Vibrational spectroscopic characterization of the arsenate mineral barahonaite: Implications for the molecular structure

The mineral barahonaite is in all probability a member of the smolianinovite group. The mineral is an arsenate mineral formed as a secondary mineral in the oxidized zone of sulphide deposits. We have studied the barahonaite mineral using a combination of Raman and infrared spectroscopy. The mineral is characterized by a series of Raman bands at 863 cm−1 with low wavenumber shoulders at 802 and 828 cm−1. These bands are assigned to the arsenate and hydrogen arsenate stretching vibrations. The infrared spectrum shows a broad spectral profile. Two Raman bands at 506 and 529 cm−1 are assigned to the triply degenerate arsenate bending vibration (F 2, ν4), and the Raman bands at 325, 360, and 399 cm−1 are attributed to the arsenate ν2 bending vibration. Raman and infrared bands in the 2500–3800 cm−1 spectral range are assigned to water and hydroxyl stretching vibrations. The application of Raman spectroscopy to study the structure of barahonaite is better than infrared spectroscopy, probably because of the much higher spatial resolution.

Raman and infrared spectroscopic characterization of the arsenate-bearing mineral tangdanite– and in comparison with the discredited mineral clinotyrolite

The minerals clinotyrolite and fuxiaotuite are discredited in terms of the mineral tangdanite. The mixed anion mineral tangdanite Ca2Cu9(AsO4)4(SO4)0.5(OH)9 9H2O has been studied using a combination of Raman and infrared spectroscopy. Characteristic bands associated with arsenate, sulphate and hydroxyl units are identified. Broad bands in the OH stretching region are observed and are resolved into component bands. These bands are assigned to water and hydroxyl stretching vibrations. Two intense Raman bands at 837 and approximately 734 cm−1 are assigned to the ν1 (AsO4)3− symmetric stretching and ν3 (AsO4)3− antisymmetric stretching modes. Infrared bands at 1023 cm−1 are assigned to the (SO4)2− ν1 symmetric stretching mode, and infrared bands at 1052, 1110 and 1132 cm−1 assigned to (SO4)2− ν3 antisymmetric stretching modes, confirming the presence of the sulphate anion in the tangdanite structure. Raman bands at 593 and 628 cm−1 are attributed to the (SO4)2− ν4 bending modes. Low-intensity Raman bands found at 457 and 472 cm−1 are assigned to the (AsO4)3− ν2 bending modes. A comparison is made with the previously obtained spectral data on the discredited mineral clinotyrolite.

Methylenetetrahydrofolate reductase CpG islands: Epigenotyping

Background Determination of the differential DNA methylation patterns of methylenetetrahydrofolate reductase (MTHFR) that are associated with differential MTHFR activity is important to understand the pathogenesis of ischemic stroke. However, to date, no data are available on the differential DNA methylation profiles of Kelantanese Malays. Therefore, we developed a rapid and efficient serial pyrosequencing assay to determine differential DNA methylation profiles of MTHFR, which help to further our understanding of the pathogenesis of ischemic stroke. The developed assay also served as the validation platform for our previous computational epigenetic research on MTHFR. Methods Polymerase chain reaction primers were designed and validated to specifically amplify the cytosine that is followed by guanine residues (CpGs) A and B regions. Prior epigenotyping on 110 Kelantanese Malays, the serial pyrosequencing assays for the CpGs A and B regions were validated using five validation controls. The mean values of the DNA methylation profiles of CpGs A and B were calculated. Results The mean DNA methylation levels for CpGs A and B were 0.984 ± 0.582 and 2.456 ± 1.406, respectively. The CpGs 8 and 20 showed the highest (5.581 ± 4.497) and the lowest (0.414 ± 2.814) levels of DNA methylation at a single-base resolution. Conclusion We have successfully developed and validated a pyrosequencing assay that is fast and can yield high-quality pyrograms for DNA methylation analysis and is therefore applicable to high throughput study. Using this newly developed pyrosequencing assay, the MTHFR DNA methylation profiles of 110 Kelantanese Malays were successfully determined. It also validated our computational epigenetic research on MTHFR.

Raman spectroscopic study of the uranyl mineral natrouranospinite (Na2,Ca)[(UO2)(AsO4)]2•5H2O

Raman spectra of natrouranospinite complemented with infrared spectra were studied and related to the structure of the mineral. Observed bands were assigned to the stretching and bending vibrations of (UO2)2+ and (AsO4)3- units and of water molecules. U-O bond lengths in uranyl and O-H…O hydrogen bond lengths were calculated from the Raman and infrared spectra.

Raman spectroscopic study of the uranyl mineral metauranospinite Ca[(UO2)(AsO4)]2.8H2O

Raman spectra of metauranospinite Ca[(UO2)(AsO4)]2.8H2O complemented with infrared spectra were studied. Observed bands were assigned to the stretching and bending vibrations of (UO2)2+ and (AsO4)3- units and of water molecules. U-O bond lengths in uranyl and O-H…O hydrogen bond lengths were calculated from the Raman and infrared spectra.

Raman spectroscopic study of the phosphate mineral Churchite-(Y) YPO4.2H2O

Raman spectroscopy has been used to study the rare earth mineral churchite-(Y) of formula (Y,REE)(PO4) •2H2O. The mineral contains yttrium and depending on the locality, a range of rare earth metals. The Raman spectra of two churchite-(Y) mineral samples from Jáchymov and Medvědín in the Czech Republic were compared with the Raman spectra of churchite-(Y) downloaded from the RRUFF data base. The Raman spectra of churchite-(Y) are characterized by an intense sharp band at 975 cm-1 assigned to the ν1 (PO4)3- symmetric stretching mode. A lower intensity band observed at around 1065 cm-1 is attributed to the ν3 (PO43-) antisymmetric stretching mode. The (PO43-) bending modes are observed at 497 cm-1 (ν2) and 563 cm-1(ν4). Some small differences in the band positions between the four churchite-(Y) samples from four different localities were found. These differences are possible to explain as different compositions of the churchite-(Y) minerals.

Raman spectroscopic study of the arsenite minerals leiteite ZnAs2O4 , reinerite Zn3(AsO3)2 and cafarsite Ca5(Ti,Fe,Mn)7(AsO3)12.4H2O

The selected arsenite minerals leiteite, reinerite and cafarsite have been studied by Raman spectroscopy. DFT calculations enabled the position of AsO22- symmetric stretching mode at 839 cm-1, the antisymmetric stretching mode at 813 cm-1, and the deformation mode at 449 cm-1 to be calculated. The Raman spectrum of leiteite shows bands at 804 and 763 cm-1 assigned to the As2O42- symmetric and antisymmetric stretching modes. The most intense Raman band of leiteite is the band at 457 cm-1 and is assigned to the ν2 As2O42- bending mode. A comparison of the Raman spectrum of leiteite is made with the arsenite minerals reinerite and cafarsite.

Raman spectroscopic study of the multi-anion mineral dixenite CuMn2+14Fe3+(AsO3)5(SiO4)2(AsO4)(OH)6

The mixed anion mineral dixenite has been studied by Raman spectroscopy, complimented with infrared spectroscopy. The Raman spectrum of dixenite shows bands at 839 and 813 cm-1 assigned to the (AsO3)3- symmetric and antisymmetric stretching modes. The most intense Raman band of dixenite is the band at 526 cm-1 and is assigned to the ν2 AsO33- bending mode. DFT calculations enabled the position of AsO22- symmetric stretching mode at 839 cm-1, the antisymmetric stretching mode at 813 cm-1, and the deformation mode at 449 cm-1 to be calculated. Raman bands at 1026 and 1057 cm-1 are assigned to the SiO42- symmetric stretching vibrations and at 1349 and 1386 cm-1 to the SiO42- antisymmetric stretching vibrations. Both Raman and infrared spectra indicate the presence of water in the structure of dixenite. This brings into question the commonly accepted formula of dixenite as CuMn2+14Fe3+(AsO3)5(SiO4)2(AsO4)(OH)6. The formula may be better written as CuMn2+14Fe3+(AsO3)5(SiO4)2(AsO4)(OH)6•xH2O.

Raman microscopy of haidingerite Ca(AsO3OH)•H2O and brassite Mg(AsO3OH)•4H2O

Raman spectroscopy has been used to study the arsenate minerals haidingerite Ca(AsO3OH)•H2O and brassite Mg(AsO3OH)•4H2O. Intense Raman bands in haidingerite spectrum observed at 745 and 855 cm-1 are assigned to the (AsO3OH)2- ν3 antisymmetric stretching and ν1 symmetric stretching vibrational modes. For brassite two similarly assigned intense bands are found at 809 and 862 cm-1. The observation of multiple Raman bands in the (AsO3OH)2- stretching and bending regions suggests that the arsenate tetrahedrons in the crystal structures of both minerals studied are strongly distorted. Broad Raman bands observed at 2842 cm-1 for haidingerite and 3035 cm-1 for brassite indicate strong hydrogen bonding of water molecules in the structure of these minerals. OH…O hydrogen bond lengths were calculated from the Raman spectra based on empiric relations.

Spectroscopy of selected copper group minerals : chalcophyllite and chenevixite-implications for hydrogen bonding

NIR and IR spectroscopy has been applied for detection of chemical species and the nature of hydrogen bonding in arsenate complexes. The structure and spectral properties of copper(II) arsenate minerals chalcophyllite and chenevixite are compared with copper(II) sulphate minerals devilline, chalcoalumite and caledonite. Split NIR bands in the electronic spectrum of two ranges 11700-8500 cm-1 and 8500-7200 cm-1 confirm distortion of octahedral symmetry for Cu(II) in the arsenate complexes. The observed bands with maxima at 9860 and 7750 cm-1 are assigned to Cu(II) transitions 2B1g ® 2B2g and 2B1g ® 2A1g. Overlapping bands in the NIR region 4500-4000 cm-1 is the effect of multi anions OH-, (AsO4)3- and (SO4)2-. The observation of broad and diffuse bands in the range 3700-2900 cm-1 confirms strong hydrogen bonding in chalcophyllite relative to chenevixite. The position of the water bending vibrations indicates the water is strongly hydrogen bonded in the mineral structure. The strong absorption feature centred at 1644 cm-1 in chalcophyllite indicates water is strongly hydrogen bonded in the mineral structure. The H2O-bending vibrations shift to low wavenumbers in chenevixite and an additional band observed at 1390 cm-1 is related to carbonate impurity. The characterisation of IR spectra by ν3 antisymmetric stretching vibrations of (SO4)2- and (AsO4)3 ions near 1100 and 800 cm-1 respectively is the result of isomorphic substitution for arsenate by sulphate in both the minerals of chalcophyllite and chenevixite.

Use of hydrotalcites for the removal of toxic anions from aqueous solutions

The removal of toxic anions has been achieved using hydrotalcite via two methods: (1) coprecipitation and (2) thermal activation. Hydrotalcite formed via the coprecipitation method, using solutions containing arsenate and vanadate up to pH 10, are able to remove more than 95% of the toxic anions (0.2 M) from solution. The removal of toxic anions in solutions with a pH of >10 reduces the removal uptake percentage to 75%. Raman spectroscopy observed multiple A1 stretching modes of V−O and As−O at 930 and 810 cm−1, assigned to vanadate and arsenate, respectively. Analysis of the intensity and position of the A1 stretching modes helped to identify the vanadate and arsenate specie intercalated into the hydrotalcite structure. It has been determined that 3:1 hydrotalcite structure predominantly intercalate anions into the interlayer region, while the 2:1 and 4:1 hydrotalcite structures shows a large portion of anions being removed from solution by adsorption processes. Treatment of carbonate solutions (0.2 M) containing arsenate and vanadate (0.2 M) three times with thermally activated hydrotalcite has been shown to remove 76% and 81% of the toxic anions, respectively. Thermally activated hydrotalcite with a Mg:Al ratio of 2:1, 3:1, and 4:1 have all been shown to remove 95% of arsenate and vanadate (25 ppm). At increased concentrations of arsenate and vanadate, the removal uptake percentage decreased significantly, except for the 4:1 thermally activated hydrotalcite. Thermally activated Bayer hydrotalcite has also been shown to be highly effective in the removal of arsenate and vanadate. The thermal activation of the solid residue component (red mud) removes 30% of anions from solution (100 ppm of both anions), while seawater-neutralized red mud removes 70%. The formation of hydrotalcite during the seawater neutralization process removes anions via two mechanisms, rather than one observed for thermally activated red mud.

Cystine-mediated oxidative defence in Lactobacillus reuteri BR11

Lactobacillus reuteri BR11 possesses an abundant cystine uptake (Cyu) ABC-transporter that was previously found to be involved in a novel mechanism of oxidative defence mediated by cystine. The current study aimed to elucidate this mechanism with a focus on the role of the co-transcribed cystathionine ã-lyase (Cgl). Growth studies of wild-type L. reuteri BR11 and mutants inactivated in cgl and the cystine-binding protein encoding gene cyuC showed that in contrast to the Cyu transporter, whose inactivation led to growth arrest in aerated cultures, Cgl is not crucial for oxidative defence. However, the role of Cgl in oxidative defence became apparent in the presence of severe oxidative damage and cysteine deprivation. Cysteine was found to be protective against oxidative stress, and the action of Cgl in both cysteine biosynthesis and degradation poses a seemingly futile pathway that deprives the intracellular cysteine pool. To further characterise the relationship between Cgl activity and cysteine and their roles in oxidative defence, enzymatic assays were performed on purified Cgl, and intracellular concentrations of cysteine, cystathionine and methionine were determined. Cgl was highly active towards cystine and cystathionine and less active towards cysteine in vitro, suggesting the main function of Cgl to be cysteine biosynthesis. Cysteine was found at high concentrations in the cell, but the levels were not significantly affected by inactivation of cgl or growth under aerobic conditions. It was concluded that both anabolic and catabolic activities of Cgl towards cysteine contribute to oxidative defence, the former by maintaining an intracellular reservoir of thiol analogous to glutathione, and the latter by producing H2S which is readily secreted, thus creating a reducing extracellular environment. The significance of the Cyu transporter to the physiology of L. reuteri BR11 prompted a phylogenetic study to determine its presence in bacteria. Orthologs of the Cyu transporter that are closest matches to the Cyu transporter are only limited to several species of Lactobacillus and Leuconostoc. Outside the Lactobacillales order, the closest matching orthologs belong to Proteobacteria, and there are more orthologs in Proteobacteria than non-Lactobacillales Firmicutes, suggesting that the Cyu transporter locus was present in the ancestor of the Proteobacteria and Firmicutes, and over evolutionary time has been lost or diverged in many Firmicutes. The clustering of the Cyu transporter locus with a gene encoding a Cgl family protein is even rarer. It was only found in L. reuteri, Lactobacillus vaginalis, Weissella paramesenteroides, the Lactobacillus casei group, and several Campylobacter sp. An accompanying phylogenetic study of L. reuteri BR11 using multi-locus sequence analysis showed that L. reuteri BR11 had diverged from more than 100 strains of L. reuteri isolated from various hosts and geographical locations. However, comparison with other Lactobacillus species supported the current classification of BR11 as L. reuteri. The most closely related species to L. reuteri is L. vaginalis or Lactobacillus antri, depending on the housekeeping gene used for analysis. The close evolutionary relationship of L. vaginalis to L. reuteri and the high degree of sequence identity between the cgl-cyuABC loci in both species suggest that the Cyu system is highly likely to perform similar functions in L. vaginalis. In search of other genes that function in oxidative defence, a number of mutants which were inactivated in genes that confer increased resistance to oxidative stress in other bacteria were constructed. The genes targeted were ahpC (peroxidase component of the alkyl hydroperoxide reductase system), tpx (thiol peroxidase), osmC (osmotically induced protein C), mntH (Mn2+/Fe2+ transporter), gshA (ã-glutamylcysteine synthetase) and msrA (methionine sulfoxide reductase). The ahpC and mntH mutants had slightly lower minimum inhibitory concentrations of organic peroxides, suggesting these genes might be involved in resistance to organic peroxides in L. reuteri. However, none of the mutants exhibited growth defects in aerated cultures, in stark contrast to the cyuC mutant. This may be due to compensatory functions of other genes, a hypothesis which cannot be tested until a robust protocol for constructing markerless multiple gene deletion mutants in L. reuteri is developed. These results highlight the importance of the Cyu transporter in oxidative defence and provide a foundation for extending the research of this system in other bacteria.

A Near-infrared and Raman spectroscopic study of the mineral richelsdorfite Ca2Cu5Sb[Cl|(OH)6|(AsO4)4]•6H2O

Raman spectroscopy has enabled insights into the molecular structure of the richelsdorfite Ca2Cu5Sb[Cl|(OH)6|(AsO4)4]·6H2O. This mineral is based upon the incorporation of arsenate or phosphate with chloride anion into the structure and as a consequence the spectra reflect the bands attributable to these anions, namely arsenate or phosphate and chloride. The richelsdorfite Raman spectrum reflects the spectrum of the arsenate anion and consists of ν1 at 849, ν2 at 344 cm−1, ν3 at 835 and ν4 at 546 and 498 cm−1. A band at 268 cm−1 is attributed to CuO stretching vibration. Low wavenumber bands at 185 and 144 cm−1 may be assigned to CuCl TO/LO optic vibrations.