiquitous in nature and occur as both biological and abiotic minerals, but empirically distinguishing between the two remains a problem. Recently, electron paramagnetic resonance (EPR) spectroscopy has been proposed for this purpose. It has been reported that biogenic Mn oxides display a characteristic narrow linewidth in contrast to their pure abiotic counterparts, which is explained in part by the large number of cation vacancies that form within the layers of biogenic Mn oxides. It was, therefore, proposed that natural samples that display a narrow EPR linewidth, delta H-pp < 580G, could be assigned to a biogenic origin. However, in poorly crystalline or amorphous solids, both dipolar broadening and exchange narrowing simultaneously determine the linewidth. Considering that the spectral linewidth is governed by several mechanisms, this approach might be questioned. In this study, we report synthetic chemical garden Mn oxide biomorphs that exhibit both morphologically life-like structures and narrow EPR linewidths, suggesting that a narrow EPR line may be unsuitable as reliable evidence in assessment of biogenicity. Key Words: Mn oxides & mdash;EPR & mdash;Chemical gardens & mdash;Biomorphs. Astrobiology 23, 24-32.
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| 7. |
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| 8. |
- Sjöberg, Susanne, 1969-
(författare)
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Microbially mediated formation of birnessite-type manganese oxides and subsequent incorporation of rare earth elements, Ytterby mine, Sweden
- 2017
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Microbes exert extensive control on redox element cycles. They participate directly orindirectly in the concentration and fractionation of elements by influencing the partitioningbetween soluble and insoluble species. Putative microbially mediated manganese (Mn) oxidesof the birnessite-type, enriched in rare earth elements (REE) + yttrium (Y) were recentlyfound in the Ytterby mine, Sweden. A poorly crystalline birnessite-type phyllomanganate isregarded as the predominant initial phase formed during microbial Mn oxidation. Owing to ahigher specific surface area, this biomineral also enhances the known sorption property of Mnoxides with respect to heavy metals (e.g. REE) and therefore has considerable environmentalimpact.The concentration of REE + Y (2±0.5% of total mass, excluding oxygen, carbon and silicon)in the Ytterby Mn oxide deposit is among the highest ever observed in secondary precipitateswith Mn and/or iron. Sequential extraction provides evidence of a mineral structure where theREE+Y are firmly included, even at pH as low as 1.5. Concentration ratios of Mn oxideprecipitates to fracture water indicate a strong preference for the trivalent REE+Y overdivalent and monovalent metals. A culture independent molecular phylogenetic approach wasadopted as a first step to analyze the processes that microbes mediate in this environment andspecifically how the microbial communities interact with the Mn oxides. Plausible players inthe formation of the investigated birnessite-type Mn oxides are mainly found within theferromanganese genera Hyphomicrobium and Pedomicrobium and a newly identified YtterbyBacteroidetes cluster most closely related to the Terrimonas. Data also indicate that thedetected microorganisms are related to the environmental constraints of the site including lowconstant temperature (8°C), absence of light, high metal content and possibly proximity to theformer storage of petroleum products.
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| 9. |
- Sjöberg, Susanne, 1969-
(författare)
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Microbially mediated manganese oxides enriched in yttrium and rare earth elements in the Ytterby mine, Sweden
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Microorganisms are able to manipulate redox reactions and thus exert extensive control on chemical speciation and element partitioning in nature, affecting the formation and dissolution of certain minerals. One of these redox active elements is manganese (Mn), which in its oxidized states (III/IV), commonly forms Mn oxide-hydroxide minerals. A microbially mediated birnessite-type Mn oxide enriched in yttrium (Y) and rare earth elements (REE) has been studied in our research. The YREE-enriched birnessite was found in a tunnel to the main shaft of the former Ytterby mine in Sweden, well known as the place of discovery of scandium, yttrium, tantalum and five of the REEs. The thesis aims to define preconditions and processes leading to the formation of this Ytterby birnessite, with particular focus on microbial involvement and the potentially promoting role of biofilms. Dynamics and mineral products of the natural system are studied in combination with analyses of Mn phases produced in vitro by microbes isolated from this system. In addition, the nature of the YREE association with the birnessite-type Mn oxides is investigated.Natural birnessite has the composition Mx(Mn3+, Mn4+)2O4•(H2O)n with M ususally being (Na,Ca) and x=0.5. An empirical formula based on element analyses for the Ytterby birnessite has been assessed as M = (Ca0,37-0,41YREE0.02Mg0.04Other metals0.02-0.03), with [Mn3+]/[Mn4+] = 0.86-1.00 to achieve charge balance. We find that there is a preference for the trivalent YREEs over divalent and monovalent metals. There is also a preferential uptake of light rare earth elements (LREE) relative to heavy rare earth elements (HREE), likely due to mineralogical preferences for charge and ionic radius. The YREEs are strongly bound to the mineral structure and not merely adsorbed on the surface. The Mn deposit subsystems (fracture water, Mn oxide precipitating biofilm and bubble biofilm) are phylogenetically significantly different and the microbial community composition of the feeding water has little impact on the derived biofilms. The signature microbial groups of the Mn oxide producing biofilm Rhizobiales (e.g., Pedomicrobium), PLTA13 Gammaproteobacteria, Pirellulaceae, Blastocatellia and Nitrospira are adapted to the specific characteristics of the biofilm: an emerging extreme environment (low temperature, no light, high metal concentration) which is in part generated by the biofilm components themselves. Known Mn oxidizers are identified among these niched microbial groups and four of the isolated bacterial species (Hydrogenophaga sp., Pedobacter sp., Rhizobium sp. and Nevskia sp.) as well as one fungal species (Cladosporium sp.) are involved in Mn oxide production. Hydrogenophaga sp. and Pedobacter sp. produce Mn oxides independently while results imply a synergistic relationship between Rhizobium sp. and selected species. Members of the Pedobacter and Nevskia genera are previously not known to oxidize Mn. Microstructural characterizaton show that the growth pattern of the birnessite-type Mn oxides is either dendritic/shrublike or spherulitic/botryoidal. Nucleation takes place in close association to the biofilm and initial Mn precipitates are observed at different locations depending on the mediating species. Encrustations of cells and other organic structures by Mn precipitates serve as stable nuclei for further growth. The close relationship appears to decrease in importance as the aggregates of poorly crystalline precipitates grow. In the more developed crystals, a repetitive pattern, Liesegang-type of rings, suggests that abiotic factors take over.
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| 10. |
- Sjöberg, Susanne, 1969-, et al.
(författare)
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Mn oxide precipitation by epilithic biofilms in the Ytterby mine, Sweden : formation of an YREE-enriched birnessite
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Biofilms scavenge and bind reduced Mn(II) as well as stabilize highly reactive Mn(III), favouring formation of Mn oxides. Mn oxidation and precipitation involve closely connected and concomitant abiotic and biotic biogeochemical mechanisms, often making the biogenicity of the mineral product difficult to determine. In order to use these precipitates as potential biosignatures, profound knowledge of the formation pathways is required. Here we have access to an underground Mn oxide producing ecosystem in which epilithic biofilms precipitate yttrium and rare earth element enriched birnessite-type Mn oxides. Microbial community composition combined with elemental data is investigated to provide insight into how different subsystems of this ecosystem (fracture water, Mn oxide producing biofilm, and bubble biofilm) interact with each other to form the birnessite. We find that the microbial assembly of the feeding water has little impact on the derived biofilms, in which the signature microbial groups rather results from water chemistry and environmental conditions. In the Mn oxide producing biofilm, bacteria are adapted to the emerging extreme environment (low temperature, no light, high metal concentration) which is generated by the biofilm itself. Microstructural characterizations show that the birnessite has a dendritic/shrublike or spherulitic/botryoidal growth pattern. Nucleation occurs in close association to the biofilm and Mn encrustations of cells and other organic structures serve as stable nuclei for further growth. The influence of organics decrease in importance as precipitates grow. In more evolved crystals, a repetitive pattern, Liesegang-type of rings, implies that abiotic factors dominate. Grown on a solid substrate, four bacterial (Hydrogenophaga sp., Pedobacter sp., Rhizobium sp. and Nevskia sp.) and one fungal species (Cladosporium sp.) are involved in Mn oxide production. Hydrogenophaga and Pedobacter oxidize Mn independently while Rhizobium needs a synergistic relationship with selected species (e.g., Nevskia). Members of the Pedobacter and Nevskia genera are previously not known Mn oxidizers. The onset of Mn precipitaiton takes place at different locations with respect to the cells for the different species. Precipitates are located intracellularly (possibly post mortem), on the bacterial cell walls, at the outer edges of more well developed crystals, within the extracellular organic matter (EOM) and on hyphal surfaces.
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