Mechanism and Structural Insights Into a Novel Esterase, E53, Isolated From Erythrobacter longus

Esterases are a class of enzymes that split esters into an acid and an alcohol in a chemical reaction with water, having high potential in pharmaceutical, food and biofuel industrial applications. To advance the understanding of esterases, we have identified and characterized E53, an alkalophilic esterase from a marine bacterium Erythrobacter longus. The crystal structures of wild type E53 and three variants were solved successfully using the X-ray diffraction method. Phylogenetic analysis classified E53 as a member of the family IV esterase. The enzyme showed highest activity against p-nitrophenyl butyrate substrate at pH 8.5–9.5 and 40°C. Based on the structural feature, the catalytic pocket was defined as R1 (catalytic center), R2 (pocket entrance), and R3 (end area of pocket) regions. Nine variants were generated spanning R1–R3 and thorough functional studies were performed. Detailed structural analysis and the results obtained from the mutagenesis study revealed that mutations in the R1 region could regulate the catalytic reaction in both positive and negative directions; expanding the bottleneck in R2 region has improved the enzymatic activity; and R3 region was associated with the determination of the pH pattern of E53. N166A in R3 region showed reduced activity only under alkaline conditions, and structural analysis indicated the role of N166 in stabilizing the loop by forming a hydrogen bond with L193 and G233. In summary, the systematic studies on E53 performed in this work provide structural and functional insights into alkaliphilic esterases and further our knowledge of these enzymes.

Comparative And Phylogenetic Analyses of Six Kenya Polystachya (Orchidaceae) Species Based On The Complete Chloroplast Genome Sequences

Background: Polystachya Hook. is a large pantropical orchid genus (c. 240 species) distributed in Africa, southern Asia and the Americas, with the centre of diversity in Africa. Chloroplast (cp) genomes of plants are highly conserved and can provide much more informative DNA sites and generate much better resolution for plant phylogenies. However, for Polystachya, the whole cp genome including its structure features are yet unknown and its phylogenetic placement of the genus within the Orchidaceae is still unclear.Results: In this study, the complete cp genomes of six Polystachya species were assembled based on genome skimming. We subjected them to comparative genomic analyses and reconstructed their phylogenetic relationships. The results exhibited that the cp genomes had a typical quadripartite structure with conserved genome arrangement and moderate divergence. The cp genomes of the six Polystachya species ranged from 145,484 bp to 149,274 bp in length and had almost similar GC content of 36.9%-37.0%. Gene annotation revealed 113 unique genes. In additions, 19 genes are duplicated in the inverted regions, and 17 gene possessed intron. Comparative analysis of the overall sequence identity among six complete cp genomes confirmed that for both coding and non-coding regions in Polystachya, SC regions exhibit higher sequence variation than IRs. Furthermore, there were various amplifications in the IR region among the six Polystachya species. Most of the protein-coding genes of these species had a high degree of codon preference. We screened out specific SSR and found seven relatively highly variable loci. Moreover, 13 genes were discovered with significant positive selection. Phylogenetic analysis suggested that the six Polystachya species formed a monophyletic clade and had more closely related to tribe Vandeae. Phylogenetic relationships of the family Orchidaceae inferred from the 85 cp genome sequences were generally consistent with previous studies and robust. Conclusions: Our study reported the complete cp genomes of the six Polystachya species, and provided detailed structural analysis and comparative analysis results, which can contribute to the development of DNA markers for use in the study of genetic variability and evolutionary studies in Polystachya. In addition, the present results further demonstrate the phylogenetic position of Polystachya.

Permeability variation in crystalline rocks due to low-grade solution phenomena

Permeability of crystalline rocks depends on parameters such as density and interconnectivity of fractures and pores. While in pristine crystalline rocks porosity is usually considered to be low, low-grade solution phenomena such as the formation of episyenites occur occasionally and may cause a local dramatic increase in porosity and permeability. These solution phenomena can be effective in otherwise unaltered rocks and may result in the preferential removal of certain mineral phases, especially of quartz so that porosities correspond to the spatial distribution of the previously existing mineral phase if no subsequent mineralization occurs (e.g., Pennacchioni et al., 2016). Using light-optical and scanning electron microscopy, X-ray tomography, micro-XRD, as well as digital image analysis, the differences in connectivity and hence permeability between, for example, quartz-depleted granite, gneiss, and schist can be characterized and quantified. We demonstrate that such porosities do not necessarily result in high permeabilities in an undeformed granodiorite from the Central Gneiss unit of the Tauern Window (Lago di Neves area, Italy), since former quartz aggregates are not interconnected due to their relatively late crystallization age and the preservation of the magmatic fabric; however, in the case of moderate mylonitic deformation, quartz as rheologically weak phase forms interconnected aggregates and layers. Its dissolution results in an extremely increased permeability. Therefore, not only the content and grain size but also the distribution, shape and alignment of minerals are crucial for rock permeability and need to be carefully investigated when searching for a final repository of highly radioactive waste in crystalline rocks. Especially since local shear zones may form in otherwise undeformed intrusive bodies, a detailed structural analysis beyond the exclusion of the presence of fractures is required to mitigate the risk of a long-lasting nuclear waste disposal.

Structural Digital Twin of FPSO for Monitoring the Hull and Topsides Based on Inspection Data and Load Measurement

A high-fidelity FPSO Structural Digital Twin (SDT) based on Reduced Basis Finite Element Analysis (RB-FEA) coupled with inspection data and physical sensor measurements (advisory hull monitoring system) is presented to demonstrate a complete FPSO "digital thread" that combines operational data feeds, detailed structural analysis based on as-is asset condition, and automated structural integrity reporting. This lays the groundwork for a philosophical shift for asset lifecycle management by enabling the use of "as-measured" conditions in lieu of assumed "design-conditions" for a more accurate, and robust understanding of asset health. We demonstrate the deployment of this methodology for the Bonga FPSO and discuss the value that it brings during day-to-day operations.

Chemical Modification of Combusted Coal Gangue for U(VI) Adsorption: Towards a Waste Control by Waste Strategy

Uranium mining waste causes serious radiation-related health and environmental problems. This has encouraged efforts toward U(VI) removal with low cost and high efficiency. Typical uranium adsorbents, such as polymers, geopolymers, zeolites, and MOFs, and their associated high costs limit their practical applications. In this regard, this work found that the natural combusted coal gangue (CCG) could be a potential precursor of cheap sorbents to eliminate U(VI). The removal efficiency was modulated by chemical activation under acid and alkaline conditions, obtaining HCG (CCG activated with HCl) and KCG (CCG activated with KOH), respectively. The detailed structural analysis uncovered that those natural mineral substances, including quartz and kaolinite, were the main components in CCG and HCG. One of the key findings was that kalsilite formed in KCG under a mild synthetic condition can conspicuous enhance the affinity towards U(VI). The best equilibrium adsorption capacity with KCG was observed to be 140 mg/g under pH 6 within 120 min, following a pseudo-second-order kinetic model. To understand the improved adsorption performance, an adsorption mechanism was proposed by evaluating the pH of uranyl solutions, adsorbent dosage, as well as contact time. Combining with the structural analysis, this revealed that the uranyl adsorption process was mainly governed by chemisorption. This study gave rise to a utilization approach for CCG to obtain cost-effective adsorbents and paved a novel way towards eliminating uranium by a waste control by waste strategy.

Time-resolved dissolution elucidates the mechanism of zeolite MFI crystallization

Zeolite crystal growth mechanisms are not fully elucidated owing to their complexity wherein the formation of a particular zeolite can occur by more than one crystallization pathway. Here, we have conducted time-resolved dissolution experiments of MFI-type zeolite crystals in ammonium fluoride medium where detailed structural analysis allowed us to extrapolate and elucidate the possible mechanism of nucleation and crystal growth. A combination of electron and scanning probe microscopy shows that dissolution initiates preferentially at lattice defects and progressively removes defect zones to reveal a mosaic structure of crystalline domains within each zeolite crystal. This mosaic architecture evolves during the growth process, reflecting the changing conditions of zeolite formation that can be retroactively assessed during zeolite crystal dissolution. Moreover, a more general implication of this study is the establishment that dissolution can be used successfully as an ex situ technique to uncover details about crystal growth features inaccessible by other methods.

Targeting the ALS/FTD-associated A-DNA kink with anthracene-based metal complex causes DNA backbone straightening and groove contraction

The use of a small molecule compound to reduce toxic repeat RNA transcripts or their translated aberrant proteins to target repeat-expanded RNA/DNA with a G4C2 motif is a promising strategy to treat C9orf72-linked disorders. In this study, the crystal structures of DNA and RNA–DNA hybrid duplexes with the -GGGCCG- region as a G4C2 repeat motif were solved. Unusual groove widening and sharper bending of the G4C2 DNA duplex A-DNA conformation with B-form characteristics inside was observed. The G4C2 RNA–DNA hybrid duplex adopts a more typical rigid A form structure. Detailed structural analysis revealed that the G4C2 repeat motif of the DNA duplex exhibits a hydration shell and greater flexibility and serves as a ‘hot-spot’ for binding of the anthracene-based nickel complex, NiII(Chro)2 (Chro = Chromomycin A3). In addition to the original GGCC recognition site, NiII(Chro)2 has extended specificity and binds the flanked G:C base pairs of the GGCC core, resulting in minor groove contraction and straightening of the DNA backbone. We have also shown that Chro-metal complexes inhibit neuronal toxicity and suppresses locomotor deficits in a Drosophila model of C9orf72-associated ALS. The approach represents a new direction for drug discovery against ALS and FTD diseases by targeting G4C2 repeat motif DNA.

Taking Advantage of Ortho- and Peri-Substitution to Design Original 9-Membered P,O,Si-Heterocycles

A family of 9 cyclic phosphine-disiloxane featuring peri-substituted naphthyl(Nap)/acenaphthyl(Ace) scaffolds have been prepared and fully characterized including X-ray structure, which allows a detailed structural analysis. This straightforward synthesis takes advantage of both ortho- and peri-substitution of Nap/Ace-substituted phosphine oxides. The synthetic method allows diversifying the polyaromatic platform (Nap and Ace) as well as the Si substituents (Me and Ph). Despite a strong steric congestion, the P-atom remains reactive toward oxidation or coordination. In particular, Au(I) complex could be prepared. All the compounds display absorption/luminescence in the UV-Vis range. Surprisingly, the P-trivalent derivatives display unexpected luminescence in the green in solid-state.