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The selective recognition of tyrosine residues in peptides is an appealing approach to inhibiting their tyrosine kinase (TK)‐mediated phosphorylation. Herein, we describe pseudopeptidic cages that efficiently protect substrates from the action of the Src TK enzyme, precluding the corresponding Tyr phosphorylation. Fluorescence emission titrations show that the most efficient cage inhibitors strongly bind the peptide substrates with a very good correlation between the binding constant and the inhibitory potency. Structural insights and additional control experiments further support the proposed mechanism of selective supramolecular protection of the substrates. Moreover, the approach also works in a completely different kinase‐substrate system. These results illustrate the potential of supramolecular complexes for the efficient and selective modulation of TK signaling., How to spare Tyr: The selective recognition of tyrosine residues by pseudopeptidic cages protects the substrates from Src kinase‐promoted phosphorylation. The Tyr kinase‐inhibiting activity of the cages can be satisfactorily explained by the formation of host‐guest complexes. This supramolecular approach represents an appealing alternative to modulating Tyr kinase activity by substrate recognition.

HIV‐1 entry requires the redistribution of envelope glycoproteins (Env) into a cluster and the presence of cholesterol (chol) in the viral membrane. However, the molecular mechanisms underlying the specific role of chol in infectivity and the driving force behind Env clustering remain unknown. Here, gp41 is demonstrated to directly interact with chol in the viral membrane via residues 751–854 in the cytoplasmic tail (CT751–854). Super‐resolution stimulated emission depletion (STED) nanoscopy analysis of Env distribution further demonstrates that both truncation of gp41 CT751–854 and depletion of chol leads to dispersion of Env clusters in the viral membrane and inhibition of virus entry. This work reveals a direct interaction of gp41 CT with chol and indicates that this interaction is an important orchestrator of Env clustering., The authors are grateful to Barbara Müller, N. Landau, and Tom Hope for providing the plasmids pCHIV and pCAGGS NL4‐3 Env, pMM310, and peGFP‐Vpr, respectively. Proteomic analysis was performed by the SGIKER service of the University of the Basque Country. The authors would like to thank Advanced Light Microscopy Unit at the Centre for Genomic Regulation (CRG), Barcelona, Spain for the access to Leica STED microscope. The following reagents were obtained through the NIH AIDS Reagent Program (Division of NIAID, NIH): Anti‐HIV‐1 gp41 Hybridome (Chessie 8) (Cat# 526) from Dr. George Lewis; Antiviral bicyclam JM‐2987 (hydrobromide salt of AMD‐3100) from NIAID, DAIDS (cat# 8128). This project was supported by the Basque Government (grant number IT1264‐19 to M.L. and F.‐X.C.) and the Spanish Ministry of Science, Innovation, and Universities (BFU‐2015‐68981‐P). This work was supported in part by the Fundación Biofísica Bizkaia and the Basque Excellence Research Centre (BERC) program of the Basque Government. J.A.N.‐G. was supported by a FI predoctoral fellowship from the Basque Government and currently by Fundación Biofísica Bizkaia. A.A. was supported by Fundación Biofísica Bizkaia. S.O. was supported by an IKASIKER fellowship from the Basque Government. J.C. was supported by European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska‐Curie grant agreement No. 793830. H.G.‐K. was supported by a grant from the Deutsche Forschungsgemeischaft within TRR86.

Ligand‐based NMR techniques to study protein–ligand interactions are potent tools in drug design. Saturation transfer difference (STD) NMR spectroscopy stands out as one of the most versatile techniques, allowing screening of fragments libraries and providing structural information on binding modes. Recently, it has been shown that a multi‐frequency STD NMR approach, differential epitope mapping (DEEP)‐STD NMR, can provide additional information on the orientation of small ligands within the binding pocket. Here, the approach is extended to a so‐called DEEP‐STD NMR fingerprinting technique to explore the binding subsites of cholera toxin subunit B (CTB). To that aim, the synthesis of a set of new ligands is presented, which have been subject to a thorough study of their interactions with CTB by weak affinity chromatography (WAC) and NMR spectroscopy. Remarkably, the combination of DEEP‐STD NMR fingerprinting and Hamiltonian replica exchange molecular dynamics has proved to be an excellent approach to explore the geometry, flexibility, and ligand occupancy of multi‐subsite binding pockets. In the particular case of CTB, it allowed the existence of a hitherto unknown binding subsite adjacent to the GM1 binding pocket to be revealed, paving the way to the design of novel leads for inhibition of this relevant toxin., Fingerprinting: A powerful protocol by using NMR spectroscopy and molecular dynamics to study multi‐subsite binding pockets has been developed. For cholera toxin subunit B (CTB), the combination of differential epitope mapping saturation transfer difference (DEEP‐STD) NMR, STD competition experiments, transfer‐NOESY, and Hamiltonian replica exchange molecular dynamics (HREMD) unveiled the presence of a novel subsite adjacent to the known subsites of GM1 on CTB.

BACKGROUND AND PURPOSE: 3', 5'-cyclic adenosine monophosphate (cAMP) is a central second messenger that broadly regulates cell function and can underpin pathophysiology. In chronic obstructive pulmonary disease (COPD), a lung disease primarily provoked by cigarette smoke (CS), the induction of cAMP-dependent pathways, via inhibition of hydrolyzing phosphodiesterases (PDEs), is a prime therapeutic strategy. Mechanisms that disrupt cAMP signaling in airway cells, in particular regulation of endogenous PDEs are poorly understood.EXPERIMENTAL APPROACH: We used a novel Förster resonance energy transfer (FRET) based cAMP biosensor in mouse in vivo, ex vivo precision cut lung slices (PCLS), and in human in vitro cell models to track the effects of CS exposure.KEY RESULTS: Under fenoterol stimulated conditions, FRET responses to cilostamide were significantly increased in in vivo, ex vivo PCLS exposed to CS and in human airway smooth muscle cells exposed to CS extract. FRET signals to rolipram were only increased in the in vivo CS model. Under basal conditions, FRET responses to cilostamide and rolipram were significantly increased in in vivo, ex vivo PCLS exposed to CS. Elevated FRET signals to rolipram correlated with a protein upregulation of PDE4 subtypes. In ex vivo PCLS exposed to CS extract, rolipram reversed downregulation of ciliary beating frequency, whereas only cilostamide significantly increased airway relaxation of methacholine pre-contracted airways.CONCLUSION AND IMPLICATIONS: We show that CS upregulates expression and activity of both PDE3 and PDE4, which regulate real-time cAMP dynamics. These mechanisms determine the availability of cAMP and can contribute to CS-induced pulmonary pathophysiology.

A universal anti-Xa assay for the determination of rivaroxaban, apixaban and edoxaban drug concentrations would simplify laboratory procedures and facilitate widespread implementation. Following two pilot studies analysing spiked samples and material from 698 patients, we conducted a prospective multicentre cross-sectional study, including 867 patients treated with rivaroxaban, apixaban or edoxaban in clinical practice to comprehensively evaluate a simple, readily available anti-Xa assay that would accurately measure drug concentrations and correctly predict relevant levels in clinical practice. Anti-Xa activity was measured by an assay calibrated with low-molecular-weight heparin (LMWH) in addition to ultra-high performance liquid chromatography-tandem mass spectrometry (LC-MS/MS). As an external validation, LMWH-calibrated anti-Xa activity was also determined in nine external laboratories. The LMWH-calibrated anti-Xa activity correlated strongly with rivaroxaban, apixaban or edoxaban drug levels [r s = 0·98, 95% confidence interval (CI) 0·98-0·98]. The sensitivity for the clinically relevant cut-off levels of 30, 50 and 100 µg/l was 96·2% (95% CI 94·4-97·4), 96·4% (95% CI 94·4-97·7) and 96·7% (95% CI 94·3-98·1) respectively. Concordant results were obtained in the external validation study. In conclusion, a universal, LMWH-calibrated anti-Xa assay accurately measured rivaroxaban, apixaban and edoxaban concentrations and correctly predicted relevant drug concentrations in clinical practice.

BACKGROUND: The occurrence of pharmaceutical compounds in wastewater has become a major concern for human health and the environment. Therefore, it is an important challenge to improve conventional wastewater treatment to remove these compounds. Coupling biological treatment with advanced oxidation technology has been widely studied in the literature, but only sequential associations of the two processes have been used. This study proposes an innovative concept based on a real integration of the photocatalytic oxidation process in a continuous recycling loop on a membrane bioreactor. The role of the oxidation here is not to completely degrade pharmaceuticals, but instead to oxidize them moderately to increase their biodegradability so that they can be eliminated by the biological process. RESULTS: Preliminary experiments on the oxidation process indicated that a flux density of 5 W m−2 was sufficient to increase biodegradability and decrease the toxicity of a cocktail of three pharmaceuticals. Then the performance of a 20-L continuous membrane bioreactor treating wastewater with seven pharmaceuticals, without and with pre-oxidation at 5 W m−2, were compared. Pre-oxidation increased the global removal for some recalcitrant pharmaceuticals (from 3% to 47% for diclofenac and from 1% to 44% for furosemide) without affecting either the removal of carbon, nitrogen or phosphorous by activated sludge, or of already highly removed pharmaceuticals. CONCLUSION: This work proves the feasibility of an innovative concept of a continuous hybrid process coupling a photocatalytic oxidation process and a membrane bioreactor for the treatment of pharmaceuticals in wastewater, with low cost and size. © 2020 Society of Chemical Industry (SCI)., This work was supported by the Program ‘SUDOE’ on the project Innovec'EAU 2016-2019 under award number SUDOE SOE1/P1/F0173. We thank R. Garcia and J. J. Huc for their help in designing and building the demonstrator, and Victor Pueyo for doing the analysis.

Journal of synchrotron radiation 28(5), 1518 - 1527 (2021). doi:10.1107/S1600577521007074, Many processes and materials in heterogeneous catalysis undergo dynamic structural changes depending on their chemical environment. Monitoring such dynamic changes can be challenging using conventional spectroscopic characterization tools, due to the high time resolution required. Here, a high-resolution 2D X-ray camera operating at 50 Hz full-frame rate was synchronized with a QEXAFS monochromator, enabling rapid spectro-microscopic imaging with chemical contrast over individual pixels. This was used to monitor chemical gradients within a model Pt/Al2O3 catalyst during catalytic partial oxidation of methane to synthesis gas. The transition from methane combustion (partly oxidized Pt) to combustion-reforming and partial oxidation (fully reduced Pt) was observed by a characteristic reduction front, which progressed from the end of the catalyst bed towards its beginning on the second time scale. The full-field QEXAFS imaging method applied here allows acquisition of entire XANES spectra `on the fly' in a rapid and spatially resolved manner. The combination of high spatial and temporal resolution with spectroscopic data offers new opportunities for observing dynamic processes in catalysts and other functional materials at work. The methodology is flexible and can be applied at beamlines equipped with a QEXAFS or other fast-scanning monochromators and a suitable sample environment for gas phase analytics to allow for catalytic studies at the same time., Published by Wiley-Blackwell, [S.l.]

Acta crystallographica / B 77(4), 594 - 604 (2021). doi:10.1107/S2052520621005655, The crystal structure of CrAs was investigated using synchrotron X-ray single-crystal diffraction for separate dependences on temperature (30–400 K) and on pressure (0–9.46 GPa). The isosymmetrical magnetostructural phase transition at T$_N$ = 267 K can induce a change in the microstructure by twinning due to a crossing of the orthohexagonal setting of the unit-cell parameter ratio c/b. Within the crystal structure, one particular Cr–Cr distance exhibits anomalous behavior in that it is nearly unaffected by temperature and pressure in the paramagnetic phase, which is stable above 267 K and at high pressures. The distinction of this shortest Cr–Cr distance might be of importance for the superconducting properties of CrAs., Published by Wiley-Blackwell, Oxford [u.a.]

A comparative study on the self‐assembly of sexiphenyl‐dicarbonitrile on highly oriented pyrolytic graphite and single‐layer graphene on Cu(111) is presented. Despite an overall low molecule–substrate interaction, the close‐packed structures exhibit a peculiar shift repeating every four to five molecules. This shift has hitherto not been reported for similar systems and is hence a unique feature induced by the graphitic substrates.

The new phytologist 221(2), 881-895 (2019). doi:10.1111/nph.15442, Published by Wiley-Blackwell, Oxford [u.a.]

To obtain insights into the dynamics of nutrient exchange in arbuscular mycorrhizal (AM) symbiosis, we modelled mathematically the two‐membrane system at the plant–fungus interface and simulated its dynamics. In computational cell biology experiments, the full range of nutrient transport pathways was tested for their ability to exchange phosphorus (P)/carbon (C)/nitrogen (N) sources. As a result, we obtained a thermodynamically justified, independent and comprehensive model of the dynamics of the nutrient exchange at the plant–fungus contact zone. The predicted optimal transporter network coincides with the transporter set independently confirmed in wet‐laboratory experiments previously, indicating that all essential transporter types have been discovered. The thermodynamic analyses suggest that phosphate is released from the fungus via proton‐coupled phosphate transporters rather than anion channels. Optimal transport pathways, such as cation channels or proton‐coupled symporters, shuttle nutrients together with a positive charge across the membranes. Only in exceptional cases does electroneutral transport via diffusion facilitators appear to be plausible. The thermodynamic models presented here can be generalized and adapted to other forms of mycorrhiza and open the door for future studies combining wet‐laboratory experiments with computational simulations to obtain a deeper understanding of the investigated phenomena.

Journal of synchrotron radiation 27(3), 625 - 632 (2020). doi:10.1107/S1600577520002192, The unique diagnostic possibilities of X-ray diffraction, small X-ray scattering and phase-contrast imaging techniques applied with high-intensity coherent X-ray synchrotron and X-ray free-electron laser radiation can only be fully realized if a sufficient dynamic range and/or spatial resolution of the detector is available. In this work, it is demonstrated that the use of lithium fluoride (LiF) as a photoluminescence (PL) imaging detector allows measuring of an X-ray diffraction image with a dynamic range of ∼107 within the sub-micrometre spatial resolution. At the PETRA III facility, the diffraction pattern created behind a circular aperture with a diameter of 5 µm irradiated by a beam with a photon energy of 500 eV was recorded on a LiF crystal. In the diffraction pattern, the accumulated dose was varied from 1.7 × 10$^5$ J cm$^{−3}$ in the central maximum to 2 × 10$^{−2}$ J cm$^{−3}$ in the 16th maximum of diffraction fringes. The period of the last fringe was measured with 0.8 µm width. The PL response of the LiF crystal being used as a detector on the irradiation dose of 500 eV photons was evaluated. For the particular model of laser-scanning confocal microscope Carl Zeiss LSM700, used for the readout of the PL signal, the calibration dependencies on the intensity of photopumping (excitation) radiation (λ = 488 nm) and the gain have been obtained., Published by Wiley-Blackwell, [S.l.]

Choosing the optimal catalyst for a new transformation is challenging because the ideal molecular requirements of the catalyst for one reaction do not always simply translate to another. Large groups at the 3,3′ positions of the binaphthol rings are important for efficient stereoinduction but if they are too large this can lead to unusual or poor results. By applying a quantitative steric assessment of the substituents at the 3,3′ positions of the binaphthol ring, we have systematically studied the effect of modulating this group on enantioselectivity for a wide range of reactions involving imines, and verified this analysis using ONIOM calculations. We have shown that in most reactions, the stereochemical outcome depends on both proximal and remote sterics. Summarising detailed calculations into a simple qualitative model identifies and explains the steric features required for high selectivity. This model is consistent with seventy seven papers reporting reactions (over 1000 transformations in total), and provides a straightforward decision tree for selecting the best catalyst.

Fish oil rich in polyunsaturated omega-3 fatty acids is extracted in high yield from anchovy filleting waste using d-limonene as green biosolvent in a simple solid-liquid extraction performed by mechanically stirring and maceration followed by limonene removal via evaporation under reduced pressure. As limonene is renewably obtained from waste orange peel, this method closes the materials cycle and establishes a circular economy process to obtain high quality fish oil from biowaste available worldwide in several million t/year amount. Significant economic, social and environmental benefits are anticipated.

Crystallographic methods are used to identify the primary mineral phase of pseudomorphs of crystals embedded in 3.48 Ga bedded carbonate-chert rocks from the Dresser Formation, Pilbara Craton, Australia. This identification provides valuable information on the chemical environments at the onset of life on Earth., Crystallography has a long history of providing knowledge and methods for applications in other disciplines. The identification of minerals using X-ray diffraction is one of the most important contributions of crystallography to earth sciences. However, when the crystal itself has been dissolved, replaced or deeply modified during the geological history of the rocks, diffraction information is not available. Instead, the morphology of the crystal cast provides the only crystallographic information on the original mineral phase and the environment of crystal growth. This article reports an investigation of crystal pseudomorphs and crystal casts found in a carbonate-chert facies from the 3.48 Ga-old Dresser Formation (Pilbara Craton, Australia), considered to host some of the oldest remnants of life. A combination of X-ray microtomography, energy-dispersive X-ray spectroscopy and crystallographic methods has been used to reveal the original phases of these Archean pseudomorphs. It is found with a high degree of confidence that the original crystals forming in Archean times were hollow aragonite, the high-temperature polymorphs of calcium carbonate, rather than other possible alternatives such as gypsum (CaSO4·2H20) and nahcolite (NaHCO3). The methodology used is described in detail.

Acta crystallographica / D 73(7), 581 - 590(2017). doi:10.1107/S2059798317006970, Cadmium ions can be effectively used to promote crystal growth and for experimental phasing. Here, the use of cadmium ions as a suitable anomalous scatterer at the standard wavelength of 1 Å is demonstrated. The structures of three different proteins were determined using cadmium single-wavelength anomalous dispersion (SAD) phasing. Owing to the strong anomalous signal, the structure of lysozyme could be automatically phased and built using a very low anomalous multiplicity (1.1) and low-completeness (77%) data set. Additionally, it is shown that cadmium ions can easily substitute divalent ions in ATP–divalent cation complexes. This property could be generally applied for phasing experiments of a wide range of nucleotide-binding proteins. Improvements in crystal growth and quality, good anomalous signal at standard wavelengths (i.e. no need to change photon energy) and rapid phasing and refinement using a single data set are benefits that should allow cadmium ions to be widely used for experimental phasing., Published by Wiley-Blackwell, Oxford

Recent developments in microbial techniques (such as PCR, GE, FISH) have allowed researchers to detect, identify and quantify microorganisms without the limitation of culture-dependent methods. This has given both engineers and scientists a more fundamental understanding about systems containing microorganisms. These techniques can be used to monitor bacteria in wastewater treatment systems, soil and sea, industrial fermentation, food technology, and improve floccability, etc. However, despite these techniques being readily available and relatively cheap, they are not widely used by engineers. Hence, the aim of this paper is to introduce these techniques, and their applications, to chemical engineers. Two different studies related to industrial wastewater treatment, but applicable to general microorganism systems, will be presented: (1) microbial stability of pure cultures, and (2) bioreactor population shifts during alternating operational conditions. In (1), two bioreactors, inoculated with two different pure cultures, (A) Xanthobacter aut GJ10 and (B) Bulkholderia sp JS150, degrading 1,2-dichloroethane (DCE) and monochlorobenzene (MCB), respectively, were followed over time (Emanuelsson et al., 2005)(Emanuelsson et al., 2005). Specific and universal 16S rRNA oligonucleotide probes were used to identify the bacteria. It was found that bioreactor (A) remained pure for 290 days, whereas bioreactor (B) became contaminated within one week. The difference in behaviour is attributed to the pathway required to degrade DCE. In (2), the stability of a bacterial strain, which was isolated on the basis of its capability to degrade 2-fluorobenzoate from contaminated soil, in three different, up-flow fixed bed reactors operated under shock loads and starvation periods, was followed by denaturing gradient gel electrophoresis (DGGE) (Emanuelsson et al., 2006)(Emanuelsson et al., 2006). All bioreactors were rapidly colonised by different bacteria; however, the communities remained fairly stable over time, and shifts in bacterial populations were mainly found during the starvation periods. Copyright © 2007 Curtin University of Technology and John Wiley & Sons, Ltd.

Bioconversion of syngas/waste gas components to produce ethanol appears to be a promising alternative compared to the existing chemical techniques. Recently, several laboratory-scale studies have demonstrated the use of acetogens that have the ability to convert various syngas components (CO, CO2, and H2) to multicarbon com- pounds, such as acetate, butyrate, butanol, lactate, and ethanol, in which ethanol is often produced as a minor end- product. This bioconversion process has several advantages, such as its high specifi city, the fact that it does not require a highly specifi c H2/CO ratio, and that biocatalysts are less susceptible to metal poisoning. Furthermore, this process occurs under mild temperature and pressure and does not require any costly pre-treatment of the feed gas or costly metal catalysts, making the process superior over the conventional chemical catalytic conversion process. The main challenge faced for commercializing this technology is the poor aqueous solubility of the gaseous sub- strates (mainly CO and H2). In this paper, a critical review of CO-rich gas fermentation to produce ethanol has been analyzed systematically and published results have been compared. Special emphasis has been given to under- stand the microbial aspects of the conversion process, by highlighting the role of different micro-organisms used, pathways, and parameters affecting the bioconversion. An analysis of the process fundamentals of various bioreac- tors used for the biological conversion of CO-rich gases, mainly syngas to ethanol, has been made and reported in this paper. Various challenges faced by the syngas fermentation process for commercialization and future research requirements are also discussed. © 2011 Society of Chemical Industry and John Wiley & Sons, Ltd

Cocoa bean fermentation is still a spontaneous curing process to facilitate drying of nongerminating cocoa beans by pulp removal as well as to stimulate colour and flavour development of fermented dry cocoa beans. As it is carried out on farm, cocoa bean fermentation is subjected to various agricultural and operational practices and hence fermented dry cocoa beans of variable quality are obtained. Spontaneous cocoa bean fermentations carried out with care for approximate four days are characterized by a succession of particular microbial activities of three groups of micro-organisms, namely yeasts, lactic acid bacteria (LAB) and acetic acid bacteria (AAB), which results in well-fermented fully brown cocoa beans. This has been shown through a plethora of studies, often using a multiphasic experimental approach. Selected strains of several of the prevailing microbial species have been tested in appropriate cocoa pulp simulation media to unravel their functional roles and interactions as well as in small plastic vessels containing fresh cocoa pulp-bean mass to evaluate their capacity to dominate the cocoa bean fermentation process. Various starter cultures have been proposed for successful fermentation, encompassing both cocoa-derived and cocoa nonspecific strains of (hybrid) yeasts, LAB and AAB, some of which have been implemented on farms successfully.