Microbial methanogenesis in aerobic water: A key driver of surface methane enrichment in a deep reservoir.

Significant amounts of the greenhouse gas methane (CH4) are released into the atmosphere worldwide via freshwater sources. The surface methane maximum (SMM), where methane is supersaturated in surface water, has been observed in aquatic systems and contributes significantly to emissions. However, little is known about the temporal and spatial variability of SMM or the mechanisms underlying its development in artificial reservoirs. Here, the community composition of methanogens as major methane producers in the water column and the mcrA gene was investigated, and the cause of surface methane supersaturation was analyzed. In accordance with the findings, elevated methane concentration of SMM in the transition zone, with an annually methane emission flux 2.47 times higher than the reservoir average on a large and deep reservoir. In the transition zone, methanogens with mcrA gene abundances ranging from 0.5 × 103-1.45 × 104 copies/L were found. Methanobacterium, Methanoseata and Methanosarcina were the three dominate methanogens, using both acetic acid and H2/CO2 pathways. In summary, this study contributes to our comprehension of CH4 fluxes and their role in the atmospheric methane budget. Moreover, it offers biological proof of methane generation, which could aid in understanding the role of microbial methanogenesis in aerobic water.

Functional characterization of MaEXPA11 and its roles in response to biotic and abiotic stresses in mulberry.

Mulberry is a traditional economic tree with various values in sericulture, ecology, food industry and medicine. Expansins (EXPs) are known as cell wall expansion related proteins and have been characterized to involve in plant development and responses to diverse stresses. In present study, twenty EXP and expansin-like (EXL) genes were identified in mulberry. RNA-seq results indicated that three EXP and EXL genes showed up-regulated expression level under sclerotiniose pathogen infection in three independent RNA-seq datasets. The most significant upregulated EXPA11 was selected as key EXP involving in response to sclerotiniose pathogen infection in mulberry. Furthermore, a comprehensive functional analysis was performed to reveal subcellular location, tissue expression profile of MaEXPA11 in mulberry. Down-regulation of MaEXPA11 using virus induced gene silence (VIGS) was performed to explore the function of MaEXPA11 in Morus alba. Results showed that MaEXPA11 can positively regulate mulberry resistance to Ciboria shiraiana infection and negatively regulate mulberry resistance to cold or drought stress.

Altered T-cell receptor ß repertoire in adults with SARS CoV-2 inactivated vaccine of BBIBP-CorV.

OBJECTIVE: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the prolonged and widespread epidemic of coronavirus disease 2019 (COVID-19). The inactivated BBIBP-CorV vaccine has shown safety, efficacy and immunogenicity against COVID-19 in in-vitro studies and clinical trials. However, the characteristics changes of the TCRß repertoire in patients receiving BBIBP-CorV remain unclear. METHODS: TCRß repertoire difference were analyzed between 54 uninfected subjects who received a third dose of the enhanced BBIBP-CorV vaccine and the 16 healthy donors who did not receive the vaccine and 44 COVID-19 patients with different courses of disease (asymptomatic, symptomatic and convalescent). Furthermore, antibody response, anti-inflammatory and pro-inflammatory cytokines also were examined. RESULTS: We found that the third dose inactivated coronavirus vaccine induced widespread changes including the increased TCRß repertoire diversity, a much shorter CDR3 length and high usage of V-J genes segments. Meanwhile, the vaccine-responding clones were also predicted. The results of the antibody response showed that 90.7 % of the vaccinated individuals were positive for NAb seroconversion and 88.9 % for IgG antibody about 60 days after the third dose. The concentration of IL-2 increased significantly compared to baseline inoculation. CONCLUSION: Altered TCRß repertoire in adults with SARS CoV-2 inactivated vaccine of BBIBP-CorV clarified the specific immunity induced by inactivated vaccines. Our research provides insights into the adaptive immune response induced by the new inactivated SARS-CoV-2 vaccine and strengthens the development of immunotherapy.

Extraction, structural characterization, and antioxidant activity of polysaccharides derived from Arctium lappa L.

Introduction: Arctium lappa L. root has high nutritional and medicinal values and has been identified as a healthy food raw material by the Ministry of Health of the People's Republic of China. Methods: In the present study, an aqueous two-phase system (ATPS) of polyethylene glycol (PEG)-(NH4)2SO4 was used to extract Arctium lappa L. polysaccharides (ALPs) from the Arctium lappa L. roots, the optimal extraction conditions of crude ALPs were optimized by using the single-factor experiment and response surface methodology. The structure and composition of ALPs were determined by fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), and high-performance liquid chromatography (HPLC). At the same time, the antioxidant activity of ALPs was investigated by in vitro antioxidant experiment. Results: The optimized extraction parameters for extraction ALPs were as follows: the PEG relative molecular weight of 6,000, a quality fraction of PEG 25%, a quality fraction of (NH4)2SO4 18%, and an extraction temperature of 80°C. Under these conditions, the extraction rate of ALPs could reach 28.83%. FTIR, SEM and HPLC results showed that ALPs were typical acidic heteropolysaccharides and had uneven particle size distribution, an irregular shape, and a rough surface. The ALPs were chiefly composed of glucose, rhamnose, arabinose, and galactose with a molar ratio of 70.19:10.95:11.16:6.90. In addition, the ALPs had intense antioxidant activity in vitro with IC50 values in the ·OH radical (1.732 mg/ml), DPPH radical (0.29 mg/ml), and superoxide anion (0.15 mg/ml) scavenging abilities. Discussion: The results showed that ATPS was an efficient method to extract polysaccharides and could be used for the extraction of other polysaccharides. These results indicated that ALPs had great prospects as a functional food and could be exploited in multiple fields.

Microneedle-based interstitial fluid extraction for drug analysis: Advances, challenges, and prospects.

Similar to blood, interstitial fluid (ISF) contains exogenous drugs and biomarkers and may therefore substitute blood in drug analysis. However, current ISF extraction techniques require bulky instruments and are both time-consuming and complicated, which has inspired the development of viable alternatives such as those relying on skin or tissue puncturing with microneedles. Currently, microneedles are widely employed for transdermal drug delivery and have been successfully used for ISF extraction by different mechanisms to facilitate subsequent analysis. The integration of microneedles with sensors enables in situ ISF analysis and specific compound monitoring, while the integration of monitoring and delivery functions in wearable devices allows real-time dose modification. Herein, we review the progress in drug analysis based on microneedle-assisted ISF extraction and discuss the related future opportunities and challenges.

CD163 as a Potential Biomarker in Colorectal Cancer for Tumor Microenvironment and Cancer Prognosis: A Swedish Study from Tissue Microarrays to Big Data Analyses.

(1) Background: CD163, a specific macrophage receptor, affects the progression of malignant tumors. Unfortunately, the regulation and expression of CD163 are poorly understood. In this study, we determined the expressions of CD163 in TMA samples from CRC patients and combined them with patient data from several Swedish hospitals. (2) Methods: The expressions of CD163 in tissue samples from CRC patients were examined. After combining 472 CRC patients' gene expression and 438 CRC patients' clinical data with the TCGA database, 964 cases from the GEO database, and experimental expression data from 1247 Swedish CRC patients, we selected four genes (PCNA, LOX, BCL2, and CD163) and analyzed the tumor-infiltrating immune cells (TICs) and CRC prognosis. (3) Results: Based on histopathological TMA analysis, CD163 was strongly expressed in the stroma of both normal and cancer tissues, and the expressions in normal and cancer cells varied from negative to strong. The results from public databases show decreased expression of CD163 in cancer tissue compared to normal mucosa (|log FC| > 1 and FDR < 0.01), and it is a negative prognostic factor for CRC patients (p-value < 0.05). Through tumor microenvironment (TME) analysis, we found a potential influence of CD163 on immune cell infiltration. Furthermore, the enrichment analysis indicated the possible interaction with other proteins and biological pathways. (4) Conclusions: CD163 is expressed differently in CRC tissue and is a negative prognostic factor. Its expression is associated with the TME and tumor purity of CRC. Considering all results, CD163 has the potential to be a predictive biomarker in the investigation of CRC.

Observation of broken detailed balance in polymorphic transformation of bacterial flagellar filament.

Living systems operate far from thermodynamic equilibrium, which usually manifests as broken detailed balance at the molecular scale. At larger scales with collective function of many molecules, the presence of non-equilibrium thermodynamics may not be evident. In bacterial motility, the switching dynamics of the flagellar rotary motor was recently discovered to be operating in non-equilibrium. However, the resulting motility pattern at the mesoscale, the run-and-tumble behavior, was normally considered to be a Poisson process that can be described by a two-state equilibrium model. Here, we studied the details of the run-and-tumble behavior by following the polymorphic transformation of the flagellar filaments, observing broken detailed balance that reveals its non-equilibrium nature. Evaluation of entropy production provided a direct measure of the lack of detailed balance and a quantification of the rate of energy dissipation for bacterial run-and-tumble regulation.

The relationship between LncRNAs and lung adenocarcinoma as well as their ceRNA network.

BACKGROUND: More and more studies have shown that long non-coding RNA (LncRNA) as a competing endogenous RNA (ceRNA) plays an important role in lung cancer. Therefore, we analyzed the RNA expression profiles of 82 lung cancer patients which were all from Gene Expression Omnibus (GEO). METHODS: Firstly, we used BLASTN (evalue = 1e-10) to annotate the gene sets, performed in-group correction and batched normalization of the three data sets with R. Secondly, we used the limma and sva packages to compare tumor tissues with normal tissues. Then through WGCNA, we obtained the 4 gene modules most related to the trait. RESULTS: We intersected the genes of above 4 modules with the differential expression genes: 28 LncRNAs (up: 5, down: 23) and 265 mRNAs (up:11, down: 254). Based on these genes, we picked up 6 LncRNAs (CCDC39, FAM182A, SRGAP3-AS2, ADAMTS9-AS2, AC020907.2, SFTA1P), then set and visualized the LncRNA-miRNA-mRNA ceRNA network with 12 miRNAs related to 12 mRNAs. Finally, we performed downstream analysis of 265 mRNAs by Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and Protein-Protein Interaction (PPI) network. CONCLUSION: After analyzing, we think this study provides a new direction for basic and clinical research related to LAD, and is expected to provide new targets for early diagnosis, prognostic evaluation and clinical treatment of lung cancer.

Spatial organization of Clostridium difficile S-layer biogenesis.

Surface layers (S-layers) are protective protein coats which form around all archaea and most bacterial cells. Clostridium difficile is a Gram-positive bacterium with an S-layer covering its peptidoglycan cell wall. The S-layer in C. difficile is constructed mainly of S-layer protein A (SlpA), which is a key virulence factor and an absolute requirement for disease. S-layer biogenesis is a complex multi-step process, disruption of which has severe consequences for the bacterium. We examined the subcellular localization of SlpA secretion and S-layer growth; observing formation of S-layer at specific sites that coincide with cell wall synthesis, while the secretion of SlpA from the cell is relatively delocalized. We conclude that this delocalized secretion of SlpA leads to a pool of precursor in the cell wall which is available to repair openings in the S-layer formed during cell growth or following damage.

Candidate lncRNA-microRNA-mRNA networks in predicting non-small cell lung cancer and related prognosis analysis.

PURPOSE: The role of non-coding RNA, once thought to be dark matter, is increasingly prominent in cancer. Our article explores the effect of non-coding RNA in lung adenocarcinoma and lung squamous cell carcinoma by mining TCGA public database. METHODS: Download the data by applying the official TCGA software. The data were analyzed by R data analysis packages, 'edgeR', 'gplots' and 'survival'. We better illustrate the potential networks of lung cancer genes by constructing ceRNAs, using Cytoscape software. RESULTS: We obtained genes which were differentially expressed in lung adenocarcinoma and lung squamous cell carcinoma analysis. Within these differentially expressed genes, we also conducted a survival analysis to find differentially expressed genes associated with prognosis in both lung adenocarcinoma and lung squamous cell carcinoma. Based on genes differentially expressed of both lung adenocarcinoma and lung squamous cell carcinoma, we constructed a ceRNA network to illustrate the mechanism of lung adenocarcinoma and lung squamous cell carcinoma. Our study analyzed genes which were differentially expressed in lung adenocarcinoma and lung squamous cell carcinoma using the TCGA database. CONCLUSION: Based on this, the prognosis in both lung squamous cell carcinoma and lung adenocarcinoma was analyzed. We have also constructed a ceRNA network to provide a basis for the study of ceRNA in lung adenocarcinoma and lung squamous cell carcinoma.

A hidden state in the turnover of a functioning membrane protein complex.

Most membrane proteins exist in complexes that carry out critical cellular functions and exhibit rich dynamics. The bacterial flagellar motor, a large membrane-spanning ion-driven rotary motor that propels the bacteria to swim, provides a canonical example. Rotation of the motor is driven by multiple torque-generating units (stators). Turnover of the stators has been shown previously, demonstrating the exchange of stator units between the motor and a membrane pool. But the details of the turnover kinetics remain unclear. Here, we directly measured the kinetics of stator turnover in individual motors via analysis of a large dataset of long-term high-resolution recordings of motor speed at high load. We found that the dwell time distribution of the stator units exhibits a multi-exponential shape, suggesting the existence of a hidden state in the turnover of the stators.

Co-Association Matrix-Based Multi-Layer Fusion for Community Detection in Attributed Networks.

Community detection is a challenging task in attributed networks, due to the data inconsistency between network topological structure and node attributes. The problem of how to effectively and robustly fuse multi-source heterogeneous data plays an important role in community detection algorithms. Although some algorithms taking both topological structure and node attributes into account have been proposed in recent years, the fusion strategy is simple and usually adopts the linear combination method. As a consequence of this, the detected community structure is vulnerable to small variations of the input data. In order to overcome this challenge, we develop a novel two-layer representation to capture the latent knowledge from both topological structure and node attributes in attributed networks. Then, we propose a weighted co-association matrix-based fusion algorithm (WCMFA) to detect the inherent community structure in attributed networks by using multi-layer fusion strategies. It extends the community detection method from a single-view to a multi-view style, which is consistent with the thinking model of human beings. Experiments show that our method is superior to the state-of-the-art community detection algorithms for attributed networks.

Structural Variability of 4f and 5f Thiocyanate Complexes and Dissociation of Uranium(III)-Thiocyanate Bonds with Increased Ionicity.

A series of complexes [Et4N][Ln(NCS)4(H2O)4] (Ln = Pr, Tb, Dy, Ho, Yb) have been structurally characterized, all showing the same structure, namely a distorted square antiprismatic coordination geometry, and the Ln-O and Ln-N bond lengths following the expected lanthanide contraction. When the counterion is Cs+, a different structural motif is observed and the eight-coordinate complex Cs5[Nd(NCS)8] isolated. The thorium compounds [Me4N]4[Th(NCS)7(NO3)] and [Me4N]4[Th(NCS)6(NO3)2] have been characterized, and high coordination numbers are also observed. Finally, attempts to synthesize a U(III) thiocyanate compound has been unsuccessful; from the reaction mixture, a heterocycle formed by condensation of five MeCN solvent molecules, possibly promoted by U(III), was isolated and structurally characterized. To rationalize the inability to isolate U(III) thiocyanate compounds, thin-layer cyclic voltammetry and IR spectroelectrochemistry have been utilized to explore the cathodic behavior of [Et4N]4[U(NCS)8] and [Et4N][U(NCS)5(bipy)2] along with a related uranyl compound [Et4N]3[UO2(NCS)5]. In all examples, the reduction triggers a rapid dissociation of [NCS]- ions and decomposition. Interestingly, the oxidation chemistry of [Et4N]3[UO2(NCS)5] in the presence of bipy gives the U(IV) compound [Et4N]4[U(NCS)8], an unusual example of a ligand-based oxidation triggering a metal-based reduction. The experimental results have been augmented by a computational investigation, concluding that the U(III)-NCS bond is more ionic than the U(IV)-NCS bond.