High-Throughput Host-Microbe Single-Cell RNA Sequencing Reveals Ferroptosis-Associated Heterogeneity during Acinetobacter baumannii Infection.

Interactions between host and bacterial cells are integral to human physiology. The complexity of host-microbe interactions extends to different cell types, spatial aspects, and phenotypic heterogeneity, requiring high-resolution approaches to capture their full complexity. The latest breakthroughs in single-cell RNA sequencing (scRNA-seq) have opened up a new era of studies in host-pathogen interactions. Here, we first report a high-throughput cross-species dual scRNA-seq technology by using random primers to simultaneously capture both eukaryotic and bacterial RNAs (scRandom-seq). Using reference cells, scRandom-seq can detect individual eukaryotic and bacterial cells with high throughput and high specificity. Acinetobacter baumannii (A.b) is a highly opportunistic and nosocomial pathogen that displays resistance to many antibiotics, posing a significant threat to human health, calling for discoveries and treatment. In the A.b infection model, scRandom-seq witnessed polarization of THP-1 derived-macrophages and the intracellular A.b-induced ferroptosis-stress in host cells. The inhibition of ferroptosis by Ferrostatin-1 (Fer-1) resulted in the improvement of cell vitality and resistance to A.b infection, indicating the potential to resist related infections. scRandom-seq provides a high-throughput cross-species dual single-cell RNA profiling tool that will facilitate future discoveries in unraveling the complex interactions of host-microbe interactions in infection systems and tumor micro-environments.

Discovery of Novel Biphenyl Carboxylic Acid Derivatives as Potent URAT1 Inhibitors.

Urate transporter 1 (URAT1) is a clinically validated target for the treatment of hyperuricemia and gout. Due to the absence of protein structures, the molecular design of new URAT1 inhibitors generally resorts to ligand-based approaches. Two series of biphenyl carboxylic acids were designed based on the structures of URAT1 inhibitors Epaminurad and Telmisartan via a strategy of pharmacophore fusion. Fifty-one novel compounds were synthesized and most of them showed obvious inhibition against human URAT1. A1 and B21 were identified as the most potent URAT1 inhibitors in series A and B, respectively. They exhibited IC50 values of 0.93 µM and 0.17 µM, which were comparable or superior to the clinical uricosuric drug benzbromarone. The results confirmed the effectiveness of ligand-based approaches in identifying novel and potent URAT1 inhibitors.

OpenNAU: An open-source platform for normalizing, analyzing, and visualizing cancer untargeted metabolomics data.

Objective: As an important part of metabolomics analysis, untargeted metabolomics has become a powerful tool in the study of tumor mechanisms and the discovery of metabolic markers with high-throughput spectrometric data which also poses great challenges to data analysis, from the extraction of raw data to the identification of differential metabolites. To date, a large number of analytical tools and processes have been developed and constructed to serve untargeted metabolomics research. The different selection of analytical tools and parameter settings lead to varied results of untargeted metabolomics data. Our goal is to establish an easily operated platform and obtain a repeatable analysis result. Methods: We used the R language basic environment to construct the preprocessing system of the original data and the LAMP (Linux+Apache+MySQL+PHP) architecture to build a cloud mass spectrum data analysis system. Results: An open-source analysis software for untargeted metabolomics data (openNAU) was constructed. It includes the extraction of raw mass data and quality control for the identification of differential metabolic ion peaks. A reference metabolomics database based on public databases was also constructed. Conclusions: A complete analysis system platform for untargeted metabolomics was established. This platform provides a complete template interface for the addition and updating of the analysis process, so we can finish complex analyses of untargeted metabolomics with simple human-computer interactions. The source code can be downloaded from https://github.com/zjuRong/openNAU.

Exploring the structure, bonding and stability of noble gas compounds promoted by superhalogens. A case study on HNgMX3 (Ng = Ar-Rn, M = Be-Ca, X = F-Br) via combined high-level ab initio and DFT calculations.

A series of complexes (HNgMX3), formed from superhalogen MX3 (M = Be-Ca, X = F-Br) noble gas (Ar-Rn) and the hydrogen atom, were investigated via combined high-level ab initio and DFT calculations. The high vertical electron detachment energy (VDE) of the superhalogen part will lead to charge transfer from the noble gas hydride to it. This charge transfer gives rise to attractive ionic interaction between the two components and to the existence of these complexes as local minima on the potential energy surface eventually. However, the VDE value of the superhalogen part is not always monotonically correlated with the thermodynamic/kinetic stability of the whole complexes. Therefore the superhalogen itself might not be enough to provide information for the correct prediction of the properties of the whole composites. Although there are exothermic channels of dissociation, the existence of energy barrier might ensure the existence of these Ng hydrides under certain conditions. Our analysis indicates the existence of two important factors, functioning in opposite directions, for the energy barriers along the exothermic channel. To achieve a high energy barrier, the attractive interaction between superhalogen and the H atom in the TS, which lowers the barrier, needs to be suppressed effectively. An understanding of the superhalogen-based composites will provide valuable information on the functional properties and potential application of superhalogens. The details of the interaction between different parts of these composites should be one of the areas of focus in these studies.

Investigation of Conversion and Decay Processes in Thermally Activated Delayed Fluorescence Copper(I) Molecular Crystal: Theoretical Estimations from an ONIOM Approach Combined with the Tuned Range-Separated Density Functional Theory.

Accurate research of the photophysical processes is of great significance for the rational design of excellent thermally activated delayed fluorescence (TADF) materials. Herein, the interconversion and decay rates of the first excited singlet state (S1) and triplet states (T1) in the Cu(pop)(pz2BH2) complex are computed using the thermal vibration correlation function (TVCF) theory at different temperature. For consideration of the solid-state environment, a methodology that is based on the ONIOM model, combined with the optimally tuned range-separated hybrid functional (CAM-B3LYP*) method, was applied. Our calculated results are in excellent agreement with the experimentally available data. It has been found that the energy dissipation of the nonradiative processes from the S1 to ground state is promoted by low frequency vibrational modes in the solution phase, resulting in the high knr(S) = 1.68 × 108 s-1 at 300 K. However, for the crystal phase, they are easily hindered through intermolecular interactions, knr(S) is predicted to be decreased by about 5 orders of magnitude upon aggregation (2.98 × 103 s-1). With temperature increase, the reverse intersystem crossing (RISC) rate kRISC from T1 to S1 is drastically increased to 6.12 × 104 s-1 at 300 K, while the change of other rates is still small, which can compete with the radiative decay rate of kr(T) = 4.75 × 104 s-1 and nonradiative intersystem crossing rate of kISC(T1-S0) = 6.63 × 102 s-1 at the T1 state. This implies that the S1 state can be an efficient thermal population from the T1 state, leading to an occurrence of delayed fluorescence, and the complexes exhibit high emission quantum yields, 58.7%. But, at low temperature T < 100 K, the RISC rate is sharply change, kRISC ≪ kr(T) or kISC, which cannot induce an occurrence of delayed fluorescence. Our investigation would be helpful for designing novel, high-efficiency TADF materials.

Integrated whole-genome and transcriptome sequence analysis reveals the genetic characteristics of a riboflavin-overproducing Bacillus subtilis.

Commercial riboflavin production with Bacillus subtilis has been developed by combining rational and classical strain development for almost two decades, but how an improved riboflavin producer can be created rationally is still not completely understood. In this study, we demonstrate the combined use of integrated genomic and transcriptomic analysis of the genetic basis for riboflavin over-production in B. subtilis. This methodology succeeded in discerning the positive mutations in the mutagenesis derived riboflavin producer B. subtilis 24/pMX45 through whole-genome sequencing and transcriptome sequencing. These included RibC (G199D), ribD+(G+39A), PurA (P242L), CcpN(A44S), YvrH (R222Q) and two nonsense mutations YhcF (R90*) and YwaA (Q68*). Reintroducing these specific mutations into the wild-type strain recovered the riboflavin overproduction phenotype and subsequent metabolic engineering greatly improved riboflavin production, achieving an up to 3.4-fold increase of the riboflavin titer over the sequenced producer. A novel mutation, YvrH (R222Q), involved in a typical two-component regulatory system deregulated the purine de novo synthesis pathway and increased the pool of intracellular purine metabolites, which in turn increased riboflavin production. Taken together, we present a case study of combining genome and transcriptome analysis to elucidate the genetic underpinnings of a complex cellular property, which enabled the transfer of beneficial mutations to engineer a reference strain into an overproducer.

Carboxylic Acid-Promoted Single-Step Indole Construction from Simple Anilines and Ketones via Aerobic Cross-Dehydrogenative Coupling.

The cross-dehydrogenative coupling (CDC) reaction is an efficient strategy for indole synthesis. However, most CDC methods require special substrates, and the presence of inherent groups limits the versatility for further transformation. A carboxylic acid-promoted aerobic catalytic system is developed herein for a single-step synthesis of indoles from simple anilines and ketones. This versatile system is featured by the broad substrate scope and the use of ambient oxygen as an oxidant and is convenient and economical for both laboratory and industry applications. The existence of the labile hydrogen at C-3 and the highly transformable carbonyl at C-2 makes the indoles versatile building blocks for organic synthesis in different contexts. Computational studies based on the density functional theory (DFT) suggest that the rate-determining step is carboxylic acid-assisted condensation of the substrates, rather than the functionalization of aryl C-H. Accordingly, a pathway via imine intermediates is deemed to be the preferred mechanism. In contrast to the general deduction, the in situ formed imine, instead of its enamine isomer, is believed to be involved in the first ligand exchange and later carbopalladation of the α-Me, which shed new light on this indolization mechanism.

Basic photophysical analysis of a thermally activated delayed fluorescence copper(i) complex in the solid state: theoretical estimations from a polarizable continuum model (PCM)-tuned range-separated density functional approach.

A quantitative understanding of photophysical processes is fundamental for designing novel thermally activated delayed fluorescence (TADF) materials. Taking a Cu(pop)(pz2Bph2) crystal as a typical TADF molecular model, we computed the conversion and decay rates of the first excited singlet state (S1) and triplet state (T1) at different temperatures by employing the thermal vibration correlation function (TVCF) approach. For the consideration of the solid-state environment, a methodology, which is based on the combination of a nonempirical, optimally tuned range-separated hybrid functional with the polarizable continuum model, was applied. Our calculated results are in excellent agreement with the experimentally available data. It is found that the reverse intersystem crossing (RISC) from T1 to S1 proceeds at a rate of kRISC = 6.34 × 105 s-1 and can compete with the radiative decay rate (k = 3.29 × 103 s-1) and nonradiative intersystem crossing rate (k = 1.48 × 102 s-1) of T1 at 300 K. This implies that the S1 state can be repopulated from the T1 state, TADF should be observed and the TADF decay time was found to be τ (300 K) = 9.68 µs by fitting calculations. In addition, the calculations indicate that the free rotation of the phenylene ring in the pop ligand can provide an important channel to energy conversion between T1 and S1. But, at a low temperature of T < 100 K, the situation will experience a larger change. The RISC rate becomes very small, kRISC ≪ k or kISC, and it cannot induce an occurrence of delayed fluorescence. As a consequence, Cu(pop)(pz2Bph2) is a highly attractive candidate for applications of TADF.

A NiFe Alloy Reduced on Graphene Oxide for Electrochemical Nonenzymatic Glucose Sensing.

A NiFe alloy nanoparticle/graphene oxide hybrid (NiFe/GO) was prepared for electrochemical glucose sensing. The as-prepared NiFe/GO hybrid was characterized by transmission electron microscopy (TEM) and X-ray diffraction (XRD). The results indicated that NiFe alloy nanoparticles can be successfully deposited on GO. The electrochemical glucose sensing performance of the as-prepared NiFe/GO hybrid was studied by cyclic voltammetry and amperometric measurement. Results showed that the NiFe/GO-modified glassy carbon electrode had sensitivity of 173 µA mM-1 cm-2 for glucose sensing with a linear range up to 5 mM, which is superior to that of commonly used Ni nanoparticles. Furthermore, high selectivity for glucose detection could be achieved by the NiFe/GO hybrid. All the results demonstrated that the NiFe/GO hybrid has promise for application in electrochemical glucose sensing.

Transition metal oxide hierarchical nanotubes for energy applications.

We report a general synthetic method for transition metal oxide (TMO) hierarchical nanotube (HNT) structures by a solution-phase cation exchange method from Cu2O nanowire templates. This method leads to the formation of hollow, tubular backbones with secondary, thin nanostructures on the tube surface, which substantially increases the surface reactive sites for electrolyte contacts and electrochemical reactions. As proofs-of-concept, several representative first-row TMO HNTs have been synthesized, including CoOx, NiOx, MnOx, ZnOx and FeOx, with specific surface areas much larger than nanotubes or nanoparticles of corresponding materials. An example of the potential energy storage applications of CoOx HNTs as supercapacitors is also demonstrated.

Theoretical Study on the Reaction Mechanism of Ti with CH3CN in the Gas Phase.

To gain a deeper understanding of the reaction mechanisms of Ti with acetonitrile molecules, the triplet and singlet spin-state potential energy surfaces (PESs) has been investigated at B3LYP level of density functional theory (DFT). Crossing points between the different PESs and possible spin inversion processes are discussed by spin-orbit coupling (SOC) calculation. In addition, the bonding properties of the species along the reaction were analyzed by electron localization function (ELF), atoms in molecules (AIM) and natural bond orbital (NBO). The results showed that acetonitrile activation by Ti is a typical spin-forbidden process; larger SOC (by 220.12 cm(-1)) and the possibility of crossing between triplet and singlet imply that intersystem crossing (ISC) would occur near the minimum energy crossing point (MECP) during the transfer of the hydrogen atom.

Nanoparticle Superlattices as Efficient Bifunctional Electrocatalysts for Water Splitting.

The solar-driven water splitting process is highly attractive for alternative energy utilization, while developing efficient, earth-abundant, bifunctional catalysts for both oxygen evolution reaction and hydrogen evolution reaction has remained as a major challenge. Herein, we develop an ordered CoMnO@CN superlattice structure as an efficient bifunctional water-splitting electrocatalyst, in which uniform Co-Mn oxide (CoMnO) nanoparticles are coated with a thin, continuous nitrogen-doped carbon (CN) framework. The CoMnO nanoparticles enable optimized OER activity with effective electronic structure configuration, and the CN framework serves as an excellent HER catalyst. Importantly, the ordered superlattice structure is beneficial for enhanced reactive sites, efficient charge transfer, and structural stability. This bifunctional superlattice catalyst manifests optimized current densities and electrochemical stability in overall water splitting, outperforming most of the previously reported single- or bifunctional electrocatalysts. Combining with a silicon photovoltaic cell, this CoMnO@CN superlattice bifunctional catalyst enables unassisted solar water splitting continuously for ∼5 days with a solar-to-hydrogen conversion efficiency of ∼8.0%. Our discovery suggests that these transition metal oxide-based superlattices may serve as a unique structure modality for efficient bifunctional water splitting electrocatalysts with scale-up potentials.

Solar-Energy-Driven Photoelectrochemical Biosensing Using TiO2 Nanowires.

Photoelectrochemical sensing represents a unique means for chemical and biological detection, with foci of optimizing semiconductor composition and electronic structures, surface functionalization layers, and chemical detection methods. Here, we have briefly discussed our recent developments of TiO2 nanowire-based photoelectrochemical sensing, with particular emphasis on three main detection mechanisms and corresponding examples. We have also demonstrated the use of the photoelectrochemical sensing of real-time molecular reaction kinetic measurements, as well as direct interfacing of living cells and probing of cellular functions.

Solar-driven photoelectrochemical probing of nanodot/nanowire/cell interface.

We report a nitrogen-doped carbon nanodot (N-Cdot)/TiO2 nanowire photoanode for solar-driven, real-time, and sensitive photoelectrochemical probing of the cellular generation of H2S, an important endogenous gasotransmitter based on a tunable interfacial charge carrier transfer mechanism. Synthesized by a microwave-assisted solvothermal method and subsequent surface chemical conjugation, the obtained N-Cdot/TiO2 nanowire photoanode shows much enhanced photoelectrochemical photocurrent compared with pristine TiO2 nanowires. This photocurrent increase is attributed to the injection of photogenerated electrons from N-Cdots to TiO2 nanowires, confirmed by density functional theory simulation. In addition, the charge transfer efficiency is quenched by Cu(2+), whereas the introduction of H2S or S(2-) ions resets the charge transfer and subsequently the photocurrent, thus leading to sensitive photoelectrochemical recording of the H2S level in buffer and cellular environments. Moreover, this N-Cdot-TiO2 nanowire photoanode has been demonstrated for direct growth and interfacing of H9c2 cardiac myoblasts, with the capability of interrogating H2S cellular generation pathways by vascular endothelial growth factor stimulation as well as inhibition.

Fully solar-powered photoelectrochemical conversion for simultaneous energy storage and chemical sensing.

We report the development of a multifunctional, solar-powered photoelectrochemical (PEC)-pseudocapacitive-sensing material system for simultaneous solar energy conversion, electrochemical energy storage, and chemical detection. The TiO2 nanowire/NiO nanoflakes and the Si nanowire/Pt nanoparticle composites are used as photoanodes and photocathodes, respectively. A stable open-circuit voltage of ∼0.45 V and a high pseudocapacitance of up to ∼455 F g(-1) are obtained, which also exhibit a repeating charging-discharging capability. The PEC-pseudocapacitive device is fully solar powered, without the need of any external power supply. Moreover, this TiO2 nanowire/NiO nanoflake composite photoanode exhibits excellent glucose sensitivity and selectivity. Under the sun light illumination, the PEC photocurrent shows a sensitive increase upon different glucose additions. Meanwhile in the dark, the open-circuit voltage of the charged pseudocapacitor also exhibits a corresponding signal over glucose analyte, thus serving as a full solar-powered energy conversion-storage-utilization system.

Growth of Single-Layered Two-Dimensional Mesoporous Polymer/Carbon Films by Self-Assembly of Monomicelles at the Interfaces of Various Substrates.

Single-layered two-dimensional (2D) ultrathin mesoporous polymer/carbon films are grown by self-assembly of monomicelles at the interfaces of various substrates, which is a general and common modification strategy. These unconventional 2D mesoporous films possess only a single layer of mesopores, while the size of the thin films can grow up to inch size in the plane. Free-standing transparent mesoporous carbon ultrathin films, together with the ordered mesoporous structure on the substrates of different compositions (e.g. metal oxides, carbon) and morphologies (e.g. nanocubes, nanodiscs, flexible and patterned substrates) have been obtained. This strategy not only affords controllable hierarchical porous nanostructures, but also appends the easily modified and multifunctional properties of carbon to the primary substrate. By using this method, we have fabricated Fe2 O3 -mesoporous carbon photoelectrochemical biosensors, which show excellent sensitivity and selectivity for glutathione.

Oriented mesoporous nanopyramids as versatile plasmon-enhanced interfaces.

We developed a facile interfacial oriented growth and self-assembly process to fabricate three-dimensional (3D) aligned mesoporous iron oxide nanopyramid arrays (NPAs). The unique NPAs possess a 3D mesostructure with multiple features, including high surface area (~175 m(2)/g), large pore size (~20 nm), excellent flexibility (bent over 150 times), and scalability at the foot scale for practical applications. More importantly, these NPAs structures enable versatile enhancement of localized surface plasmon resonance and photoelectrochemical conversion. The integration of plasmonic gold with 3D NPAs remarkably improves the performance of photoelectrochemical conversion, leading to ~6- and 83-fold increases of the photocurrent under simulated solar and visible-light illumination, respectively. The fabrication and investigation of NPAs provide a new paradigm for preparing unconventional mesoporous oriented thin films and further suggest a new strategy for designing plasmonic metal/semiconductor systems for effective solar energy harvesting.

Surface plasmon resonance enhanced real-time photoelectrochemical protein sensing by gold nanoparticle-decorated TiO2 nanowires.

Recently developed photoelectrochemical (PEC) sensing systems represent a unique potential detection method for real-time analysis of chemical/biological molecules, while the low absorption of TiO2 nanomaterials in the visible wavelength region and the slow surface charge transfer efficiency limit the ultimate sensitivity. Here we develop a gold nanoparticle-decorated TiO2 nanowire sensor for PEC detection of protein binding. The direct attachment of Au nanoparticles to TiO2 nanowires offers strong surface plasmon resonance for electrochemical field effect amplification, yielding a ~100% increase of photocurrent density. In addition, the surface functionalization of gold nanoparticles allows for direct capturing of target proteins near the Au/TiO2 interface and thus substantially enhances the capability of attenuation of energy coupling between Au and TiO2, leading to much-improved sensor performance. As a proof of concept, cholera toxin subunit B has been robustly detected by the TiO2-Au nanowire sensor functionalized with ganglioside GM1, with a high sensitivity of 0.167 nM and excellent selectivity. Furthermore, the real-time feature of photoelectrochemical sensing enables direct measurement of binding kinetics between cholera toxin subunit B and GM1, yielding association and disassociation rate constants and an equilibrium constant K(d) of 4.17 nM. This surface plasmon resonance-enhanced real-time, photoelectrochemical sensing design may lead to exciting biodetection capabilities with high sensitivity and real-time kinetic studies.

Reversible chemical tuning of charge carriers for enhanced photoelectrochemical conversion and probing of living cells.

A facile, solution method for reversible tuning of oxygen vacancies inside TiO2 nanowires, in which the reducing treatment of TiO2 by NaBH4 leads to 2.4-fold increase of photocurrent density, compared to pristine TiO2 nanowires, is reported. Subsequent oxidizing treatment using KMnO4 or annealing in air can reset the photocurrent density to the original values. The incident photo-to-current conversion efficiency measurement exhibits that the reduced TiO2 nanowires present both enhanced photoactivity in both UV and visible regions. Density functional theory calculations reveal that the oxygen vacancies in the reduced TiO2 cause defect states in the band structure and result in enhanced carrier density and conductivity. In addition, the enhanced solar energy-driven photoelectrochemical conversion allows real-time, sensitive chemical probing of living cells that are directly grown on the TiO2 nanowire photoanodes. As proofs-of-concept, after functionalized with horseradish peroxidase (HRP) on the surface, the reduced TiO2 NWs demonstrate sensitive, real-time monitoring of the H2O2 levels in several distinctive living cell lines, with the lowest detectable H2O2 concentration of 7.7 nM. This reversible tuning of oxygen vacancies suggests a facile means for transition metal oxides, with enhanced photoconversion activity and electrochemical sensitivity.

Deregulation of purine pathway in Bacillus subtilis and its use in riboflavin biosynthesis.

BACKGROUND: Purine nucleotides are essential metabolites for living organisms because they are involved in many important processes, such as nucleic acid synthesis, energy supply, and biosynthesis of several amino acids and riboflavin. Owing to the pivotal roles of purines in cell physiology, the pool of intracellular purine nucleotides must be maintained under strict control, and hence the de novo purine biosynthetic pathway is tightly regulated by transcription repression and inhibition mechanism. Deregulation of purine pathway is essential for this pathway engineering in Bacillus subtilis. RESULTS: Deregulation of purine pathway was attempted to improve purine nucleotides supply, based on a riboflavin producer B. subtilis strain with modification of its rib operon. To eliminate transcription repression, the pur operon repressor PurR and the 5'-UTR of pur operon containing a guanine-sensing riboswitch were disrupted. Quantitative RT-PCR analysis revealed that the relative transcription levels of purine genes were up-regulated about 380 times. Furthermore, site-directed mutagenesis was successfully introduced into PRPP amidotransferase (encoded by purF) to remove feedback inhibition by homologous alignment and analysis. Overexpression of the novel mutant PurF (D293V, K316Q and S400W) significantly increased PRPP amidotransferase activity and triggered a strong refractory effect on purine nucleotides mediated inhibition. Intracellular metabolite target analysis indicated that the purine nucleotides supply in engineered strains was facilitated by a stepwise gene-targeted deregulation. With these genetic manipulations, we managed to enhance the metabolic flow through purine pathway and consequently increased riboflavin production 3-fold (826.52 mg/L) in the purF-VQW mutant strain. CONCLUSIONS: A sequential optimization strategy was applied to deregulate the rib operon and purine pathway of B. subtilis to create genetic diversities and to improve riboflavin production. Based on the deregulation of purine pathway at transcription and metabolic levels, an extended application is recommended for the yield of products, like inosine, guanosine, adenosine and folate which are directly stemming from purine pathway in B. subtilis.