Differential protein expression during growth on model and commercial mixtures of naphthenic acids in Pseudomonas fluorescens Pf-5.

Naphthenic acids (NAs) are carboxylic acids with the formula (Cn H2n+Z O2 ) and are among the most toxic, persistent constituents of oil sands process-affected waters (OSPW), produced during oil sands extraction. Currently, the proteins and mechanisms involved in NA biodegradation are unknown. Using LC-MS/MS shotgun proteomics, we identified proteins overexpressed during the growth of Pseudomonas fluorescens Pf-5 on a model NA (4'-n-butylphenyl)-4-butanoic acid (n-BPBA) and commercial NA mixture (Acros). By day 11, >95% of n-BPBA was degraded. With Acros, a 17% reduction in intensity occurred with 10-18 carbon compounds of the Z family -2 to -14 (major NA species in this mixture). A total of 554 proteins (n-BPBA) and 631 proteins (Acros) were overexpressed during growth on NAs, including several transporters (e.g., ABC transporters), suggesting a cellular protective response from NA toxicity. Several proteins associated with fatty acid, lipid, and amino acid metabolism were also overexpressed, including acyl-CoA dehydrogenase and acyl-CoA thioesterase II, which catalyze part of the fatty acid beta-oxidation pathway. Indeed, multiple enzymes involved in the fatty acid oxidation pathway were upregulated. Given the presumed structural similarity between alkyl-carboxylic acid side chains and fatty acids, we postulate that P. fluorescens Pf-5 was using existing fatty acid catabolic pathways (among others) during NA degradation.

Advanced Identification and Quantification of In-Bearing Minerals by Scanning Electron Microscope-Based Image Analysis.

The identification and accurate characterization of discrete grains of rare minerals in sulfide base-metal ores is usually a cumbersome procedure due to the small grain sizes (typically <10 µm) and complex mineral assemblages in the material. In this article, a new strategy for finding and identifying indium minerals, and quantifying their composition and abundance is presented, making use of mineral liberation analysis (MLA) and electron probe microanalysis (EPMA). The method was successfully applied to polymetallic massive sulfide ores from the Neves-Corvo deposit in Portugal. The presence of roquesite and sakuraiite could be systematically detected, their concentration quantified by MLA measurements, and their identity later confirmed by EPMA analyses. Based on these results, an almost complete indium deportment could be obtained for the studied samples. This validates the approach taken, combining automated mineralogy data with electron microprobe analysis. A similar approach could be used to find minerals of other common minor and trace elements in complex base-metal sulfide ores, for example Se, Ge, Sb, or Ag, thus permitting the targeted development of resource technologies suitable for by-product recovery.

Reservoir Souring - Latest developments for application and mitigation.

Sulphate-reducing prokaryotes (SRP) have been identified in oil field fluids since the 1920s. SRP reduce sulphate to sulphide, a toxic and corrosive species that impacts on operational safety, metallurgy and both capital and operational cost. Differences in water cut, temperature, pressure and fluid chemistry can impact on the observed H2S concentration, meaning that an increase in H2S concentration does not always correlate with activity of SRP. However it wasn't until the 1990s that SRP activity was accepted as the leading cause of reservoir souring (i.e. an increase in H2S concentrations) in water flooded oil fields. The process of sulphate-reduction has been well documented at the genetic, enzymatic and physiological level in pure cultures under laboratory conditions. DNA sequencing has also identified new groups of microorganisms, such as archaea which are capable of contributing to reservoir souring. This has led to some recent advances in microbial control and detection, however, despite this, many of the methods used routinely for microbial control and detection are over a century old. We therefore look towards emerging and novel mitigation technologies that may be used in mitigating against reservoir souring, along with tried and tested methods. Modelling and prediction is another important but often under-used tool in managing microbial reservoir souring. To be truly predictive, models need to take into account not only microbial H2S generation but also partitioning and mineral scavenging. The increase in 'big data' available through increased integration of sensors in the digital oil field and the increase in the DNA sequencing capabilities through next-generation sequencing (NGS) therefore offer a unique opportunity to develop and refine microbial reservoir souring models. We therefore review a number of different reservoir souring models and identify how these can be used in the future. With this comprehensive overview of the current and emerging technologies we will highlight areas where significant development effort could generate rewards that can improve detection, prediction and control of microbial reservoir souring.

Uptake and toxicity of methylmethacrylate-based nanoplastic particles in aquatic organisms.

The uptake and toxicity of 2 poly(methylmethacrylate)-based plastic nanoparticles (PNPs) with different surface chemistries (medium and hydrophobic) were assessed using aquatic organisms selected for their relevance based on the environmental behavior of the PNPs. Pure poly(methylmethacrylate) (medium; PMMA PNPs) and poly(methylmethacrylate-co-stearylmethacrylate) copolymer (hydrophobic; PMMA-PSMA PNPs) of 86 nm to 125 nm were synthesized using a miniemulsion polymerization method. Fluorescent analogs of each PNP were also synthesized using monomer 7-[4-(trifluoromethyl)coumarin]acrylamide and studied. Daphnia magna, Corophium volutator, and Vibrio fischeri were employed in a series of standard acute ecotoxicity tests, being exposed to the PNPs at 3 different environmentally realistic concentrations (0.01 mg/L, 0.1 mg/L, and 1.0 mg/L) and a high concentration 500 mg/L to 1000 mg/L. In addition, sublethal effects of PNPs in C. volutator were determined using a sediment reburial test, and the uptake and depuration of fluorescent PNPs was studied in D. magna. The PNPs and fluorescent PNPs did not exhibit any observable toxicity at concentrations up to 500 mg/L to 1000 mg/L in any of the tests except for PMMA-PSMA PNPs and fluorescent PNPs following 48-h exposure to D. magna (median lethal concentration values of 879 mg/L and 887 mg/L, respectively). No significant differences were observed between labeled and nonlabeled PNPs, indicating the suitability of using fluorescent labeling. Significant uptake and rapid excretion of the fluorescent PNPs was observed in D. magna. Environ Toxicol Chem 2016;35:1641-1649. © 2015 SETAC.

Reexamination of pure qubit work extraction.

Many work extraction or information erasure processes in the literature involve the raising and lowering of energy levels via external fields. But even if the actual system is treated quantum mechanically, the field is assumed to be classical and of infinite strength, hence not developing any correlations with the system or experiencing back-actions. We extend these considerations to a fully quantum mechanical treatment by studying a spin-1/2 particle coupled to a finite-sized directional quantum reference frame, a spin-l system, which models an external field. With this concrete model together with a bosonic thermal bath, we analyze the back-action a finite-size field suffers during a quantum-mechanical work extraction process and the effect this has on the extractable work and highlight a range of assumptions commonly made when considering such processes. The well-known semiclassical treatment of work extraction from a pure qubit predicts a maximum extractable work W=kTlog2 for a quasistatic process, which holds as a strict upper bound in the fully quantum mechanical case and is attained only in the classical limit. We also address the problem of emergent local time dependence in a joint system with a globally fixed Hamiltonian.

Nanostructure and crystallography of aberrant columnar vaterite in Corbicula fluminea (Mollusca).

Both the crystallographic and nanostructural organisation of aberrant columnar vaterite occurring in Corbicula fluminea were characterised in detail for the first time using electron microscopic and X-ray powder diffraction techniques. At the millimetre scale, only a confinement of the otherwise randomly oriented c-axis to the growth surface is observed. Domains of 100 or more individual vaterite columns with common c-axis orientation exist within this disordered material. Each column behaves as a single crystal on the scale of EBSD measurements, but is internally composed of smaller irregularly shaped and slightly misaligned crystalline units (0.3-1.3µm in dimension). These are in turn partitioned by porous boundaries into rounded nanodomains, up to 600nm in size. The geometry of the nanodomains and their respective boundaries might suggest formation by the accretion of vesicles. In addition to crystallographic textures, this observation indicates formation under significant biological control with wider implications for possible causes of the condition.

Micro-structure and chemical composition of vateritic deformities occurring in the bivalve Corbicula fluminea (Müller, 1774).

Vateritic deformities occurring in the invasive heterodont bivalve Corbicula fluminea from several locations in the UK were characterised in detail for the first time using scanning electron microscopy, X-ray diffraction and different geochemical techniques (electron microprobe, ICP-AES, and mass spectrometry). Large volumes of vaterite are produced abnormally in the animals' shells in the form of yellow-green bulges. These are distinguished from the aragonitic parts of the shell by their characteristic micro-structures, content of organic material, trace elemental composition and carbon stable isotope signatures. The most commonly observed micro-structures include columnar vaterite, lamellar vaterite and different irregular structures occurring in all parts of the shell. There are indications that organic material is present largely as intracrystalline impurities or nano-scale phases and not as envelopes around microstructural units. These micro-structures are novel, nothing equivalent having yet been described for other vateritic systems. Euhedral vaterite crystals also occur occasionally. The vaterite has generally higher Mg/Ca and lower Na/Ca, K/Ca than the aragonite. In addition, δ¹³C is also always lower. Microstructural characteristics would suggest loss of biological control probably due to physiological stress(es) inducing the switch to vaterite production. The vaterite might be stabilised by its higher content of organic material and magnesium.

Molecular effects of diethanolamine exposure on Calanus finmarchicus (Crustacea: Copepoda).

Alkanolamines are surface-active chemicals used in a wide range of industrial, agricultural and pharmaceutical applications and products. Of particular interest is the use of alkanolamines such as diethanolamine (DEA) in the removal of CO(2) from natural gas and for CO(2) capture following fossil fuel combustion. Despite this widespread use, relatively little is known about the ecotoxicological impacts of these compounds. In an attempt to assess the potential effects of alkanolamines in the marine environment, a key species in the North Atlantic, the planktonic copepod Calanus finmarchicus, was studied for molecular effects following sublethal exposure to DEA. DEA-induced alterations in transcriptome and metabolome profiling were assessed using a suppression subtractive hybridization (SSH) gene library method and high resolution magic angle spinning nuclear magnetic resonance (HR-MAS NMR), respectively. Effects were observed on transcription of genes reportedly involved in lipid metabolism, antioxidant systems, metal binding, and amino acid and protein catabolism. These effects were accompanied by altered expression of fatty acid derivates, amino acids (threonine, methionine, glutamine, arginine, alanine and leucine) and cholines (choline, phosphocholine and glycerophosphocholine). Together, SSH and HR-MAS NMR offer complementary screening tools for the assessment of molecular responses of C. finmarchicus to DEA and can be used in the study of other chemicals and organisms. Concentration-response and time-response relationships between DEA exposure and single gene transcription were investigated using quantitative PCR. Specific relationships were found between DEA exposure and the transcription of genes involved in protein catabolism (ubiquitin-specific protease-7), metal ion homeostasis (ferritin) and defence against oxidative stress (gamma-glutamylcysteine synthase, glutathione synthase and Cu/Zn-superoxide dismutase). At the lowest alkanolamine concentration used in these experiments, which corresponded to 0.5% of the LC(50) concentration, no transcriptional effects were observed, giving information regarding the lower molecular effect level. Finally, similar transcription patterns were observed for a number of different genes following exposure to DEA, which indicates analogous mechanisms of toxicity and response.

Complications with remediation strategies involving the biodegradation and detoxification of recalcitrant contaminant aromatic hydrocarbons.

Environmentally persistent aromatic hydrocarbons known as unresolved complex mixtures (UCMs) derived from crude oil can be accumulated by, and elicit toxicological responses in, marine organisms (e.g. mussels, Mytilus edulis). Comprehensive two-dimensional gas chromatography time-of-flight mass-spectrometry (GCxGC-ToF-MS) previously revealed that these UCMs included highly branched alkylated aromatic hydrocarbons. Here, the effects of biodegradation on the toxicity and chemical composition of an aromatic UCM hydrocarbon fraction isolated from Tia Juana Pesado (TJP) crude oil were examined. 48h exposure of mussels to the aromatic hydrocarbon fraction (F2) resulted in tissue concentrations of 900microgg(-1) (dry wt.) and approximately 45% decrease in clearance rate. Over 90% of the hydrocarbon burden corresponded to an UCM. Following a 5day recovery period, GCxGC-ToF-MS analysis of the tissues indicated depuration of most accumulated hydrocarbons and clearance rates returned to those observed in controls. To assess the potential of biodegradation to reduce UCM toxicity, TJP F2 was exposed to bacteria isolated from Whitley Bay, UK, for 46days. Mussels exposed to the undegraded TJP F2 from the abiotic control exhibited a reduction in clearance rate comparable with values for the pure crude oil TJP F2. Clearance rates of mussels exposed to biodegraded TJP F2 were statistically similar to seawater controls, suggesting biodegradation had reduced the TJP F2 toxicity. GCxGC-ToF-MS analysis revealed the same compound groups in the tissue of mussels exposed to pure TJP F2, undegraded TJP F2 and biodegraded TJP F2 samples; however >300 fewer compounds were observed in the biodegraded (954 compounds) compared to the undegraded TJP F2 (1261). The compound distributions were markedly different, possibly accounting for the decrease in toxicity. Extraction and analysis of pelleted bacterial cell material revealed that a significant proportion of the TJP F2 had adsorbed onto the cells. Thus extreme care must be taken in interpreting biodegradation data from recalcitrant UCM hydrocarbons.

Suzuki-Miyaura coupling reactions in aqueous microdroplets with catalytically active fluorous interfaces.

Using microfluidic techniques and a novel fluorous-tagged palladium catalyst, we generated droplet reactors with catalytically active walls and used these compartments for small molecule synthesis.