Novel strain-level resolution of Crohn’s disease mucosa-associated microbiota via an ex vivo combination of microbe culture and metagenomic sequencing

The mucosa-associated microbiota is widely recognized as a potential trigger for Crohn’s disease pathophysiology but remains largely uncharacterised beyond its taxonomic composition. Unlike stool microbiota, the functional characterisation of these communities using current DNA/RNA sequencing approaches remains constrained by the relatively small microbial density on tissue, and the overwhelming amount of human DNA recovered during sample preparation. Here, we have used a novel ex vivo approach that combines microbe culture from anaerobically preserved tissue with metagenome sequencing (MC-MGS) to reveal patient-specific and strain-level differences among these communities in post-operative Crohn’s disease patients. The 16 S rRNA gene amplicon profiles showed these cultures provide a representative and holistic representation of the mucosa-associated microbiota, and MC-MGS produced both high quality metagenome-assembled genomes of recovered novel bacterial lineages. The MC-MGS approach also produced a strain-level resolution of key Enterobacteriacea and their associated virulence factors and revealed that urease activity underpins a key and diverse metabolic guild in these communities, which was confirmed by culture-based studies with axenic cultures. Collectively, these findings using MC-MGS show that the Crohn’s disease mucosa-associated microbiota possesses taxonomic and functional attributes that are highly individualistic, borne at least in part by novel bacterial lineages not readily isolated or characterised from stool samples using current sequencing approaches.Subject terms: Biomarkers, Microbiome, Next-generation sequencing, Clinical microbiology, Metagenomics     

Generating Correlated Binary Variables with Complete Specification of the Joint Distribution

Most statistical methods for the analysis of correlated binary data are based on asymptotic theory. Therefore it is important to generate correlated binary data efficiently for Monte Carlo simulation studies to investigate the finite sample performance of these methods. This article provides a simple method for generating correlated binary data with a given joint distribution. The key idea is to consider k‐variate binary data as a multinomial distribution with 2^k possible outcomes.     

Perspectives on Li Dendrite Penetration in Li7La3Zr2O12-Based Solid-State Electrolytes and Batteries: Materials,Interfaces, and Charge Transfer

Garnet-type Li₇La₃Zr₂O₁₂ (LLZO) solid-state electrolytes have gained significant attention as one of the most promising electrolyte candidates for high-energy-density energy storage devices due to their superior stability and high ionic conductivity. However, the problem of lithium (Li) dendrite penetration into LLZO hinders the practical application of LLZO in solid-state Li metal batteries (SSLMBs). Multidisciplinary evaluations are carried out to understand the mechanism of dendrite penetration. Herein, the formation and evolution of different types of Li dendrites within LLZO are reviewed. The Li dendrite penetration process is addressed from the perspectives of material design, Li/LLZO interfacial adaptability, and the interfacial charge transfer process. On this basis, recent efforts and solutions to inhibiting the penetration of Li dendrites in LLZO, including stabilizing LLZO phase and densification techniques, interfacial modifications, and grain boundary manipulations, are summarized. It is expected that the in-depth understanding of the Li dendrite penetration and corresponding solutions will provide a systemic guideline toward the development of LLZO-based solid-state electrolytes and the commercialization of ultra-stable SSLMBs.     

Local Steric Hindrance for CO2 Electroreduction at a Thermodynamic Potential and Wide Working Window

To improve the energy-conversion efficiency and adaptability between a CO₂ electroreduction system and intermittent renewable energy, small onset potentials, and wide working windows are highly important. Here, three indium metal–organic frameworks (In-MOFs) have been projected using different ligands to adjust the local steric hindrance and electronic structure of In nodes, manipulating the whole workflow of CO₂ during electroreduction including local CO₂ transport, adsorption, activation, hydrogenation, and product desorption. Significantly, a CO₂ electroreduction to formate process promoted by 2,5-TDC In-MOF shows an onset potential of −0.1 V versus RHE around the therymodynamic potential, over 90% FE_foramte in a wide current-density window from 0.1 to 0.9 A cm⁻². Driven by solar cells, the system displays a high solar-to-chemical efficiency of 17.39%. In depth mechanism study indicates that the local CO₂ transport and adsorption of all In-MOFs are thermodynamically and kinetically favorable, while the energy barrier of potential-determine step (*HCOOH desorption) is the lowest for 2,5-TDC In-MOF.     

A Safe Organic/Inorganic Composite Anode for Sodium-Ion Batteries

Sodium-ion batteries (SIBs), based on hard carbon anodes and Na⁺-intercalation compound cathodes, have gained significant attention. Nonetheless, hard carbon anodes involve the storage of Na⁺ at a low potential, typically below 0.1 V (vs Na/Na⁺), which increases the risk of dendritic Na growth on the anode surface during overcharging. Herein, a safe organic/inorganic composite anode containing tetrasodium 3,4,9,10-perylenetetracarboxylate (Na₄PTC) and Metallic bismuth (Bi) with a weight ratio of 7:2, which exhibits an average potential of 0.7 V (vs Na⁺/Na) and a capacity of 150 mAh g⁻¹ is proposed. The electrode reaction involves a reversible coordination reaction within the organic host and alloying reactions within the metallic Bi component. Importantly, the organic component efficiently buffers the volume changes in Bi during the alloying reaction, while the metallic Bi enhances the electronic conductivity of the organic material. As a result, this composite anode shows high cycle stability and rate performance, even under high mass loadings ranging from 10 to 50 mg cm⁻². Furthermore, it is demonstrated that the Na-ion full cell, consisting of the composite anode and the Na₃V₂O₂(PO₄)₂F cathode, exhibits minimal capacity degradation over 100 cycles while maintaining a high areal capacity of 1.1 mA cm⁻².     

A novel fluorescent aptasensor for the detection of theophylline based on cryonase-driven signal amplification strategy

In the study, we have developed an expedient and efficient method for the detection of theophylline based on the amplification of the signal intensity of fluorescence based on oxidized single-walled carbon nanohorns (oxSWCNHs)/cryonase. When theophylline was not present in the system, oxSWCNHs can adequately adsorb nucleic acid probes labeled by carboxyfluorescein (FAM). In the presence of theophylline, the nucleic acid probe forms the tertiary probe–theophylline complex, which detaches from the surface of the oxSWCNHs. Then, upon reaction with cryonase, the complex can release the FAM and theophylline into the next cycle. The fluorescence signal of the system exhibits a 1:N magnification, enabling quantitative detection of theophylline. The linear range was 30–150 ng/mL, and the limit of detection (LOD) was 6.04 ng/mL. At the same time, it can also be used to detect theophylline in mouse serum.     

The long rod-shaped Sr2MgSi2O7:Eu2+,Dy3+ with ultrahigh afterglow performance

The afterglow properties of long afterglow luminescent materials are greatly affected by their defects, which are distributed on the grain surface. Increasing the exposed surface area is an important method to improve the afterglow performance. In this research, long rod-shaped long afterglow materials Sr₂MgSi₂O₇:Eu²⁺,Dy³⁺ were prepared using the hydrothermal-coprecipitation method. When the reaction time reached 96 h, the length of the afterglow materials could grow to 2 mm, and the sintering temperature was just 1150°C. The emission spectra of all obtained samples upon excitation at 397 nm had a maximum of 465 nm, which belonged to the representative transition of Eu²⁺. The initial brightness was 1.35 cd/m². The afterglow time could reach 19 h, giving a good afterglow performance. The research on this kind of material has essential significance in the exploration of luminescence mechanisms and their applications.     

Conformational study of asialo-GM1 (GA1) ganglioside

In order to investigate the significance of preferred conformations of the saccharide for the steric orientation and recognition of glycosphingolipids at the membrane surface, the conformational free energy calculations were carried out on the asialo-GM1 [GA1; β-D -Gal(1 → 3) β-D -GalNAc(1 → 4) β-D -Gal(1 → 4) β-D -Glc-O-ceramide] using a new program CONCARB (CONformational study program for CARBohydrate) in the unhydrated and hydrated states. The overall backbone conformation of GA1 appears nearly to be extended with a little bent at the glycosidic II–III linkage, in which two pyranose rings of Gal(IV)-GalNAc-(III) moiety orient approximately perpendicular to those of Gal(II)-Glc(I) moiety. This is consistent with the structures deduced from high-sensitivity differential scanning calorimetry experiments and the nmr study on GA1. The calculated glycosidic torsion angles of the lowest free energy conformation of GA1 in the hydrated state are in accord with the structures of relevant oligosaccharides deduced from nmr experiments and hard sphere exoanomeric calculations. A comparison of the values of glycosidic torsion angles ϕ and π of GA1 and its constituent oligosaccharides indicates that the overall backbone conformation of each oligosaccharide is retained when the oligosaccharide chain becomes longer. This implies that the short-range interactions between the nearest-neighbored saccharides are of significant importance in stabilizing the overall backbone conformation of GA1 in both the unhydrated and hydrated states. The different orientation and hydrogen bonds of hydroxymethyl and hydroxyl groups from one oligosaccharide to another suggest that the medium- and long-range interactions are also of consequence. Hydration seems to affect significantly the conformation of these groups, but not to perturb remarkably the overall backbone conformation of GA1. © 1997 John Wiley & Sons, Inc. Biopoly 42: 19–35, 1997