Use of the frc gene as a molecular marker to characterize oxalate-oxidizing bacterial abundance and diversity structure in soil.

Oxalate catabolism, which can have both medical and environmental implications, is performed by phylogenetically diverse bacteria. The formyl-CoA-transferase gene was chosen as a molecular marker of the oxalotrophic function. Degenerated primers were deduced from an alignment of frc gene sequences available in databases. The specificity of primers was tested on a variety of frc-containing and frc-lacking bacteria. The frc-primers were then used to develop PCR-DGGE and real-time SybrGreen PCR assays in soils containing various amounts of oxalate. Some PCR products from pure cultures and from soil samples were cloned and sequenced. Data were used to generate a phylogenetic tree showing that environmental PCR products belonged to the target physiological group. The extent of diversity visualised on DGGE pattern was higher for soil samples containing carbonate resulting from oxalate catabolism. Moreover, the amount of frc gene copies in the investigated soils was detected in the range of 1.64x10(7) to 1.75x10(8)/g of dry soil under oxalogenic tree (representing 0.5 to 1.2% of total 16S rRNA gene copies), whereas the number of frc gene copies in the reference soil was 6.4x10(6) (or 0.2% of 16S rRNA gene copies). This indicates that oxalotrophic bacteria are numerous and widespread in soils and that a relationship exists between the presence of the oxalogenic trees Milicia excelsa and Afzelia africana and the relative abundance of oxalotrophic guilds in the total bacterial communities. This is obviously related to the accomplishment of the oxalate-carbonate pathway, which explains the alkalinization and calcium carbonate accumulation occurring below these trees in an otherwise acidic soil. The molecular tools developed in this study will allow in-depth understanding of the functional implication of these bacteria on carbonate accumulation as a way of atmospheric CO(2) sequestration.

Caracterització de les metal·lotioneïnes CnMT1 i CnMT2 del fong Cryptococcus neoformans. Estudi de la capacitat coordinant davant dels ions Zn(II), Cd(II) i Cu(I)

En aquest treball de recerca, s’han estudiat les dues isoformes de metal·lotioneïna CnMT1 i CnMT2 presents en el fong patogen Cryptococcus neoformans. Recentment s’ha descobert que aquest fong té com a factor de virulència, els nivells de coure del medi on es troba. Les dues isoformes produïdes en medis rics en Zn(II) s’han utilitzat per a fer valoracions amb Cu(I) i Cd(II), i s’ha seguit l’evolució dels experiments mitjançant les tècniques DC, UV-vis, i ESI-MS. S’ha pogut observar que les dues isoformes tenen preferència per enllaçar Cu(I). Per altra banda també s’ha establert una gran homologia entre les dues seqüències.

Variability in urinary oxalate measurements between six international laboratories.

BACKGROUND: Hyperoxaluria is a major risk factor for kidney stone formation. Although urinary oxalate measurement is part of all basic stone risk assessment, there is no standardized method for this measurement. METHODS: Urine samples from 24-h urine collection covering a broad range of oxalate concentrations were aliquoted and sent, in duplicates, to six blinded international laboratories for oxalate, sodium and creatinine measurement. In a second set of experiments, ten pairs of native urine and urine spiked with 10 mg/L of oxalate were sent for oxalate measurement. Three laboratories used a commercially available oxalate oxidase kit, two laboratories used a high-performance liquid chromatography (HPLC)-based method and one laboratory used both methods. RESULTS: Intra-laboratory reliability for oxalate measurement expressed as intraclass correlation coefficient (ICC) varied between 0.808 [95% confidence interval (CI): 0.427-0.948] and 0.998 (95% CI: 0.994-1.000), with lower values for HPLC-based methods. Acidification of urine samples prior to analysis led to significantly higher oxalate concentrations. ICC for inter-laboratory reliability varied between 0.745 (95% CI: 0.468-0.890) and 0.986 (95% CI: 0.967-0.995). Recovery of the 10 mg/L oxalate-spiked samples varied between 8.7 ± 2.3 and 10.7 ± 0.5 mg/L. Overall, HPLC-based methods showed more variability compared to the oxalate oxidase kit-based methods. CONCLUSIONS: Significant variability was noted in the quantification of urinary oxalate concentration by different laboratories, which may partially explain the differences of hyperoxaluria prevalence reported in the literature. Our data stress the need for a standardization of the method of oxalate measurement.

Influence of nutrition on urinary oxalate and calcium in preterm and term infants.

Few data for normal urinary oxalate (Ox) and calcium (Ca) excretion related both to gestational age and nutritional factors have been reported in preterm or term infants. We therefore determined the molar Ox and Ca to creatinine (Cr) ratios in spot urines from 64 preterm and 37 term infants aged 1-60 days, either fed formula or human milk (HM). Only vitamin D was supplemented; renal or metabolic diseases were excluded. Urinary Ox/Cr ratio was higher in preterm than in term infants, both when formula fed (1st month 253 vs. 180 mmol/mol and 2nd month 306 vs. 212 mmol/mol; P<0.05) or HM fed (206 vs. 169 mmol/ mol and 283* vs. 232 mmol/mol; *P<0.05). Ox/Cr was also higher in formula- than HM-fed preterm infants. The ratio increased during the first 2 months of life irrespective of nutrition. Urinary Ca/Cr ratio was comparable in all groups during the 1st month of life, except for a lower (P < 0.05) value in term infants fed HM (0.10 mol/mol). It increased in all groups during the 2nd month of life, being highest in HM-fed preterm infants (1.86 mol/mol). In conclusion, urinary Ox and Ca excretion is influenced by both gestational age and nutrient intake in preterm and term infants.

Silicon nanocluster sensitization of erbium ions under low-energy optical excitation

The sensitizing action of amorphous silicon nanoclusters on erbium ions in thin silica films has been studied under low-energy (long wavelength) optical excitation. Profound differences in fast visible and infrared emission dynamics have been found with respect to the high-energy (shortwavelength) case. These findings point out to a strong dependence of the energy transfer process on the optical excitation energy. Total inhibition of energy transfer to erbium states higher than thefirst excited state (4I13/2) has been demonstrated for excitation energy below 1.82 eV (excitation wavelength longer than 680 nm). Direct excitation of erbium ions to the first excited state (4I13/2)has been confirmed to be the dominant energy transfer mechanism over the whole spectral range of optical excitation used (540 nm¿680 nm).

Extraction and concentration of biogenic calcium oxalate from plant leaves

The objective of this study was to extract and concentrate calcium oxalate (CaOx) crystals from plant leaves that form the above mentioned crystals. The chemical and physical studies of CaOx from plant to be performed depend on an adequate amount of the crystals. The plant used in this study was croton (Codiaeum variegatum). The leaves were ground in a heavy duty blender and sieved through a 0.20 mm sieve. The suspension obtained was suspended in distilled water. The crystals were concentrated at the bottom of a test tube. The supernatant must be washed until it is free of plant pigments and other organic substances. Biogenic CaOx crystals have well-defined and sharp peaks, indicating very high crystallinity. Moreover, the CaOx crystals were not damaged during the extraction procedure, as can be seen on the scanning electron microscope images. The porposed method can be considered efficient to extract and concentrate biogenic calcium oxalate.

Model for the emission of Si+ ions during oxygen bombardment of Si(100) surfaces

The variation in the emission of Si+ ions from ion-beam-induced oxidized silicon surfaces has been studied. The stoichiometry and the electronic structure of the altered layer has been characterized using x-ray photoelectron spectroscopy (XPS). The XPS analysis of the Si 2p core level indicates the strong presence of suboxide chemical states when bombarding at angles of incidence larger than 30 °. Since the surface stoichiometry or degree of oxidation varies with the angle of incidence, the corresponding valence-band structures also differ among each other. A comparison between experimental measurements and theoretically calculated Si and SiO2 valence bands indicates that the valence bands for the altered layers are formed by a combination of those two. Since Si-Si bonds are present in the suboxide molecules, the top of the respective new valence bands are formed by the corresponding 3p-3p Si-like subbands, which extend up to the Si Fermi level. The changes in stoichiometry and electronic structure have been correlated with the emission of Si+ ions from these surfaces. From the results a general model for the Si+ ion emission is proposed combining the resonant tunneling and local-bond-breaking models.

Phosphorus saturation of Finnish soils : evaluating an easy oxalate extraction method

Selostus: Alumiini- ja rautaoksidien fosforikyllästysasteen arvioiminen suomalaisista peltomaista

Rôle des champignons dans la voie oxalate-carbonate

La présente thèse met en évidence trois rôles des champignons dans la voie oxalate-carbonate. (i) La dynamique fongique de production des cristaux d'oxalate de calcium montre une diminution du nombre de ces cristaux comparativement à ceux préalablement produits. Afin de confirmer ce résultat, une méthode analytique faisant usage de la chromatographie liquide mesurant l'oxalate total, a été mise en pratique. De plus, des champignons à pourriture blanche ont été cultivés sur un milieu Schlegel couramment utilisé par les bactériologistes pour montrer la dissolution bactérienne des oxalates de calcium. Certains champignons se sont révélés positifs au test. (ii) Une approche en microcosme a été employée pour comprendre le rôle respectif des champignons et des bactéries dans la voie oxalate-carbonate. Champignons et bactéries sont la composante biologique du système oxalate-carbonate et sont donc ajoutés au sol des microcosmes selon les séries : (A) champignons seuls, (B) bactéries seules et (C) champignons et bactéries ensemble. En prenant en considération la variable oxalate et en opérant une approche factorielle en accord avec la théorie de la hiérarchie, les séries additionnelles suivantes ont été étudiées : (D) champignon plus oxalate, (E) bactéries plus oxalate et (F) champignon et bactéries ensemble plus oxalate. En présence d'oxalate de calcium les résultats des quantités de champignon vivant (évaluées par dosage de l'ergostérol) au cours du temps montrent que la rapidité de colonisation des microcosmes est accélérée de trois semaines ; c'est une fertilisation du sol opérée par l'oxalate qui favorise la biomasse vivante du champignon. Les champignons à leur tour survivent sur le long terme (3 mois) seulement en présence des bactéries sinon leur biomasse vivante reste faible. Par conséquent, c'est l'interaction entre champignons et bactéries sous forme de coexistence qui permet leur survie réciproque. Les champignons interagissent en synergie avec les bactéries dans le sol du microcosme mais les bactéries, moteur de l'alcalinisation du sol, survivent plus longtemps et atteignent des populations plus élevées seulement quand le champignon et l'oxalate sont présents. En plus des résultats sur les quantités de champignons et de bactéries, le suivi du pH pour toutes les séries des microcosmes examinées laisse apparaître une propriété émergente. Pour l'unique série (F), il se produit une alcalinisation du milieu de deux unités et demie de pH. L'hypothèse de base selon laquelle l'oxalate est responsable d'une favorisation de la voie oxalate-carbonate a été vérifiée. Le rôle des champignons est de favoriser les populations bactériennes sous l'action fertilisante de l'oxalate. (iii) L'origine du calcium, une des questions à résoudre les plus importantes afin que la voie oxalate-carbonate agisse comme un puits de carbone, a été abordée théoriquement, par une littérature élargie, et expérimentalement en boîte de Pétri, en utilisant la colonisation fongique. Le rôle des champignons est de transloquer et libérer du calcium activement et passivement dans le sol.