ABSTRACT
Broadband spectrum detectors exhibit great promise in fields such as multispectral imaging and optical communications. Despite significant progress, challenges like materials instability in such devices, complex manufacturing process, and high cost still hinder their further application. Here, we present a method that achieves broadband spectral detection by impurity-level in SrSnO3. We report over 500 mA/W photoresponsivity at 275 nm (ultraviolet C solar-bind) and 367 nm (ultraviolet A) and â¼60 mA/W photoresponsivity at 532 and 700 nm (visible) with a voltage bias of -5 V. Further transport and photoluminescence results reveal a new phase transition at 88 K, which would significantly affect the impurity level of the La-doped SrSnO3 film, indicating that the broadband response attributes to the impurity levels and mutual interactions. Additionally, the photodetector demonstrates excellent robustness and stability under repeated tests and prolonged exposure in air. These findings show the potential of SrSnO3 as a material for photodetectors and propose a method to achieve broadband spectrum detection, creating new possibility for the development of single-phase, low-cost, simple structure, and high-efficiency photodetectors.
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Heart failure (HF) is an increasingly prevalent disease in humans; it induces multiple symptoms and damages health. The animal gut microbiota has critical roles in host health, which might be related to HF symptoms. Currently, several options are used to treat HF, including non-invasive ventilation (NIV). However, studies on gut microbiota responses to acute HF and associated treatments effects on gut communities in patients are scarce. Here, short-term (1 week after treatments) and long-term (3 months after treatment) variations in gut microbiota variations in rats with acute HF treated were examined NIV through high-throughput sequencing of the bacterial 16S rRNA gene. Through comparison of gut microbiota alpha diversity, it was observed lower gut microbiota richness and diversity in animals with acute HF than in normal animals. Additionally, beta-diversity analysis revealed significant alterations in the gut microbiota composition induced by acute HF, as reflected by increased Firmicutes/Bacteroidetes (F/B) ratios and Proteobacteria enrichment. When network analysis results were combined with the null model, decreased stability and elevated deterministic gut microbiota assemblies were observed in animals with acute HF. Importantly, in both short- and long-term periods, NIV was found to restore gut microbiota dysbiosis to normal states in acute HF rats. Finally, it was shown that considerable gut microbiota variations existed in rats with acute HF, that underlying microbiota mechanisms regulated these changes, and confirmed that NIV is suitable for HF treatment. In future studies, these findings should be validated with different model systems or clinical samples.
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Coptis chinensis Franch. (Ranunculaceae, Coptis), a traditional Chinese medicine (TCM) with thousands of years of clinical use history, also a natural medicine available in many countries, has wide pharmacological mechanisms and significant bioactivity according to its traditional efficacy combined with modern scientific research. The quality marker (Q-marker) of C. chinensis Franch. is predicted in this paper based on the chemical composition and pharmacological effects of the plant, as well as the current system pharmacology, plant relatedness, biosynthetic pathways and quantitative analysis of multi-components (QAMS). Natural medicine has the advantage of being multi-component, multi-pathway and multi-target. However, there are few reports on safety evaluation. This review predicts the Q-marker of C. chinensis, and the safety and efficacy of C. chinensis is provided. Studies from 1975 to 2023 were reviewed from PubMed, Elsevier, ScienceDirect, Web of Science, SpringerLink, and Google Scholar. Alkaloids and organic acids are the two main component categories of Q-Markers. The specific alkaloids identified through predictive results include berberine, coptisine, palmatine, epiberberine, jatrorrhizine, columbamine, and berberrubine. Quinic acid and malic acid, due to their influence on the content of alkaloids and their ability to aid in identifying the active components of C. chinensis, are also considered Q-markers. The research strategy of "exploring chemical components, exploring pharmacological activities, constructing pharmacological mechanism network and locating biosynthetic pathways" was used to accurately screen the quality markers of C. chinensis in this review and summarise the quality evaluation methods and criteria. In addition, we updated the biosynthetic pathway of C. chinensis and refined the specific synthetic pathways of jatrorrhizine (quality markers) and epiberberine (quality markers). Finally, we summarised the quality evaluation methods of C. chinensis, which provide an important reference for resource evaluation and provide a key reference for the discovery of new functional chemical entities for natural medicines.
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Feature extraction plays a pivotal role in the context of single image super-resolution. Nonetheless, relying on a single feature extraction method often undermines the full potential of feature representation, hampering the model's overall performance. To tackle this issue, this study introduces the wide-activation feature distillation network (WFDN), which realizes single image super-resolution through dual-path learning. Initially, a dual-path parallel network structure is employed, utilizing a residual network as the backbone and incorporating global residual connections to enhance feature exploitation and expedite network convergence. Subsequently, a feature distillation block is adopted, characterized by fast training speed and a low parameter count. Simultaneously, a wide-activation mechanism is integrated to further enhance the representational capacity of high-frequency features. Lastly, a gated fusion mechanism is introduced to weight the fusion of feature information extracted from the dual branches. This mechanism enhances reconstruction performance while mitigating information redundancy. Extensive experiments demonstrate that the proposed algorithm achieves stable and superior results compared to the state-of-the-art methods, as evidenced by quantitative evaluation metrics tests conducted on four benchmark datasets. Furthermore, our WFDN excels in reconstructing images with richer detailed textures, more realistic lines, and clearer structures, affirming its exceptional superiority and robustness.
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Staphylococcal Enterotoxin Type B (SEB), produced by Staphylococcus aureus bacteria, is notorious for inducing severe food poisoning and toxic shock syndrome. While nanobody-based treatments hold promises for combating SEB-induced diseases, the lack of structural information between SEB and nanobodies has hindered the development of nanobody-based therapeutics. Here, we present crystal structures of SEB-Nb3, SEB-Nb6, SEB-Nb8, SEB-Nb11, and SEB-Nb20 at resolutions ranging from 1.59 Å to 2.33 Å. Crystallographic analysis revealed that Nb3, Nb8, Nb11, and Nb20 bind to SEB at the T-cell receptor (TCR) interface, while Nb6 binds at the major histocompatibility complex (MHC) interface, suggesting their potential to inhibit SEB function by disrupting interactions with TCR or MHC molecules. Molecular biological analyses confirmed the thermodynamic and kinetic parameters of Nb3, Nb5, Nb6, Nb8, Nb11, Nb15, Nb18, and Nb20 to SEB. The competitive inhibition was further confirmed by cell-based experiments demonstrating nanobody neutralization. These findings elucidate the structural basis for developing specific nanobodies to neutralize SEB threats, providing crucial insights into the underlying mechanisms and offering significant assistance for further optimization towards future therapeutic strategies.
Subject(s)
Enterotoxins , Protein Binding , Single-Domain Antibodies , Enterotoxins/chemistry , Enterotoxins/immunology , Enterotoxins/metabolism , Single-Domain Antibodies/chemistry , Single-Domain Antibodies/immunology , Humans , Models, Molecular , Receptors, Antigen, T-Cell/metabolism , Receptors, Antigen, T-Cell/immunology , Receptors, Antigen, T-Cell/chemistry , Staphylococcus aureus/immunology , Crystallography, X-Ray , Thermodynamics , KineticsABSTRACT
BACKGROUND: Alcohol-related liver damage is the most prevalent chronic liver disease, which creates a heavy public health burden worldwide. The leaves of Ampelopsis grossedentata have been considered a popular tea and traditional herbal medicine in China for more than one thousand years, and possess anti-inflammatory, antioxidative, hepatoprotective, and antiviral activities. PURPOSE: We explored the protective effects of Ampelopsis grossedentata extract (AGE) against chronic alcohol-induced hepatic injury (alcoholic liver disease, ALD), aiming to elucidate its underlying mechanisms. METHODS: Firstly, UPLC-Q/TOF-MS analysis and network pharmacology were used to identify the constituents and elucidate the potential mechanisms of AGE against ALD. Secondly, C57BL/6 mice were pair-fed the Lieber-DeCarli diet containing either isocaloric maltodextrin or ethanol, AGE (150 and 300 mg/kg/d) and silymarin (200 mg/kg) were administered to chronic ethanol-fed mice for 7 weeks to evaluate the hepatoprotective effects. Serum biochemical parameters were determined, hepatic and ileum sections were used for histologic examination, and levels of inflammatory cytokines and oxidative stress in the liver were examined. The potential molecular mechanisms of AGE in improving ALD were demonstrated by RNA-seq, Western blotting analysis, and immunofluorescence staining. RESULTS: Ten main constituents of AGE were identified using UPLC-Q/TOF-MS and 274 potential ALD-related targets were identified. The enriched KEGG pathways included Toll-like receptor signaling pathway, NF-κB signaling pathway, and necroptosis. Moreover, in vivo experimental studies demonstrated that AGE significantly reduced serum aminotransferase levels and improved pathological abnormalities after chronic ethanol intake. Meanwhile, AGE improved ALD in mice by down-regulating oxidative stress and inflammatory cytokines. Furthermore, AGE notably repaired damaged intestinal epithelial barrier and suppressed the production of gut-derived lipopolysaccharide by elevating intestinal tight junction protein expression. Subsequent RNA-seq and experimental validation indicated that AGE inhibited NF-κB nuclear translocation, suppressed IκB-α, RIPK3 and MLKL phosphorylation and alleviated hepatic necroptosis in mice. CONCLUSION: In this study, we have demonstrated for the first time that AGE protects against alcoholic liver disease by regulating the gut-liver axis and inhibiting the TLR4/NF-κB/MLKL-mediated necroptosis pathway. Therefore, our present work provides important experimental evidence for AGE as a promising candidate for protection against ALD.
Subject(s)
Ampelopsis , Liver Diseases, Alcoholic , Mice, Inbred C57BL , NF-kappa B , Network Pharmacology , Toll-Like Receptor 4 , Animals , Toll-Like Receptor 4/metabolism , Liver Diseases, Alcoholic/drug therapy , Liver Diseases, Alcoholic/prevention & control , NF-kappa B/metabolism , Ampelopsis/chemistry , Male , Mice , Signal Transduction/drug effects , Plant Extracts/pharmacology , Liver/drug effects , Oxidative Stress/drug effects , Plant Leaves/chemistry , Ethanol , Cytokines/metabolismABSTRACT
The Chinese mitten crab (Eriocheir sinensis), an economically important crustacean that is endemic to China, has recently experienced high-temperature stress. The high thermal tolerance of E. sinensis points to its promise in being highly productive in an aquacultural context. However, the mechanisms underlying its high thermal tolerance remain unknown. In this study, female E. sinensis that were heat exposed for 24 h at 38.5 °C and 33 °C were identified as high-temperature-stressed (HS) and normal-temperature-stressed (NS) groups, respectively. The hepatopancreas of E. sinensis from the HS and NS groups were used for transcriptome and proteomic analyses. A total of 2350 upregulated and 1081 downregulated differentially expressed genes (DEGs) were identified between the HS and NS groups. In addition, 126 differentially expressed proteins (DEPs) were upregulated and 35 were downregulated in the two groups. An integrated analysis showed that 2641 identified genes were correlated with their corresponding proteins, including 25 genes that were significantly differentially expressed between the two omics levels. Ten Gene Ontology terms were enriched in the DEGs and DEPs. A functional analysis revealed three common pathways that were significantly enriched in both DEGs and DEPs: fluid shear stress and atherosclerosis, leukocyte transendothelial migration, and thyroid hormone synthesis. Further analysis of the common pathways showed that MGST1, Act5C, HSP90AB1, and mys were overlapping genes at the transcriptome and proteome levels. These results demonstrate the differences between the HS and NS groups at the two omics levels and will be helpful in clarifying the mechanisms underlying the thermal tolerance of E. sinensis.
Subject(s)
Brachyura , Heat-Shock Response , Hepatopancreas , Proteome , Transcriptome , Animals , Female , Hepatopancreas/metabolism , Proteome/genetics , Proteome/metabolism , Brachyura/genetics , Brachyura/metabolism , Brachyura/physiology , Heat-Shock Response/genetics , Gene Expression Profiling , Proteomics/methods , Gene Ontology , Gene Expression RegulationABSTRACT
Cobalt (Co) is a promising candidate to replace noble metals in the hydrogenation process, which is widely employed in the chemical industry. Although the catalytic performance for this reaction has been considered to be significantly dependent on the Co crystal phase, no satisfactory systematic studies have been conducted, because it is difficult to synthesize metal nanoparticles that have different crystalline structures with similar sizes. Here we report a new method for the synthesis of cobalt nanoparticles using hydrosilane as a reducing agent (hydrosilane-assisted method). This new method uses 1,3-butanediol and propylene glycol to successfully prepare fcc and hcp cobalt nanoparticles, respectively. These two types of Co nanoparticles have similar sizes and surface areas. The hcp Co nanoparticles exhibit higher catalytic performance than fcc nanoparticles for the hydrogenation of benzonitrile under mild conditions. The present hcp Co catalyst is also effective for highly selective benzyl amine production from benzonitrile without ammonia addition, whereas many catalytic systems require ammonia addition for selective benzyl amine production. Mechanistic studies revealed that the fast formation of the primary amine and the prevention of condensation and secondary amine hydrogenation promote selective benzonitrile hydrogenation for benzylamine over hcp Co nanoparticles.
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OBJECTIVES: To investigate the epidemic patterns of pretreatment drug resistance (PDR) and acquired drug resistance (ADR) in HIV-1 sequences from China. METHODS: HIV-1 pol sequences and associated epidemiological data were collected from the Los Alamos HIV Sequence Database, NCBI, HIV Gene Sequence Database and PubMed. Genotypic resistance and subtypes were identified using the Stanford HIV Drug Resistance Database. RESULTS: A total of 36â263 sequences from ART-naïve individuals and 1548 sequences from ART-experienced individuals with virological failure were evaluated. PDR prevalence was 6.64%, initially decreasing and then increasing to 7.84% (2018-22) due to NNRTI. Pooled ADR prevalence (44.96%) increased, with NNRTI and NRTI aligning with the overall trend. The percentage of multidrug resistance was more than that of single-drug resistance in PDR and especially ADR annually. PDR was most prevalent in Central China followed by Southwest and North. ADR prevalence was highest in North China followed by Northwest and Southwest. In ADR sequences, high-level resistance was more common, especially in NRTI. PDR sequences exhibited low-level or intermediate resistance, especially PI. Drug resistance mutations revealed distinct patterns in PDR and ADR. CRF01_AE, the predominant subtype in China, exhibited the highest proportions among most ART drugs and drug resistance mutations, with a few exceptions where CRF07_BC (prominent in the Northwest), CRF55_01B and CRF08_BC (prominent in the Southwest) showed the highest proportions. CONCLUSIONS: HIV-1 PDR and ADR prevalence in China exhibited diverse epidemiological characteristics, underscoring the importance of ongoing national monitoring of PDR, ADR and subtype; patient education on adherence; and personalized regimens.
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BACKGROUND: Dental pulp stem cells (DPSCs) have self-renewal and multidirectional differentiation potentials. As such, DPSCs have a wide range of clinical applications. Low-level laser therapy (LLLT) has positive photobiostimulatory effects on cell proliferation, angiogenesis, osteogenic differentiation, bone regeneration, and fracture healing. However, there have been few studies on the effect of low-energy lasers on DPSC proliferation. METHODS: DPSCs were obtained from dental pulp tissue. The effects of LLLT on the proliferation of DPSCs and the associated mechanisms were investigated by in vitro culture and laser irradiation. RESULTS: LLLT with energy densities of 3.5 J/cm2 and 14 J/cm2promoted the proliferation of DPSCs. Differential protein expression studies suggested the stimulation of DPSC proliferation by LLLT involved the PI3K-Akt and Rap1 signaling pathways, as well as the apoptosis-related pathway. CONCLUSION: This preliminary study demonstrated that low-energy lasers have a pro-proliferative effect on DPSCs, and identified possible associated mechanisms. Our findings provide a theoretical basis for the clinical application of DPSCs and suggest novel strategies for the treatment of related diseases.
Subject(s)
Cell Proliferation , Dental Pulp , Low-Level Light Therapy , Stem Cells , Dental Pulp/cytology , Dental Pulp/radiation effects , Cell Proliferation/radiation effects , Humans , Stem Cells/radiation effects , Stem Cells/cytology , Stem Cells/metabolism , Low-Level Light Therapy/methods , Cells, Cultured , Signal Transduction/radiation effects , Apoptosis/radiation effects , Cell Differentiation/radiation effectsABSTRACT
Lacticaseibacillus rhamnosus is applied as a probiotic to alleviate various metabolic, gastrointestinal, and psychological symptoms and diseases, and its probiotic effectiveness is strain-specific. In this study, we obtained 21 strains of Ls. rhamnosus, and their genomes were sequenced. We defined the pan- and core-genomes of Ls. rhamnosus. Phenotypes such as the assimilation of carbohydrates and antibiotic resistance were experimentally characterized and associated with genome annotations. Nine strains were selected and tested for growth rates, tolerance to acidity/alkalinity and bile acids, the production of short-chain fatty acids, and competition with pathogenic microbes. Strains WL11 and WL17 were targeted as potential probiotics and were applied in mouse model tests for the alleviation of chronic fatigue syndrome (CFS) and irritable bowel syndrome (IBS). The results showed that WL11 and WL17 effectively alleviated slow body weight gain, anxiety, poor memory, and cognitive impairment in CFS mouse models. They also reduced the expression of pro-inflammatory factors, such as TNF-α and IL-6, and alleviated intestinal peristalsis, visceral hypersensitivity, and anxiety-like behavior in IBS mouse models. This study reports new Ls. rhamnosus strain resources and their effect on alleviation of both IBS and CFS symptoms with mouse models; the probiotic functions of those strains in human patients remain to be further tested.
ABSTRACT
Work function of organometallic halide perovskite (OHP) films is one of the most crucial photoelectric properties, which dominates the carrier dynamics in OHP-based devices. Despite surface treatments by additives being widely used to promote crystallization and passivate defects in OHP films, these chemical strategies for modulation of work functions face two trade-offs: homogeneity on the surface versus along the thickness; the range versus the accuracy of modulation. Herein, by using ferroelectric substrates of uniform polarization and subnanometer roughness, homogeneous CH3NH3PbI3 films are fabricated with five states of work functions with large spanning (â¼0.8 eV) and high precision (sd â¼ 0.01 eV). We reveal that the ferroelectric polarizations and the smooth surfaces regulate CH3NH3+ orientations and suppress distortions of PbI6 octahedrons. The wide-range and multistate work functions originate from the ordered CH3NH3+ orientations and PbI6 octahedrons, which result in intensity enhancements and wavelength shifts in photoluminescence with a 30-fold increase of photoexcited carrier lifetime.
ABSTRACT
RNA sequencing (RNAseq) technology has become increasingly important in precision medicine and clinical diagnostics, and emerged as a powerful tool for identifying protein-coding genes, performing differential gene analysis, and inferring immune cell composition. Human peripheral blood samples are widely used for RNAseq, providing valuable insights into individual biomolecular information. Blood samples can be classified as whole blood (WB), plasma, serum, and remaining sediment samples, including plasma-free blood (PFB) and serum-free blood (SFB) samples that are generally considered less useful byproducts during the processes of plasma and serum separation, respectively. However, the feasibility of using PFB and SFB samples for transcriptome analysis remains unclear. In this study, we aimed to assess the suitability of employing PFB or SFB samples as an alternative RNA source in transcriptomic analysis. We performed a comparative analysis of WB, PFB, and SFB samples for different applications. Our results revealed that PFB samples exhibit greater similarity to WB samples than SFB samples in terms of protein-coding gene expression patterns, detection of differentially expressed genes, and immunological characterizations, suggesting that PFB can serve as a viable alternative to WB for transcriptomic analysis. Our study contributes to the optimization of blood sample utilization and the advancement of precision medicine research. Supplementary Information: The online version contains supplementary material available at 10.1007/s43657-023-00121-1.
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The core task of neuromorphic devices is to effectively simulate the behavior of neurons and synapses. Based on the functionality of ferroelectric domains with the advantages of low power consumption and high-speed response, great progress has been made in realizing neuromimetic behaviors such as ferroelectric synaptic devices. However, the correlation between the ferroelectric domain dynamics and neuromimetic behavior remains unclear. Here, we reveal the correlation between domain/domain wall dynamics and neuromimetic behaviors from a microscopic perspective in real-time by using high temporal and spatial resolution in situ transmission electron microscopy. Furthermore, we propose utilizing ferroelectric microstructures for the simultaneous simulation of neuronal and synaptic plasticity, which is expected to improve the integration and performance of ferroelectric neuromorphic devices. We believe that this work to study neuromimetic behavior from the perspective of domain dynamics is instructive for the development of ferroelectric neuromorphic devices.
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A photorechargeable supercapacitor was constructed using vanadium pentoxide (V2O5), reduced graphene oxide hydrogel (rGH), and zinc trifluoromethanesulfonate (Zn(CF3SO3)2) as the photoanode, cathode, and electrolyte, respectively. The phase composition, microstructure, chemical structure, light absorption, and specific surface area of the synthesized products and the electrochemical performance of the rGH/V2O5 supercapacitor were investigated using X-ray diffraction (XRD), scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FT-IR), Raman spectroscopy, UV-Vis spectroscopy, the Brunauer-Emmett-Teller (BET) method, and an electrochemical workstation, respectively. The results show that the device has a specific capacity of 164 F g-1 at 0.5 A g-1 under illumination with 95 mW cm-2 light intensity, which is 20.5% higher than that under normal electrical charging. The supercapacitor has a 75% capacity retention rate and 100% coulombic efficiency, respectively, after 10 000 testing cycles under photoelectric synergistic charging and discharging. The as-constructed rGH/V2O5 photorechargeable supercapacitor exhibits promising application potential in electric vehicles and wearable electronics.
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Neurexins play diverse functions as presynaptic organizers in various glutamatergic and GABAergic synapses. However, it remains unknown whether and how neurexins are involved in shaping functional properties of the glycinergic synapses, which mediate prominent inhibition in the brainstem and spinal cord. To address these issues, we examined the role of neurexins in a model glycinergic synapse between the principal neuron in the medial nucleus of the trapezoid body (MNTB) and the principal neuron in the lateral superior olive (LSO) in the auditory brainstem. Combining RNAscope with stereotactic injection of AAV-Cre in the MNTB of neurexin1/2/3 conditional triple knockout mice, we showed that MNTB neurons highly express all isoforms of neurexins although their expression levels vary remarkably. Selective ablation of all neurexins in MNTB neurons not only reduced the amplitude but also altered the kinetics of the glycinergic synaptic transmission at LSO neurons. The synaptic dysfunctions primarily resulted from an impaired Ca2+ sensitivity of release and a loosened coupling between voltage-gated Ca2+ channels and synaptic vesicles. Together, our current findings demonstrate that neurexins are essential in controlling the strength and temporal precision of the glycinergic synapse, which therefore corroborates the role of neurexins as key presynaptic organizers in all major types of fast chemical synapses.
Subject(s)
Glycine , Mice, Knockout , Trapezoid Body , Animals , Glycine/metabolism , Mice , Trapezoid Body/metabolism , Trapezoid Body/physiology , Synaptic Transmission/physiology , Neural Cell Adhesion Molecules/metabolism , Neural Cell Adhesion Molecules/genetics , Superior Olivary Complex/physiology , Superior Olivary Complex/metabolism , Brain Stem/physiology , Brain Stem/metabolism , Synapses/metabolism , Synapses/physiology , Neurons/metabolism , Neurons/physiology , Cell Adhesion Molecules, Neuronal/metabolism , Cell Adhesion Molecules, Neuronal/genetics , Nerve Tissue Proteins/metabolism , Nerve Tissue Proteins/genetics , Neurexins , Calcium-Binding ProteinsABSTRACT
Two-dimensional (2D) semiconductors possess exceptional electronic, optical, and magnetic properties, making them highly desirable for widespread applications. However, conventional mechanical exfoliation and epitaxial growth methods are insufficient in meeting the demand for atomically thin films covering large areas while maintaining high quality. Herein, leveraging liquid metal oxidation reaction, we propose a motorized spin-coating exfoliation strategy to efficiently produce large-area 2D metal oxide (2DMO) semiconductors with high crystallinity, atomically thin thickness, and flat surfaces on diverse substrates. Moreover, we realized a 2D gallium oxide-based deep ultraviolet solar-blind photodetector featuring a metal-semiconductor-metal structure, showcasing high responsivity (8.24 A W-1) at 254 nm and excellent sensitivity (4.3 × 1012 cm Hz1/2 W-1). This novel liquid-metal-based spin-coating exfoliation strategy offers great potential for synthesizing atomically thin 2D semiconductors, opening new avenues for future functional electronic and optical applications.
ABSTRACT
The gut commensal bacteria Christensenellaceae species are negatively associated with many metabolic diseases, and have been seen as promising next-generation probiotics. However, the cultured Christensenellaceae strain resources were limited, and their beneficial mechanisms for improving metabolic diseases have yet to be explored. In this study, we developed a method that enabled the enrichment and cultivation of Christensenellaceae strains from fecal samples. Using this method, a collection of Christensenellaceae Gut Microbial Biobank (ChrisGMB) was established, composed of 87 strains and genomes that represent 14 species of 8 genera. Seven species were first described and the cultured Christensenellaceae resources have been significantly expanded at species and strain levels. Christensenella strains exerted different abilities in utilization of various complex polysaccharides and other carbon sources, exhibited host-adaptation capabilities such as acid tolerance and bile tolerance, produced a wide range of volatile probiotic metabolites and secondary bile acids. Cohort analyses demonstrated that Christensenellaceae and Christensenella were prevalent in various cohorts and the abundances were significantly reduced in T2D and OB cohorts. At species level, Christensenellaceae showed different changes among healthy and disease cohorts. C. faecalis, F. tenuis, L. tenuis, and Guo. tenuis significantly reduced in all the metabolic disease cohorts. The relative abundances of C. minuta, C. hongkongensis and C. massiliensis showed no significant change in NAFLD and ACVD. and C. tenuis and C. acetigenes showed no significant change in ACVD, and Q. tenuis and Geh. tenuis showed no significant change in NAFLD, when compared with the HC cohort. So far as we know, this is the largest collection of cultured resource and first exploration of Christensenellaceae prevalences and abundances at species level.
Subject(s)
Feces , Gastrointestinal Microbiome , Humans , Feces/microbiology , Clostridiales/genetics , Clostridiales/metabolism , Clostridiales/isolation & purification , Clostridiales/classification , Probiotics/metabolism , Metabolomics , Genomics , Male , Phylogeny , Female , Genome, BacterialABSTRACT
Three Gram-positive, obligately anaerobic bacterial strains, namely CSJ-1T, CSJ-3T, and CSJ-4T, were isolated from faeces of healthy persons. They were characterized through a combination of whole-genome sequencing, phenotypic traits, and metabolomic analysis. The genome sizes of CSJ-1T, CSJ-4T, and CSJ-3T were 3.3, 3.8, and 6.1 Mbp, with DNA G+C contents of 47.2, 48.3, and 48.8 mol%, respectively. Strain CSJ-3T was identified as representing a novel species, Diplocloster hominis (type strain CSJ-3T=CGMCC 1.18033T=JCM 36512T) of the genus Diplocloster. The 16S rRNA gene sequence similarity and whole genome average nucleotide identity (gANI) of CSJ-4T to its closest related species, Diplocloster modestus ASD 4241T, were 98.3 and 91.4â%, respectively. Comparative analysis of 16S rRNA gene sequences showed 91.6â% similarity between CSJ-1T and its closest phylogenetic neighbour, Catenibacillus scindens DSM 106146T, and 93.3â% similarity between CSJ-4T and its closest relative strain, Clostridium fessum SNUG30386T. Based on the polyphasic taxonomic results, we proposed two novel genera and three novel species. Strain CSJ-1T was identified as representing a novel species of novel genus, Anaerolentibacter hominis gen. nov. sp. nov. (type strain CSJ-1T=CGMCC 1.18046T=JCM 36511T) of the family Lachnospiraceae, and strain CSJ-4T was identified as representing a novel species of novel genus Pilosibacter fragilis gen. nov. sp. nov. (type strain CSJ-4T=CGMCC 1.18026T= JCM 36513T) of the family Clostridiaceae.
Subject(s)
Bacterial Typing Techniques , Base Composition , DNA, Bacterial , Feces , Phylogeny , RNA, Ribosomal, 16S , Sequence Analysis, DNA , RNA, Ribosomal, 16S/genetics , Feces/microbiology , DNA, Bacterial/genetics , Humans , Fatty Acids/analysis , Genome, Bacterial , Whole Genome SequencingABSTRACT
Association networks are widely applied for the prediction of bacterial interactions in studies of human gut microbiomes. However, the experimental validation of the predicted interactions is challenging due to the complexity of gut microbiomes and the limited number of cultivated bacteria. In this study, we addressed this challenge by integrating in vitro time series network (TSN) associations and co-cultivation of TSN taxon pairs. Fecal samples were collected and used for cultivation and enrichment of gut microbiome on YCFA agar plates for 13 days. Enriched cells were harvested for DNA extraction and metagenomic sequencing. A total of 198 metagenome-assembled genomes (MAGs) were recovered. Temporal dynamics of bacteria growing on the YCFA agar were used to infer microbial association networks. To experimentally validate the interactions of taxon pairs in networks, we selected 24 and 19 bacterial strains from this study and from the previously established human gut microbial biobank, respectively, for pairwise co-cultures. The co-culture experiments revealed that most of the interactions between taxa in networks were identified as neutralism (51.67%), followed by commensalism (21.67%), amensalism (18.33%), competition (5%) and exploitation (3.33%). Genome-centric analysis further revealed that the commensal gut bacteria (helpers and beneficiaries) might interact with each other via the exchanges of amino acids with high biosynthetic costs, short-chain fatty acids, and/or vitamins. We also validated 12 beneficiaries by adding 16 additives into the basic YCFA medium and found that the growth of 66.7% of these strains was significantly promoted. This approach provides new insights into the gut microbiome complexity and microbial interactions in association networks. Our work highlights that the positive relationships in gut microbial communities tend to be overestimated, and that amino acids, short-chain fatty acids, and vitamins are contributed to the positive relationships.