Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing

Biogas production from renewable resources is attracting increased attention as an alternative energy source due to the limited availability of traditional fossil fuels. Many countries are promoting the use of alternative energy sources for sustainable energy production. In this study, a metagenome from a production-scale biogas fermenter was analysed employing Roche's GS FLX Titanium technology and compared to a previous dataset obtained from the same community DNA sample that was sequenced on the GS FLX platform. Taxonomic profiling based on 16S rRNA-specific sequences and an Environmental Gene Tag (EGT) analysis employing CARMA demonstrated that both approaches benefit from the longer read lengths obtained on the Titanium platform. Results confirmed Clostridia as the most prevalent taxonomic class, whereas species of the order Methanomicrobiales are dominant among methanogenic Archaea. However, the analyses also identified additional taxa that were missed by the previous study, including members of the genera Streptococcus, Acetivibrio, Garciella, Tissierella, and Gelria, which might also play a role in the fermentation process leading to the formation of methane. Taking advantage of the CARMA feature to correlate taxonomic information of sequences with their assigned functions, it appeared that Firmicutes, followed by Bacteroidetes and Proteobacteria, dominate within the functional context of polysaccharide degradation whereas Methanomicrobiales represent the most abundant taxonomic group responsible for methane production. Clostridia is the most important class involved in the reductive CoA pathway (Wood-Ljungdahl pathway) that is characteristic for acetogenesis. Based on binning of 16S rRNA-specific sequences allocated to the dominant genus Methanoculleus, it could be shown that this genus is represented by several different species. Phylogenetic analysis of these sequences placed them in close proximity to the hydrogenotrophic methanogen Methanoculleus bourgensis. While rarefaction analyses still indicate incomplete coverage, examination of the GS FLX Titanium dataset resulted in the identification of additional genera and functional elements, providing a far more complete coverage of the community involved in anaerobic fermentative pathways leading to methane formation

Anaerobic degradation of m-cresol by Desulfobacterium cetonicum is initiated by formation of 3-hydroxybenzylsuccinate

The anaerobic bacterium Desulfobacterium cetonicum oxidized m-cresol completely with sulfate as electron acceptor. During growth, 3-hydroxybenzylsuccinate (identified by gas chromatography/mass spectroscopy and by comparison of high-performance liquid chromatography retention time and UV spectrum with a chemically synthesized reference compound) accumulated in the medium. This finding indicates that the methyl group of mcresol is activated by addition to fumarate as in the case of anaerobic toluene metabolism. In cell-free extracts of D. cetonicum, the formation of 3-hydroxybenzylsuccinate from m-cresol and fumarate was detected at an activity of 0.5 nmol min 1 (mg protein) 1. This reaction depended strictly on anoxic assay conditions. Treatment with air resulted in a complete loss of activity; however, some activity could be recovered after restoring anoxic conditions. The activity was slightly membrane-associated. 3-Hydroxybenzylsuccinate was degraded via CoA thioesterification and further oxidation to 3-hydroxybenzoyl-CoA as subsequent steps in the degradation pathway

Initiation of Anaerobic Degradation of p-Cresol by Formation of 4-Hydroxybenzylsuccinate in Desulfobacterium cetonicum

The anaerobic bacterium Desulfobacterium cetonicum oxidized p-cresol completely to CO(2) with sulfate as the electron acceptor. During growth, 4-hydroxybenzylsuccinate accumulated in the medium. This finding indicated that the methyl group of p-cresol is activated by addition to fumarate, analogous to anaerobic toluene, m-xylene, and m-cresol degradation. In cell extracts, the formation of 4-hydroxybenzylsuccinate from p-cresol and fumarate was detected at an initial rate of 0.57 nmol min(−1) (mg of protein)(−1). This activity was specific for extracts of p-cresol-grown cells. 4-Hydroxybenzylsuccinate was degraded further to 4-hydroxybenzoyl-coenzyme A (CoA), most likely via β-oxidation. 4-Hydroxybenzoyl-CoA was reductively dehydroxylated to benzoyl-CoA. There was no evidence of degradation of p-cresol via methyl group oxidation by p-cresol-methylhydroxylase in this bacterium

Low-field MRI for assessing synovitis in patients with rheumatoid arthritis. Impact of Gd-DTPA dose on synovitis scoring

Objective: To investigate the impact of a double dose compared to a single dose of contrast material in low- field magnetic resonance imaging ( MRI) on semi- quantitative scoring of synovitis in patients with rheumatoid arthritis ( RA). Methods: This prospective study included 38 RA patients ( 23 women and 15 men, mean age 51 years). All patients underwent low- field MRI of the hand before administration of contrast medium, after intravenous injection of 0.1 mmol/kg gadolinium diethylenetriaminepentaacetic acid (Gd- DTPA), and after another dose of 0.1 mmol/ kg Gd- DTPA. Two readers ( A and B) blinded to dosage independently scored the single dose and double dose image sets for synovitis according to outcome measures in rheumatology (OMERACT) recommendations. Contrast- to-noise ratio ( CNR) and signal-to-noise ratio ( SNR) were also calculated for each set. Results: 149 metacarpophalangeal (MCP) joints were evaluated. There was good inter-reader agreement for each of the two sets ( intra- class correlation coefficient of 0.75 for the single dose set and 0.83 for the double dose). Median CNR and SNR values were 5.4 and 15.9, respectively, for the single dose set and 8.5 and 16.6, respectively, for the double dose set (p < 0.0001). Single dose set mean synovitis scores were 1.7 and 1.6 for readers A and B, respectively. Double dose set scores were 1.9 and 2.0, respectively. Thus, higher synovitis scores were recorded for the double dose sets than the single dose sets ( pv0.005). Conclusion: In low- field MRI, when evaluating RA, the dose of the contrast material influences synovitis scoring. Therefore, dosage of contrast material should be taken into consideration when using extremity dedicated low- field MRI

Diagnostic quality and scoring of synovitis, tenosynovitis and erosions in low‐field MRI of patients with rheumatoid arthritis: a comparison with conventional MRI

OBJECTIVE: To compare dedicated low‐field MRI (lfMRI) with conventional MRI (cMRI) in the detection and scoring of synovitis, tenosynovitis and erosions in patients with rheumatoid arthritis. PATIENTS AND METHODS: The wrist and finger joints of 17 patients with rheumatoid arthritis (median (range) disease duration 8 years (7–12); Disease Activity Score 3.3 (2.6–4.5)) were examined by 0.2 T lfMRI and 1.5 TcMRI. The protocols comprised coronal spin‐echo and three‐dimensional gradient‐echo sequences before and after contrast medium administration. Synovitis of the metacarpophalangeal and proximal interphalangeal joints 2–5 and the wrist joints was scored according to Outcome Measures in Rheumatology recommendations. Tenosynovitis and erosions were scored using 4‐point and 6‐point scales, respectively. The results were analysed by calculating κ values and performing McNemar's test intra‐individually on a joint‐by‐joint basis. RESULTS: Agreement between the two MRI techniques was good to excellent for synovitis and erosions, and moderate for tenosynovitis. Of the 306 joints evaluated, 245 and 200 joints showed synovitis in lfMRI and cMRI, respectively. Scoring of synovitis of the finger joints yielded κ values from 0.69 to 0.94. Of the 68 flexor tendons evaluated, tenosynovitis was diagnosed by lfMRI in 24 and by cMRI in 33 instances. Of the 391 bones evaluated, 154 and 139 showed erosions in lfMRI and cMRI, respectively. κ values for erosion scores were between 0.65 and 1. CONCLUSION: Dedicated, lfMRI shows high agreement with cMRI in diagnosing and scoring synovitis, tenosynovitis and erosions in rheumatoid arthritis when using standardised scoring systems

On the Spectrophotometric determination of dissolved silica in natural waters

The precision and accuracy of methods for the determination of dissolved silica in natural waters can be greatly improved by taking account of the time courses of some of the reactions involved. The kinetics of these reactions are dependent on the concentrations of electrolytes present in the samples. Based on results from a metol-sulfite reduction method, the molar absorptivity of a reduced mixture of the α-and β-isomers of molybdosilicic acid in sea water is apparently affected only by the ionic strength but not by the nature of the component salts of the solution. © 1973, American Chemical Society. All rights reserved