Small RNA-modulated anaerobic respiration allows bacteria to survive under antibiotic stress conditions.

Despite extensive knowledge of antibiotic-targeted bacterial cell death, deeper understanding of antibiotic tolerance mechanisms is necessary to combat multi-drug resistance in the global healthcare settings. Regulatory RNAs in bacteria control important cellular processes such as cell division, cellular respiration, metabolism, and virulence. Here, we investigated how exposing Escherichia coli to the moderately effective first-generation antibiotic cephalothin alters transcriptional and post-transcriptional dynamics. Bacteria switched from active aerobic respiration to anaerobic adaptation via an FnrS and Tp2 small RNA-mediated post-transcriptional regulatory circuit. From the early hours of antibiotic exposure, FnrS was involved in regulating reactive oxygen species levels, and delayed oxygen consumption in bacteria. We demonstrated that bacteria strive to maintain cellular homeostasis via sRNA-mediated sudden respiratory changes upon sublethal antibiotic exposure.

Multimodal Golden DNA Superstructures (GDSs) for Highly Efficient Photothermal Immunotherapy.

DNA-templated metallization has emerged as an efficient strategy for creating nanoscale-metal DNA hybrid structures with a desirable conformation and function. Despite the potential of DNA-metal hybrids, their use as combinatory therapeutic agents has rarely been examined. Herein, we present a simple approach for fabricating a multipurpose DNA superstructure that serves as an efficient photoimmunotherapy agent. Specifically, we adsorb and locally concentrate Au ions onto DNA superstructures through induced local reduction, resulting in the formation of Au nanoclusters. The mechanical and optical properties of these metallic nanoclusters can be rationally controlled by their conformations and metal ions. The resulting golden DNA superstructures (GDSs) exhibit significant photothermal effects that induce cancer cell apoptosis. When sequence-specific immunostimulatory effects of DNA are combined, GDSs provide a synergistic effect to eradicate cancer and inhibit metastasis, demonstrating potential as a combinatory therapeutic agent for tumor treatment. Altogether, the DNA superstructure-templated metal casting system offers promising materials for future biomedical applications.

DECIPHERING GUT MICROBIOTA IN PATIENTS WITH SEVERE SEPSIS AND SEPTIC SHOCK.

ABSTRACT: Introduction: Gut microbiota dysbiosis is associated with susceptibility to sepsis and poor outcomes. However, changes to the intestinal microbiota during sepsis and their value as biomarkers are unclear. In this study, we compared the intestinal microbiota of patients with sepsis and healthy controls. Methods: Stool was collected from patients with sepsis (subdivided according to mortality) and controls. Microbiome diversity and composition were analyzed by 16S rRNA gene pyrosequencing. The α-diversity of the intestinal microbiome was determined using operational taxonomic unit counts and the Chao1, Shannon, and ACE indices. Adjusted Cox regression analyses assessed 6-month mortality risk factors. Results: Fifty-nine patients (14 in-hospital deaths) and 29 healthy controls were enrolled. Operational taxonomic unit counts and Chao1 and ACE indices were lower in the nonsurvivor than in the other groups. The controls showed a higher Shannon and lower Simpson index than did the sepsis group. The genus Blautia was more abundant in controls than in the sepsis group, and Faecalibacterium less abundant in the nonsurvivor than in the other groups. Regression analysis associated low Shannon index with 6-month mortality. Conclusions: Survivors of sepsis, nonsurvivors, and healthy controls have different gut microbiomes, and a low Shannon index is a risk factor for 6-month mortality.

Repeated Intravenous Administration of Human Neural Stem Cells Producing Choline Acetyltransferase Exerts Anti-Aging Effects in Male F344 Rats.

Major features of aging might be progressive decreases in cognitive function and physical activity, in addition to withered appearance. Previously, we reported that the intracerebroventricular injection of human neural stem cells (NSCs named F3) encoded the choline acetyltransferase gene (F3.ChAT). The cells secreted acetylcholine and growth factors (GFs) and neurotrophic factors (NFs), thereby improving learning and memory function as well as the physical activity of aged animals. In this study, F344 rats (10 months old) were intravenously transplanted with F3 or F3.ChAT NSCs (1 × 106 cells) once a month to the 21st month of age. Their physical activity and cognitive function were investigated, and brain acetylcholine (ACh) and cholinergic and dopaminergic system markers were analyzed. Neuroprotective and neuroregenerative activities of stem cells were also confirmed by analyzing oxidative damages, neuronal skeletal protein, angiogenesis, brain and muscle weights, and proliferating host stem cells. Stem cells markedly improved both cognitive and physical functions, in parallel with the elevation in ACh levels in cerebrospinal fluid and muscles, in which F3.ChAT cells were more effective than F3 parental cells. Stem cell transplantation downregulated CCL11 and recovered GFs and NFs in the brain, leading to restoration of microtubule-associated protein 2 as well as functional markers of cholinergic and dopaminergic systems, along with neovascularization. Stem cells also restored muscular GFs and NFs, resulting in increased angiogenesis and muscle mass. In addition, stem cells enhanced antioxidative capacity, attenuating oxidative damage to the brain and muscles. The results indicate that NSCs encoding ChAT improve cognitive function and physical activity of aging animals by protecting and recovering functions of multiple organs, including cholinergic and dopaminergic systems, as well as muscles from oxidative injuries through secretion of ACh and GFs/NFs, increased antioxidant elements, and enhanced blood flow.

Design of a Flexible Thin-Film Encapsulant with Sandwich Structures of Perhydropolysilazane Layers.

Perovskite solar cells (PSCs) have attracted considerable attention due to their excellent photovoltaic properties, but stability issues have prevented their widespread application. PSCs must be protected by encapsulation to extend their lifetime. Here, we show that perhydropolysilazane (PHPS)-based multilayered encapsulation improves the lifetime of PSCs. The PSCs were encapsulated by converting PHPS into silica under vacuum ultraviolet (UV) irradiation. The PHPS-based multilayer encapsulation method achieved a sandwich structure of PHPS/poly(ethylene terephthalate) (PET)/PHPS with a water vapor transmission rate (WVTR) of 0.92 × 10-3 gm-2 d-1 (at 37.8 °C and 100% relative humidity). We then performed a reservoir test of the encapsulated PSCs to confirm the moisture stability of the encapsulation based on PHPS/PET/PHPS barrier films. The cell lifetime remained stable even after 1000 h of ambient-temperature operation. Finally, we analyzed the mechanical flexibility of the PHPS/PET/PHPS multibarrier through bending tests. The multibarrier exhibited high mechanical stability with no large increase in WVTR after bending.

Multimeric RNAs for efficient RNA-based therapeutics and vaccines.

There has been a growing interest in RNA therapeutics globally, and much progress has been made in this area, which has been further accelerated by the clinical applications of RNA-based vaccines against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Following these successful clinical trials, various technologies have been developed to improve the efficacy of RNA-based drugs. Multimerization of RNA therapeutics is one of the most attractive approaches to ensure high stability, high efficacy, and prolonged action of RNA-based drugs. In this review, we offer an overview of the representative approaches for generating repetitive functional RNAs by chemical conjugation, structural self-assembly, enzymatic elongation, and self-amplification. The therapeutic and vaccine applications of engineered multimeric RNAs in various diseases have also been summarized. By outlining the current status of multimeric RNAs, the potential of multimeric RNA as a promising treatment strategy is highlighted.

Salmonella enterica serovar Typhimurium uses anaerobic respiration to overcome propionate-mediated colonization resistance.

The gut microbiota benefits the host by limiting enteric pathogen expansion (colonization resistance), partially via the production of inhibitory metabolites. Propionate, a short-chain fatty acid produced by microbiota members, is proposed to mediate colonization resistance against Salmonella enterica serovar Typhimurium (S. Tm). Here, we show that S. Tm overcomes the inhibitory effects of propionate by using it as a carbon source for anaerobic respiration. We determine that propionate metabolism provides an inflammation-dependent colonization advantage to S. Tm during infection. Such benefit is abolished in the intestinal lumen of Salmonella-infected germ-free mice. Interestingly, S. Tm propionate-mediated intestinal expansion is restored when germ-free mice are monocolonized with Bacteroides thetaiotaomicron (B. theta), a prominent propionate producer in the gut, but not when mice are monocolonized with a propionate-production-deficient B. theta strain. Taken together, our results reveal a strategy used by S. Tm to mitigate colonization resistance by metabolizing microbiota-derived propionate.

RNA polymerization actuating nucleic acid membrane (RANAM)-based biosensing for universal RNA virus detection.

The coronavirus disease (COVID-19) pandemic has shown the importance of early disease diagnosis in preventing further infection and mortality. Despite major advances in the development of highly precise and rapid detection approaches, the time-consuming process of designing a virus-specific diagnostic kit has been a limiting factor in the early management of the pandemic. Here, we propose an RNA polymerase activity-sensing strategy utilizing an RNA polymerization actuating nucleic acid membrane (RANAM) partially metallized with gold for colorimetric RNA virus detection. Following RANAM-templated amplification of newly synthesized RNA, the presence of the RNA polymerase was determined by visualization of the inhibition of an oxidation/reduction (redox) reaction between 3,3',5,5'-tetramethylbenzidine (TMB) and blocked Au3+. As a proof of concept, a viral RNA-dependent RNA polymerase (RdRP), which is found in various RNA virus-infected cells, was chosen as a target molecule. With this novel RANAM biosensor, as little as 10 min of RdRP incubation could significantly reduce the colorimetric signal. Further development into an easy-to-use prototype kit in viral infection diagnosis detected RdRP present at levels even as low as 100 aM. Color formation based on the presence of RdRP could be simply and clearly confirmed through smartphone-assisted color imaging of the prototype kit. This study provides a non-PCR-based RNA virus detection including its variants using RdRP-mediated polymerization.

Construction of a two-dimensional DNA-RNA hybridized membrane for collecting tumor-derived exosomes.

Macroscopic nucleic acid-based structures have attracted much attention in biomedical fields. Here, we introduce a novel DNA-RNA hybridized membrane structure via enzymatic dual polymerization. The membrane exhibited enhanced rigidity and functionality. Encoded with an aptamer, the membrane showed great potential as a collecting platform of tumor-derived exosomes without additional labeling.

Stamina-Enhancing Effects of Human Adipose-Derived Stem Cells.

Stamina-enhancing effects of human adipose derived stem cells (hADSCs) were investigated in young Sprague-Dawley rats. Ten-day-old male rats were transplanted intravenously (IV) or intracerebroventricularly (ICV) with hADSCs (1 × 106 cells/rat), and physical activity was measured by locomotor activity and rota-rod performance at post-natal day (PND) 14, 20, 30, and 40, as well as a forced swimming test at PND 41. hADSCs injection increased the moving time in locomotor activity, the latency in rota-rod performance, and the maximum swimming time. For the improvement of physical activity, ICV transplantation was superior to IV injection. In biochemical analyses, ICV transplantation of hADSCs markedly reduced serum creatine phosphokinase, lactate dehydrogenase, alanine transaminase, and muscular lipid peroxidation, the markers for muscular and hepatic injuries, despite the reduction in muscular glycogen and serum triglycerides as energy sources. Notably, hADSCs secreted brain-derived neurotrophic factor (BDNF) and nerve growth factor in vitro, and increased the level of BDNF in the brain and muscles in vivo. The results indicate that hADSCs enhance physical activity including stamina not only by attenuating tissue injury, but also by strengthening the muscles via production of BDNF.

Viscosity-Regulated Control of RNA Microstructure Fabrication.

The development of RNA self-assemblies offers a powerful platform for a wide range of biomedical applications. The fabrication process has become more elaborate in order to achieve functional structures with maximized potential. As a facile means to control the structure, here, we report a new approach to manipulate the polymerization rate and subsequent self-assembly process through regulation of the reaction viscosity. As the RNA polymerization rate has a dependence on solution viscosity, the resulting assembly, crystallization, and overall sizes of the product could be manipulated. The simple and precise control of RNA polymerization and self-assembly by reaction viscosity will provide a way to widen the utility of RNA-based materials.

An enzymatically self-assembled DNA patch for enhanced blood coagulation.

DNA has been widely investigated as a carrier for drug delivery. Here, we describe a macroscopic DNA film that has been generated enzymatically. This DNA film was subsequently coated with thrombin (TB) using an aptamer-protein interaction, to expedite hemostasis over a large area. The DNA film coated with TB (DNA patch) significantly improved plasma hemostasis by acting as a coagulative scaffold for TB, as well as carrying localized TB. This study elucidates the benefits of using enzymatic amplification-based DNA structures in the context of topical drug treatment.

Engineered extracellular vesicles and their mimetics for clinical translation.

Cells secrete extracellular vesicles (EVs) to external environments to achieve cellular homeostasis and cell-to-cell communication. Their therapeutic potential has been constantly spotlighted since they mirror both cytoplasmic and membranous components of parental cells. Meanwhile, growing evidence suggests that EV engineering could further promote EVs with a maximized capacity. In this review, a range of engineering techniques as well as upscaling approaches to exploit EVs and their mimetics are introduced. By laying out the pros and cons of each technique from different perspectives, we sought to provide an overview potentially helpful for understanding the current state of the art EV engineering and a guideline for choosing a suitable technique for engineering EVs. Furthermore, we envision that the advances in each technique will give rise to the combinatorial engineering of EVs, taking us a step closer to a clinical translation of EV-based therapeutics.

Quantitative Surface-Enhanced Raman Spectroscopy Analysis through 3D Superlattice Arrays of Au Nanoframes with Attomolar Detection.

This paper reports a methodology for synthesizing and ordering gold nanoframes into three-dimensional (3D) arrays with a controlled thickness, leading to homogeneous plasmonic superstructures, with which quantitative analysis via surface-enhanced Raman spectroscopy (SERS) has been successfully demonstrated. Because this preparation method allows for systematic control of nanoframe film thickness and the resulting 3D plasmonic superstructure, which exhibits a unique nanoporous network of hot-spots, detection limits down to 10-18 M, corresponding to ≈6000 molecules, have been measured. Compared to analogous solid nanoparticle superstructures, the nanoframe superstructures with their unique nanoporous architecture effectively dissipate the heat inevitably generated by laser excitation during measurement, effectively suppressing the formation of carbonaceous materials and therefore their accompanying fluorescence interference, especially important for low concentration detection.

Pediatric codeine prescriptions in outpatient and inpatient settings in Korea.

OBJECTIVES: To examine the extent of codeine prescriptions for children younger than 12 years in Korea and to investigate characteristics associated with pediatric codeine use. STUDY DESIGN: A retrospective observational study was conducted to examine codeine prescriptions and patients' characteristics. METHODS: We used the Korea Health Insurance Review and Assessment Service National Patient Sample database. The study participants were patients younger than 12 years who were prescribed codeine as inpatients or outpatients between 2011 and 2016. Pediatric codeine use was defined as codeine prescribed at least once for a child younger than 12 years. The frequency and proportion of pediatric codeine users were analyzed by age group (0-2, 3-6, or 7-11 years), sex, year, region, diagnosis, type of medical institution, and coprescribed medication. Logistic regression analyses were performed to identify characteristics associated with pediatric codeine use. RESULTS: Of all patients younger than 12 years, 518,895 (55.8%) and 16,337 (1.7%) were treated with codeine in outpatient and inpatient settings, respectively. Odds of pediatric codeine prescriptions were highest for outpatients at clinics (adjusted odds ratio [OR], 1.19; 95% CI, 1.16-1.21) and public hospitals (adjusted OR, 1.56; 95% CI, 1.28-1.91) and for inpatients at public hospitals (adjusted OR, 8.38; 95% CI, 6.64-10.58). CONCLUSIONS: Codeine was frequently prescribed for pediatric outpatients in Korea, especially in primary care clinics. Efforts to limit codeine use in children are required to prevent the occurrence of codeine-related adverse events.

Programmed Delay of a Virulence Circuit Promotes Salmonella Pathogenicity.

Signal transduction systems dictate various cellular behaviors in response to environmental changes. To operate cellular programs appropriately, organisms have sophisticated regulatory factors to optimize the signal response. The PhoP/PhoQ master virulence regulatory system of the intracellular pathogen Salmonella enterica is activated inside acidic macrophage phagosomes. Here we report that Salmonella delays the activation of this system inside macrophages using an inhibitory protein, EIIANtr (a component of the nitrogen-metabolic phosphotransferase system). We establish that EIIANtr directly restrains PhoP binding to its target promoter, thereby negatively controlling the expression of PhoP-activated genes. PhoP furthers its activation by promoting Lon-mediated degradation of EIIANtr at acidic pH. These results suggest that Salmonella ensures robust activation of its virulence system by suspending the activation of PhoP until a sufficient level of active PhoP is present to overcome the inhibitory effect of EIIANtr Our findings reveal how a pathogen precisely and efficiently operates its virulence program during infection.IMPORTANCE To accomplish successful infection, pathogens must operate their virulence programs in a precise, time-sensitive, and coordinated manner. A major question is how pathogens control the timing of virulence gene expression during infection. Here we report that the intracellular pathogen Salmonella controls the timing and level of virulence gene expression by using an inhibitory protein, EIIANtr A DNA binding master virulence regulator, PhoP, controls various virulence genes inside acidic phagosomes. Salmonella decreases EIIANtr amounts at acidic pH in a Lon- and PhoP-dependent manner. This, in turn, promotes expression of the PhoP-activated virulence program because EIIANtr hampers activation of PhoP-regulated genes by interfering with PhoP binding to DNA. EIIANtr enables Salmonella to impede the activation of PhoP-regulated gene expression inside macrophages. Our findings suggest that Salmonella achieves programmed delay of virulence gene activation by adjusting levels of an inhibitory factor.

Self-assembled DNA hollow spheres from microsponges.

We report a novel approach for generating nanosized DNA hollow spheres (HSs) using enzymatically produced DNA microsponges in a self-templating manner. In previous studies, preparation of DNA nanostructures with specified functions required multiple complicated steps. In this study, however, a simple treatment with the nucleophilic agent 4-dimethylaminopyridine (DMAP) enabled a gradual disentanglement of DNA in microsponges by electrostatic interactions between DMAP and DNA, and the DNA underwent a reassembly process to generate hollow shell structures without denaturation/annealing by thermal cycling. In addition, this synthetic process was conducted in a water-based system without organic solvents, enabling the synthesis of biologically and environmentally friendly products. Based on the benefits of hollow shell structures, which include their high surface-to-volume ratio and ability to encapsulate small molecules, we envision that this simple approach for synthesizing DNA HSs will provide a new platform for maximizing their potential use in drug delivery and bio-imaging.

Structural basis for HOCl recognition and regulation mechanisms of HypT, a hypochlorite-specific transcriptional regulator.

Hypochlorous acid (HOCl) is generated in the immune system to kill microorganisms. In Escherichia coli, a hypochlorite-specific transcription regulator, HypT, has been characterized. HypT belongs to the LysR-type transcriptional regulator (LTTR) family that contains a DNA-binding domain (DBD) and a regulatory domain (RD). Here, we identified a hypT gene from Salmonella enterica serovar Typhimurium and determined crystal structures of the full-length HypT protein and the RD. The full-length structure reveals a type of tetrameric assembly in the LTTR family. Based on HOCl-bound and oxidation-mimicking structures, we identified a HOCl-driven methionine oxidation mechanism, in which the bound HOCl oxidizes a conserved methionine residue lining the putative ligand-binding site in the RD. Furthermore, we proposed a molecular model for the oxidized HypT, where methionine oxidation by HOCl results in a conformational change of the RD, inducing a counter rotation of the DBD dimers. Target genes that are regulated by HypT and their roles in Salmonella were also investigated. DNase I footprinting experiments revealed a DNA segment containing two pseudopalindromic motifs that are separated by ∼100 bp, suggesting that only the oxidized structure makes a concomitant binding, forming a DNA loop. An understanding of the HypT-mediated mechanism would be helpful for controlling many pathogenic bacteria by counteracting bacterial HOCl defense mechanisms.

3D PtAu nanoframe superstructure as a high-performance carbon-free electrocatalyst.

In this work, we demonstrate how to synthesize a three-dimensional (3D) ordered PtAu nanoframe superstructure and evaluated its performance as an electrocatalyst. Compared to carbon supported platinum (Pt) nanocrystal electrocatalysts (wherein the aggregation- and carbon corrosion-induced fast degradation is a well-known drawback), the 3D PtAu nanoframe superstructure is free from aggregation and carbon corrosion. The 3D superstructure was self-assembled via drop-casting and evaporation using truncated octahedral PtAu nanoframes (TOh PtAu NFs) as building blocks that were produced by controlled wet-chemical etching of a TOh Au core whose edges and vertexes were selectively deposited with Pt atoms. Density functional theory calculations revealed that the surface alloy state of PtAu gave rise to an enhanced catalytic activity compared to pure Pt. Experimental investigations showed that such 3D superstructure electrocatalysts exhibited excellent mass transfer efficiency, higher catalytic activity and stability towards the methanol oxidation reaction (MOR) compared to a commercial Pt/C catalyst. The demonstrated 3D nanoframe superstructure shows great potential for practical catalytic application due to its high structural stability, high catalytic activity, high surface area and ease of fabrication.

Immunostimulatory Effects Triggered by Self-Assembled Microspheres with Tandem Repeats of Polymerized RNA Strands.

Self-assembled RNA particles have been exploited widely to maximize the therapeutic potential of RNA. However, the immune response via RNA particles is not fully understood. In addition, the investigation of the immunogenicity from RNA-based particles is required owing to inherent immunostimulatory effects of RNA for clinical translation. To examine the immune stimulating potency, rationally designed microsized RNA particles, called RNA microspheres (RMSs), are generated with single or double strands via rolling circle transcription. The RMSs show an exceptional stability in the presence of serum, while they are selectively degraded under endolysosomal conditions. With precisely controlled size, both RMSs are successfully taken up by macrophages. Unlike the nature of RNA fragments, RMSs induce only basal-level expression of inflammatory cytokines as well as type I interferon from macrophages, suggesting that RMSs are immunocompatible in the therapeutic dose range. Taken together, this study could help accelerate clinical translation and broaden the applicability of the self-assembled RNA-based particles without being limited by their potential immunotoxicity, while a systematic controllability study observing the release of RNA fragments from RMSs would provide self-assembled RNA-based structures with a great potential for immunomodulation.