Biomedical subjects

D R Noguera

Publications and source records attributed to D R Noguera.

10 recordsLinked to original sources

PubMed2004

Introduction to the IWA task group on biofilm modeling.

An International Water Association (IWA) Task Group on Biofilm Modeling was created with the purpose of comparatively evaluating different biofilm modeling approaches. The task group developed three benchmark problems for this comparison, and used a diversity of modeling techniques that included analytical, pseudo-analytical, and numerical solutions to the biofilm problems. Models in one, two, and three dimensional domains were also compared. The first benchmark problem (BM1) described a monospecies biofilm growing in a completely mixed reactor environment and had the purpose of comparing the ability of the models to predict substrate fluxes and concentrations for a biofilm system of fixed total biomass and fixed biomass density. The second problem (BM2) represented a situation in which substrate mass transport by convection was influenced by the hydrodynamic conditions of the liquid in contact with the biofilm. The third problem (BM3) was designed to compare the ability of the models to simulate multispecies and multisubstrate biofilms. These three benchmark problems allowed identification of the specific advantages and disadvantages of each modeling approach. A detailed presentation of the comparative analyses for each problem is provided elsewhere in these proceedings.

Bacteria↗

PubMed2004

Comparing biofilm models for a single species biofilm system.

A benchmark problem was defined to evaluate the performance of different mathematical biofilm models. The biofilm consisted of heterotrophic bacteria degrading organic substrate and oxygen. Mathematical models tested ranged from simple analytical to multidimensional numerical models. For simple and more or less flat biofilms it was shown that analytical biofilm models provide very similar results compared to more complex numerical solutions. When considering a heterogeneous biofilm morphology it was shown that the effect of an increased external mass transfer resistance was much more significant compared to the effect of an increased surface area inside the biofilm.

Bacteria↗

PubMed2004

Modelling a spatially heterogeneous biofilm and the bulk fluid: selected results from benchmark problem 2 (BM2).

The numerical simulation of mass transfer and conversion in spatially heterogeneous biofilms on the meso-scale requires an accurate description of the hydrodynamics in the biofilm systems and of spatial effects. This leads to systems of three-dimensional nonlinear partial differential equations that are numerically very expensive to solve and to data requirements that are not easy to meet. In this paper several modeling approaches to reduce the physical complexity and, hence, accelerate the computation are compared. They range from a mere reduction of dimensionality by lumping the problem along a secondary flow direction to global mass balances or empirical correlations, at the core of which a one-dimensional boundary value problem must be solved. It is found that even strongly simplified models can describe the qualitative behaviour of the model with regard to variations in the geometrical and hydrodynamic model parameters quite well. In order to obtain also quantitatively reliable results the hydrodynamics must be considered in an appropriate manner.

Bacteria↗

PubMed2004

Results from the multi-species benchmark problem 3 (BM3) using two-dimensional models.

In addition to the one-dimensional solutions of a multi-species benchmark problem (BM3) presented earlier (Rittmann et al., 2004), we offer solutions using two-dimensional (2-D) models. Both 2-D models (called here DN and CP) used numerical solutions to BM3 based on a similar mathematical framework of the one-dimensional AQUASIM-built models submitted by Wanner (model W) and Morgenroth (model M1), described in detail elsewhere (Rittmann et al., 2004). The CP model used differential equations to simulate substrate gradients and biomass growth and a particle-based approach to describe biomass division and biofilm growth. The DN model simulated substrate and biomass using a cellular automaton approach. For several conditions stipulated in BM3, the multidimensional models provided very similar results to the 1-D models in terms of bulk substrate concentrations and fluxes into the biofilm. The similarity can be attributed to the definition of BM3, which restricted the problem to a flat biofilm in contact with a completely mixed liquid phase, and therefore, without any salient characteristics to be captured in a multidimensional domain. On the other hand, the models predicted significantly different accumulations of the different types of biomass, likely reflecting differences in the way biomass spread within the biofilm is simulated.

Bacteria↗

PubMed2003

Simultaneous determination of bacterial viability and identity in biofilms using ethidium monoazide and fluorescent in situ hybridization.

A protocol for simultaneously interrogating bacterial viability and identity using in situ, culture-independent methods is described. Viability is assayed using ethidium monoazide (EMA) staining of cells with compromised membranes, and identity is determined using fluorescent in situ hybridization (FISH). Experiments with planktonic cultures were used to demonstrate the compatibility of EMA staining and FISH after covalently bonding EMA to nucleic acids by photoreaction. Applications to biofilm samples showed that diffusion limitations in the biofilm matrix were not problematic and that effective discrimination of viable target cells within a mixed microbial community was possible.

Affinity Labels↗

PubMed2002

Presence of Rhodocyclus in a full-scale wastewater treatment plant and their participation in enhanced biological phosphorus removal.

The objective of this research was to assess the relevance of organisms related to Rhodocyclus in enhanced biological phosphorus removal in full-scale wastewater treatment plants. The presence of these organisms in full-scale plants was first confirmed by fluorescent in situ hybridization. To address which organisms were involved in phosphorus removal, a method was developed which selected polyphosphate-accumulating organisms from activated sludge samples by DAPI staining and flow cytometry. Sorted samples were characterized using fluorescent in situ hybridization. The results of these analyses confirmed the presence of organisms related to Rhodocyclus in full-scale wastewater treatment plants and supported the involvement of these organisms in enhanced biological phosphorus removal. However, a significant fraction of the polyphosphate-accumulating organisms were not related to Rhodocyclus.

Bioreactors↗

PubMed2002

Molecular analysis of ammonia-oxidizing bacterial populations in aerated-anoxic orbal processes.

Aerated-anoxic processes operate under the principle that small additions of oxygen to an anoxic reactor induce simultaneous nitrification and denitrification. In these systems, ammonia oxidation in the anoxic zone can easily account for 30-50% of the total nitrification in the reactor, even though the dissolve oxygen concentration is usually below detection limit. To investigate whether the nitrification efficiency in aerated-anoxic processes was due to the presence of specialized ammonia-oxidizing bacteria (AOB), an analysis of the AOB population in an aerated-anoxic Orbal process and a conventional nitrogen removal process was carried out using phylogenetic analyses based on the ammonia monooxygenase A (amoA) gene. Terminal restriction fragment length polymorphism (TRFLP) analyses revealed that Nitrosospira-like organisms were one of the major contributors to ammonia oxidation in a full-scale aerated-anoxic Orbal reactor. However, the relative populations of Nitrosospira-like and Nitrosomonas-like AOB were not constant and appeared to have seasonal variability. Cloning and sequence comparison of amoA gene fragments demonstrated that most of the AOB in the aerated-anoxic Orbal process belonged to the Nitrosospira sp. and Nitrosomonas oligotropha lineages. The abundance of Nitrosospira-like organisms in aerated-anoxic reactors is significant, since this group of AOB has not been usually associated with nitrification in wastewater treatment plants.

Ammonia↗

PubMed2000

Transformation of 2,4,6-trinitrotoluene by purified xenobiotic reductase B from Pseudomonas fluorescens I-C.

The enzymatic transformation of 2,4,6-trinitrotoluene (TNT) by purified XenB, an NADPH-dependent flavoprotein oxidoreductase from Pseudomonas fluorescens I-C, was evaluated by using natural abundance and [U-(14)C]TNT preparations. XenB catalyzed the reduction of TNT either by hydride addition to the aromatic ring or by nitro group reduction, with the accumulation of various tautomers of the protonated dihydride-Meisenheimer complex of TNT, 2-hydroxylamino-4,6-dinitrotoluene, and 4-hydroxylamino-2, 6-dinitrotoluene. Subsequent reactions of these metabolites were nonenzymatic and resulted in predominant formation of at least three dimers with an anionic m/z of 376 as determined by negative-mode electrospray ionization mass spectrometry and the release of approximately 0.5 mol of nitrite per mol of TNT consumed. The extents of the initial enzymatic reactions were similar in the presence and in the absence of O(2), but the dimerization reaction and the release of nitrite were favored under aerobic conditions or under anaerobic conditions in the presence of NADP(+). Reactions of chemically and enzymatically synthesized and high-pressure liquid chromatography-purified TNT metabolites showed that both a hydroxylamino-dinitrotoluene isomer and a tautomer of the protonated dihydride-Meisenheimer complex of TNT were required precursors for the dimerization and nitrite release reactions. The m/z 376 dimers also reacted with either dansyl chloride or N-1-naphthylethylenediamine HCl, providing evidence for an aryl amine functional group. In combination, the experimental results are consistent with assigning the chemical structures of the m/z 376 species to various isomers of amino-dimethyl-tetranitrobiphenyl. A mechanism for the formation of these proposed TNT metabolites is presented, and the potential enzymatic and environmental significance of their formation is discussed.

Anaerobiosis↗

PubMed1996

Reduction and Acetylation of 2,4-Dinitrotoluene by a Pseudomonas aeruginosa Strain.

Aerobic and anoxic biotransformation of 2,4-dinitrotoluene (DNT) was examined by using a Pseudomonas aeruginosa strain isolated from a plant treating propellant manufacturing wastewater. DNT biotransformation in the presence and absence of oxygen was mostly reductive and was representative of the type of cometabolic transformations that occur when a high concentration of an easily degradable carbon source is present. P. aeruginosa reduced both nitro groups on DNT, with the formation of mainly 4-amino-2-nitrotoluene and 2-amino-4-nitrotoluene and small quantities of 2,4-diaminotoluene. Acetylation of the arylamines was a significant reaction. 4-Acetamide-2-nitrotoluene and the novel compounds 2-acetamide-4-nitrotoluene, 4-acetamide-2-aminotoluene, and 2,4-diacetamidetoluene were identified as DNT metabolites. The biotransformation of 2,4-diaminotoluene to 4-acetamide-2-aminotoluene was 24 times faster than abiotic transformation. 2-Nitrotoluene and 4-nitrotoluene were also reduced to their corresponding toluidines and then acetylated. However, the yield of 4-acetamidetoluene was much higher than that of 2-acetamidetoluene, demonstrating that acetylation at the position para to the methyl group was favored.

Journal Article↗

PubMed1994

Quantification of methanogenic groups in anaerobic biological reactors by oligonucleotide probe hybridization.

The microbial community structure of anaerobic biological reactors was evaluated by using oligonucleotide probes complementary to conserved tracts of the 16S rRNAs of phylogenetically defined groups of methanogens. Phylogenetically defined groups of methanogens were quantified and visualized, respectively, by hybridization of 32P- and fluorescent-dye-labeled probes to the 16S rRNAs from samples taken from laboratory acetate-fed chemostats, laboratory municipal solid waste digestors, and full-scale sewage sludge digestors. Methanosarcina species, members of the order Methanobacteriales, and Methanosaeta species were the most abundant methanogens present in the chemostats, the solid-waste digestors, and the sewage sludge digestors, respectively.

Anaerobiosis↗