Bacterial phosphorothioate (PT) DNA modifications are incorporated by Dnd proteins A-E and often function with DndF-H as a restriction-modification (R-M) system, as in Escherichia coli B7A. However, bacteria such as Vibrio cyclitrophicus FF75 lack dndF-H, which points to other PT functions. To better understand PT biology, we report two novel, orthogonal technologies to map PTs across the genomes of B7A and FF75 with >90% agreement: real-time (SMRT) sequencing and deep sequencing of iodine-induced cleavage at PT (ICDS). In B7A, we detect PT on both strands of GpsAAC/GpsTTC motifs, but with only 18% of 40,701 possible sites modified. In contrast, PT in FF75 occurs as a single-strand modification at CpsCA, again with only 14% of 160,541 sites modified. Single-molecule analysis indicates that modification could be partial at any particular genomic site even with active restriction by DndF-H, with direct interaction of modification proteins with GAAC/GTTC sites demonstrated with oligonucleotides. These results point to highly unusual target selection by PT modification proteins and rule out known R-M mechanisms.

Microscopic understanding of interaction between H2O and MAPbI3 (CH3NH3PbI3) is essential to further improve efficiency and stability of perovskite solar cells. A complete picture of perovskite from initial physical uptake of water molecules to final chemical transition to its monohydrate MAPbI3·H2O is obtained with in situ infrared spectroscopy, mass monitoring, and X-ray diffraction. Despite strong affinity of MA to water, MAPbI3 absorbs almost no water from ambient air. Water molecules penetrate the perovskite lattice and share the space with MA up to one H2O per MA at high-humidity levels. However, the interaction between MA and H2O through hydrogen bonding is not established until the phase transition to monohydrate where H2O and MA are locked to each other. This lack of interaction in water-infiltrated perovskite is a result of dynamic orientational disorder imposed by tetragonal lattice symmetry. The apparent inertness of H2O along with high stability of perovskite in an ambient environment provides a solid foundation for its long-term application in solar cells and optoelectronic devices.

Development of highly active and stable electrocatalysts is a key to realize efficient hydrogen evolution through water electrolysis. Here, the development of a 3D self-supported integrated electrode constituting few layered N, P dual-doped carbon-encapsulated ultrafine MoP nanocrystal/MoP cluster hybrids on carbon cloth (FLNPC@MoP-NC/MoP-C/CC) is demonstrated. Benefiting from novel structural features including fully open and accessible nanoporosity, ultrasmall size of MoP-NCs on MoP-Cs as well as strong synergistic effects of N, P dual-doped carbon layers with MoP-NCs, the FLNPC@ MoP-NC/MoP-C/CC as a 3D self-supported binder-free integrated electrode exhibits extraordinary catalytic activity for the hydrogen evolution reaction (HER) with extremely low overpotentials at all pH values ( j = 10 mA cm −2 at η = 74, 106, and 69 mV in 0.5 m H 2 SO 4 , 1.0 m PBS, and 1.0 m KOH electrolytes, respectively). To the best of our knowledge, the ultrahigh electrocatalytic performance represents one of the best MoP-based HER electrocatalysts reported so far. Additionally, few layered N, P dual-doped carbon can effectively prevent MoP-NC/MoP-C from corrosion, making the FLNPC@ MoP-NC/MoP-C/CC exhibit nearly unfading stability after 50 h testing in acidic, neutral, and alkaline media, which shows great promise for electrocatalytic water splitting application.

The construction of a novel 3D self‐supported integrated NixCo2−xP@NC (0 < x < 2) nanowall array (NA) on Ni foam (NF) electrode constituting highly dispersed NixCo2−xP nanoparticles, nanorods, nanocapsules, and nanodendrites embedded in N‐doped carbon (NC) NA grown on NF is reported. Benefiting from the collective effects of special morphological and structural design and electronic structure engineering, the NixCo2−xP@NC NA/NF electrodes exhibit superior electrocatalytic performance for water splitting with an excellent stability in a wide pH range. The optimal NiCoP@NC NA/NF electrode exhibits the best hydrogen evolution reaction (HER) activity in acidic solution so far, attaining a current density of 10 mA cm−2 at an overpotential of 34 mV. Moreover, the electrode manifests remarkable performances toward both HER and oxygen evolution reaction in alkaline medium with only small overpotentials of 37 mV at 10 mA cm−2 and 305 mV at 50 mA cm−2, respectively. Most importantly, when coupling with the NiCoP@NC NA/NF electrode for overall water splitting, an alkali electrolyzer delivers a current density of 20 mA cm−2 at a very low cell voltage of ≈1.56 V. In addition, the NiCoP@NC NA/NF electrode has outstanding long‐term durability at j = 10 mA cm−2 with a negligible degradation in current density over 22 h in both acidic and alkaline media.

The formation of (Fe, Cr)(OH)3 nanoparticles determines the fate of aqueous Cr in many aquatic environments. Using small-angle X-ray scattering, precipitation rates of (Fe, Cr)(OH)3 nanoparticles in solution and on quartz were quantified from 0.1 mM Fe(III) solutions containing 0-0.25 mM Cr(III) at pH = 3.7 ± 0.2. Concentration ratio of aqueous Cr(III)/Fe(III) controlled the chemical composition (x) of (Fex, Cr1-x)(OH)3 precipitates, solutions' supersaturation with respect to precipitates, and the surface charge of quartz. Therefore, the aqueous Cr(III)/Fe(III) ratio affected homogeneous (in solution) and heterogeneous (on quartz) precipitation rates of (Fex, Cr1-x)(OH)3 through different mechanisms. The sequestration mechanisms of Cr(III) in precipitates were also investigated. In solutions with high aqueous Cr(III)/Fe(III) ratios, surface enrichment of Cr(III) on the precipitates occurred, resulting in slower particle growth in solutions. From solutions with 0-0.1 mM Cr(III), the particles on quartz grew from 2 to 4 nm within 1 h. Interestingly, from solution with 0.25 mM Cr(III), particles of two distinct sizes (2 and 6 nm) formed on quartz, and their sizes remained unchanged throughout the reaction. Our study provided new insights on homogeneous and heterogeneous precipitation of (Fex, Cr1-x)(OH)3 nanoparticles, which can help determine the fate of Cr in aquatic environments.

Genomic modification with sulfur as phosphorothioate (PT) is widespread among prokaryotes, including human pathogens. Apart from its physiological functions, the redox and nucleophilic properties of PT sulfur suggest effects on bacterial fitness in stressful environments. Here we show that PTs are dynamic and labile DNA modifications that cause genomic instability during oxidative stress. Using coupled isotopic labeling-mass spectrometry, we observed sulfur replacement in PTs at a rate of ~2%/h in unstressed Escherichia coli and Salmonella enterica. While PT levels were unaffected by exposure to hydrogen peroxide (H2O2) or hypochlorous acid (HOCl), PT turnover increased to 3.8–10%/h for HOCl and was unchanged for H2O2, consistent with repair of HOCl-induced sulfur damage. PT-dependent HOCl sensitivity extended to cytotoxicity and DNA strand-breaks, which occurred at orders-of-magnitude lower doses of HOCl than H2O2. The genotoxicity of HOCl in PT-containing bacteria suggests reduced fitness in competition with HOCl-producing organisms and during human infections.

Xantholipin and several related polycyclic xanthone antibiotics feature a unique xanthone ring nucleus within a highly oxygenated, angular, fused hexacyclic system. In this study, we demonstrated that a flavin-dependent monooxygenase (FMO) XanO4 catalyzes the oxidative transformation of an anthraquinone to a xanthone system during the biosynthesis of xantholipin. In vitro isotopic labeling experiments showed that the reaction involves sequential insertion of two oxygen atoms, accompanied by an unexpected cryptic demethoxylation reaction. Moreover, characterizations of homologous FMOs of XanO4 suggested the generality of the XanO4-like-mediated reaction for the assembly of a xanthone ring in the biosynthesis of polycyclic xanthone antibiotics. These findings not only expand the repertoire of FMO activities but also reveal a novel mechanism for xanthone ring formation.

Abstract DNA damage and epigenetic marks are well established to have profound influences on genome stability and cell phenotype, yet there are few technologies to obtain high-resolution genomic maps of the many types of chemical modifications of DNA. Here we present Nick-seq for quantitative, sensitive, and accurate mapping of DNA modifications at single-nucleotide resolution across genomes. Pre-existing breaks are first blocked and DNA modifications are then converted enzymatically or chemically to strand-breaks for both 3′-extension by nick-translation to produce nuclease-resistant oligonucleotides and 3′-terminal transferase tailing. Following library preparation and next generation sequencing, the complementary datasets are mined with a custom workflow to increase sensitivity, specificity and accuracy of the map. The utility of Nick-seq is demonstrated with genomic maps of site-specific endonuclease strand-breaks in purified DNA from Eschericia coli, phosphorothioate epigenetics in Salmonella enterica Cerro 87, and oxidation-induced abasic sites in DNA from E. coli treated with a sublethal dose of hydrogen peroxide. Nick-seq applicability is demonstrated with strategies for &gt;25 types of DNA modification and damage.