243 research outputs found
Conservation of Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 and rejection of Rhodococcus hoagii (Morse 1912) KĂ€mpfer et al. 2014
Characterization and Phylogeny of the pfp Gene of Amycolatopsis methanolica Encoding PPi-Dependent Phosphofructokinase
Characterization and Phylogeny of the pfp Gene of Amycolatopsis methanolica Encoding PPi-Dependent Phosphofructokinase
Mining Explainable Predictive Features for Water Quality Management
With water quality management processes, identifying and interpreting
relationships between features, such as location and weather variable tuples,
and water quality variables, such as levels of bacteria, is key to gaining
insights and identifying areas where interventions should be made. There is a
need for a search process to identify the locations and types of phenomena that
are influencing water quality and a need to explain how the quality is being
affected and which factors are most relevant. This paper addresses both of
these issues. A process is developed for collecting data for features that
represent a variety of variables over a spatial region and which are used for
training models and inference. An analysis of the performance of the features
is undertaken using the models and Shapley values. Shapley values originated in
cooperative game theory and can be used to aid in the interpretation of machine
learning results. Evaluations are performed using several machine learning
algorithms and water quality data from the Dublin Grand Canal basin
Demethylation of dimethylsulfoniopropionate to 3-S-methylmercaptopropionate by marine sulfate-reducing bacteria
Demethylation of dimethylsulfoniopropionate to 3-S-methylmercaptopropionate by marine sulfate-reducing bacteria
The initial step in the anaerobic degradation of the algal osmolyte dimethylsulfoniopropionate (DMSP) in anoxic marine sediments involves either a cleavage to dimethylsulfide and acrylate or a demethylation to 3-S-methylmercaptopropionate. Thus far, only one anaerobic bacterial strain has been shown to carry out the demethylation, namely, Desulfobacterium sp. strain PM4, The aims of the present work were to study how common this property is among certain groups of anaerobic bacteria and to obtain information on the affinities for DMSP of DMSP-demethylating strains, Screening of several pure cultures of sulfate-reducing and acetogenic bacteria showed that Desulfobacterinm vacuolatum DSM 3385 and Desulfobacterium niacini DSM 2059 are also able to demethylate DMSP; a very slow demethylation of DMSP was observed with a salt-tolerant strain of Eubacterium limosum. From a 10(5) dilution of intertidal sediment a new marine DMSP-demethylating sulfate-reducing bacterium (strain WN) was isolated, Strain WN was a short, gram-negative, nonmotile rod that grew on betaine, sarcosine, palmitate, H-2 plus CO2, and several alcohols, organic acids, and amino acids, Extracts of betaine-grown cells had hydrogenase, formate dehydrogenase, and CO dehydrogenase activities but no alpha-ketoglutarate oxidoreductase activity, indicating the presence of the acetyl coenzyme A-CO dehydrogenase pathway, Analysis of the 16S rRNA gene sequence of strain WN revealed a close relationship with Desulfobacter hydrogenophilus, Desulfobacter latus, and Desulfobacula toluolica. Strain PM4 was shown to group with Desulfobacterium niacini, The K-m of strain WN for DMSP, as derived from substrate progress curves in cell suspensions, was approximately 10 mu M. A similar value was found for D. niacini PM4.</p
Implementation and integration of microbial source tracking in a river watershed monitoring plan
Fecal pollution of water bodies poses a serious threat for public health and ecosystems. Microbial source tracking (MST) is used to track the source of this pollution facilitating better management of pollution at the source. In this study we tested 12 MST markers to track human, ruminant, sheep, horse, pig and gull pollution to assess their usefulness as an effective management tool of water quality. First, the potential of the selected markers to track the source was evaluated using fresh fecal samples. Subsequently, we evaluated their performance in a catchment with different impacts, considering land use and environmental conditions. All MST markers showed high sensitivity and specificity, although none achieved 100% for both. Although some of the MST markers were detected in hosts other than the intended ones, their abundance in the target group was always several orders of magnitude higher than in the non-target hosts, demonstrating their suitability to distinguish between sources of pollution. The MST analysis matched the land use in the watershed allowing an accurate assessment of the main sources of pollution, in this case mainly human and ruminant pollution. Correlating environmental parameters including temperature and rainfall with MST markers provided insight into the dynamics of the pollution in the catchment. The levels of the human marker showed a significant negative correlation with rainfall in human polluted areas suggesting a dilution of the pollution, whereas at agricultural areas the ruminant marker increased with rainfall. There were no seasonal differences in the levels of human marker, indicating human pollution as a constant pressure throughout the year, whereas the levels of the ruminant marker was influenced by the seasons, being more abundant in summer and autumn. MST analysis integrated with land use and environmental data can improve the management of fecal polluted areas and set up best practice
The Use of Transport Time Scales as Indicators of Pollution Persistence in a Macro-Tidal Setting
An understanding of water exchange processes is essential for assessing water quality management issues in coastal bays. This paper evaluates the impact of water exchange processes on pollution persistence in a macro-tidal semi-closed coastal bay through two transport time scales (TTS), namely residence time and exposure time. The numerical model was calibrated against field-measured data for various tidal conditions. Simulated current speeds and directions were shown to agree well with the field data. By considering different release scenarios of a conservative tracer by the refinement of an integrated hydrodynamic and solute transport model (the EFDC), the two TTS were used for interpreting the water exchange processes in a semi-closed system, and for describing the effects of advective and dispersive processes on the transport and fate of pollutants. The results indicate that the magnitudes of river inflows to the bay, tidal ranges, and tracer release times significantly influence the residence and exposure times. Return coefficients were shown to be variable, confirming the different effects of returning water for the different conditions that were studied. For the tested river flow magnitudes and tide conditions, the exposure times were generally higher than the residence times, but particularly so for neap tide conditions. The results, therefore, highlight the risks associated with pollutants leaving a specified domain on an outgoing tide but re-entering on subsequent incoming tides. The spatial distributions of the exposure and residence times across the model domain confirmed that for the case of Dublin Bay, river inputs have a potentially greater impact on water quality on the northern side of the bay
A protein having similarity with methylmalonyl-CoA mutase is required for the assimilation of methanol and ethanol by Methylobacterium extorquens AM1
A 4.0 kb region of Methylobacterium extorquens AM1 DNA which complements three mutants unable to convert acetyl-CoA to glyoxylate (and therefore defective in the assimilation of methanol and ethanol) has been isolated and sequenced. It contains two ORFs and the 3'-end of a third one. The mutations in all three mutants mapped within the first ORF, which was designated meaA; it encodes a protein having similarity with methylmalonyl-CoA mutase. However, methylmalonyl-CoA mutase was measured in extracts of one of the mutants and the specific activity was found to be similar to that in extracts of wild-type cells. Furthermore, although the predicted meaA gene product has the proposed cobalamin-binding site, it does not contain a highly conserved sequence (RIARNT) which is present in all known methylmalonyl-CoA mutases; meaA may therefore encode a novel vitamin-B-12-dependent enzyme. The predicted polypeptide encoded by the second ORF did not have similarity with any known proteins. The partial ORF encoded a protein with similarity with the 3-oxoacyl-[acyl-carrier-protein] reductases; it was not essential for growth on methanol or ethanol
Erratum to: âIntegrated analysis of the local and systemic changes preceding the development of post-partum cytological endometritisâ
ErratumErratum to: âIntegrated analysis of the local and systemic changes preceding the development of post-partum cytological endometritisâ -http://hdl.handle.net/11019/90
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