Recent bcoe_cee_oapolicydeposits items

M13 bacteriophage spheroids as scaffolds for directed synthesis of spiky gold nanostructures

Fri, 27 Feb 2026 00:00:00 +0000

The spherical form (s-form) of a genetically-modified gold-binding M13 bacteriophage was investigated as a scaffold for gold synthesis. Repeated mixing of the phage with chloroform caused a 15-fold contraction from a nearly one micron long filament to an approximately 60 nm diameter spheroid. The geometry of the viral template and the helicity of its major coat protein were monitored throughout the transformation process using electron microscopy and circular dichroism spectroscopy, respectively. The transformed virus, which retained both its gold-binding and mineralization properties, was used to assemble gold colloid clusters and synthesize gold nanostructures. Spheroid-templated gold synthesis products differed in morphology from filament-templated ones. Spike-like structures protruded from the spherical template while isotropic particles developed on the filamentous template. Using inductively coupled plasma-mass spectroscopy (ICP-MS), gold ion adsorption was found to be comparatively...

Modeling Microenvironmental Effects in Heterogeneous Catalysis

Thu, 12 Feb 2026 00:00:00 +0000

Heterogeneous catalysis involves a complex interplay of adsorption, charge transfer, and catalyst restructuring at solid–gas or solid–liquid interfaces. While first-principles methods such as KS-DFT and AIMD accurately describe chemisorbed species, they struggle to capture weakly bound or dynamic molecules subject to thermal fluctuations. Continuum models provide macroscopic insight into electrostatics and transport but often neglect the interfacial molecular structure, especially within the Stern layer. The challenge is even greater at gas–solid interfaces, where the gas phase is typically ignored, giving rise to a long-standing pressure gap between theory and experiment. This Perspective advocates a statistical-mechanical description of interfacial species using classical density functional theory (cDFT), in which physisorption and gas/liquid-phase inhomogeneity near catalytic surfaces are represented by molecular density distributions rather than fixed atomic configurations....

Simultaneous hyperspectral imaging and pyrometry for multi-phase temperature profiling of energetic composite reactions

Thu, 15 Jan 2026 00:00:00 +0000

High-temperature, multi-phase reactions in energetic composites present significant challenges in understanding their chemical processes and underlying mechanisms. These systems often involve rapid, heterogeneous reactions which require temporally and spatially resolved diagnostic tools. To address this need, this work develops a dual-camera system that integrates hyperspectral emission spectroscopy and three-color pyrometry, enabling simultaneous, high-speed measurements of gas-phase and condensed-phase temperatures. One camera captures RGB video for three-color pyrometry, while the other captures emission spectra using a slit-array mask and diffraction grating system. The slit-array mask is designed to achieve spatial coverage, allowing for 2D gas-phase temperature profiling. Gas-phase temperatures are derived using emission spectra based on Boltzmann equation, utilizing the intensity ratios of potassium emission lines near 580 nm and 693 nm. Demonstration experiments were conducted...

Heterogeneous catalysis: Optimal performance at a phase boundary?

Fri, 21 Nov 2025 00:00:00 +0000

Most of the industrially used heterogeneous catalysts have been discovered by trial and error, and despite decades of experience, the discovery of new catalysts continues to be extremely challenging. The drive to uncover guiding principles in catalyst design is more present than ever. We share a series of observations indicating that optimal catalysts typically function at characteristic phase boundaries (e.g., abrupt changes in adsorbate coverage, catalyst structure, etc.) accessed in the reaction conditions. The catalyst exploits the associated instability—the desire to exist in multiple states simultaneously—as a driving force for chemical transformations. In other words, phase boundaries are good places to start the catalyst search, and indeed, we should focus on at least two phases at once rather than just one. We substantiate this claim with several studies that combine statistical operando modeling and experiments. Transpiring from these observations is a hitherto unrecognized...

Defect-Driven Redox Interplay on Anatase TiO2: Surface-Structure Dependent Activation for CO2 Hydrogenation Catalysis

Fri, 21 Nov 2025 00:00:00 +0000

Titanium dioxide (TiO₂) is one of the most extensively studied oxides as an active catalyst or catalyst support, particularly in energy and environmental applications, but the atomistic mechanisms governing its dynamic response to reactive environments and their correlation to reactivity remain largely elusive. Using in situ environmental transmission electron microscopy (ETEM), synchrotron X-ray diffraction (XRD), ambient-pressure X-ray photoelectron spectroscopy (AP-XPS), temperature-programmed reduction (TPR), reactivity measurements, and theoretical modeling, we reveal the dynamic interplay between oxygen loss and replenishment of anatase TiO₂ under varying reactive conditions. Under H₂ exposure, anatase TiO₂ undergoes surface reduction via lattice oxygen loss, forming Ti₃O₅. In contrast, CO₂ exposure induces oxygen replenishment, reversing stoichiometry. In mixed H₂/CO₂ environments,...

Kingdom-wide CRISPR guide design with ALLEGRO

Thu, 28 Aug 2025 00:00:00 +0000

Designing CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) single guide RNA (sgRNA) libraries targeting entire kingdoms of life will significantly advance genetic research in diverse and underexplored taxa. Current sgRNA design tools are often species-specific and fail to scale to large, phylogenetically diverse datasets, limiting their applicability to comparative genomics, evolutionary studies, and biotechnology. Here, we introduce ALLEGRO, a combinatorial optimization algorithm designed to compose minimal, yet highly effective sgRNA libraries targeting thousands of species at the same time. Leveraging integer linear programming, ALLEGRO identified compact sgRNA sets simultaneously targeting multiple genes of interest for over 2000 species across the fungal kingdom. We experimentally validated sgRNAs designed by ALLEGRO in Kluyveromyces marxianus, Komagataella phaffii, Yarrowia lipolytica, and Saccharomyces cerevisiae, confirming successful genome...

Modeling thermocatalytic systems for CO 2 hydrogenation to methanol

Fri, 11 Apr 2025 00:00:00 +0000

The hydrogenation of CO₂ to CH₃OH over Cu-based catalysts holds significant potential for advancing carbon sequestration and sustainable chemical processes. While numerous studies have focused on catalyst development, the environmental effects on underlying reaction mechanisms have yet to be fully understood. In this work, we develop a grand potential theory for a comprehensive analysis of CO₂ hydrogenation to CH₃OH over Cu (111) and Cu (211) surfaces. By integrating electronic and classical density functional calculations to bridge the "pressure gap", the theoretical results revealed that the HCOO* formation rate may vary by several orders of magnitude depending on reaction conditions. The grand potential theory enables us to elucidate the molecular mechanisms underlying the need for high H₂ pressure, the prevalence of saturated CO₂ adsorption, and the important roles of CO and H₂O in hydrogenation....

Oxidation of V(IV) by Birnessite: Kinetics and Surface Complexation

Sat, 5 Apr 2025 00:00:00 +0000

Vanadium is a redox-active metal that has been added to the EPA's Contaminant Candidate List with a notification level of 50 μg L^-1 due to mounting evidence that V^V exposure can lead to adverse health outcomes. Groundwater V concentration exceeds the notification level in many locations, yet geochemical controls on its mobility are poorly understood. Here, we examined the redox interaction between V^IV and birnessite (MnO₂), a well-characterized oxidant and a scavenger of many trace metals. In our findings, birnessite quickly oxidized sparingly soluble V^IV species such as häggite [V₂O₃(OH)₂] into highly mobile and toxic vanadate (H_nVO₄^(3-n)-) in continuously stirred batch reactors under neutral pH conditions. Synchrotron X-ray absorption spectroscopic (XAS) analysis of in situ and ex situ experiments showed that oxidation of V^IV occurs...

Near-Complete Phosphorus Recovery from Challenging Water Matrices Using Multiuse Ceramsite Made from Water Treatment Residual (WTR)

Tue, 1 Apr 2025 00:00:00 +0000

Water treatment residual (WTR) is a burden for many water treatment plants due to the large volumes and associated management costs. In this study, we transform aluminum-salt WTR (Al-WTR) into ceramsite (ASC) to recover phosphate from challenging waters. ASC showed remarkably higher specific surface area (SSA, 70.53 m²/g) and phosphate adsorption capacity (calculated 47.2 mg P/g) compared to previously reported ceramsite materials (< 40 m²/g SSA and < 20 mg P/g). ASC recovered over 94.9% of phosphate across a wide pH range (3 - 11) and generally sustained > 90% of its phosphate recovery at high concentrations of competing anions (i.e., Cl^-, F^-, SO₄ ^2-, or HCO₃ ^-) or humic acid (HA). We challenged the material with real municipal wastewater at 10°C and achieved simultaneous phosphate (>97.1%) and COD removal (71.2%). Once saturated with phosphate, ASC can be repurposed for landscaping...

Dual feedback inhibition of ATP-dependent caffeate activation economizes ATP in caffeate-dependent electron bifurcation

Mon, 3 Mar 2025 00:00:00 +0000

The acetogen Acetobacterium woodii couples caffeate reduction with ferredoxin reduction and NADH oxidation via electron bifurcation, providing additional reduced ferredoxin for energy conservation and cell synthesis. Caffeate is first activated by an acyl-CoA synthetase (CarB), which ligates CoA to caffeate at the expense of ATP. After caffeoyl-CoA is reduced to hydrocaffeoyl-CoA, the CoA moiety in hydrocaffeoyl-CoA could be recycled for caffeoyl-CoA synthesis by an ATP-independent CoA transferase (CarA) to save energy. However, given that CarA and CarB are co-expressed, it was not well understood how ATP could be saved when both two competitive pathways of caffeate activation are present. Here, we reported a dual feedback inhibition of the CarB-mediated caffeate activation by the intermediate hydrocaffeoyl-CoA and the end-product hydrocaffeate. As the product of CarA, hydrocaffeate inhibited CarB-mediated caffeate activation by serving as another substrate of CarB with...

Defluorination Mechanisms and Real-Time Dynamics of Per- and Polyfluoroalkyl Substances on Electrified Surfaces

Thu, 27 Feb 2025 00:00:00 +0000

Per- and polyfluoroalkyl substances (PFAS) are persistent environmental contaminants found in groundwater sources and a wide variety of consumer products. In recent years, electrochemical approaches for the degradation of these harmful contaminants have garnered a significant amount of attention due to their efficiency and chemical-free modular nature. However, these electrochemical processes occur in open, highly non-equilibrium systems, and a detailed understanding of PFAS degradation mechanisms in these promising technologies is still in its infancy. To shed mechanistic insight into these complex processes, we present the first constant-electrode potential (CEP) quantum calculations of PFAS degradation on electrified surfaces. These advanced CEP calculations provide new mechanistic details about the intricate electronic processes that occur during PFAS degradation in the presence of an electrochemical bias, which cannot be gleaned from conventional density functional theory...

GPU Implementation of a Gas-Phase Chemistry Solver in the CMAQ Chemical Transport Model

Tue, 25 Feb 2025 00:00:00 +0000

The Community Multiscale Air Quality (CMAQ) model simulates atmospheric phenomena, including advection, diffusion, gas-phase chemistry, aerosol physics and chemistry, and cloud processes. Gas-phase chemistry is often a major computational bottleneck due to its representation as large systems of coupled nonlinear stiff differential equations. We leverage the parallel computational performance of graphics processing unit (GPU) hardware to accelerate the numerical integration of these systems in CMAQ's CHEM module. Our implementation, dubbed CMAQ-CUDA, in reference to its use in the Compute Unified Device Architecture (CUDA) general purpose GPU (GPGPU) computing solution, migrates CMAQ's Rosenbrock solver from Fortran to CUDA Fortran. CMAQ-CUDA accelerates the Rosenbrock solver such that simulations using the chemical mechanisms RACM2, CB6R5, and SAPRC07 require only 51%, 50%, or 35% as much time, respectively, as CMAQv5.4 to complete a chemistry time step. Our results demonstrate...

Synergistic material–microbe interface toward deeper anaerobic defluorination

Wed, 5 Feb 2025 00:00:00 +0000

Per- and polyfluoroalkyl substances (PFAS), particularly the perfluorinated ones, are recalcitrant to biodegradation. By integrating an enrichment culture of reductive defluorination with biocompatible electrodes for the electrochemical process, a deeper defluorination of a C₆-perfluorinated unsaturated PFAS was achieved compared to the biological or electrochemical system alone. Two synergies in the bioelectrochemical system were identified: i) The in-series microbial-electrochemical defluorination and ii) the electrochemically enabled microbial defluorination of intermediates. These synergies at the material-microbe interfaces surpassed the limitation of microbial defluorination and further turned the biotransformation end products into less fluorinated products, which could be less toxic and more biodegradable in the environment. This material-microbe hybrid system brings opportunities in the bioremediation of PFAS driven by renewable electricity and warrants future...

Signaling Strategies of Malaria Parasite for Its Survival, Proliferation, and Infection during Erythrocytic Stage

Fri, 31 Jan 2025 00:00:00 +0000

Irrespective of various efforts, malaria persist the most debilitating effect in terms of morbidity and mortality. Moreover, the existing drugs are also vulnerable to the emergence of drug resistance. To explore the potential targets for designing the most effective antimalarial therapies, it is required to focus on the facts of biochemical mechanism underlying the process of parasite survival and disease pathogenesis. This review is intended to bring out the existing knowledge about the functions and components of the major signaling pathways such as kinase signaling, calcium signaling, and cyclic nucleotide-based signaling, serving the various aspects of the parasitic asexual stage and highlighted the Toll-like receptors, glycosylphosphatidylinositol-mediated signaling, and molecular events in cytoadhesion, which elicit the host immune response. This discussion will facilitate a look over essential components for parasite survival and disease progression to be implemented in...

Development of a self-powered digital LAMP microfluidic chip (SP-dChip) for the detection of emerging viruses

Fri, 24 Jan 2025 00:00:00 +0000

Point-of-care (POC) diagnostics have emerged as a crucial technology for emerging pathogen detections to enable rapid and on-site detection of infectious diseases. However, current POC devices often suffer from limited sensitivity with poor reliability to provide quantitative readouts. In this paper, we present a self-powered digital loop-mediated isothermal amplification (dLAMP) microfluidic chip (SP-dChip) for the rapid and quantitative detection of nucleic acids. The SP-dChip utilizes a vacuum lung design to passively digitize samples into individual nanoliter wells for high-throughput analysis. The superior digitization scheme is further combined with reverse transcription loop-mediated isothermal amplification (RT-LAMP) to demonstrate dLAMP detection of Zika virus (ZIKV). Firstly, the LAMP assay is loaded into the chip and passively digitized into individual wells. Mineral oil is then pipetted through the chip to differentiate each well as an individual reactor. The chip...

Food packaging solutions in the post‐per‐ and polyfluoroalkyl substances (PFAS) and microplastics era: A review of functions, materials, and bio‐based alternatives

Fri, 17 Jan 2025 00:00:00 +0000

Food packaging (FP) is essential for preserving food quality, safety, and extending shelf-life. However, growing concerns about the environmental and health impacts of conventional packaging materials, particularly per- and polyfluoroalkyl substances (PFAS) and microplastics, are driving a major transformation in FP design. PFAS, synthetic compounds with dual hydro- and lipophobicity, have been widely employed in food packaging materials (FPMs) to impart desirable water and grease repellency. However, PFAS bioaccumulate in the human body and have been linked to multiple health effects, including immune system dysfunction, cancer, and developmental problems. The detection of microplastics in various FPMs has raised significant concerns regarding their potential migration into food and subsequent ingestion. This comprehensive review examines the current landscape of FPMs, their functions, and physicochemical properties to put into perspective why there is widespread use of PFAS...

Photoinduced Electron–Nuclear Dynamics of Fullerene and Its Monolayer Networks in Solvated Environments

Tue, 7 Jan 2025 00:00:00 +0000

The recently synthesized monolayer fullerene network in a quasi-hexagonal phase (qHP-C₆₀) exhibits superior electron mobility and optoelectronic properties compared to molecular fullerene (C₆₀), making it highly promising for a variety of applications. However, the microscopic carrier dynamics of qHP-C₆₀ remain unclear, particularly in realistic environments, which are of significant importance for applications in optoelectronic devices. Unfortunately, traditional ab initio methods are prohibitive for capturing the real-time carrier dynamics of such large systems due to their high computational cost. In this work, we present the first real-time electron-nuclear dynamics study of qHP-C₆₀ using velocity-gauge density functional tight binding, which enables us to perform several picoseconds of excited-state electron-nuclear dynamics simulations for nanoscale systems with periodic boundary conditions. When applied to C₆₀,...

Micropillar enhanced FRET-CRISPR biosensor for nucleic acid detection

Mon, 6 Jan 2025 00:00:00 +0000

CRISPR technology has gained widespread adoption for pathogen detection due to its exceptional sensitivity and specificity. Although recent studies have investigated the potential of high-aspect-ratio microstructures in enhancing biochemical applications, their application in CRISPR-based detection has been relatively rare. In this study, we developed a FRET-based biosensor in combination with high-aspect-ratio microstructures and Cas12a-mediated trans-cleavage for detecting HPV 16 DNA fragments. Remarkably, our results show that micropillars with higher density exhibit superior molecular binding capabilities, leading to a tenfold increase in detection sensitivity. Furthermore, we investigated the effectiveness of two surface chemical treatment methods for enhancing the developed FRET assay. A simple and effective approach was also developed to mitigate bubble generation in microfluidic devices, a crucial issue in biochemical reactions within such devices. Overall, this work introduces...

Pyrolysis of Two Perfluoroalkanesulfonates (PFSAs) and PFSA-Laden Granular Activated Carbon (GAC): Decomposition Mechanisms and the Role of GAC

Fri, 27 Dec 2024 00:00:00 +0000

Thermal treatment of perfluoroalkyl and polyfluoroalkyl substances (PFASs) presents a promising opportunity to halt the PFAS cycle. However, how co-occurring materials such as granular activated carbon (GAC) influence thermal decomposition products of PFASs, and underlying mechanisms remain unclear. We studied the pyrolysis of two potassium salts of perfluoroalkanesulfonates (PFSAs, C_nF_2n+1SO₃K), perfluorobutanesulfonate (PFBS-K), and perfluorooctanesulfonate (PFOS-K), with or without GAC. PFBS-K is more stable than PFOS-K for pure standards, but when it is adsorbed onto GAC, its thermal stabilities and decomposition behaviors are similar. Temperatures and heating rates can significantly influence the decomposition mechanisms and products for pure standards, while these effects are less pronounced when PFSAs are adsorbed onto GAC. We further studied the underlying decomposition mechanisms. Pure standards of C_nF_2n+1SO₃K...

Chemical Fate of Particulate Sulfur from Nighttime Oxidation of Thiophene

Fri, 27 Dec 2024 00:00:00 +0000

Sulfur-containing volatile organic compounds emitted during wildfire events, such as dimethyl sulfide, are known to form secondary aerosols containing inorganic sulfate (SO₄ ^2-) and surfactant-like organic compounds; however, little is known about the fate of sulfur in other emitted reduced organosulfur species. This study aimed to determine the sulfurous product distribution resulting from the nighttime oxidation of thiophene as a model system. Ion chromatography (IC) and aerosol mass spectrometry (a mini aerosol mass spectrometer, mAMS) were used to constrain the proportions of sulfurous compounds produced under wildfire-relevant conditions ([NO₂]/[O₃] = 0.1). With constraints from IC, results indicated that the sulfurous particle mass consisted of 30.3 ± 6.6% SO₄ ^2-, while mAMS fractionation attributed 24.5 ± 1.6% of total sulfate signal to SO₄ ^2-, 15.4 ± 1.9% to organosulfates, and 60.1...

VAN-DAMME: GPU-accelerated and symmetry-assisted quantum optimal control of multi-qubit systems

Fri, 20 Dec 2024 00:00:00 +0000

We present an open-source software package, VAN-DAMME (Versatile Approaches to Numerically Design, Accelerate, and Manipulate Magnetic Excitations), for massively-parallelized quantum optimal control (QOC) calculations of multi-qubit systems. To enable large QOC calculations, the VAN-DAMME software package utilizes symmetry-based techniques with custom GPU-enhanced algorithms. This combined approach allows for the simultaneous computation of hundreds of matrix exponential propagators that efficiently leverage the intra-GPU parallelism found in high-performance GPUs. In addition, to maximize the computational efficiency of the VAN-DAMME code, we carried out several extensive tests on data layout, computational complexity, memory requirements, and performance. These extensive analyses allowed us to develop computationally efficient approaches for evaluating complex-valued matrix exponential propagators based on Padé approximants. To assess the computational performance of our GPU-accelerated...

Development of an Electrochemical Paper-Based Device Modified with Functionalized Biochar for the Screening of Paracetamol in Substandard Medicines

Wed, 11 Dec 2024 00:00:00 +0000

The global prevalence of counterfeit and low-quality pharmaceuticals poses significant health risks and challenges in medical treatments, creating a need for rapid and reliable drug screening technologies. This study introduces a cost-effective electrochemical paper-based device (ePAD) modified with functionalized bamboo-derived biochar (BCF) for the detection of paracetamol in substandard medicines. The sensor was fabricated using a custom 3D-printed stencil in PLA, designed for efficient production, and a 60:40 (m/m) graphite (GR) and glass varnish (GV) conductive ink, resulting in a robust and sensitive platform. The electroactive area of the ePAD/BCF sensor was determined as 0.37 cm². Characterization via SEM and cyclic voltammetry (CV) verified its structural and electrochemical stability. The sensor demonstrated linear detection of paracetamol from 5.0 to 60.0 µmol L^-1 with a detection limit of 3.50 µmol L^-1. Interference studies showed high...

A comprehensive transformer-based approach for high-accuracy gas adsorption predictions in metal-organic frameworks

Mon, 9 Dec 2024 00:00:00 +0000

Gas separation is crucial for industrial production and environmental protection, with metal-organic frameworks (MOFs) offering a promising solution due to their tunable structural properties and chemical compositions. Traditional simulation approaches, such as molecular dynamics, are complex and computationally demanding. Although feature engineering-based machine learning methods perform better, they are susceptible to overfitting because of limited labeled data. Furthermore, these methods are typically designed for single tasks, such as predicting gas adsorption capacity under specific conditions, which restricts the utilization of comprehensive datasets including all adsorption capacities. To address these challenges, we propose Uni-MOF, an innovative framework for large-scale, three-dimensional MOF representation learning, designed for multi-purpose gas prediction. Specifically, Uni-MOF serves as a versatile gas adsorption estimator for MOF materials, employing pure three-dimensional...

Theoretical insights on potential-dependent oxidation behaviors and antioxidant strategies of MXenes

Mon, 9 Dec 2024 00:00:00 +0000

Significant efforts have been devoted to investigating the oxidation of MXenes in various environments. However, the underlying mechanism of MXene oxidation and its dependence on the electrode potential remain poorly understood. Here we show the oxidation behavior of MXenes under the working conditions of electrochemical processes in terms of kinetics and thermodynamics by using constant-potential ab initio simulations. The theoretical results indicate that the potential effects can be attributed to the nucleophilic attack of water molecules on metal atoms, similar to that taking place in the Oxygen Evolution Reaction. Building upon these findings, we deduced the oxidation potential of the common MXenes, and proposed antioxidant strategies for MXene. Finally, we demonstrated that MBenes, the boron analogs of MXenes, may undergo a similar nucleophilic attack in water and inferred that molecule-induced Walden inversion is widely present in material reconstructions. This work contributes...

Pneumatic nano-sieve for CRISPR-based detection of drug-resistant bacteria

Tue, 3 Dec 2024 00:00:00 +0000

The increasing prevalence of antibiotic-resistant bacterial infections, particularly methicillin-resistant Staphylococcus aureus (MRSA), presents a significant public health concern. Timely detection of MRSA is crucial to enable prompt medical intervention, limit its spread, and reduce antimicrobial resistance. Here, we introduce a miniaturized nano-sieve device featuring a pneumatically-regulated chamber for highly efficient MRSA purification from human plasma samples. By using packed magnetic beads as a filter and leveraging the deformability of the nano-sieve channel, we achieved an on-chip concentration factor of ∼15-fold for MRSA. We integrated this device with recombinase polymerase amplification (RPA) and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas detection system, resulting in an on-chip limit of detection (LOD) of approximately 100 CFU mL^-1. This developed approach provides a rapid, precise, and centrifuge-free solution suitable...

Balanced Training Sets Improve Deep Learning-Based Prediction of CRISPR sgRNA Activity

Thu, 21 Nov 2024 00:00:00 +0000

CRISPR-Cas systems have transformed the field of synthetic biology by providing a versatile method for genome editing. The efficiency of CRISPR systems is largely dependent on the sequence of the constituent sgRNA, necessitating the development of computational methods for designing active sgRNAs. While deep learning-based models have shown promise in predicting sgRNA activity, the accuracy of prediction is primarily governed by the data set used in model training. Here, we trained a convolutional neural network (CNN) model and a large language model (LLM) on balanced and imbalanced data sets generated from CRISPR-Cas12a screening data for the yeast Yarrowia lipolytica and evaluated their ability to predict high- and low-activity sgRNAs. We further tested whether prediction performance can be improved by training on imbalanced data sets augmented with synthetic sgRNAs. Lastly, we demonstrated that adding synthetic sgRNAs to inherently imbalanced CRISPR-Cas9 data sets from...

Optimization of Campesterol-Producing Yeast Strains as a Feasible Platform for the Functional Reconstitution of Plant Membrane-Bound Enzymes

Tue, 19 Nov 2024 00:00:00 +0000

Campesterol is a major phytosterol that plays important roles in regulating membrane properties and serves as the precursor to multiple specialized metabolites, such as the phytohormone brassinosteroids. Recently, we established a campesterol-producing yeast strain and extended the bioproduction to 22-hydroxycampesterol and 22-hydroxycampest-4-en-3-one, the precursors to brassinolide. However, there is a trade-off in growth due to the disrupted sterol metabolism. In this study, we enhanced the growth of the campesterol-producing yeast by partially restoring the activity of the sterol acyltransferase and engineering upstream FPP supply. Furthermore, genome sequencing analysis also revealed a pool of genes possibly associated with the altered sterol metabolism. Retro engineering implies an essential role of ASG1, especially the C-terminal asparagine-rich domain of ASG1, in the sterol metabolism of yeast especially under stress. The performance of the campesterol-producing yeast...

Nanocarrier mediated delivery of insecticides into tarsi enhances stink bug mortality

Tue, 19 Nov 2024 00:00:00 +0000

Current delivery practices for insecticide active ingredients are inefficient with only a fraction reaching their intended target. Herein, we developed carbon dot based nanocarriers with molecular baskets (γ-cyclodextrin) that enhance the delivery of active ingredients into insects (southern green stink bugs, Nezara viridula L.) via their tarsal pores. Nezara viridula feeds on leguminous plants worldwide and is a primary pest of soybeans. After two days of exposure, most of the nanocarriers and their active ingredient cargo (>85%) remained on the soybean leaf surface, rendering them available to the insects. The nanocarriers enter stink bugs through their tarsi, enhancing the delivery of a fluorescent chemical cargo by 2.6 times. The insecticide active ingredient nanoformulation (10 ppm) was 25% more effective in controlling the stink bugs than the active ingredient alone. Styletectomy experiments indicated that the improved active ingredient efficacy was due to the nanoformulation...

Sulfate residuals on Ru catalysts switch CO2 reduction from methanation to reverse water-gas shift reaction

Mon, 18 Nov 2024 00:00:00 +0000

Efficient heterogeneous catalyst design primarily focuses on engineering the active sites or supports, often neglecting the impact of trace impurities on catalytic performance. Herein, we demonstrate that even trace amounts of sulfate (SO42−) residuals on Ru/TiO2 can totally change the CO2 reduction from methanation to reverse-water gas shift (RWGS) reaction under atmospheric pressure. We reveal that air annealing causes the trace amount of SO42− to migrate from TiO2 to Ru/TiO2 interface, leading to the significant changes in product selectivity from CH4 to CO. Detailed characterizations and DFT calculations show that the sulfate at Ru/TiO2 interface notably enhances the H transfer from Ru particles to the TiO2 support, weakening the CO intermediate activation on Ru particles and inhibiting the further hydrogenation of CO to CH4. This discovery highlights the vital role of trace impurities in CO2 hydrogenation reaction, and also provides broad implications for the design and development...

QRCODE: Massively parallelized real-time time-dependent density functional theory for periodic systems

Thu, 14 Nov 2024 00:00:00 +0000

We present a new software module, QRCODE (Quantum Research for Calculating Optically Driven Excitations), for massively parallelized real-time time-dependent density functional theory (RT-TDDFT) calculations of periodic systems in the open-source Qbox software package. Our approach utilizes a custom implementation of a fast Fourier transformation scheme that significantly reduces inter-node message passing interface (MPI) communication of the major computational kernel and shows impressive scaling up to 16,344 CPU cores. In addition to improving computational performance, QRCODE contains a suite of various time propagators for accurate RT-TDDFT calculations. As benchmark applications of QRCODE, we calculate the current density and optical absorption spectra of hexagonal boron nitride (h-BN) and photo-driven reaction dynamics of the ozone-oxygen reaction. We also calculate the second and higher harmonic generation of monolayer and multi-layer boron nitride structures as examples...

Unleashing plant synthetic capacity: navigating regulatory mechanisms for enhanced bioproduction and secondary metabolite discovery

Mon, 11 Nov 2024 00:00:00 +0000

Plant natural products (PNPs) hold significant pharmaceutical importance. The sessile nature of plants has led to the evolution of chemical defense mechanisms over millions of years to combat environmental challenges, making it a crucial and essential defense weapon. Despite their importance, the abundance of these bioactive molecules in plants is typically low, and conventional methods are time-consuming for enhancing production. Moreover, there is a pressing need for novel drug leads, exemplified by the shortage of antibiotics and anticancer drugs. Understanding how plants respond to stress and regulate metabolism to produce these molecules presents an opportunity to explore new avenues for discovering compounds that are typically under the detection limit or not naturally produced. Additionally, this knowledge can contribute to the advancement of plant engineering, enabling the development of new chassis for the biomanufacturing of these valuable molecules. In this perspective,...

Zeolite-promoted platinum catalyst for efficient reduction of nitrogen oxides with hydrogen

Tue, 5 Nov 2024 00:00:00 +0000

Internal combustion engine fueled by carbon-free hydrogen (H2-ICE) offers a promising alternative for sustainable transportation. Herein, we report a facile and universal strategy through the physical mixing of Pt catalyst with zeolites to significantly improve the catalytic performance in the selective catalytic reduction of nitrogen oxides (NOx) with H2 (H2-SCR), a process aiming at NOx removal from H2-ICE. Via the physical mixing of Pt/TiO2 with Y zeolite (Pt/TiO2 + Y), a remarkable enhancement of NOx reduction activity and N2 selectivity was simultaneously achieved. The incorporation of Y zeolite effectively captured the in-situ generated water, fostering a water-rich environment surrounding the Pt active sites. This environment weakened the NO adsorption while concurrently promoting the H2 activation, leading to the strikingly elevated H2-SCR activity and N2 selectivity on Pt/TiO2 + Y catalyst. This study provides a unique, easy and sustainable physical mixing approach to...

Nonthermal Plasma Activation of Adsorbates: The Case of CO on Pt

Thu, 19 Sep 2024 00:00:00 +0000

Nonthermal plasmas provide a unique approach to electrically driven heterogeneous catalytic processes. Despite much interest from the community, fundamental activation pathways in these processes remain poorly understood. Here, we investigate how exposure to a nonthermal plasma sustained in an argon nonreactive atmosphere affects the desorption of carbon monoxide (CO) from platinum nanoparticles. Temperature-programmed desorption measurements indicate that the plasma reduces the effective binding energy (BE) of CO to Pt surfaces by as much as ∼0.3 eV, with the reduction in the BE scaling linearly with the plasma density. We find that the effective CO BE is most strongly reduced for under-coordinated sites (steps and edges) compared to well-coordinated sites (terraces). Density functional theory calculations suggest that this is due to plasma-induced charging and electric fields at the catalyst surface, which preferentially affect under-coordinated sites. This study provides direct...

Functional genomic screening in Komagataella phaffii enabled by high-activity CRISPR-Cas9 library

Tue, 10 Sep 2024 00:00:00 +0000

CRISPR-based high-throughput genome-wide loss-of-function screens are a valuable approach to functional genetics and strain engineering. The yeast Komagataella phaffii is a host of particular interest in the biopharmaceutical industry and as a metabolic engineering host for proteins and metabolites. Here, we design and validate a highly active 6-fold coverage genome-wide sgRNA library for this biotechnologically important yeast containing 30,848 active sgRNAs targeting over 99% of its coding sequences. Conducting fitness screens in the absence of functional non-homologous end joining (NHEJ), the dominant DNA repair mechanism in K. phaffii, provides a quantitative means to assess the activity of each sgRNA in the library. This approach allows for the experimental validation of each guide's targeting activity, leading to more precise screening outcomes. We used this approach to conduct growth screens with glucose as the sole carbon source and identify essential genes. Comparative...

Synthesis, Characterization, and Utilization of a Lignin-Based Adsorbent for Effective Removal of Azo Dye from Aqueous Solution

Sun, 18 Aug 2024 00:00:00 +0000

How to effectively remove toxic dyes from the industrial wastewater using a green low-cost lignocellulose-based adsorbent, such as lignin, has become a topic of great interest but remains quite challenging. In this study, cosolvent-enhanced lignocellulosic fractionation (CELF) pretreatment and Mannich reaction were combined to generate an aminated CELF lignin which is subsequently applied for removal of methylene blue and direct blue (DB) 1 dye from aqueous solution. ³¹P NMR was used to track the degree of amination, and an orthogonal design was applied to determine the relationship between the extent of amination and reaction parameters. The physicochemical, morphological, and thermal properties of the aminated CELF lignin were characterized to confirm the successful grafting of diethylenetriamine onto the lignin. The aminated CELF lignin proved to be an effective azo dye-adsorbent, demonstrating considerably enhanced dye decolorization, especially toward DB 1 dye...

Polygalacturonase-inhibiting proteins as an exogenously applied natural solution for prevention of postharvest fungal infections

Sat, 17 Aug 2024 00:00:00 +0000

Polygalacturonase inhibiting proteins (PGIPs) are plant proteins involved in the inhibition of polygalacturonases (PGs), cell-wall degrading enzymes often secreted by phytopathogenic fungi. Previously, we confirmed that PGIP2 from Phaseolus vulgaris (PvPGIP2) can inhibit the growth of Aspergillus niger and Botrytis cinerea on agar plate. In this study, we further validated the feasibility of using PGIP as an environmental and ecological friendly agent to prevent fungal infection post-harvest. We found that application of either purified PGIP (full length PvPGIP2 or truncated tPvPGIP2_5-8), or PGIP-secreting Saccharomyces cerevisiae strains can effectively inhibit fungal growth and necrotic lesions on tobacco leaf. We also examined the effective amount and thermostability of PGIP when applied on plants. A concentration of 0.75 mg/mL or higher can significantly reduce the area of B. cinerea lesions. The activity of full-length PvPGIPs is not...

Author Correction: Genome-wide identification and expression analysis of E2 ubiquitin-conjugating enzymes in tomato

Fri, 16 Aug 2024 00:00:00 +0000

A correction has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

Genome-wide identification and expression analysis of E2 ubiquitin-conjugating enzymes in tomato

Fri, 16 Aug 2024 00:00:00 +0000

The ubiquitin-proteasomal degradation mechanism has gained the attention over the past decade. The E2 ubiquitin conjugating enzymes are the crucial part of ubiquitination mechanism and they are believed to hold imperative association for plant development. It accepts ubiquitin from the E1 enzyme and interacts with the E3 ligase to transfer ubiquitin or directly transfers ubiquitin to the substrate. The functional aspects of E2 ubiquitin enzymes in plant systems are unclear. Tomato is being used as a model plant and rarely explored to study E2 ubiquitin enzyme. We have utilized in-silico methods to analyze E2 enzymes in Solanum lycopersicum and 59 genes were identified with UBC family domains. The physio-chemical properties, chromosomal localization, structural organization, gene duplication, promoter analysis, gene ontology and conserved motifs were investigated along with phylogenetic analysis of tomato E2 genes exploring evolutionary relations. The gene expression analysis of...

Genome-wide analysis of HECT E3 ubiquitin ligase gene family in Solanum lycopersicum

Fri, 16 Aug 2024 00:00:00 +0000

The E3 ubiquitin ligases have been known to intrigue many researchers to date, due to their heterogenicity and substrate mediation for ubiquitin transfer to the protein. HECT (Homologous to the E6-AP Carboxyl Terminus) E3 ligases are spatially and temporally regulated for substrate specificity, E2 ubiquitin-conjugating enzyme interaction, and chain specificity during ubiquitylation. However, the role of the HECT E3 ubiquitin ligase in plant development and stress responses was rarely explored. We have conducted an in-silico genome-wide analysis to identify and predict the structural and functional aspects of HECT E3 ligase members in tomato. Fourteen members of HECT E3 ligases were identified and analyzed for the physicochemical parameters, phylogenetic relations, structural organizations, tissue-specific gene expression patterns, and protein interaction networks. Our comprehensive analysis revealed the HECT domain conservation throughout the gene family, close evolutionary relationship...

Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato

Fri, 16 Aug 2024 00:00:00 +0000

E3 ubiquitin ligases are a central modifier of plant signaling pathways that act through targeting proteins to the degradation pathway. U-box E3 ubiquitin ligases are a distinct class of E3 ligases that utilize intramolecular interactions for its scaffold stabilization. U-box E3 ubiquitin ligases are prevalent in plants in comparison to animals. However, the evolutionary aspects, genetic organizations, and functional fate of the U-box E3 gene family in plant development, especially in tomato is not well understood. In the present study, we have performed in-silico genome-wide analysis of the U-box E3 ubiquitin ligase gene family in Solanum lycopersicum. We have identified 62 U-box genes with U-box/Ub Fusion Degradation 2 (UFD2) domain. The chromosomal localization, phylogenetic analysis, gene structure, motifs, gene duplication, syntenic regions, promoter, physicochemical properties, and ontology were investigated. The U-box gene family showed significant conservation of the U-box...

Role of Ubiquitin-Mediated Degradation System in Plant Biology

Fri, 16 Aug 2024 00:00:00 +0000

Ubiquitin-mediated proteasomal degradation is an important mechanism to control protein load in the cells. Ubiquitin binds to a protein on lysine residue and usually promotes its degradation through 26S proteasome system. Abnormal proteins and regulators of many processes, are targeted for degradation by the ubiquitin-proteasome system. It allows cells to maintain the response to cellular level signals and altered environmental conditions. The ubiquitin-mediated proteasomal degradation system plays a key role in the plant biology, including abiotic stress, immunity, and hormonal signaling by interfering with key components of these pathways. The involvement of the ubiquitin system in many vital processes led scientists to explore more about the ubiquitin machinery and most importantly its targets. In this review, we have summarized recent discoveries of the plant ubiquitin system and its involvement in critical processes of plant biology.

Influence of soil characteristics and metal(loid)s on antibiotic resistance genes in green stormwater infrastructure in Southern California

Thu, 15 Aug 2024 00:00:00 +0000

The synergetic effects of metal(loid)s and soil characteristics on bacterial antibiotic resistance genes (ARGs) in green stormwater infrastructure (GSI) has been relatively understudied. Surface soil samples from six GSIs in Southern California over three time periods were assessed for selected ARGs, class 1 integron-integrase genes (intI1), 16S rRNA genes, and bioavailable and total concentrations of nine metal(loid)s, to investigate the relationships among ARGs, soil characteristics, and co-occurring metal(loid)s. Significant correlations existed among relative gene abundances (sul1, sul2, tetW, and intI1), total metal(loid)s (arsenic, copper, lead, vanadium, and zinc), and bioavailable metal(loid) (arsenic) (r = 0.29-0.61, p_adj < 0.05). Additionally, soil texture, organic matter, and nutrients within GSI appeared to be significantly correlated with relative gene abundances of sul1, sul2, and tetW (r = -0.57 to 0.59, p_adj < 0.05)....

Effect of Aerosol Size on Glass Transition Temperature

Thu, 15 Aug 2024 00:00:00 +0000

The amorphous phase state of suspended nanoparticles affects their atmospheric lifetimes and environmental impact. Influence of relative humidity and chemical composition on the glass-to-liquid transition is well-known. However, the influence of the particle size on the phase transition remains uncertain. Here we show experimental data that probe the amorphous phase transition of suspended sucrose particles as a function of particle size. The depression in glass-transition temperature follows the Gibbs-Thomson or Keesom-Laplace predicted proportionality of ΔT_g ∝ D^-1 for particles 100-700 nm in diameter, but the proportionality changes to ΔT_g ∝ D^-1/2 for smaller sizes. Literature data for glass-transition temperature depression in thin films and nanoconfined compounds show similar and strong deviations from the expected D^-1 behavior. While the observed proportionalities remain incompletely...

Metal doped nitrogenous hydroxyapatite nanohybrids slowly release nitrogen to crops and mitigate ammonia volatilization: An impact assessment

Thu, 15 Aug 2024 00:00:00 +0000

To supply adequate food, the ongoing and unrestrained administration of nitrogen fertilizer to agricultural fields is polluting the climate and living organisms. On the other hand, the agriculture sector urgently needs a technological upgrade to effectively confront hunger and poverty. Here, we report a rapid synthesis of zinc and magnesium-doped hydroxyapatite-urea nanohybrids for slow release and delivery of nitrogen to wheat and rice crops. Nanohybrids slowly release nitrogen for up to six weeks compared to the burst release of nitrogen from urea, and their use substantially reduces, by at least 3.8 times, ammonia emissions into the environment compared with that of urea fertilizer. A half‑nitrogen dose applied as multi-nutrient complexed nanohybrids maintained crop growth, yield, and nutritional compositions in wheat and subsequent rice crops. Nanohybrids enhanced the wheat crop yield and nitrogen uptake by 22.13% and 58.30%, respectively. The synthesized nitrogen nanohybrids...

Zinc- and magnesium-doped hydroxyapatite-urea nanohybrids enhance wheat growth and nitrogen uptake

Thu, 15 Aug 2024 00:00:00 +0000

The ongoing and unrestrained application of nitrogen fertilizer to agricultural lands has been directly linked to climate change and reductions in biodiversity. The agricultural sector needs a technological upgrade to adopt sustainable methods for maintaining high yield. We report synthesis of zinc and magnesium doped and undoped hydroxyapatite nanoparticles, and their urea nanohybrids, to sustainably deliver nitrogen to wheat. The urea nanohybrids loaded with up to 42% nitrogen were used as a new source of nitrogen and compared with a conventional urea-based fertilizer for efficient and sufficient nitrogen delivery to pot-grown wheat. Doping with zinc and magnesium manipulated the hydroxyapatite crystallinity for smaller size and higher nitrogen loading capacity. Interestingly, 50% and 25% doses of urea nanohybrids significantly boosted the wheat growth and yield compared with 100% doses of urea fertilizer. In addition, the nutritional elements uptake and grain protein and...

Role of F-box E3-ubiquitin ligases in plant development and stress responses

Thu, 15 Aug 2024 00:00:00 +0000

Key message

F-box E3-ubiquitin ligases regulate critical biological processes in plant development and stress responses. Future research could elucidate why and how plants have acquired a large number of F-box genes. The ubiquitin-proteasome system (UPS) is a predominant regulatory mechanism employed by plants to maintain the protein turnover in the cells and involves the interplay of three classes of enzymes, E1 (ubiquitin-activating), E2 (ubiquitin-conjugating), and E3 ligases. The diverse and most prominent protein family among eukaryotes, F-box proteins, are a vital component of the multi-subunit SCF (Skp1-Cullin 1-F-box) complex among E3 ligases. Several F-box proteins with multifarious functions in different plant systems have evolved rapidly over time within closely related species, but only a small part has been characterized. We need to advance our understanding of substrate-recognition regulation and the involvement of F-box proteins in biological processes and...

Dichloramine Hydrolysis in Membrane Desalination Permeate: Mechanistic Insights and Implications for Oxidative Capacity in Potable Reuse Applications

Mon, 12 Aug 2024 00:00:00 +0000

Dichloramine (NHCl₂) naturally exists in reverse osmosis (RO) permeate due to its application as an antifouling chemical in membrane-based potable reuse treatment. This study investigated mechanisms of background NHCl₂ hydrolysis associated with the generation of oxidative radical species in RO permeate, established a kinetic model to predict the oxidative capacity, and examined its removal efficiency on trace organic contaminants in potable reuse. Results showed that NHCl₂ hydrolysis generated transient peroxynitrite (ONOO^-) and subsequently dissociated into hydroxyl radical (HO^•). The maximal HO^• exposure was observed at an RO permeate pH of 8.4, higher than that from typical ultraviolet (UV)-based advanced oxidation processes. The HO^• exposure during NHCl₂ hydrolysis also peaked at a NH₂Cl-to-NHCl₂ molar ratio of 1:1. The oxidative capacity rapidly degraded 1,4-dioxane,...

Electrospray-Differential Mobility Hyphenated with Single Particle Inductively Coupled Plasma Mass Spectrometry for Characterization of Nanoparticles and Their Aggregates

Fri, 9 Aug 2024 00:00:00 +0000

The novel hyphenation of electrospray-differential mobility analysis with single particle inductively coupled plasma mass spectrometry (ES-DMA-spICPMS) was demonstrated with the capacity for real-time size, mass, and concentration measurement of nanoparticles (NPs) on a particle-to-particle basis. In this proof-of-concept study, the feasibility of this technique was validated through both concentration and mass calibration using NIST gold NP reference materials. A detection limit of 10(5) NPs mL(-1) was determined under current experimental conditions, which is about 4 orders of magnitude lower in comparison to that of a traditional ES-DMA setup using a condensation particle counter as detector. Furthermore, independent and simultaneous quantification of both size and mass of NPs provides information regarding NP aggregation states. Two demonstrative applications include gold NP mixtures with a broad size range (30-100 nm), and aggregated gold NPs with a primary size of 40 nm....

Enhancing the Carbon Monoxide Oxidation Performance through Surface Defect Enrichment of Ceria-Based Supports for Platinum Catalyst

Sat, 3 Aug 2024 00:00:00 +0000

Effective synthesis and application of single-atom catalysts on supports lacking enough defects remain a significant challenge in environmental catalysis. Herein, we present a universal defect-enrichment strategy to increase the surface defects of CeO₂-based supports through H₂ reduction pretreatment. The Pt catalysts supported by defective CeO₂-based supports, including CeO₂, CeZrO_x, and CeO₂/Al₂O₃ (CA), exhibit much higher Pt dispersion and CO oxidation activity upon reduction activation compared to their counterpart catalysts without defect enrichment. Specifically, Pt is present as embedded single atoms on the CA support with enriched surface defects (CA-HD) based on which the highly active catalyst showing embedded Pt clusters (Pt_C) with the bottom layer of Pt atoms substituting the Ce cations in the CeO₂ surface lattice can be obtained through reduction activation....

Host and Pathway Engineering for Enhanced Lycopene Biosynthesis in Yarrowia lipolytica