Toxicity Assessment of an Anti-Cancer Drug of p-Toluene Sulfonamide in Zebrafish Larvae Based on Cardiovascular and Locomotion Activities.

p-Toluene sulfonamide (p-TSA), a small molecular drug with antineoplastic activity is widely gaining interest from researchers because of its pharmacological activities. In this study, we explored the potential cardio and neural toxicity of p-TSA in sublethal concentrations by using zebrafish as an in vivo animal model. Based on the acute toxicity assay, the 96hr LC50 was estimated as 204.3 ppm, suggesting the overall toxicity of p-TSA is relatively low in zebrafish larvae. For the cardiotoxicity test, we found that p-TSA caused only a minor alteration in treated larvae after no overall significant alterations were observed in cardiac rhythm and cardiac physiology parameters, as supported by the results from expression level measurements of several cardiac development marker genes. On the other hand, we found that acute p-TSA exposure significantly increased the larval locomotion activity during the photomotor test while prolonged exposure (4 days) reduced the locomotor startle reflex activities in zebrafish. In addition, a higher respiratory rate and blood flow velocity was also observed in the acutely treated fish groups compared to the untreated group. Finally, by molecular docking, we found that p-TSA has a moderate binding affinity to skeletal muscle myosin II subfragment 1 (S1), ATPase activity, actin- and Ca2+-stimulated myosin S1 ATPase, and v-type proton ATPase. These binding interactions between p-TSA and proteins offer insights into the potential molecular mechanism of action of p-TSA on observed altered responses toward photo and vibration stimuli and minor altered vascular performance in the zebrafish larvae.

An optical detection module-based biosensor using fortified bacterial beads for soil toxicity assessment.

An optical biosensor module for soil contamination assessment is presented, employing bioluminescent bacterial bioreporters encapsulated in poly-dopamine (PD)-coated alginate microbeads. The PD-coated beads displayed improved mechanical strength and stability, but somewhat delayed responses to the inducing toxicant. Using toluene as a model soil contaminant, two bioluminescent reporter strains were employed for its detection in the ambient light-blocking, temperature-controlled biosensor module. Bioluminescence of strain TV1061 (harboring an inducible grpE::luxCDABE fusion) increased and that of strain GC2 (harboring a constitutive lac::luxCDABE fusion) decreased in the presence of increasing toluene concentrations. In the former case, a maximal effect was observed in the presence of 1% toluene. This simple optical detection biosensor module may potentially be utilized for monitoring soil contamination from areas suspected of chemical pollution such petrochemical industrial zones or petrol stations.

Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo.

Accurately predicting protein-ligand binding affinities and binding modes is a major goal in computational chemistry, but even the prediction of ligand binding modes in proteins poses major challenges. Here, we focus on solving the binding mode prediction problem for rigid fragments. That is, we focus on computing the dominant placement, conformation, and orientations of a relatively rigid, fragment-like ligand in a receptor, and the populations of the multiple binding modes which may be relevant. This problem is important in its own right, but is even more timely given the recent success of alchemical free energy calculations. Alchemical calculations are increasingly used to predict binding free energies of ligands to receptors. However, the accuracy of these calculations is dependent on proper sampling of the relevant ligand binding modes. Unfortunately, ligand binding modes may often be uncertain, hard to predict, and/or slow to interconvert on simulation time scales, so proper sampling with current techniques can require prohibitively long simulations. We need new methods which dramatically improve sampling of ligand binding modes. Here, we develop and apply a nonequilibrium candidate Monte Carlo (NCMC) method to improve sampling of ligand binding modes. In this technique, the ligand is rotated and subsequently allowed to relax in its new position through alchemical perturbation before accepting or rejecting the rotation and relaxation as a nonequilibrium Monte Carlo move. When applied to a T4 lysozyme model binding system, this NCMC method shows over 2 orders of magnitude improvement in binding mode sampling efficiency compared to a brute force molecular dynamics simulation. This is a first step toward applying this methodology to pharmaceutically relevant binding of fragments and, eventually, drug-like molecules. We are making this approach available via our new Binding modes of ligands using enhanced sampling (BLUES) package which is freely available on GitHub.

Bioelectrochemical BTEX removal at different voltages: assessment of the degradation and characterization of the microbial communities.

BTEX compounds (Benzene, Toluene, Ethylbenzene and Xylenes) are toxic hydrocarbons that can be found in groundwater due to accidental spills. Bioelectrochemical systems (BES) are an innovative technology to stimulate the anaerobic degradation of hydrocarbons. In this work, single chamber BESs were used to assess the degradation of a BTEX mixture at different applied voltages (0.8V, 1.0V, 1.2V) between the electrodes. Hydrocarbon degradation was linked to current production and to sulfate reduction, at all the tested potentials. The highest current densities (about 200mA/m2 with a maximum peak at 480mA/m2) were observed when 0.8V were applied. The application of an external voltage increased the removal of toluene, m-xylene and p-xylene. The highest removal rate constants at 0.8V were: 0.4±0.1days-1, 0.34±0.09days-1 and 0.16±0.02days-1, respectively. At the end of the experiment, the microbial communities were characterized by high throughput sequencing of the 16S rRNA gene. Microorganisms belonging to the families Desulfobulbaceae, Desulfuromonadaceae and Geobacteraceae were enriched on the anodes suggesting that both direct electron transfer and sulfur cycling occurred. The cathodic communities were dominated by the family Desulfomicrobiaceae that may be involved in hydrogen production.

Proteomic Assessment of the Expression of Genes Related to Toluene Catabolism and Porin Synthesis in Pseudomonas stutzeri ST-9.

The organization and expression of Pseudomonas stutzeri ST-9 genes related to toluene catabolism and porin synthesis was investigated. Toluene-degrading genes were found to be localized in the chromosome close to a phage-type integrase. A regulatory gene and 21 genes related to an aromatics degradation pathway are organized as a putative operon. These proteins are upregulated in the presence of toluene. Fourteen outer membrane proteins were identified as porins in the ST-9 genome. The identified porins showed that the main detected porins are related to the OmpA and OprD superfamilies. The percentage of porins in the outer membrane protein fraction, as determined by mass spectrometry, was 73% and 54% when the cells were cultured with toluene and with glucose, respectively. Upregulation of OmpA and downregulation of OprD occurred in the presence of toluene. A porin fraction (90% OprD) from both cultures was isolated and examined as a toluene uptake system using the liposome-swelling assay. Liposomes were prepared with the porin fraction from a culture that was grown on toluene (T-proteoliposome) or glucose (G-proteoliposome). There was no significant difference in the permeability rate of the different solutes through the T-proteoliposome and the G-proteoliposome.

[Use of comet assay for the risk assessment of oil- and chemical-industry workers]. / Comet assay alkalmazása olaj- és vegyipari exponált dolgozók kockázatbecslésében.

INTRODUCTION: The comet assay is a fluorescent microscopic method that is able to detect DNA strand-breaks even in non-proliferative cells in samples with low cell counts. AIM: The aim of the authors was to measure genotoxic DNA damage and assess oxidative DNA damage caused by occupational exposure in groups exposed to benzene, polycyclic aromatic carbohydrates and styrene at the workplace in order to clarify whether the comet assay can be used as an effect marker tool in genotoxicology monitoring. METHOD: In addition to the basic steps of the comet assay, one sample was treated with formamido-pirimidine-DNA-glycolase restriction-enzyme that measures oxidative DNA damage. RESULTS: An increase was observed in tail moments in each group of untreated and Fpg-treated samples compared to the control. CONCLUSIONS: It can be concluded that occupational exposure can be detected with the method. The comet assay may prove to be an excellent effect marker and a supplementary technique for monitoring the presence or absence of genotoxic effects.

Model selection for microbial nutrient uptake using a cost-benefit approach.

We consider the uptake of various carbon sources by microorganisms based on four fundamental assumptions: (1) the uptake of nutrient follows a saturation characteristics (2) substrate processing has a benefit but comes at costs of maintaining the process chain (3) substrate uptake is controlled and (4) evolution optimized the control of substrate uptake. These assumptions result in relatively simple mathematical models. In case of two substrates, our main finding is the following: Depending on the overall topology of the metabolic pathway, three different behavioral patterns can be identified. (1) both substrates are consumed at a time, (2) one substrate is preferred and represses the uptake of the other (catabolite repression), or (3) a cell feeds exclusively on one or the other substrate, possibly leading to a population that splits in two sub-populations, each of them specialized on one substrate only. Batch-culture and retentostat data of toluene, benzoate, and acetate uptake by Geobacter metallireducens are used to demonstrate that the model structure is suited for a quantitative description of uptake dynamics.

Assessment of volatile organic compound removal by indoor plants--a novel experimental setup.

Indoor plants can remove volatile organic compounds (VOCs) from the air. The majority of knowledge comes from laboratory studies where results cannot directly be transferred to real-life settings. The aim of this study was to develop an experimental test system to assess VOC removal by indoor plants which allows for an improved real-life simulation. Parameters such as relative humidity, air exchange rate and VOC concentration are controlled and can be varied to simulate different real-life settings. For example, toluene diffusion through a needle gave concentrations in the range of 0.10-2.35 µg/L with deviations from theoretical values of 3.2-10.5%. Overall, the system proved to be functional for the assessment of VOC removal by indoor plants with Hedera helix reaching a toluene removal rate of up to 66.5 µg/m(2)/h. The mode of toluene exposure (semi-dynamic or dynamic) had a significant influence on the removal rate obtained by H. helix.

Assessment of anaerobic toluene biodegradation activity by bssA transcript/gene ratios.

Benzylsuccinate synthase (bssA) genes associated with toluene degradation were profiled across a groundwater contaminant plume under nitrate-reducing conditions and were detected in significant numbers throughout the plume. However, differences between groundwater and core sediment samples suggested that microbial transport, rather than local activity, was the underlying cause of the high copy numbers within the downgradient plume. Both gene transcript and reactant concentrations were consistent with this hypothesis. Expression of bssA genes from denitrifying toluene degraders was induced by toluene but only in the presence of nitrate, and transcript abundance dropped rapidly following the removal of either toluene or nitrate. The drop in bssA transcripts following the removal of toluene could be described by an exponential decay function with a half-life on the order of 1 h. Interestingly, bssA transcripts never disappeared completely but were always detected at some level if either inducer was present. Therefore, the detection of transcripts alone may not be sufficient evidence for contaminant degradation. To avoid mistakenly associating basal-level gene expression with actively degrading microbial populations, an integrated approach using the ratio of functional gene transcripts to gene copies is recommended. This approach minimizes the impact of microbial transport on activity assessment and allows reliable assessments of microbial activity to be obtained from water samples.

Assessment of potential anaerobic biotransformation of organic pollutants in sediment caps.

In situ capping is a remedial approach for reducing the risk of biota exposure to sediment contaminants. Biotransformation of contaminants in sand-based sediment caps, rarely considered in sediment cap design, could further reduce the exposure risk. The anaerobic biotransformation of benzene, toluene, ethylbenzene, xylenes (BTEX), monochlorobenzene, dichlorobenzenes and naphthalene was evaluated with sediments from Onondaga Lake in dilute sediment slurries and in sand-capped sediment laboratory-scale columns. The percentage of sediment samples demonstrating biotransformation under anaerobic conditions in slurries incubated at 12°C was greatest for BTEX, followed by monochlorobenzene, 1,4-dichlorobenzene, 1,2-dichlorobenzene and 1,3-dichlorobenzene. Only toluene biotransformation was observed in sand cap columns. The rate of toluene biotransformation diminished over time, which might be due to inhibition caused by hydrogen from the experimental setup. Results suggest potential for the biotransformation of toluene, and possibly other pollutants, in sand-based sediment caps under anaerobic conditions at low temperatures.

A mechanistic modeling framework for predicting metabolic interactions in complex mixtures.

BACKGROUND: Computational modeling of the absorption, distribution, metabolism, and excretion of chemicals is now theoretically able to describe metabolic interactions in realistic mixtures of tens to hundreds of substances. That framework awaits validation. OBJECTIVES: Our objectives were to a) evaluate the conditions of application of such a framework, b) confront the predictions of a physiologically integrated model of benzene, toluene, ethylbenzene, and m-xylene (BTEX) interactions with observed kinetics data on these substances in mixtures and, c) assess whether improving the mechanistic description has the potential to lead to better predictions of interactions. METHODS: We developed three joint models of BTEX toxicokinetics and metabolism and calibrated them using Markov chain Monte Carlo simulations and single-substance exposure data. We then checked their predictive capabilities for metabolic interactions by comparison with mixture kinetic data. RESULTS: The simplest joint model (BTEX interacting competitively for cytochrome P450 2E1 access) gives qualitatively correct and quantitatively acceptable predictions (with at most 50% deviations from the data). More complex models with two pathways or back-competition with metabolites have the potential to further improve predictions for BTEX mixtures. CONCLUSIONS: A systems biology approach to large-scale prediction of metabolic interactions is advantageous on several counts and technically feasible. However, ways to obtain the required parameters need to be further explored.

Assessment of toluene/biphenyl dioxygenase gene diversity in benzene-polluted soils: links between benzene biodegradation and genes similar to those encoding isopropylbenzene dioxygenases.

The PCR-single-strand conformation polymorphism (SSCP) technique was used to assess the diversity and distribution of Rieske nonheme iron oxygenases of the toluene/biphenyl subfamily in soil DNA and bacterial isolates recovered from sites contaminated with benzene, toluene, ethylbenzene, and xylenes (BTEX). The central cores of genes encoding the catalytic alpha subunits were targeted, since they are responsible for the substrate specificities of these enzymes. SSCP functional genotype fingerprinting revealed a substantial diversity of oxygenase genes in three differently BTEX-contaminated soil samples, and sequence analysis indicated that in both the soil DNA and the bacterial isolates, genes for oxygenases related to the isopropylbenzene (cumene) dioxygenase branch of the toluene/biphenyl oxygenase subfamily were predominant among the detectable genotypes. The peptide sequences of the two most abundant alpha subunit sequence types differed by only five amino acids (residues 258, 286, 288, 289, and 321 according to numbering in cumene dioxygenase alpha subunit CumA1 of Pseudomonas fluorescens IP01). However, a strong correlation between sequence type and substrate utilization pattern was observed in isolates harboring these genes. Two of these residues were located at positions contributing, according to the resolved crystal structure of cumene dioxygenase from Pseudomonas fluorescens IP01, to the inner surface of the substrate-binding pocket. Isolates containing an alpha subunit with isoleucine and leucine at positions 288 and 321, respectively, were capable of degrading benzene and toluene, whereas isolates containing two methionine substitutions were found to be incapable of degrading toluene, indicating that the more bulky methionine residues significantly narrowed the available space within the substrate-binding pocket.

Prediction of the adaptability of Pseudomonas putida DOT-T1E to a second phase of a solvent for economically sound two-phase biotransformations.

The strain Pseudomonas putida DOT-T1E was tested for its ability to tolerate second phases of different alkanols for their use as solvents in two-liquid-phase biotransformations. Although 1-decanol showed an about 10-fold higher toxicity to the cells than 1-octanol, the cells were able to adapt completely to 1-decanol only and could not be adapted in order to grow stably in the presence of a second phase of 1-octanol. The main explanation for this observation can be seen in the higher water and membrane solubility of 1-octanol. The hydrophobicity (log P) of a substance correlates with a certain partitioning of that compound into the membrane. Combining the log P value with the water solubility, the maximum membrane concentration of a compound can be calculated. With this simple calculation, it is possible to predict the property of an organic chemical for its potential applicability as a solvent for two-liquid-phase biotransformations with solvent-tolerant P. putida strains. Only compounds that show a maximum membrane concentration of less than 400 mM, such as 1-decanol, seem to be tolerated by these bacterial strains when applied in supersaturating concentrations to the medium. Taking into consideration that a solvent for a two-liquid-phase system should possess partitioning properties for potential substrates and products of a fine chemical synthesis, it can be seen that 1-decanol is a suitable solvent for such biotransformation processes. This was also demonstrated in shake cultures, where increasing amounts of a second phase of 1-decanol led to bacteria tolerating higher concentrations of the model substrate 3-nitrotoluene. Transferring this example to a 5-liter-scale bioreactor with 10% (vol/vol) 1-decanol, the amount of 3-nitrotoluene tolerated by the cells is up to 200-fold higher than in pure aqueous medium. The system demonstrates the usefulness of two-phase biotransformations utilizing solvent-tolerant bacteria.

In situ assessment of biodegradation potential using biotraps amended with 13C-labeled benzene or toluene.

Stable isotope fractionation analysis of an aquifer heavily contaminated with benzene (up to 850 mg L(-1)) and toluene (up to 50 mg L(-1)) at a former hydrogenation plant in Zeitz (Saxonia, Germany) has suggested that significant biodegradation of toluene was occurring. However, clear evidence of benzene biodegradation has been lacking at this site. Determining the fate of benzene is often a determining factor in regulatory approval of a risk-based management strategy. The objective of the work described here was the demonstration of a new tool that can be used to provide proof of biodegradation of benzene or other organics by indigenous microorganisms under actual aquifer conditions. Unique in situ biotraps containing Bio-Sep beads, amended with 13C-labeled or 12C nonlabeled benzene and toluene, were deployed at the Zeitz site for 32 days in an existing groundwater monitoring well and used to collect and enrich microbial biofilms. Lipid biomarkers or remaining substrate was extracted from the beads and analyzed by mass spectrometry and molecular methods. Isotopic analysis of the remaining amounts of 13C-labeled contaminants (about 15-18% of the initial loading) showed no alteration of the 12C/13C ratio during incubation. Therefore, no measurable exchange of labeled compounds in the beads by the nonlabeled compounds in the aquifer materials occurred. Isotopic ratio analysis of microbial lipid fatty acids (as methyl ester derivatives) from labeled benzene- and toluene-amended biotraps showed 13C enrichment in several fatty acids of up to delta (13C) 13400%o, clearly verifying benzene and toluene biodegradation and the transformation of the labeled carbon into biomass by indigenous organisms under aquifer conditions. Fatty acid profiles of total lipid fatty acids and the phospholipid fatty acid fraction and their isotopic composition showed significant differences between benzene- and toluene-amended biotraps, suggesting that different microbial communities were involved in the biodegradation of the two compounds.

Assessment of microbial natural attenuation in groundwater polluted with gasworks residues.

Intrinsic biodegradation, representing the key process in Natural Attenuation, was examined at a tar-oil polluted disposal site. Methods to assess microbial natural attenuation of BTEX and PAH included analysis of groundwater hydrochemistry, pollutant profiles, composition of the microflora, and microcosm studies. In the polluted groundwater downgradient the disposal site, oxygen and nitrate were only available adjacent to the groundwater table and at the plume fringes. In the anaerobic core of the plume, a sequence of predominating redox zones (methanogenic, sulphate-reducing, Fe(III)-reducing) was observed. Changing pollutant profiles in the plume indicated active biodegradation processes, e.g. biodegradation of toluene and naphthalene in the anaerobic zones. High numbers of microorganisms capable of growing under anaerobic conditions and of aerobic pollutant degrading organisms confirmed the impact of biodegradation at this site. In microcosm studies, the autochthonous microflora utilised toluene, ethylbenzene, and naphthalene under sulfate- and Fe(III)-reducing conditions. Additionally, benzene and phenanthrene were degraded in the presence of Fe(III). Under aerobic conditions, all BTEX and PAH were rapidly degraded. The microcosm studies in particular were suitable to examine the role of specific electron acceptors, and represented an important component of the multiple line of evidence concept to assess natural attenuation.

Biofilters based on the action of fungi.

Traditional biofilters for waste gas treatment are mainly based on the degradation activity of bacteria. The application of fungi in biofilters has several advantages: fungi are more resistant to acidification and drying out, and the aerial mycelia of fungi form a larger surface area in the gas phase than bacterial biofilms, which may facilitate the uptake of hydrophobic volatile compounds. The research described here identifies important conditions for the operation of fungal-based biofilters. Biofilters with perlite packing were operated at different pHs and relative inlet gas humidities. Toluene was used as a model pollutant. It was shown that a low pH is a prerequisite for fungal growth in biofilters. Also, the fungal biofilters were more resistant to drying out and more active than the bacterial biofilters. Fungal biofilters eliminated 80-125 g toluene/m3 filterbed/h. Several measures that could limit the clogging of fungal biofilters with fungal biomass were investigated. The introduction of mites helped to control excessive fungal growth and pressure drop. The pressure drop of a perlite/fungi/mites filter of 1 m height, loaded with 200 m3 gas/m3 filter/h stabilised around 130 Pa. Biofilters based on the action of fungi are cost-effective for the treatment of waste gases containing aromatic compounds, alkenes and other hydrophobic compounds.

Assessment of the biodegradation potential of psychrotrophic microorganisms.

Bioremediation of polluted temperate and cold temperature environments may require the activity of psychrotrophic bacteria, because their low temperature growth range parallels the ambient temperatures encountered in these environments. In the present study, 135 psychrotrophic microorganisms isolated from a variety of ecosystems in Canada were examined for their ability to mineralize 14C-labelled toluene, naphthalene, dodecane, hexadecane, 2-chlorobiphenyl, and pentachlorophenol. A number of the psychrotrophic strains mineralized toluene, naphthalene, dodecane, and hexadecane. None of the psychrotrophs were capable of mineralizing 2-chlorobiphenyl or pentachlorophenol. Those strains demonstrating mineralization activity were subsequently screened by the polymerase chain reaction (PCR) and Southern hybridization of PCR products for the presence of catabolic genes (alkB, ndoB, todCl, and xylE) involved in known bacterial biodegradative pathways for these compounds. Some of the psychrotrophs able to mineralize toluene and naphthalene possessed catabolic genes that hybridized to xylE or todCl, and ndoB, respectively. The alkB PCR fragments obtained from the strains that mineralized dodecane and hexadecane did not hybridize to an alkB gene probe derived from Pseudomonas oleovorans. Psychrotrophic strain Q15, identified as a Rhodococcus sp., also mineralized the C28 n-paraffin octacosane. A gene probe constructed from the "alkB" PCR fragment from strain Q15 did hybridize with the alkB PCR fragments from most of the psychrotrophic alkane biodegraders, indicating that the alkB primers may be amplifying another gene(s), perhaps with low homology to P. oleovorans alkB, which may be involved in the biodegradation of both short chain (dodecane) and longer chain alkanes (hexadecane, octacosane). All of the psychrotrophic biodegradative isolates examined were capable of mineralization activity at both 23 and 5 degrees C, indicating their potential for low temperature bioremediation of petroleum hydrocarbon contaminated sites.

Immunochemical assessment of the influence of nutritional, physiological and environmental factors on the metabolism of toluene.

Factors influencing the metabolism of toluene were investigated in rats using monoclonal antibody (MAb) to cytochrome P450 (P450). At low toluene concentrations, P450 IIE1 was primarily involved in the metabolism of toluene, whereas P450 IIC11/6 was involved at high concentrations. A low-carbohydrate diet induced P450 IIE1 and resulted in an increase in toluene metabolism. The intake of fat did not influence the metabolism. A lowered protein intake decreased not only the total content of P450 but also the P450 IIC11/6. Fasting and ethanol consumption also enhanced toluene metabolism via the induction of P450 IIE1. The metabolic rate of toluene in adult male rats was 4-fold higher than in immature males and adult females at a high substrate concentration because of the high level of P450 IIC11/6 in adult males, whereas no difference was noted between adult and immature females. Although development did not influence toluene metabolism in males at a low substrate concentration, the metabolic rate in adult female rats was significantly lower than that of immature females and males; this may be due to the decrease in P450 IE1 with development. Diabetic status influenced toluene metabolism in rats by affecting several kinds of P450 isozymes. Toluene exposure also affected its own metabolism by increasing P450 IIE1 and P450 IIB 1/2, and decreasing P450 IIC11/6. A significant difference in toluene metabolism was observed among rat, mouse and human liver microsomes. Thus, when considering the factors affecting toluene metabolism, it is important to elucidate the change in specific P450 isozyme composition related to the modifications, and their affinities to toluene.