Identification of a therapeutic interfering particle-A single-dose SARS-CoV-2 antiviral intervention with a high barrier to resistance.

Viral-deletion mutants that conditionally replicate and inhibit the wild-type virus (i.e., defective interfering particles, DIPs) have long been proposed as single-administration interventions with high genetic barriers to resistance. However, theories predict that robust, therapeutic DIPs (i.e., therapeutic interfering particles, TIPs) must conditionally spread between cells with R0 >1. Here, we report engineering of TIPs that conditionally replicate with SARS-CoV-2, exhibit R0 >1, and inhibit viral replication 10- to 100-fold. Inhibition occurs via competition for viral replication machinery, and a single administration of TIP RNA inhibits SARS-CoV-2 sustainably in continuous cultures. Strikingly, TIPs maintain efficacy against neutralization-resistant variants (e.g., B.1.351). In hamsters, both prophylactic and therapeutic intranasal administration of lipid-nanoparticle TIPs durably suppressed SARS-CoV-2 by 100-fold in the lungs, reduced pro-inflammatory cytokine expression, and prevented severe pulmonary edema. These data provide proof of concept for a class of single-administration antivirals that may circumvent current requirements to continually update medical countermeasures against new variants.

A defective viral genome strategy elicits broad protective immunity against respiratory viruses.

RNA viruses generate defective viral genomes (DVGs) that can interfere with replication of the parental wild-type virus. To examine their therapeutic potential, we created a DVG by deleting the capsid-coding region of poliovirus. Strikingly, intraperitoneal or intranasal administration of this genome, which we termed eTIP1, elicits an antiviral response, inhibits replication, and protects mice from several RNA viruses, including enteroviruses, influenza, and SARS-CoV-2. While eTIP1 replication following intranasal administration is limited to the nasal cavity, its antiviral action extends non-cell-autonomously to the lungs. eTIP1 broad-spectrum antiviral effects are mediated by both local and distal type I interferon responses. Importantly, while a single eTIP1 dose protects animals from SARS-CoV-2 infection, it also stimulates production of SARS-CoV-2 neutralizing antibodies that afford long-lasting protection from SARS-CoV-2 reinfection. Thus, eTIP1 is a safe and effective broad-spectrum antiviral generating short- and long-term protection against SARS-CoV-2 and other respiratory infections in animal models.

Genetic mechanism regulating diversity in the placement of eyes on the head of animals.

Despite the conservation of genetic machinery involved in eye development, there is a strong diversity in the placement of eyes on the head of animals. Morphogen gradients of signaling molecules are vital to patterning cues. During Drosophila eye development, Wingless (Wg), a ligand of Wnt/Wg signaling, is expressed anterolaterally to form a morphogen gradient to determine the eye- versus head-specific cell fate. The underlying mechanisms that regulate this process are yet to be fully understood. We characterized defective proventriculus (dve) (Drosophila ortholog of human SATB1), a K50 homeodomain transcription factor, as a dorsal eye gene, which regulates Wg signaling to determine eye versus head fate. Across Drosophila species, Dve is expressed in the dorsal head vertex region where it regulates wg transcription. Second, Dve suppresses eye fate by down-regulating retinal determination genes. Third, the dve-expressing dorsal head vertex region is important for Wg-mediated inhibition of retinal cell fate, as eliminating the Dve-expressing cells or preventing Wg transport from these dve-expressing cells leads to a dramatic expansion of the eye field. Together, these findings suggest that Dve regulates Wg expression in the dorsal head vertex, which is critical for determining eye versus head fate. Gain-of-function of SATB1 exhibits an eye fate suppression phenotype similar to Dve. Our data demonstrate a conserved role for Dve/SATB1 in the positioning of eyes on the head and the interocular distance by regulating Wg. This study provides evidence that dysregulation of the Wg morphogen gradient results in developmental defects such as hypertelorism in humans where disproportionate interocular distance and facial anomalies are reported.

VODKA2: a fast and accurate method to detect non-standard viral genomes from large RNA-seq data sets.

During viral replication, viruses carrying an RNA genome produce non-standard viral genomes (nsVGs), including copy-back viral genomes (cbVGs) and deletion viral genomes (delVGs), that play a crucial role in regulating viral replication and pathogenesis. Because of their critical roles in determining the outcome of RNA virus infections, the study of nsVGs has flourished in recent years, exposing a need for bioinformatic tools that can accurately identify them within next-generation sequencing data obtained from infected samples. Here, we present our data analysis pipeline, Viral Opensource DVG Key Algorithm 2 (VODKA2), that is optimized to run on a parallel computing environment for fast and accurate detection of nsVGs from large data sets.

Pt Single Atoms Supported on Defect Ceria as an Active and Stable Dual-Site Catalyst for Alkaline Hydrogen Evolution.

This work evaluates the feasibility of alkaline hydrogen evolution reaction (HER) using Pt single-atoms (1.0 wt %) on defect-rich ceria (Pt1/CeOx) as an active and stable dual-site catalyst. The catalyst displayed a low overpotential and a small Tafel slope in an alkaline medium. Moreover, Pt1/CeOx presented a high mass activity and excellent durability, competing with those of the commercial Pt/C (20 wt %). In this picture, the defective CeOx is active for water adsorption and dissociation to create H* intermediates, providing the first site where the reaction occurs. The H* intermediate species then migrate to adsorb and react on the Pt2+ isolated atoms, the site where H2 is formed and released. DFT calculations were also performed to obtain mechanistic insight on the Pt1/CeOx catalyst for the HER. The results indicate a new possibility to improve the state-of-the-art alkaline HER catalysts via a combined effect of the O vacancies on the ceria support and Pt2+ single atoms.

Uncoupling neurogenic gene networks in the Drosophila embryo.

The EGF signaling pathway specifies neuronal identities in the Drosophila embryo by regulating developmental patterning genes such as intermediate neuroblasts defective (ind). EGFR is activated in the ventral midline and neurogenic ectoderm by the Spitz ligand, which is processed by the Rhomboid protease. CRISPR/Cas9 was used to delete defined rhomboid enhancers mediating expression at each site of Spitz processing. Surprisingly, the neurogenic ectoderm, not the ventral midline, was found to be the dominant source of EGF patterning activity. We suggest that Drosophila is undergoing an evolutionary transition in central nervous system (CNS)-organizing activity from the ventral midline to the neurogenic ectoderm.

Creating cell type-specific mutants by enhancer mutagenesis.

Cell signaling plays an essential role in development, and knowledge of the identities of the cells sending the signal is critical. This can be a challenge, since signaling pathways and ligands are commonly used at multiple times and in multiple cell types during development. One solution to this problem is to create cell type-specific mutants using CRISPR/Cas9 to mutate enhancers that control different patterns of expression. In this issue of Genes & Development, Rogers and colleagues (pp. 634-638) provide the first use of this method in Drosophila to solve a long-standing issue in patterning of the embryonic central nervous system.

Transcriptionally Active Defective HIV-1 Proviruses and Their Association With Immunological Nonresponse to Antiretroviral Therapy.

A subset of antiretroviral therapy-treated persons with human immunodeficiency virus (HIV), referred to as immunological nonresponders (INRs), fails to normalize CD4+ T-cell numbers. In a case-control study involving 26 INRs (CD4 < 250 cells/µL) and 25 immunological responders (IRs; CD4 ≥ 250 cells/µL), we evaluated the potential contribution of transcriptionally competent defective HIV-1 proviruses to poor CD4+ T-cell recovery. Compared to the responders, the INRs had higher levels of cell-associated HIV RNA (P = .034) and higher percentages of HLA-DR+ CD4+ T cells (P < .001). While not encoding replication-competent viruses, the RNA transcripts frequently encoded HIV-1 Gag-p17 and Nef proteins. These transcripts and/or resulting proteins may activate pathway(s) leading to the immunological nonresponse phenotype.

Ru-Induced Defect Engineering in Co3O4 Lattice for High Performance Electrochemical Reduction of Nitrate to Ammonium.

Amidst these growing sustainability concerns, producing NH4 + via electrochemical NO3 - reduction reaction (NO3RR) emerges as a promising alternative to the conventional Haber-Bosch process. In a pioneering approach, this study introduces Ru incorporation into Co3O4 lattices at the nanoscale and further couples it with electroreduction conditioning (ERC) treatment as a strategy to enhance metal oxide reducibility and induce oxygen vacancies, advancing NH4 + production from NO3RR. Here, supported by a suite of ex situ and in situ characterization measurements, the findings reveal that Ru enrichment promotes Co species reduction and oxygen vacancy formation. Further, as evidenced by the theoretical calculations, Ru integration lowers the energy barrier for oxygen vacancy formation, thereby facilitating a more energy-efficient NO3RR-to-NH4 + pathway. Optimal catalytic activity is realized with a Ru loading of 10 at.% (named 10Ru/Co3O4), achieving a high NH4 + production rate (98 nmol s-1 cm-2), selectivity (97.5%) and current density (≈100 mA cm-2) at -1.0 V vs RHE. The findings not only provide insights into defect engineering via the incorporation of secondary sites but also lay the groundwork for innovative catalyst design aimed at improving NH4 + yield from NO3RR. This research contributes to the ongoing efforts to develop sustainable electrochemical processes for nitrogen cycle management.

CeO2-Based Frustrated Lewis Pairs via Defective Engineering: Formation Theory, Site Characterization, and Small Molecule Activation.

Activation of small molecules is considered to be a central concern in the theoretical investigation of environment- and energy-related catalytic conversions. Sub-nanostructured frustrated Lewis pairs (FLPs) have been an emerging research hotspot in recent years due to their advantages in small molecule activation. Although the progress of catalytic applications of FLPs is increasingly reported, the fundamental theories related to the structural formation, site regulation, and catalytic mechanism of FLPs have not yet been fully developed. Given this, it is attempted to demonstrate the underlying theory of FLPs formation, corresponding regulation methods, and its activation mechanism on small molecules using CeO2 as the representative metal oxide. Specifically, this paper presents three fundamental principles for constructing FLPs on CeO2 surfaces, and feasible engineering methods for the regulation of FLPs sites are presented. Furthermore, cases where typical small molecules (e.g., hydrogen, carbon dioxide, methane oxygen, etc.) are activated over FLPs are analyzed. Meanwhile, corresponding future challenges for the development of FLPs-centered theory are presented. The insights presented in this paper may contribute to the theories of FLPs, which can potentially provide inspiration for the development of broader environment- and energy-related catalysis involving small molecule activation.

Defects Healing of the ZnO Surface by Filling with Au Atom Catalysts for Efficient Photocatalytic H2 Production.

Healed defects on photocatalysts surface and their interaction with plasmonic nanoparticles (NPs) have attracted attention in H2 production process. In this study, surface oxygen vacancy (Vo ) defects are created on ZnO (Vo -ZnO) NPs by directly pyrolyzing zeolitic imidazolate framework. The surface defects on Vo -ZnO provide active sites for the diffusion of single Au atoms and as nucleation sites for the formation of Au NPs by the in situ photodeposition process. The electronically healed surface defects by single Au atoms help in the formation of a heterojunction between the ZnO and plasmonic Au NPs. The formed Au/Vo -Au:ZnO-4 heterojunction prolongs photoelectron lifetimes and increases donor charge density. Therefore, the optimized photocatalysts of Au/Vo -Au:ZnO-4 has 21.28 times higher H2 production rate than the pristine Vo -ZnO under UV-visible light in 0.35 m Na2 SO4 and 0.25 m Na2 SO3 . However in 0.35 m Na2 S and 0.25 m Na2 SO3 , the H2 production rate is 25.84 mmole h-1 g-1 . Furthermore, Au/Vo -Au:ZnO-4 shows visible light activity by generating hot carries via induced surface plasmonic effects. It has 48.58 times higher H2 production rate than pristine Vo -ZnO. Therefore, this study infers new insight for defect healing mediated preparation of Au/Vo -Au:ZnO heterojunction for efficient photocatalytic H2 production.

Defect-Rich Functional HfO2-x for Highly Reversible Zn Metal Anode.

Interface engineering attracted tremendous attention owing to its remarkable ability to impede dendrite growth and side reactions in aqueous zinc-ion batteries. Artificial interface layers composed of crystalline materials have been extensively employed to stabilize the Zn anode. However, the diffusion kinetics of Zn2+ in highly crystalline materials are hindered by steric effects from the lattice, thereby limiting the high-rate performance of the cell. Here, defect-rich HfO2-x polycrystals derived from metal-organic frameworks (MOFs) (D-HfO2-x) are developed to enhance the Zn deposition behavior. The discrepancy of dielectric constants between metallic Zn and HfO2 enables the building of an electrostatic shielding layer for uniform Zn deposition. More importantly, the oxygen vacancies in D-HfO2-x provide abundant active sites for Zn2+ adsorption, accelerating the kinetics of Zn2+ migration, which contributes to the preferential exposure of the Zn (002) plane during plating. Consequently, the D-HfO2-x-modified Zn anode delivers ultrastable durability of over 5000 h at 1 mA cm-2 and a low voltage hysteresis of 30 mV. The constructed defective coating provides a guarantee for the stable operation of Zn anodes, and the innovative approach of defective engineering also offers new ideas for the protection of other energy storage devices.

α-MnO2 Cathode with Oxygen Vacancies Accelerated Affinity Electrolyte for Dual-Ion Co-Encapsulated Aqueous Aluminum Ion Batteries.

Aluminum batteries (ABs) are identified as one of the most promising candidates for the next generation of large-scale energy storage elements because of their efficient three-electron reaction. Compared to ionic electrolytes, aqueous aluminum-ion batteries (AAIBs) are considered safer, less costly, and more environmentally friendly. However, considerable cycling performance is a key issue limiting the development of AAIBs. Stable, efficient, and electrolyte-friendly cathodes are most desirable for AAIBs. Herein, a rod-shaped defect-rich α-MnO2 is designed as a cathode, which is capable to deliver high performance with stable cycling for 180 cycles at 500 mA g-1 and maintains a discharge specific capacity of ≈100 mAh g-1. In addition, the infiltrability simulation is effectively utilized to corroborate the rapid electrochemical reaction brought about by the defective mechanism. With the formation of oxygen vacancies, the dual embedding of protons and metal ions is activated. This work provides a brand-new design for the development and characterization of cathodes for AAIBs.

Defect Engineered Bi2Te3 Nanosheets with Enhanced Haloperoxidase Activity for Marine Antibiofouling.

Defective bismuth telluride (Bi2Te3) nanosheets, an artificial nanozyme mimicking haloperoxidase activity (hPOD), show promise as eco-friendly, bactericidal, and antimicrofouling materials by enhancing cytotoxic hypohalous acid production from halides and H2O2. Microscopic and spectroscopic characterization reveals that controlled NaOH (upto X = 250 µL) etching of the nearly inactive non-transition metal chalcogenide Bi2Te3 nanosheets creates controlled defects (d), such as Bi3+species, in d-Bi2Te3-X that induces enhanced hPOD activity. d-Bi2Te3-250 exhibits approximately eight-fold improved hPOD than the as-grown Bi2Te3 nanosheets. The antibacterial activity of d-Bi2Te3-250 nanozymes, studied by bacterial viability, show 1, and 45% viability for Staphylococcus aureus and Pseudomonas aeruginosa, respectively, prevalent in marine environments. The hPOD mechanism is confirmed using scavengers, implicating HOBr and singlet oxygen for the effect. The antimicrofouling property of the d-Bi2Te3-250 nanozyme has been studied on Pseudomonas aeruginosa biofilm in a lab setting by multiple assays, and also on titanium (Ti) plates coated with the nanozyme mixed commercial paint, exposed to seawater in a real setting. All studies, including direct microscopic evidence, exhibit inhibition of microfouling, up to ≈73%, in the presence of nanozymes. This approach showcases that defect engineering can induce antibacterial, and antimicrofouling activity in non-transition metal chalcogenides, offering an inexpensive alternative to noble metals.

Thermocatalytic Hydrogen Production from Water at Boiling Condition.

Thermochemical water-splitting cycles are technically feasible for hydrogen production from water. However, the ultrahigh operation temperature and low efficiency seriously restrict their practical application. Herein, one-step and one-pot thermocatalytic water-splitting process is reported at water boiling condition catalyzed by single atomic Pt on defective In2O3. Water splitting into hydrogen is verified by D2O isotopic experiment, with an optimized hydrogen production rate of 36.4 mmol·h-1·g-1 as calculated on Pt active sites. It is revealed that three-centered Pt1In2 surrounding oxygen vacancy as catalytic ensembles promote the dissociation of the adsorbed water into H, which transfers to singlet atomic Pt sites for H2 production. Remaining OH groups on adjacent In sites from Pt1In2 ensembles undergoes O─O bonding, hyperoxide formation and diminishing via triethylamine oxidation, water re-adsorption for completing the catalytic cycle. Current work represents an isothermal and continuous thermocatalytic water splitting under mild condition, which can re-awaken the research interest to produce H2 from water using low-grade heat and competes with photocatalytic, electrolytic, and photoelectric reactions.

In-Situ Derived Defective Ru Particles Anchored on Ru-Ni Layered Double Hydroxides for Enhanced Alkaline Hydrogen Evolution.

Developing active, stable, and cost-efficient electrocatalysts to replace platinum for the alkaline hydrogen evolution reaction (HER) is highly desirable yet represents a great challenge. Here, it is reported on a facile one-pot synthesis of RuxNi layered double hydroxides (RuxNi-LDHs) that exhibit remarkable HER activity and stability after an in-situ activation treatment, surpassing most state-of-the-art Ru-based catalysts as well as commercial Ru/C and Pt/C catalysts. The structural and chemical changes triggered by in-situ activation are systematically investigated, and the results clearly show that the pristine, less-active RuxNi-LDHs are transformed into a highly active catalyst characterized by raft-like, defect-rich Ru° particles decorated on the surface of RuxNi-LDHs. Density functional theory (DFT) calculations reveal that the defective Ru sites can effectively optimize the reaction pathway and lower the free energies of the elemental steps involved, leading to enhanced intrinsic activity. This work highlights the importance of the currently understudied strategy of defect engineering in boosting the HER activity of Ru-based catalysts and offers an effective approach involving in-situ electrochemical activation for the development of high-performance alkaline HER catalysts.

Highly Permeable Mixed Matrix Membranes for Gas Separation via Dual Defect-Engineered Zeolitic Imidazolate Framework-8.

Defect engineering of metal-organic frameworks (MOFs) is a promising strategy for tailoring the interfacial characteristics between MOFs and polymers, aiming to create high-performance mixed matrix membranes (MMMs). This study introduces a new approach using dual defective alkylamine (AA)-modulated zeolitic imidazolate framework-8 (DAZIF-8), to develop high-flux MMMs. Tributylamine (TBA) and triethylamine (TEA) monodentate ligands coordinate with zinc ions in varying compositions. A mixture of Zn(CH3COO)2·2H2O:2-methylimidazole (Mim):AA in a 1:1.75:5 molar ratio facilitates high-yield coordination between Zn and multiple organic ligands, including Zn-Mim, Zn-TEA, and Zn-TBA (>80%). Remarkably, DAZIF-8 containing 3 mol% TBA and 2 mol% TEA exhibits exceptional characteristics, such as a Brunauer-Emmett-Teller surface area of 1745 m2 g-1 and enhanced framework rigidity. Furthermore, dual Zn-AA coordination sites on the framework's outer surface enhance compatibility with the polyimide (PI) matrix through electron donor-acceptor interactions, enabling the fabrication of high-loading MMMs with excellent mechanical durability. Importantly, the PI/DAZIF-8 (60/40 w/w) MMM demonstrates an unprecedented 759% enhancement in ethylene (C2H4) permeability (281 Barrer) with a moderate ethylene/ethane (C2H4/C2H6) selectivity of 2.95 compared to the PI, surpassing the polymeric upper limit for C2H4/C2H6 separation.

Adsorption and Distribution of Triplex-hybridizing Bioconjugated Gold Nanoclusters inside Spermatozoa- A Study using Confocal Microscopy and Fluorescence Lifetime Imaging.

The study of the interactions between biofunctionalized gold nanoclusters (Au NCs) and spermatozoa is highly relevant to evaluate the potential of Au NCs as imaging probes and transfection agents in the reproductive biology. In this work, confocal laser scanning microscopy (CLSM) was used to investigate the distribution of Au NCs bioconjugated with peptide (nuclear localisation sequence, NLS) and oligonucleotide (locked nucleic acid, LNA) ligands in bovine spermatozoa. Fluorescence lifetime imaging (FLIM) was employed to detect changes in the NC´s chemical environment. We observed a pronounced regio-selective accumulation of the bioconjugates in spermatozoa with high concentration at the equatorial segment. Furthermore, 3D-CLSM showed successful non-endosomal cellular uptake of the conjugates by intact sperm cells and the distribution of the bioconjugates was found to be influenced by the ligand types. Interestingly, the FLIM data showed differences in lifetime depending on membrane integrity. Furthermore, ligand-dependent changes in lifetime between NC bioconjugates carrying peptide and oligonucleotide ligands were found, probably attributed to specific interactions with sperm cell compartments.

sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs.

Coronavirus RNA-dependent RNA polymerases produce subgenomic RNAs (sgRNAs) that encode viral structural and accessory proteins. User-friendly bioinformatic tools to detect and quantify sgRNA production are urgently needed to study the growing number of next-generation sequencing (NGS) data of SARS-CoV-2. We introduced sgDI-tector to identify and quantify sgRNA in SARS-CoV-2 NGS data. sgDI-tector allowed detection of sgRNA without initial knowledge of the transcription-regulatory sequences. We produced NGS data and successfully detected the nested set of sgRNAs with the ranking M > ORF3a > N>ORF6 > ORF7a > ORF8 > S > E>ORF7b. We also compared the level of sgRNA production with other types of viral RNA products such as defective interfering viral genomes.

Shared sequence characteristics identified in non-canonical rearrangements of HSV-1 genomes.

IMPORTANCE: Mutations and genetic rearrangements are the primary driving forces of evolution. Viruses provide valuable model systems for investigating these mechanisms due to their rapid evolutionary rates and vast genetic variability. To investigate genetic rearrangements in the double-stranded DNA genome of herpes simplex virus type 1, the viral population was serially passaged in various cell types. The serial passaging led to formation of defective genomes, resulted from cell-specific non-canonical rearrangements (NCRs). Interestingly, we discovered shared sequence characteristics underlying the formation of these NCRs across all cell types. Moreover, most NCRs identified in clinical samples shared these characteristics. Based on our findings, we propose a model elucidating the formation of NCRs during viral replication within the nucleus of eukaryotic cells.