Abstract
Long non-coding RNAs (lncRNAs) are emerging as important regulators in different biological processes through various ways. Because the related data, especially mutations in cancers, ...increased sharply, we updated the lncRNASNP to version 2 (http://bioinfo.life.hust.edu.cn/lncRNASNP2). lncRNASNP2 provides comprehensive information of SNPs and mutations in lncRNAs, as well as their impacts on lncRNA structure and function. lncRNASNP2 contains 7260238 SNPs on 141353 human lncRNA transcripts and 3921448 SNPs on 117405 mouse lncRNA transcripts. Besides the SNP information in the first version, the following new features were developed to improve the lncRNASNP2. (i) noncoding variants from COSMIC cancer data (859534) in lncRNAs and their effects on lncRNA structure and function; (ii) TCGA cancer mutations (315234) in lncRNAs and their impacts; (iii) lncRNA expression profiling of 20 cancer types in both tumor and its adjacent samples; (iv) expanded lncRNA-associated diseases; (v) optimized the results about lncRNAs structure change induced by variants; (vi) reduced false positives in miRNA and lncRNA interaction results. Furthermore, we developed online tools for users to analyze new variants in lncRNA. We aim to maintain the lncRNASNP as a useful resource for lncRNAs and their variants.
According to the types of organic polymers, the design, preparation, performance and application value of composite membranes using MOFs as fillers were classified and summarized. The future ...development trends and priorities are also discussed and prospected.
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•Proton exchange membranes based on MOFs were reviewed.•PEMs are classified in the light of the types of polymeric matrix.•Proton conduction and conductve mechanism were concluded.•The future development trend of such PEMs was highlighted.
To overcome the defects of traditional proton exchange membranes (PEMs) (Nafion and Nafion-based membranes, etc.), the introduction of proton-conducting MOFs with performance advantages into the PEM system is a smart strategy, many exciting research results have emerged one after another in recent years. For the convenience of researchers and to explore trends for future development, in this review. MOF-based PEMs are divided into the mixed-matrix membranes using MOFs as fillers and PEMs formed by MOFs directly based on different film-forming methods, and the properties of these PEMs are concluded. The following aspects were focused on the preparation strategies and techniques, stability (covering thermal-, water-, chemical-, and mechanical stabilities, etc.), proton conductive properties under damp or anhydrous conditions, and proton conduction mechanism, and structure–activity relationship. Finally, the prospects and challenges of future research are highlighted.
It is widely accepted that β-amyloid oligomers (Aβos) play a key role in the progression of Alzheimer's disease (AD) by inducing neuron damage and cognitive impairment, but Aβos are highly ...heterogeneous in their size, structure and cytotoxicity, making the corresponding studies tough to carry out. Nevertheless, a number of studies have recently made remarkable progress in the describing the characteristics and pathogenicity of Aβos. We here review the mechanisms by which Aβos exert their neuropathogenesis for AD progression, including receptor binding, cell membrane destruction, mitochondrial damage, Ca
homeostasis dysregulation and tau pathological induction. We also summarize the characteristics and pathogenicity such as the size, morphology and cytotoxicity of dimers, trimers, Aβ*56 and spherical oligomers, and suggest that Aβos may play a different role at different phases of AD pathogenesis, resulting in differential consequences on neuronal synaptotoxicity and survival. It is warranted to investigate the temporal sequence of Aβos in AD human brain and examine the relationship between different Aβos and cognitive impairment.
Abstract
Extracellular vesicles (EVs), such as exosomes and microvesicles, acted as cell-to-cell communication vectors and potential biomarkers for diseases. microRNAs (miRNAs) are the most well ...studied molecules in EVs, thus a comprehensive investigation of miRNA expression profiles in EVs will be helpful to explore their functions and biomarkers. We curated 462 small RNA sequencing samples of EVs from 17 sources/diseases and constructed the EVmiRNA database (http://bioinfo.life.hust.edu.cn/EVmiRNA) to show the miRNA expression profiles. We found >1000 miRNAs expressed in these EVs and detected specific miRNAs for EVs of each source/disease. EVmiRNA provides three functional modules: (i) the miRNA expression profiles and the sample information of EVs from different sources (such as blood, breast milk etc.); (ii) the specifically expressed miRNAs in different EVs that would be helpful for biomarker identification; (iii) the miRNA annotations including the miRNA expression in EVs and TCGA cancer types, miRNA pathway regulations as well as miRNA function and publications. EVmiRNA has a user-friendly web interface with powerful browse and search functions, as well as data downloading. It is the first database focusing on miRNA expression profiles in EVs and will be useful for the research and application community of EV biomarker, miRNA function and liquid biopsy.
Rheumatoid arthritis (RA) is one of the chronic systemic autoimmune diseases that cardinally affect the joints. Many people all over the world suffer from the disease. Fibroblast‐like synoviocytes ...(FLSs) play a significant role in the occurrence and development of RA. The long noncoding RNA maternally expressed gene 3 (MEG3) is an imprinted gene, which participates in various cancers as a tumor suppressor. Previous studies have shown that nucleotide oligomerization domain (NOD)‐like receptors 5 (NLRC5) plays a key role in inflammatory and autoimmune diseases. Nonetheless, we know very little about the biofunctionality of MEG3 during the development of RA. In this paper, we used complete Freund's adjuvant (CFA)‐induced rats as RA animal models. The level of MEG3 significantly reduced in CFA‐induced synovial tissues and FLSs, whereas the NLRC5 levels were increased. Enforced expression of MEG3 may be responsible for the decreased level of NLRC5 and inflammatory cytokine level. The results of methylation‐specific PCR suggested that the MEG3 gene promoter was significantly methylated in CFA‐induced synovial tissues and FLSs. More important, hypermethylation of MEG3 promoter could be inhibited by 5‐aza‐2‐deoxycytidine (5‐azadC; methylation inhibitor). Besides, the expression of NLRC5 significantly decreased followed by 5‐azadc. Furthermore, DNA methyltransferases 1 (DNMT1) increased in CFA‐induced synovial tissues and cells. These results indicated that MEG3 regulates RA by targeting NLRC5 potentially.
Maternally expressed gene 3 (MEG3) may be involved in the development of rheumatoid arthritis (RA) by affecting the proliferation of fibroblast‐like synoviocytes (FLSs), whereas nucleotide oligomerization domain (NOD)‐like receptors 5 (NLRC5) promotes proliferation of FLSs in RA. Enforced expression of MEG3 decreased NLRC5 expression. These results further verified that MEG3 regulates RA by targeting NLRC5 potentially.
Transcription factors (TFs) as key regulators play crucial roles in biological processes. The identification of TF–target regulatory relationships is a key step for revealing functions of TFs and ...their regulations on gene expression. The accumulated data of chromatin immunoprecipitation sequencing (ChIP-seq) provide great opportunities to discover the TF–target regulations across different conditions. In this study, we constructed a database named hTFtarget, which integrated huge human TF target resources (7190 ChIP-seq samples of 659 TFs and high-confidence binding sites of 699 TFs) and epigenetic modification information to predict accurate TF–target regulations. hTFtarget offers the following functions for users to explore TF–target regulations: (1) browse or search general targets of a query TF across datasets; (2) browse TF–target regulations for a query TF in a specific dataset or tissue; (3) search potential TFs for a given target gene or non-coding RNA; (4) investigate co-association between TFs in cell lines; (5) explore potential co-regulations for given target genes or TFs; (6) predict candidate TF binding sites on given DNA sequences; (7) visualize ChIP-seq peaks for different TFs and conditions in a genome browser. hTFtarget provides a comprehensive, reliable and user-friendly resource for exploring human TF–target regulations, which will be very useful for a wide range of users in the TF and gene expression regulation community. hTFtarget is available at http://bioinfo.life.hust.edu.cn/hTFtarget.
Tau pathology is a hallmark of Alzheimer's disease (AD) and other tauopathies. During disease progression, abnormally phosphorylated forms of tau aggregate and accumulate into neurofibrillary ...tangles, leading to synapse loss, neuroinflammation, and neurodegeneration. Thus, targeting of tau pathology is expected to be a promising strategy for AD treatment.
The effect of rutin on tau aggregation was detected by thioflavin T fluorescence and transmission electron microscope imaging. The effect of rutin on tau oligomer-induced cytotoxicity was assessed by MTT assay. The effect of rutin on tau oligomer-mediated the production of IL-1β and TNF-α in vitro was measured by ELISA. The uptake of extracellular tau by microglia was determined by immunocytochemistry. Six-month-old male Tau-P301S mice were treated with rutin or vehicle by oral administration daily for 30 days. The cognitive performance was determined using the Morris water maze test, Y-maze test, and novel object recognition test. The levels of pathological tau, gliosis, NF-kB activation, proinflammatory cytokines such as IL-1β and TNF-α, and synaptic proteins including synaptophysin and PSD95 in the brains of the mice were evaluated by immunolabeling, immunoblotting, or ELISA.
We showed that rutin, a natural flavonoid glycoside, inhibited tau aggregation and tau oligomer-induced cytotoxicity, lowered the production of proinflammatory cytokines, protected neuronal morphology from toxic tau oligomers, and promoted microglial uptake of extracellular tau oligomers in vitro. When applied to Tau-P301S mouse model of tauopathy, rutin reduced pathological tau levels, regulated tau hyperphosphorylation by increasing PP2A level, suppressed gliosis and neuroinflammation by downregulating NF-kB pathway, prevented microglial synapse engulfment, and rescued synapse loss in mouse brains, resulting in a significant improvement of cognition.
In combination with the previously reported therapeutic effects of rutin on Aβ pathology, rutin is a promising drug candidate for AD treatment based its combinatorial targeting of tau and Aβ.
In this work, (Bi0.5Na0.5)0.94Ba0.06TiO3 (BN6BT) lead‐free ceramics were prepared via cold‐sintering followed by annealing, and effects of grain size of precursor powders and annealing temperature on ...microstructure, dielectric, and ferroelectric properties of the ceramics were studied. The precursor powders for cold sintering were obtained by mixing the powders with sub‐micrometer (average grain size, AGS = 0.26 μm) and nanometer (AGS = 73 nm) grains in various mass ratios (1:0, 1:1, 1:2, and 1:4). The precursor powders were mixed with deionized water and cold sintered at 180°C for 1 h under 500 MPa. The cold‐sintered samples were then annealed at temperatures between 800 and 1000°C for 2 h. For the ratios of 1:2 and 1:4, the corresponding ceramics annealed at 950°C exhibit dielectric and ferroelectric properties similar to those of the BN6BT ceramics sintered at 1170°C via the solid‐state sintering method. The present BN6BT ceramics exhibit dense microstructure with finer grains with AGS = 280 nm, higher breakdown strength (BDS = 160 kV· cm−1) compared to the solid‐state sintered BN6BT ceramics with AGS = 1.6 μm and BDS = 75 kV· cm−1. The results demonstrate that the cold‐sintering followed by annealing is effective in preparing BN6BT ceramics with fine grains and excellent dielectric and ferroelectric properties at relatively low temperatures.
Background
Dysregulated bile acid (BA) metabolism has been linked to steatosis, inflammation, and fibrosis in nonalcoholic fatty liver disease (NAFLD).
Aim
To determine whether circulating BA levels ...accurately stage liver fibrosis in NAFLD.
Methods
We recruited 550 Chinese adults with biopsy‐proven NAFLD and varying levels of fibrosis. Ultra‐performance liquid chromatography coupled with tandem mass spectrometry was performed to quantify 38 serum BAs.
Results
Compared to those without fibrosis, patients with mild fibrosis (stage F1) had significantly higher levels of secondary BAs, and increased diastolic blood pressure (DBP), alanine aminotransferase (ALT), body mass index, and waist circumstance (WC). The combination of serum BAs with WC, DBP, ALT, or Homeostatic Model Assessment for Insulin Resistance performed well in identifying mild fibrosis, in men and women, and in those with/without obesity, with AUROCs 0.80, 0.88, 0.75 and 0.78 in the training set (n = 385), and 0.69, 0.80, 0.61 and 0.69 in the testing set (n = 165), respectively. In comparison, the combination of BAs and clinical/biochemical biomarkers performed less well in identifying significant fibrosis (F2‐4). In women and in non‐obese subjects, AUROCs were 0.75 and 0.71 in the training set, 0.65 and 0.66 in the validation set, respectively. However, these AUROCs were higher than those observed for the fibrosis‐4 index, NAFLD fibrosis score, and Hepamet fibrosis score.
Conclusions
Secondary BA levels were significantly increased in NAFLD, especially in those with mild fibrosis. The combination of serum BAs and clinical/biochemical biomarkers for identifying mild fibrosis merits further assessment.
Secondary bile acids were significantly increased in NAFLD, especially in those with mild fibrosis. The combination of serum bile acids and clinical/biochemical biomarkers for identifying mild fibrosis is worthy of further assessment.
Cancer initiation and progression are likely caused by the dysregulation of biological pathways. Gene set analysis (GSA) could improve the signal-to-noise ratio and identify potential biological ...insights on the gene set level. However, platforms exploring cancer multi-omics data using GSA methods are lacking. In this study, we upgraded our GSCALite to GSCA (gene set cancer analysis, http://bioinfo.life.hust.edu.cn/GSCA) for cancer GSA at genomic, pharmacogenomic and immunogenomic levels. In this improved GSCA, we integrated expression, mutation, drug sensitivity and clinical data from four public data sources for 33 cancer types. We introduced useful features to GSCA, including associations between immune infiltration with gene expression and genomic variations, and associations between gene set expression/mutation and clinical outcomes. GSCA has four main functional modules for cancer GSA to explore, analyze and visualize expression, genomic variations, tumor immune infiltration, drug sensitivity and their associations with clinical outcomes. We used case studies of three gene sets: (i) seven cell cycle genes, (ii) tumor suppressor genes of PI3K pathway and (iii) oncogenes of PI3K pathway to prove the advantage of GSCA over single gene analysis. We found novel associations of gene set expression and mutation with clinical outcomes in different cancer types on gene set level, while on single gene analysis level, they are not significant associations. In conclusion, GSCA is a user-friendly web server and a useful resource for conducting hypothesis tests by using GSA methods at genomic, pharmacogenomic and immunogenomic levels.
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