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1.
Organohalide respiratory chains: composition, topology and key enzymes.
Schubert, T, Adrian, L, Sawers, RG, Diekert, G
FEMS microbiology ecology. 2018;(4)
Abstract
The utilization of halogenated organic compounds as terminal electron acceptors separates the phylogenetically diverse organohalide-respiring bacteria from other respiratory anaerobes that predominantly use nitrate, fumarate, sulfate or oxidized metals. Organohalide respiration is unique in recruiting a cobamide-containing iron-sulfur protein, the extracellular membrane-bound reductive dehalogenase, as terminal reductase in the electron transfer chain. In recent years substantial contributions have been made to the understanding of how electron transfer paths couple mechanistically to chemiosmosis in the organohalide-respiring bacteria. The structural analysis of a respiratory and a non-respiratory reductive dehalogenase revealed the intramolecular electron transfer via two cubane iron-sulfur clusters to the cobamide at the active site. Based on whether quinones are involved, two types of intermolecular electron transfer chains have been identified, which differ in their composition and mode of proton translocation. Indeed, various respiratory chain architectures have been unraveled and evidence for different putative coupling mechanisms presented. The identification of a multienzyme respiratory complex that combines uptake hydrogenase, a complex iron-sulfur molybdoenzyme and a reductive dehalogenase in Dehalococcoides mccartyi strain CBDB1 has raised new questions regarding the mode of energy conservation in these enigmatic microbes. In this mini-review, we highlight these findings and provide an outlook on potential future developments.
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2.
A review of measured bioaccumulation data on terrestrial plants for organic chemicals: Metrics, variability, and the need for standardized measurement protocols.
Doucette, WJ, Shunthirasingham, C, Dettenmaier, EM, Zaleski, RT, Fantke, P, Arnot, JA
Environmental toxicology and chemistry. 2018;(1):21-33
Abstract
Quantifying the transfer of organic chemicals from the environment into terrestrial plants is essential for assessing human and ecological risks, using plants as environmental contamination biomonitors, and predicting phytoremediation effectiveness. Experimental data describing chemical uptake by plants are often expressed as ratios of chemical concentrations in the plant compartments of interest (e.g., leaves, shoots, roots, xylem sap) to those in the exposure medium (e.g., soil, soil porewater, hydroponic solution, air). These ratios are generally referred to as "bioconcentration factors" but have also been named for the specific plant compartment sampled, such as "root concentration factors," "leaf concentration factors," or "transpiration stream (xylem sap) concentrations factors." We reviewed over 350 articles to develop a database with 7049 entries of measured bioaccumulation data for 310 organic chemicals and 112 terrestrial plant species. Various experimental approaches have been used; therefore, interstudy comparisons and data-quality evaluations are difficult. Key exposure and plant growth conditions were often missing, and units were often unclear or not reported. The lack of comparable high-confidence data also limits model evaluation and development. Standard test protocols or, at a minimum, standard reporting guidelines for the measurement of plant uptake data are recommended to generate comparable, high-quality data that will improve mechanistic understanding of organic chemical uptake by plants. Environ Toxicol Chem 2018;37:21-33. © 2017 SETAC.
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3.
Effect of Organic Solvents on Microalgae Growth, Metabolism and Industrial Bioproduct Extraction: A Review.
Miazek, K, Kratky, L, Sulc, R, Jirout, T, Aguedo, M, Richel, A, Goffin, D
International journal of molecular sciences. 2017;(7)
Abstract
In this review, the effect of organic solvents on microalgae cultures from molecular to industrial scale is presented. Traditional organic solvents and solvents of new generation-ionic liquids (ILs), are considered. Alterations in microalgal cell metabolism and synthesis of target products (pigments, proteins, lipids), as a result of exposure to organic solvents, are summarized. Applications of organic solvents as a carbon source for microalgal growth and production of target molecules are discussed. Possible implementation of various industrial effluents containing organic solvents into microalgal cultivation media, is evaluated. The effect of organic solvents on extraction of target compounds from microalgae is also considered. Techniques for lipid and carotenoid extraction from viable microalgal biomass (milking methods) and dead microalgal biomass (classical methods) are depicted. Moreover, the economic survey of lipid and carotenoid extraction from microalgae biomass, by means of different techniques and solvents, is conducted.
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4.
Biotechnological production of aromatic compounds of the extended shikimate pathway from renewable biomass.
Lee, JH, Wendisch, VF
Journal of biotechnology. 2017;:211-221
Abstract
Aromatic chemicals that contain an unsaturated ring with alternating double and single bonds find numerous applications in a wide range of industries, e.g. paper and dye manufacture, as fuel additives, electrical insulation, resins, pharmaceuticals, agrochemicals, in food, feed and cosmetics. Their chemical production is based on petroleum (BTX; benzene, toluene, and xylene), but they can also be obtained from plants by extraction. Due to petroleum depletion, health compliance, or environmental issues such as global warming, the biotechnological production of aromatics from renewable biomass came more and more into focus. Lignin, a complex polymeric aromatic molecule itself, is a natural source of aromatic compounds. Many microorganisms are able to catabolize a plethora of aromatic compounds and interception of these pathways may lead to the biotechnological production of value-added aromatic compounds which will be discussed for Corynebacterium glutamicum. Biosynthesis of aromatic amino acids not only gives rise to l-tryptophan, L-tyrosine and l-phenylalanine, but also to aromatic intermediates such as dehydroshikimate or chorismate from which value-added aromatic compounds can be derived. In this review, we will summarize recent strategies for the biotechnological production of aromatic and related compounds from renewable biomass by Escherichia coli, Pseudomonas putida, C. glutamicum and Saccharomyces cerevisiae. In particular, we will focus on metabolic engineering of the extended shikimate pathway.
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5.
Coupled Valence-Bond State Molecular Dynamics Description of an Enzyme-Catalyzed Reaction in a Non-Aqueous Organic Solvent.
Duboué-Dijon, E, Pluhařová, E, Domin, D, Sen, K, Fogarty, AC, Chéron, N, Laage, D
The journal of physical chemistry. B. 2017;(29):7027-7041
Abstract
Enzymes are widely used in nonaqueous solvents to catalyze non-natural reactions. While experimental measurements showed that the solvent nature has a strong effect on the reaction kinetics, the molecular details of the catalytic mechanism in nonaqueous solvents have remained largely elusive. Here we study the transesterification reaction catalyzed by the paradigm subtilisin Carlsberg serine protease in an organic apolar solvent. The rate-limiting acylation step involves a proton transfer between active-site residues and the nucleophilic attack of the substrate to form a tetrahedral intermediate. We design the first coupled valence-bond state model that simultaneously describes both reactions in the enzymatic active site. We develop a new systematic procedure to parametrize this model on high-level ab initio QM/MM free energy calculations that account for the molecular details of the active site and for both substrate and protein conformational fluctuations. Our calculations show that the reaction energy barrier changes dramatically with the solvent and protein conformational fluctuations. We find that the mechanism of the tetrahedral intermediate formation during the acylation step is similar to that determined under aqueous conditions, and that the proton transfer and nucleophilic attack reactions occur concertedly. We identify the reaction coordinate to be mostly due to the rearrangement of some residual water molecules close to the active site.
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6.
Improving Urban Stormwater Runoff Quality by Nutrient Removal through Floating Treatment Wetlands and Vegetation Harvest.
Xu, B, Wang, X, Liu, J, Wu, J, Zhao, Y, Cao, W
Scientific reports. 2017;(1):7000
Abstract
Two floating treatment wetlands (FTWs) in experimental tanks were compared in terms of their effectiveness on removing nutrients. The results showed that the FTWs were dominated by emergent wetland plants and were constructed to remove nutrients from simulated urban stormwater. Iris pseudacorus and Thalia dealbata wetland systems were effective in reducing the nutrient. T. dealbata FTWs showed higher nutrient removal performance than I. pseudacorus FTWs. Nitrogen (N) and phosphorous (P) removal rates in water by T. dealbata FTWs were 3.95 ± 0.19 and 0.15 ± 0.01 g/m2/day, respectively. For I. pseudacorus FTWs, the TN and TP removal rates were 3.07 ± 0.15 and 0.14 ± 0.01 g/m2/day, respectively. The maximum absolute growth rate for T. dealbata corresponded directly with the maximum mean nutrient removal efficiency during the 5th stage. At harvest, N and P uptak of T. dealbata was 23.354 ± 1.366 g and 1.489 ± 0.077 g per plant, respectively, approximate twice as high as by I. pseudacorus.
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7.
Vitamin C intervention may lower the levels of persistent organic pollutants in blood of healthy women - A pilot study.
Guo, W, Huen, K, Park, JS, Petreas, M, Crispo Smith, S, Block, G, Holland, N
Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association. 2016;:197-204
Abstract
Emerging evidence suggests that exposure to endocrine-disrupting chemicals including persistent organic pollutants (POPs) such as organochlorine pesticides (OCPs), polychlorinated biphenyls (PCBs), and polybrominated diphenyl ethers (PBDEs) has a long term impact on human health. The goal of this pilot study was to test whether antioxidant intervention by vitamin C supplementation may be a remedial approach to decrease body burden of POPs in humans. Using solid phase extraction coupled with a triple quadrupole mass spectrometer and a gas chromatography high resolution mass spectrometry, we measured 18 PCBs, 7 OCPs, and 5 PBDEs in the blood of 15 healthy California women (8 were obese/overweight and 7 had normal weight) before and after 2 months of vitamin C supplementation (1000 mg/day). We observed higher PBDE levels than PCBs and OCPs, but only PCB and OCP levels were strongly and positively correlated with participant's BMI and age. We also found statistically significant decreases in 6 PCBs (PCB-74, PCB-118, PCB-138, PCB-153, PCB-180, and PCB-187), and 2 OCPs (4,4'-DDE, and 4,4'-DDT), but not PBDEs after vitamin C supplementation. Pending confirmation of this pilot finding in a larger study of both sexes, vitamin C intervention may have important public health implications in protecting health by reducing body burdens of POPs.
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8.
Inverse modeling of the biodegradation of emerging organic contaminants in the soil-plant system.
Hurtado, C, Trapp, S, Bayona, JM
Chemosphere. 2016;:236-244
Abstract
Understanding the processes involved in the uptake and accumulation of organic contaminants into plants is very important to assess the possible human risk associated with. Biodegradation of emerging contaminants in plants has been observed, but kinetical studies are rare. In this study, we analyse experimental data on the uptake of emerging organic contaminants into lettuce derived in a greenhouse experiment. Measured soil, root and leaf concentrations from four contaminants were selected within the applicability domain of a steady-state two-compartment standard plant uptake model: bisphenol A (BPA), carbamazepine (CBZ), triclosan (TCS) and caffeine (CAF). The model overestimated concentrations in most cases, when no degradation rates in plants were entered. Subsequently, biodegradation rates were fitted so that the measured concentrations were met. Obtained degradation kinetics are in the order, BPA < CAF ≈ TCS < CBZ in roots, and BPA ≈ TCS < CBZ << CAF in leaves. Kinetics determined by inverse modeling are, despite the inherent uncertainty, indicative of the dissipation rates. The advantage of the procedure that is additional knowledge can be gained from existing experimental data. Dissipation kinetics found via inverse modeling is not a conclusive proof for biodegradation and confirmation by experimental studies is needed.
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9.
A synthesis of parameters related to the binding of neutral organic compounds to charcoal.
Hale, SE, Arp, HP, Kupryianchyk, D, Cornelissen, G
Chemosphere. 2016;:65-74
Abstract
The sorption strength of neutral organic compounds to charcoal, also called biochar was reviewed and related to charcoal and compound properties. From 29 studies, 507 individual Freundlich sorption coefficients were compiled that covered the sorption strength of 107 organic contaminants. These sorption coefficients were converted into charcoal-water distribution coefficients (K(D)) at aqueous concentrations of 1 ng/L, 1 µg/L and 1 mg/L. Reported log K(D) values at 1 µg/L varied from 0.38 to 8.25 across all data. Variation was also observed within the compound classes; pesticides, herbicides and insecticides, PAHs, phthalates, halogenated organics, small organics, alcohols and PCBs. Five commonly reported variables; charcoal production temperature T, surface area SA, H/C and O/C ratios and organic compound octanol-water partitioning coefficient, were correlated with KD values using single and multiple-parameter linear regressions. The sorption strength of organic compounds to charcoals increased with increasing charcoal production temperature T, charcoal SA and organic pollutant octanol-water partitioning coefficient and decreased with increasing charcoal O/C ratio and charcoal H/C ratio. T was found to be correlated with SA (r(2) = 0.66) and O/C (r(2) = 0.50), particularly for charcoals produced from wood feedstocks (r(2) = 0.73 and 0.80, respectively). The resulting regression: log K(D)=(0.18 ± 0.06) log K(ow) + (5.74 ± 1.40) log T + (0.85 ± 0.15) log SA + (1.60 ± 0.29) log OC + (-0.89 ± 0.20) log HC + (-13.20 ± 3.69), r(2) = 0.60, root mean squared error = 0.95, n = 151 was obtained for all variables. This information can be used as an initial screening to identify charcoals for contaminated soil and sediment remediation.
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10.
Organic acid anions: An effective defensive weapon for plants against aluminum toxicity and phosphorus deficiency in acidic soils.
Chen, ZC, Liao, H
Journal of genetics and genomics = Yi chuan xue bao. 2016;(11):631-638
Abstract
Aluminum (Al) toxicity and phosphorous (P) deficiency are two major limiting factors for plant growth on acidic soils. Thus, the physiological mechanisms for Al tolerance and P acquisition have been intensively studied. A commonly observed trait is that plants have developed the ability to utilize organic acid anions (OAs; mainly malate, citrate and oxalate) to combat Al toxicity and P deficiency. OAs secreted by roots into the rhizosphere can externally chelate Al3+ and mobilize phosphate (Pi), while OAs synthesized in the cell can internally sequester Al3+ into the vacuole and release free Pi for metabolism. Molecular mechanisms involved in OA synthesis and transport have been described in detail. Ensuing genetic improvement for Al tolerance and P efficiency through increased OA exudation and/or synthesis in crops has been achieved by transgenic and marker-assisted breeding. This review mainly elucidates the crucial roles of OAs in plant Al tolerance and P efficiency through summarizing associated physiological mechanisms, molecular traits and genetic manipulation of crops.