Application of valence-variable transition-metal-oxide-based nanomaterials in electrochemical analysis: A review.

The construction of materials with rapid electron transfer is considered an effective method for enhancing electrochemical activity in electroanalysis. It has been widely demonstrated that valence changes in transition metal ions can promote electron transfer and thus increase electrochemical activity. Recently, valence-variable transition metal oxides (TMOs) have shown popular application in electrochemical analysis by using their abundant valence state changes to accelerate electron transfer during electrochemical detection. In this review, we summarize recent research advances in valence changes of TMOs and their application in electrochemical analysis. This includes the definition and mechanism of valence change, the association of valence changes with electronic structure, and their applications in electrochemical detection, along with the use of density functional theory (DFT) to simulate the process of electron transfer during valence changes. Finally, the challenges and opportunities for developing and applying valence changes in electrochemical analysis are also identified.

scATAC-Ref: a reference of scATAC-seq with known cell labels in multiple species.

Chromatin accessibility profiles at single cell resolution can reveal cell type-specific regulatory programs, help dissect highly specialized cell functions and trace cell origin and evolution. Accurate cell type assignment is critical for effectively gaining biological and pathological insights, but is difficult in scATAC-seq. Hence, by extensively reviewing the literature, we designed scATAC-Ref (https://bio.liclab.net/scATAC-Ref/), a manually curated scATAC-seq database aimed at providing a comprehensive, high-quality source of chromatin accessibility profiles with known cell labels across broad cell types. Currently, scATAC-Ref comprises 1 694 372 cells with known cell labels, across various biological conditions, >400 cell/tissue types and five species. We used uniform system environment and software parameters to perform comprehensive downstream analysis on these chromatin accessibility profiles with known labels, including gene activity score, TF enrichment score, differential chromatin accessibility regions, pathway/GO term enrichment analysis and co-accessibility interactions. The scATAC-Ref also provided a user-friendly interface to query, browse and visualize cell types of interest, thereby providing a valuable resource for exploring epigenetic regulation in different tissues and cell types.

Sensitive sensing of Hg(II) based on lattice B and surface F co-doped CeO2: Synergies of catalysis and adsorption brought by doping site engineering.

Transition metal oxides are widely used in the detection of heavy metal ions (HMIs), and the co-doping strategy that introducing a variety of different dopant atoms to modify them can obtain a better detection performance. However, there is very little research on the co-doped transition metal oxides by non-metallic elements for electrochemical detection. Herein, boron (B) and fluorine (F) co-doped CeO2 nanomaterial (BFC) is constructed to serve as the electrochemically sensitive interface for the detection of Hg(II). B and F affect the sensitivity of CeO2 to HMIs when they were introduced at different doping sites. Through a variety of characterization, it is proved that B is successfully doped into the lattice and F is doped on the surface of the material. Through the improvement of the catalytic properties and adsorption capacity of CeO2 by different doping sites, this B and F co-doped CeO2 exhibits excellent square wave anodic stripping voltammetry (SWASV) current responses to Hg(II). Both the high sensitivity of 906.99 µA µM-1 cm-2 and the low limit of detection (LOD) of 0.006 µM are satisfactory. Besides, this BFC glassy carbon electrode (GCE) also has good anti-interference property, which has been successfully used in the detection of Hg(II) in actual water. This discovery provides a useful strategy for designing a variety of non-metallic co-doped transition metal oxides to construct trace heavy metal ion-sensitive interfaces.

SEanalysis 2.0: a comprehensive super-enhancer regulatory network analysis tool for human and mouse.

Super-enhancers (SEs) play an essential regulatory role in various biological processes and diseases through their specific interaction with transcription factors (TFs). Here, we present the release of SEanalysis 2.0 (http://licpathway.net/SEanalysis), an updated version of the SEanalysis web server for the comprehensive analyses of transcriptional regulatory networks formed by SEs, pathways, TFs, and genes. The current version added mouse SEs and further expanded the scale of human SEs, documenting 1 167 518 human SEs from 1739 samples and 550 226 mouse SEs from 931 samples. The SE-related samples in SEanalysis 2.0 were more than five times that in version 1.0, which significantly improved the ability of original SE-related network analyses ('pathway downstream analysis', 'upstream regulatory analysis' and 'genomic region annotation') for understanding context-specific gene regulation. Furthermore, we designed two novel analysis models, 'TF regulatory analysis' and 'Sample comparative analysis' for supporting more comprehensive analyses of SE regulatory networks driven by TFs. Further, the risk SNPs were annotated to the SE regions to provide potential SE-related disease/trait information. Hence, we believe that SEanalysis 2.0 has significantly expanded the data and analytical capabilities of SEs, which helps researchers in an in-depth understanding of the regulatory mechanisms of SEs.

VARAdb: a comprehensive variation annotation database for human.

With the study of human diseases and biological processes increasing, a large number of non-coding variants have been identified and facilitated. The rapid accumulation of genetic and epigenomic information has resulted in an urgent need to collect and process data to explore the regulation of non-coding variants. Here, we developed a comprehensive variation annotation database for human (VARAdb, http://www.licpathway.net/VARAdb/), which specifically considers non-coding variants. VARAdb provides annotation information for 577,283,813 variations and novel variants, prioritizes variations based on scores using nine annotation categories, and supports pathway downstream analysis. Importantly, VARAdb integrates a large amount of genetic and epigenomic data into five annotation sections, which include 'Variation information', 'Regulatory information', 'Related genes', 'Chromatin accessibility' and 'Chromatin interaction'. The detailed annotation information consists of motif changes, risk SNPs, LD SNPs, eQTLs, clinical variant-drug-gene pairs, sequence conservation, somatic mutations, enhancers, super enhancers, promoters, transcription factors, chromatin states, histone modifications, chromatin accessibility regions and chromatin interactions. This database is a user-friendly interface to query, browse and visualize variations and related annotation information. VARAdb is a useful resource for selecting potential functional variations and interpreting their effects on human diseases and biological processes.

Characterization of super-enhancer-associated functional lncRNAs acting as ceRNAs in ESCC.

Long noncoding RNAs (lncRNAs) have important regulatory roles in cancer biology. Although some lncRNAs have well-characterized functions, the vast majority of this class of molecules remains functionally uncharacterized. To systematically pinpoint functional lncRNAs, a computational approach was proposed for identification of lncRNA-mediated competing endogenous RNAs (ceRNAs) through combining global and local regulatory direction consistency of expression. Using esophageal squamous cell carcinoma (ESCC) as model, we further identified many known and novel functional lncRNAs acting as ceRNAs (ce-lncRNAs). We found that most of them significantly regulated the expression of cancer-related hallmark genes. These ce-lncRNAs were significantly regulated by enhancers, especially super-enhancers (SEs). Landscape analyses for lncRNAs further identified SE-associated functional ce-lncRNAs in ESCC, such as HOTAIR, XIST, SNHG5, and LINC00094. THZ1, a specific CDK7 inhibitor, can result in global transcriptional downregulation of SE-associated ce-lncRNAs. We further demonstrate that a SE-associated ce-lncRNA, LINC00094 can be activated by transcription factors TCF3 and KLF5 through binding to SE regions and promoted ESCC cancer cell growth. THZ1 downregulated expression of LINC00094 through inhibiting TCF3 and KLF5. Our data demonstrated the important roles of SE-associated ce-lncRNAs in ESCC oncogenesis and might serve as targets for ESCC diagnosis and therapy.

Integrative Epigenomic Analysis of Transcriptional Regulation of Human CircRNAs.

Circular RNAs (circRNAs) are evolutionarily conserved and abundant non-coding RNAs whose functions and regulatory mechanisms remain largely unknown. Here, we identify and characterize an epigenomically distinct group of circRNAs (TAH-circRNAs), which are transcribed to a higher level than their host genes. By integrative analysis of cistromic and transcriptomic data, we find that compared with other circRNAs, TAH-circRNAs are expressed more abundantly and have more transcription factors (TFs) binding sites and lower DNA methylation levels. Concordantly, TAH-circRNAs are enriched in open and active chromatin regions. Importantly, ChIA-PET results showed that 23-52% of transcription start sites (TSSs) of TAH-circRNAs have direct interactions with cis-regulatory regions, strongly suggesting their independent transcriptional regulation from host genes. In addition, we characterize molecular features of super-enhancer-driven circRNAs in cancer biology. Together, this study comprehensively analyzes epigenomic characteristics of circRNAs and identifies a distinct group of TAH-circRNAs that are independently transcribed via enhancers and super-enhancers by TFs. These findings substantially advance our understanding of the regulatory mechanism of circRNAs and may have important implications for future investigations of this class of non-coding RNAs.

SEanalysis: a web tool for super-enhancer associated regulatory analysis.

Super-enhancers (SEs) have prominent roles in biological and pathological processes through their unique transcriptional regulatory capability. To date, several SE databases have been developed by us and others. However, these existing databases do not provide downstream or upstream regulatory analyses of SEs. Pathways, transcription factors (TFs), SEs, and SE-associated genes form complex regulatory networks. Therefore, we designed a novel web server, SEanalysis, which provides comprehensive SE-associated regulatory network analyses. SEanalysis characterizes SE-associated genes, TFs binding to target SEs, and their upstream pathways. The current version of SEanalysis contains more than 330 000 SEs from more than 540 types of cells/tissues, 5042 TF ChIP-seq data generated from these cells/tissues, DNA-binding sequence motifs for ∼700 human TFs and 2880 pathways from 10 databases. SEanalysis supports searching by either SEs, samples, TFs, pathways or genes. The complex regulatory networks formed by these factors can be interactively visualized. In addition, we developed a customizable genome browser containing >6000 customizable tracks for visualization. The server is freely available at http://licpathway.net/SEanalysis.

MiR-133b targets Sox9 to control pathogenesis and metastasis of breast cancer.

The miR-133b, a commonly recognized muscle-specific miRNA, was reported to be deregulated in many kinds of cancers. However, its potential roles in tumorigenesis remain greatly elusive. Herein, we demonstrate that miR-133b is significantly suppressed in human breast cancer specimens, which is reversely correlated to histological grade of the cancer. Ectopic expression of miR-133b suppresses clonogenic ability and metastasis-relevant traits in vitro, as well as carcinogenesis and pulmonary metastasis in vivo. Further studies have identified Sox9, c-MET, and WAVE2 as direct targets of miR-133b, in which Sox9 contributes to all miR-133b-endowed effects including cell proliferation, colony formation, as well as cell migration and invasion in vitro. Moreover, re-expression of Sox9 reverses miR-133b-mediated metastasis suppression in vivo. Taken together, these findings highlight an important role for miR-133b in the regulation of tumorigenesis and metastatic potential of breast cancer and suggest a potential application of miR-133b in cancer treatment.

Fabrication of Porous Polyvinylidene Fluoride/Multi-Walled Carbon Nanotube Nanocomposites and Their Enhanced Thermoelectric Performance.

In this paper, a solvent vapor-induced phase separation (SVIPS) technique was used to create a porous structure in polyvinylidene fluoride/Multi-walled carbon nanotube (PVDF/MWNTs) composites with the aim of increasing the electrical conductivity through the incorporation of MWNTs while retaining a low thermal conductivity. By using the dimethylformamide/acetone mixture, porous networks could be generated in the PVDF/MWNTs composites upon the rapid volatilization of acetone. The electrical conductivity was gradually enhanced by the addition of MWNTs. At the same time, the thermal conductivity of the PVDF film could be retained at 0.1546 W·m-1·K-1 due to the porous structure being even by loaded with a high content of MWNTs (i.e., 15 wt.%). Thus, the Seebeck coefficient, power factor and figure of merit (ZT) were subsequently improved with maximum values of 324.45 µV/K, 1.679 µW·m-1·K-2, and 3.3 × 10-3, respectively. The microstructures, thermal properties, and thermoelectric properties of the porous PVDF/MWNTs composites were studied. It was found that the enhancement of thermoelectric properties would be attributed to the oxidation of MWNTs and the porous structure of the composites. The decrease of thermal conductivity and the increase of Seebeck coefficient were induced by the phonon scattering and energy-filtering effect. The proposed method was found to be facile and effective in creating a positive effect on the thermoelectric properties of composites.

Protein-coding genes combined with long non-coding RNAs predict prognosis in esophageal squamous cell carcinoma patients as a novel clinical multi-dimensional signature.

Esophageal carcinoma is one of the most malignant gastrointestinal cancers worldwide, and has a high mortality rate. Both protein-coding genes (PCGs) and long non-coding RNAs (lncRNAs) have been shown to play an important role in the development of malignant tumors. However, the clinical significance of PCGs combined lncRNAs is yet to be investigated in esophageal squamous cell carcinoma (ESCC). Using probe re-annotation, univariable Cox regression and the random survival forest algorithm to identify PCG-lncRNA combinations predictive of the overall survival, we found a signature comprised of three PCGs (ANGPTL7, OBP2A, SLC27A5) and two lncRNAs (RP11-702B10.1, RP11-523H24.3) to have the highest accurate prediction, with an area under ROC curve (AUC) of 0.85 in the training group and 0.63 in the test group, and it was significantly associated with the survival of ESCC patients in the training group (median survival: 32.2 months > 60 months, P < 0.001). The application of the signature to the test group showed similar prognostic values (median survival: 39.3 months vs. >60 months, P = 0.03). The chi-square test and multivariable Cox regression analysis showed that the three-PCG, two-lncRNA signature was an independent prognostic factor for patients with ESCC. Stratified analysis suggested that the PCG-lncRNA signature combined with the TNM stage could more accurately categorize ESCC patients. Our study suggests that the three-PCG, two-lncRNA signature has clinical significance for the prognosis of patients with ESCC. This signature can serve as a potential auxiliary biomarker of the TNM stage to subdivide ESCC patients more precisely.

MiR-630 suppresses breast cancer progression by targeting metadherin.

MicroRNAs have been integrated into tumorigenic programs as either oncogenes or tumor suppressor genes. The miR-630 was reported to be deregulated and involved in tumor progression of several human malignancies. However, its expression regulation shows diversity in different kinds of cancers and its potential roles remain greatly elusive. Herein, we demonstrate that miR-630 is significantly suppressed in human breast cancer specimens, as well as in various breast cancer cell lines. In aggressive MDA-MB-231-luc and BT549 breast cancer cells, ectopic expression of miR-630 strongly inhibits cell motility and invasive capacity in vitro. Moreover, lentivirus delivered miR-630 bestows MDA-MB-231-luc cells with the ability to suppress cell colony formation in vitro and pulmonary metastasis in vivo. Further studies identify metadherin (MTDH) as a direct target gene of miR-630. Functional studies shows that MTDH contributes to miR-630-endowed effects including cell migration and invasion as well as colony formation in vitro. Taken together, these findings highlight an important role for miR-630 in the regulation of metastatic potential of breast cancer and suggest a potential application of miR-630 in breast cancer treatment.

MiR-124 targets Slug to regulate epithelial-mesenchymal transition and metastasis of breast cancer.

MicroRNAs (miRNAs or miR) have been integrated into tumorigenic programs as either oncogenes or tumor suppressor genes. The miR-124 was reported to be attenuated in several tumors, such as glioma, medulloblastoma and hepatocellular carcinoma. However, its role in cancer remains greatly elusive. In this study, we show that the miR-124 expression is significantly suppressed in human breast cancer specimens, which is reversely correlated to histological grade of the cancer. More intriguingly, ectopic expression of miR-124 in aggressive breast cancer cell lines MDA-MB-231 and BT-549 strongly inhibits cell motility and invasive capacity, as well as the epithelial-mesenchymal transition process. Also, lentivirus-delivered miR-124 endows MDA-MB-231 cells with the ability to suppress cell colony formation in vitro and pulmonary metastasis in vivo. Further studies have identified the E-cadherin transcription repressor Slug as a direct target gene of miR-124; its downregulation by miR-124 increases the expression of E-cadherin, a hallmark of epithelial cells and a repressor of cell invasion and metastasis. Moreover, knockdown of Slug notably impairs the motility of MDA-MB-231 cells, whereas re-expression of Slug abrogates the reduction of motility and invasion ability induced by miR-124 in MDA-MB-231 cells. These findings highlight an important role for miR-124 in the regulation of invasive and metastatic potential of breast cancer and suggest a potential application of miR-124 in cancer treatment.

[The down-regulation of miR-129 in breast cancer and its effect on breast cancer migration and motility].

To search the microRNAs (miRNA) which suppress metastasis of breast cancer, we utilize three well known micoRNA target prediction programs, Targetscan, Pictar and miRanda, to select the microRNAs that target the genes related to tumor metastasis. We chose MDA-MB-231 with high metastasis ability as the model to evaluate the effect of miRNAs on cell motility through Transwell migration assay. After the first round of screening, miR-129 is found to significantly inhibit the migration of MDA-MB-231 both in Transwell migration assay and wound healing assay. Furthermore, miR-129 also shows great suppressive ability to cell mobility and migration in another two breast cancer cell lines BT549 and MDA-MB-435s. Most importantly, miR-129 is down-regulated both in breast cancer tissues compared with the paired adjacent normal breast tissues, and in breast cancer cell lines compared with normal breast epithelial cell MCF10A (P < 0.05). These results indicate that over-expression of miR-129 could inhibit breast cancer motility and migration, and the down-regulation of miR-129 may participate in the breast cancer migration and metastasis.

[Development of cell-penetrating peptides as vectors for drug delivery].

Biomacromolecules play an important role in the treatment of many diseases, but as a result of cell membrane serving as the natural barriers, only the small molecular compounds whose molecular weights are smaller than 600 Da can get through cell membrane and enter the cell. In recent years, some short peptides (the length less than 30 amino acids) are found to have the cell-penetrating function, called cell-penetrating peptides (CPPs). They are able to effectively translocate segments of protein, polypeptides, nucleic acid into the cells of many mammal animals with many methods. They have high transduction efficiency and will not lead to cell damage. So, the discovery of CPPs has a very good applicable prospect in such research fields as cell-biology, gene-therapy, drug transduction in vivo, evaluation of clinical medicine and medical immunology. This paper reviews the types and characteristics of CPPs, internalization mechanisms, applications, and their existing problems.

Characterization of antimicrobial peptides isolated from the skin of the Chinese frog, Rana dybowskii.

The skins of amphibians secrete small antimicrobial peptides that fight infection and are being explored as potential alternatives to conventional antibiotics. In this study we combined mass spectrometry with cDNA sequencing to examine antimicrobial peptides in skin secretions from the Chinese frog Rana dybowskii. Thirteen peptides having precursor sequences that resemble known antimicrobial peptides from this genus were identified, ten of which were members of previously described peptide families based on their primary structures; i.e., brevinin-1, Japonicin-1, brevinin-2 and temporin. The other three peptides from R. dybowskii, which were named dybowskin-1CDYa, dybowskin-2 CDYa and dybowskin-2CDYb, had different amino acid compositions and little sequence similarity to known antimicrobial peptides. The carboxyl terminus of dybowskin-1CDY lacked amidation and is therefore clearly distinct from temporin peptides, whereas dybowskin-2CDYa and dybowskin-2CDYb consisted of 18 amino acids and were rich in Arg residues. Chemically synthesized peptides corresponding to mature dybowskin-1CDYa and dybowskin-2CDYa had strong antimicrobial activity and caused little hemolysis of human erythrocytes, suggesting they may serve as interesting templates for the development of novel antibiotics.

[Molecular diversities and functions of antibacterial peptides from the skins of Ranidae of amphibians.].

Granular glands in the frog skins of Ranidae of amphibians, a widely distributed group with over 650 species, synthesize and secrete a remarkably diverse array of peptides with the broad-spectrum antibacterial, antifungal and other biologic activities to protect the organism against a wide range of pathogens, which are believed to have arisen as a result of multiple gene duplication events. Almost without exception, these components are hydrophobic, cationic and form an amphipathic a-helix in a membrane-mimetic solvent. The peptides can be grouped into families on the basis of structural similarity. To date, brevinin-1, esculentin-1, esculentin-2, and temporin peptides, ranalexin, ranatuerin-1, ranatuerin-2 and palustrin, brevinin-2, tigerinin, japonicin, nigrocin and melittin-related peptides have been found in amphibians of Ranidae. In this paper, the molecular diversity, structural feature and the biological ac-tivity of Ranidae antibacterial peptides were reviewed.

[ERIC-PCR on identification of Listeria species and strain].

Enterobacteria repetitive intergenic consensus sequences-based PCR(ERIC-PCR) was used to generate DNA fingerprints for Listeria spp. We got the specific profiles with ERIC-PCR technique that enables to identify Listeria species and the L.monocytogenes strains of different stereotype, and the same stereotype of L. monocytogenes from different sources also could be identified. Moreover,the species-specific 1600 bp DNA fragment was obtained from the fingerprint of L. monocytogenes. The study indicates that ERIC-PCR technique can be used in the identification of Listeria species and strains and its further typing, which is simple and quickly.