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Helically folded aromatic foldamers may constitute suitable candidates for the ab initiodesign of ligands for protein surfaces. As preliminary steps toward the exploration of this hypothesis, a tethering approach was developed to detect interactions between a protein and a foldamer by confining the former at the surface of the latter. Cysteine mutants of two therapeutically relevant enzymes, CypA and IL4, were produced. Two series of ten foldamers were synthesized bearing different proteinogenic side chains and either a long or a short linker functionalized with an activated disulfide. Disulfide exchange between the mutated cysteines and the activated disulfides yielded 20 foldamer-IL4 and 20 foldamer-CypA adducts. Effectiveness of the reaction was demonstrated by LC-MS, by MS analysis after proteolytic digestion, and by 2D NMR. Circular dichroism then revealed diastereoselective interactions between the proteins and the foldamers confined at their surface which resulted in a preferred handedness of the foldamer helix. Helix sense bias occurred sometimes with both the short and the long linkers and sometimes with only one of them. In a few cases, helix handedness preference is found to be close to quantitative. These cases constitute valid candidates for structural elucidation of the interactions involved.

Numerous essential biomolecular processes require the recognition of DNA surface features by proteins. Molecules mimicking these features could potentially act as decoys and interfere with pharmacologically or therapeutically relevant protein–DNA interactions. Although naturally occurring DNA-mimicking proteins have been described, synthetic tunable molecules that mimic the charge surface of double-stranded DNA are not known. Here, we report the design, synthesis and structural characterization of aromatic oligoamides that fold into single helical conformations and display a double helical array of negatively charged residues in positions that match the phosphate moieties in B-DNA. These molecules were able to inhibit several enzymes possessing non-sequence-selective DNA-binding properties, including topoisomerase 1 and HIV-1 integrase, presumably through specific foldamer–protein interactions, whereas sequence-selective enzymes were not inhibited. Such modular and synthetically accessible DNA mimics provide a versatile platform to design novel inhibitors of protein–DNA interactions.

Following exposure to xenobiotics, cellular mechanisms will take place to prevent damages relative to i) DNA, to maintain genome integrity, ii) proteins, to maintain their activities, iii) lipids, to limit peroxidation. This system of cellular defence and resistance is energetically costly. In this commentary review, we discuss the impact of DNA damage and the DNA damage response (DDR) on energetic metabolism. Conversely, we address the question about how energetic metabolism would influence DDR. These points will be highlighted in the context of cancer, in which genome instability and aerobic glycolysis are cancer hallmarks.

Beside their crucial role in xenobiotic biotransformation, AhR and Nrf2 are involved in the regulation of energetic metabolism. Nrf2, as a cytoprotective transcription factor, supply energy for detoxification and antioxidant response. AhR is ligand-activated transcriptional factor implicated in several physiological function. Following pollutant exposure, it acts as a chemosensor to eliminate harmful chemicals. Altogether, AhR and Nrf2 cooperate to contribute to protective responses upon contaminant exposure, including metabolic remodelling. This fine-tuned energetic coupling with detoxification can lead to prominent dysfunction under a chronic exposure to pollutants, and promote a long-term reprogramming that affects multiple cellular activities.

Abiotic foldamers, that is foldamers that have backbones chemically remote from peptidic and nucleotidic skeletons, may give access to shapes and functions different to those of peptides and nucleotides. However, design methodologies towards abiotic tertiary and quaternary structures are yet to be developed. Here we report rationally designed interactional patterns to guide the folding and assembly of abiotic helix bundles. Computational design facilitated the introduction of hydrogen-bonding functionalities at defined locations on the aromatic amide backbones that promote cooperative folding into helix–turn–helix motifs in organic solvents. The hydrogen-bond-directed aggregation of helices not linked by a turn unit produced several thermodynamically and kinetically stable homochiral dimeric and trimeric bundles with structures that are distinct from the designed helix–turn–helix. Relative helix orientation within the bundles may be changed from parallel to tilted on subtle solvent variations. Altogether, these results prefigure the richness and uniqueness of abiotic tertiary structure behaviour.

Constructed wetlands (CWs) have been widely applied in mariculture effluents disposal, however, the pollutants removal performance of mariculture wastewater with different salinity, especially the effect of different halophytes in CWs is rarely discussed. In this study, the nutrients removal efficiencies and absolute abundance of nitrogen (N) transformation microbes in CWs microcosms were investigated. With the increase of the salinity, both Phragmites australis (P. australis) and Suaeda salsa (S. salsa) planted CWs showed a significant reduction in chemical oxygen demand removal performance (p < 0.05), while no significant restriction on the nitrogen removal rates of all groups was obtained. The N removal efficiency was even promoted under 1.4% in these two kinds of CWs, respectively. And total phosphorus removal efficiency declined at the salinity of 1.4% and 2.1% for P. australis and S. salsa planted CWs, respectively. Further analysis showed that the presence of nitrification and denitrification was the major approaches of N removal. The absolute abundance of genes related with N transformation genes was significantly influenced by fluctuation of salinity, which affected the treatment efficiency of wastewater. The two different CWs presented high possibility of application on mariculture treatment in proper salinity.

At the molecular level, translation refers to the production of a new entity according to a template that has a different chemical composition. In this way, chemical information may be translated from one molecule to another. The process is useful to synthesize structures and thus functions that might be difficult to create otherwise, and it reaches exquisite levels of efficiency in biological systems, as illustrated by protein expression from mRNA templates or by the assembly of the tobacco mosaic virus capsid protein according to the length of its RNA. In synthetic systems, examples of template-directed syntheses are numerous, but general and versatile schemes in which a non-natural sequence actually encodes the information necessary to produce a different sequence are few and far from being optimized. Here we show a high-fidelity enzyme-free translation of long rod-like alkylcarbamate oligomers into well-defined sequences of stacked helical aromatic oligoamides. The features present in the rods, which include the number and distance between carbamate functions and stereogenic centres, template the self-assembly of complementary stacks of helices that each have a defined right (P) or left (M) handedness, length and single or double helicity. This process enables the production of very large (>20 kDa) abiotic artificial folded architectures (foldamers) that may, for example, serve as scaffolds to organize appended functional features at positions in space defined with atomic precision across nanometric distances.

Heavy oil, extra-heavy oil and tar sands account for half of the petroleum resources of the world. Due to their high viscosity their production is a major technical and economical challenge. The understanding of the origin and geological habitat of these unconventional oils is crucial in order to optimize exploration and production operations. The vast majority of these heavy oils originates from the biodegradation of conventional oils by bacterial activity. The limiting factors of the involved biological processes (temperature, nutrients, etc.) are controlled by the geological situation. In this respect, foreland basins which harbour a large part of the current deposits of heavy oils correspond to particularly favourable conditions in promoting the biodegradation of large charges of oil. They are characterized by long distance lateral oil migration draining substantial volume of the petroleum system. This migration is supported by an adequate drainage system which exhibits a large lateral continuity and consists of the first syntectonic fluvial and fluvial-deltaic sediments filling the foreland basins. As a result of this migration the oil reaches shallow situation in the forebulge where the temperature is compatible with bacterial activity. The reservoirs associated with the “forebulge” are often high porosity and high permeability sand bodies, initially hosting large volume of water and facilitating the circulation of meteoric water helping in the nutrient availability. For the sake of production, the heterogeneities associated with these fluvial and fluvial-deltaic sediments have to be carefully considered. The geological models developed for the architecture and for the stratigraphic evolution of fluvial channels and incised valleys provide useful guidelines in order to characterize the reservoirs for production purposes in such geological setting. The technical difficulties in recovering these highly viscous fluids require to integrate more detailed reservoir description than usually needed when producing conventional oil plays. The Cretaceous reservoirs of the Mannville Formation in Canada is presented to exemplify the types of heterogeneities encountered in fluvial reservoirs, their rational, their effect on the heavy oil recovery and the impact of the geological knowledge on the production strategy.

The petroleum deposits in the South Atlantic are considered in terms of the contemporary understanding of the formation of petroleum and of the petroleum system concept. These hydrocarbon reserves (7% of the global reserves), contained in the sedimentary rims along the coasts of West Africa and of the Eastern seaboard of South America, result from a favourable geological setting that is essentially the same on both sides of the ocean, giving rise to an almost symmetrical pattern. Their history is described within the general framework of the opening of the South Atlantic Ocean, which began over 140 Ma ago with the breaking up of the proto-continent Pangea. The importance of these concepts for the opening up of deep and ultra-deep offshore prospects in West Africa and Brazil is underlined.

Following a short review of the evolution of petroleum organic geochemistry in recent decades, this paper depicts the present status of research in the field and describes the guidelines dictated by the needs of the operators. Today, the industrial players are interested in increasingly deep prospects (high pressure, high temperature), in the exploration of the deep offshore, the search for gas and in the production of the planet's enormous heavy oil reserves. In this context, the challenge is to contribute effectively to the quantitative prediction of the oil and gas reserves at the scale of a basin (volume, composition, uncertainties) and to predict the quality of the fluids present in a reservoir, through a closer knowledge of the geochemical events affecting their preservation and their alteration.

In the context of reducing production costs for the oil industry, this paper aims to suggest a way for predicting wax precipitation at an early stage of the reservoir characterization and production process. In this respect, reservoir core extracts and production oil-saturated fractions have been herein analyzed by high temperature gas chromatography (HTGC) in order to quantify the high molecular weight hydrocarbons (HMWHC) which are at the origin of wax deposits in the tubing and surface facilities. Samples of oils and associated reservoir cores from two adjacent but non-communicating fields are considered in this paper. Wax deposition is documented for Field P but not for Field A. It is demonstrated that the reservoir core extract of Field P is substantially enriched in HMWHC when compared to the produced oil, whereas for Field A, with no production problems, both profiles (oil and reservoir core extracts) are similar and depleted in HMWHC. These results suggest that fields exhibiting a risk of wax precipitation could be identified during the exploration phase as soon as reservoir cores are available. Moreover, it can be envisioned that such additional data provided by the saturates distribution can potentially be used in future thermodynamic models (derived from those currently applied for assessing wax precipitation in pipelines during the transport of produced oil) in order to quantitatively predict, at an early stage of reservoir characterization, paraffins precipitation in reservoirs and tubings during production. The preliminary computed results obtained for the produced oil and the reservoir rock extract of Field P indicate that the temperature of paraffin crystallization onset is significantly under-estimated when using the composition of tank oil (42°C)-heavy paraffins are already deposited. On the other hand, the predictive calculation, using the core extract (52°C) and which can be performed as soon as a core sample is available, will allow us to minimize the risk of paraffin deposition during production and transportation. Corresponding author (I. Kowalewski)