Interplay between CTCF boundaries and a super enhancer controls cohesin extrusion trajectories and gene expression.

To understand how chromatin domains coordinate gene expression, we dissected select genetic elements organizing topology and transcription around the Prdm14 super enhancer in mouse embryonic stem cells. Taking advantage of allelic polymorphisms, we developed methods to sensitively analyze changes in chromatin topology, gene expression, and protein recruitment. We show that enhancer insulation does not rely strictly on loop formation between its flanking boundaries, that the enhancer activates the Slco5a1 gene beyond its prominent domain boundary, and that it recruits cohesin for loop extrusion. Upon boundary inversion, we find that oppositely oriented CTCF terminates extrusion trajectories but does not stall cohesin, while deleted or mutated CTCF sites allow cohesin to extend its trajectory. Enhancer-mediated gene activation occurs independent of paused loop extrusion near the gene promoter. We expand upon the loop extrusion model to propose that cohesin loading and extrusion trajectories originating at an enhancer contribute to gene activation.

Identification of hub genes and pathways associated with cellular senescence in diabetic foot ulcers via comprehensive transcriptome analysis.

This research aimed to find important genes and pathways related to cellular senescence (CS) in diabetic foot ulcers (DFU) and to estimate the possible pathways through which CS affects diabetic foot healing. The GSE80178 dataset was acquired from the Gene Expression Omnibus (GEO) database, containing six DFU and three diabetic foot skin (DFS) samples. The limma package was used to identify differentially expressed genes (DEGs). At the same time, DEGs associated with CS (CS-DEGs) were found using the CellAge database. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted on the CS-DEGs. A protein-protein interaction (PPI) network was built using the String database, and the cytoHubba plug-in within Cytoscape helped identify hub genes. Lastly, the miRNA-TF-mRNA regulatory network for these hub genes was established. In total, 66 CS-DEGs were obtained. These genes mainly focus on CS, Kaposi sarcoma-associated herpesvirus infection and Toll-like receptor signalling pathway. Eight hub genes were identified to regulate cell senescence in DFU, including TP53, SRC, SIRT1, CCND1, EZH2, CXCL8, AR and CDK4. According to miRNA-TF-mRNA regulatory network, hsa-mir-132-3p/SIRT1/EZH2 axis is involved in senescence cell accumulation in DFU.

Hsa_circ_0007321 regulates Zika virus replication through miR-492/NFKBID/NF-κB signaling pathway.

IMPORTANCE: Over the past decade, increasing evidence has shown that circular RNAs (circRNAs) play important regulatory roles in viral infection and host antiviral responses. However, reports on the role of circRNAs in Zika virus (ZIKV) infection are limited. In this study, we identified 45 differentially expressed circRNAs in ZIKV-infected A549 cells by RNA sequencing. We clarified that a downregulated circRNA, hsa_circ_0007321, regulates ZIKV replication through targeting of miR-492 and the downstream gene NFKBID. NFKBID is a negative regulator of nuclear factor-κB (NF-κB), and we found that inhibition of the NF-κB pathway promotes ZIKV replication. Therefore, this finding that hsa_circ_0007321 exerts its regulatory role on ZIKV replication through the miR-492/NFKBID/NF-κB signaling pathway has implications for the development of strategies to suppress ZIKV and possibly other viral infections.

Study on the Selectivity of Molecular Imprinting Materials Determined through Hydrogen Bonding on Template Molecular Structures of Flavonoids.

Molecular imprinting technology is widely used for the specific identification of compounds, but the selective recognition mechanisms of the same compounds still need to be further studied. Based on differences in hydrogen bond size and orientation, molecularly imprinted polymers (MIPs) were designed to adsorb flavonols with the same parent core and different hydroxyl groups. A surface-imprinted material was designed with silicon dioxide as the carrier, myricetin as the template molecule, and methacrylic acid (MAA) as the functional monomer. Scanning electron microscopy (SEM), Brunauer-Emmett-Teller surface area (BET) analyses, Fourier-transform infrared spectroscopy (FT-IR), and other characterization experiments were carried out. The intrinsic mechanism of the MIPs was also explored. The MIPs showed good adsorption of myricetin and other flavonoids through hydrogen bonding and steric hindrance. The adsorption capacity was 3.12-9.04 mg/g, and the imprinting factor was 1.78-3.37. Flavonoids with different hydroxyl groups in different numbers and directions had different hydrogen bond strengths with functional monomers. R2, R4, and R1 on 2-phenylchromogenone had stronger electronegativity, and the hydroxyl group was also more likely to form and have stronger hydrogen bonds. The hydroxyl negativity and the degree of steric hindrance of flavonoids played a major role in the recognition of molecularly imprinted materials. This study is of great significance for the synthesis of and selection of templates for analogous molecular imprinting materials.

Strategy of Choosing Templates in Molecular Imprinting to Expand the Recognition Width for Family-Selectivity.

The class-selective molecular-imprinted polymers (MIPs) have shown the recognition ability to multiple targeted molecules through using one or multiple templates. However, choosing the right templates, the core problem, still lacks a systemic guide and decision-making. In this work, we propose a strategy of selecting templates through expanding the recognition width for the improvement of class-selectivity. First, three families of genotoxic impurity (GTI) were selected as model objects, and the spatial size and binding energy of each GTI-monomer complexes were obtained and compared by computational simulation. The two indexes of energy width (WE) and size width (WL) were introduced to compare the similarity and differences on the two recognition factors, binding strength and spatial size, among these GTIs in each family. Through shortening the width to increase similarity on binding energy and size, the dual templates in the aromatic amines (AI) family and sulfonic acid esters (SI) family were successfully selected. Correspondingly, the prepared dual-template MIPs in the two GTI families can simultaneously recognize all the GTIs comparing with that of single template MIP, respectively. Meanwhile, through comparing the adsorption capacity of the selected template and its analogues in one GTI family, the recognition efficiency of the dual-template MIPs was higher than that of the single-template MIP. This indicates that though using the selected right templates, the higher class-selectivity and the larger recognition width can be realized. Thus, this work can solve the problem of blind template selection, and provide the useful theoretical guidance for designing family-selective molecular imprinting.

Improved selectivity of molecularly imprinted polymers based on the synergistic action of hydrogen bond and electrostatic interaction.

Based on the synergistic action of hydrogen bond and electrostatic interaction, provided by methacrylic acid and 2-aminoethyl ester hydrochloride (FM2), respectively, novel molecularly imprinted polymers (SA-MIPs) were designed to improve its selective recognition ability. Diclofenac sodium (DFC) was chosen as the template molecule of this study. The interaction and their recognition sites between two functional monomers and templates were confirmed by nuclear magnetic resonance hydrogen spectroscopy. Because of the synergistic action of hydrogen bond and electrostatic interaction, the imprinting factor (IF) of SA-MIPs (IF = 2.26) is superior to the corresponding monofunctional monomer imprinting materials (IF = 1.52, 1.20) and the materials using two functional monomers with an only single type of interaction (IF = 1.54, 1.75). The results of selective adsorption experiments indicate that the selective recognition ability of SA-MIPs is significantly better than that of the other four MIPs, and the difference in selectivity coefficient for methyl orange is the largest between SA-MIPs and the MIPs only using FM2, which is about 70 times. In addition, x-ray photoelectron spectroscopy was used to verify the interaction between SA-MIPs and the template. This work and its explanation of the interaction mechanism at the molecular level will be helpful for the rational design of novel MIPs with higher selectivity. Besides, SA-MIPs have good adsorption performance (37.75 mg/g) for DFC in aqueous solutions, which could be used as potential adsorption materials for the effective removal of DFC in the aquatic environment.

Profiles of Intolerance of Uncertainty Among 108,540 Adolescents: Associations with Sociodemographic Variables and Mental Health.

Intolerance of uncertainty (IU) is widely considered a transdiagnostic risk and maintaining factor for psychiatric disorders. However, little is known about the overall nature and profile of IU among adolescents. This study aims to investigate the profiles of IU among Chinese adolescents and explore their associations with sociodemographic characteristics and mental health problems. A sample of 108,540 adolescents provided data on IU, sociodemographic characteristics, and mental health via an online platform. Latent profile analysis revealed three profiles: Low IU, Medium IU, and High IU. Girls, older adolescents, and those with specific sociodemographics were more likely to belong to the "High IU" profile. Furthermore, the "High IU" profile was associated with the highest risk of several mental health problems. These findings provided valuable information for early prevention and intervention strategies targeting IU and highlighted the importance of IU-based interventions for mental health among adolescents.

Measuring the Affinities of RNA and DNA Aptamers with DNA Origami-Based Chiral Plasmonic Probes.

Reliable characterization of binding affinities is crucial for selected aptamers. However, the limited repertoire of universal approaches to obtain the dissociation constant (KD) values often hinders the further development of aptamer-based applications. Herein, we present a competitive hybridization-based strategy to characterize aptamers using DNA origami-based chiral plasmonic assemblies as optical reporters. We incorporated aptamers and partial complementary strands blocking different regions of the aptamers into the reporters and measured the kinetic behaviors of the target binding to gain insights on aptamers' functional domains. We introduced a reference analyte and developed a thermodynamic model to obtain a relative dissociation constant of an aptamer-target pair. With this approach, we characterized RNA and DNA aptamers binding to small molecules with low and high affinities.

Homomesoporous Metal-Organic Framework for High-Performance Electrochromatographic Separation.

Metal-organic frameworks (MOFs) have exhibited tremendous potential in the area of separation science. However, most of the developed MOF-based stationary phases contained only microporous structures and suffer from limited separation performance. Herein, homomesoporous MOFs with excellent mass transfer capability and strong thermodynamic interactions are first explored as the novel stationary phase for high-performance capillary electrochromatographic separations. As a proof of concept, noninterpenetrated mesoMOF-1 with uniform mesopore sizes (22.5 × 26.1 Å) and good stability was facilely grown on the inner surface of capillaries and applied as a homomesoporous MOF coating-based stationary phase for high-efficiency electrochromatographic separation. Seven types of analytes with different molecular dimensions were all baseline separated on a mesoMOF-1 coated column with high theoretical plate numbers and excellent repeatability, exhibiting significantly improved separation selectivity and column efficiency in comparison to a microporous HKUST-1 coated column. The maximum column efficiencies of the mesoMOF-1 coated column for substituted benzenes and halobenzenes reached up to 1.4 × 105 plates/m, and its mass loadability was also much higher than that of the HKUST-1 coated column. In addition, based on the analysis of adsorption kinetics and chromatographic retention behaviors, the interaction and retention mechanisms of different molecular-weight analytes on mesoMOF-1 coated stationary phases were systematically explored and disclosed in detail. These results indicate that the homomesoporous MOF-based stationary phase can effectively balance the kinetic diffusion (mass transfer capability) and thermodynamic interactions (the strength of adsorption interaction), having great potential for high-performance chromatographic separation.

MiR-146a down-regulates inflammatory response by targeting TLR3 and TRAF6 in Coxsackievirus B infection.

Coxsackievirus B (CVB) is the major cause of human myocarditis and dilated cardiomyopathy. Toll-like receptor 3 (TLR3) is an intracellular sensor to detect pathogen's dsRNA. TLR3, along with TRAF6, triggers an inflammatory response through NF-κB signaling pathway. In the cells infected with CVB type 3 (CVB3), the abundance of miR-146a was significantly increased. The role of miR-146a in CVB infection is unclear. In this study, TLR3 and TRAF6 were identified as the targets of miR-146a. The elevated miR-146a inhibited NF-κB translocation and subsequently down-regulated proinflammatory cytokine expression in the CVB3-infected cells. Therefore, the NF-κB pathway can be doubly blocked by miR-146a through targeting of TLR3 and TRAF6. MiR-146a may be a negative regulator on inflammatory response and an intrinsic protective factor in CVB infection.

Characterizing Aptamers with Reconfigurable Chiral Plasmonic Assemblies.

Aptamers have emerged as versatile affinity ligands and as promising alternatives to protein antibodies. However, the inconsistency in the reported affinities and specificities of aptamers has greatly hindered the development of aptamer-based applications. Herein, we present a strategy to characterize aptamers by using DNA origami-based chiral plasmonic assemblies as reporters and establishing a competitive hybridization reaction-based thermodynamic model. We demonstrate the characterization of several DNA aptamers, including aptamers for small molecules and macromolecules, as well as aptamers with high and low affinities. The presented characterization scheme can be readily adapted to a wide selection of aptamers. We anticipate that our approach will advance the development of aptamer-based applications by enabling reliable and reproducible characterization of aptamers.

Single-Atom Catalysts Based on the Metal-Oxide Interaction.

Metal atoms dispersed on the oxide supports constitute a large category of single-atom catalysts. In this review, oxide supported single-atom catalysts are discussed about their synthetic procedures, characterizations, and reaction mechanism in thermocatalysis, such as water-gas shift reaction, selective oxidation/hydrogenation, and coupling reactions. Some typical oxide materials, including ferric oxide, cerium oxide, titanium dioxide, aluminum oxide, and so on, are intentionally mentioned for the unique roles as supports in anchoring metal atoms and taking part in the catalytic reactions. The interactions between metal atoms and oxide supports are summarized to give a picture on how to stabilize the atomic metal centers, and rationally tune the geometric structures and electronic states of single atoms. Furthermore, several directions in fabricating single-atom catalysts with improved performance are proposed on the basis of state-of-the-art understanding in metal-oxide interactions.

Microorganisms as Bio-SPE Materials for Extraction of Pharmaceutical Drugs: Mechanism of Extraction.

In solid-phase extraction (SPE), the extraction materials depend on the physicochemical interactions to obtain the target analytes from complex systems. However, many matrix interferences existing in real samples influence the extraction efficiency through these common interactions. Therefore, extraction materials based on more special interactions for biological systems need to be developed. In this work, live microorganisms including Escherichia coli and Staphylococcus aureus were considered as the potential biological SPE (bio-SPE) materials with their biological functions in the live state. To study the enrichment and selectivity of the bio-SPE, four antibacterial drugs and two non-antibacterial drugs were employed as the target analytes. The enrichment factor (EF) was used as the evaluation index. The results showed that when using chlorpheniramine (CPM) and ofloxacin (OFLO), the enrichment capacity of E. coli was better than that of S. aureus. When extracting a single analyte, the enrichment ability of E. coli for CPM was significantly higher than other analytes, and the EF was 8.5. In a mixture solution of antibacterial analytes, OFLO could be enriched mostly by E. coli. However, in the mixture solution of antibacterial and non-antibacterial analytes, CPM was enriched more than that of antibacterial analytes. In real rat plasma, bio-SPE using live E. coli could obviously extract CPM, while traditional liquid-liquid extraction could not. The confocal microscopy results showed that the extraction mechanism may not only depend on the surface adsorption of bacteria with analytes but also on the uptake into bacteria. This provides a valuable basis for the development of more biological separation materials based on biological interactions.

Mvda is required for zebrafish early development.

BACKGROUND: The MVD gene mutations are identified in porokeratosis, which is considered a skin-specific autoinflammatory keratinization disease. However, the biological function of MVD gene remains largely unknown. Therefore, we analyzed the function of mvda gene, orthologous to the human MVD gene, in developing zebrafish. METHODS: Morpholino antisense oligonucleotide technique was used to generate mvda loss-of-function phenotypes. Knockdown of mvda was confirmed by RT-PCR and Sanger sequencing. Scanning and transmission electron microscopy were performed to analyze the morphology of the epidermis. Angiogenesis study was presented using the Tg(fli1a:EGFP)y1 transgenic strain. In addition, acridine orange staining was used to examine the apoptotic cells in vivo. RESULTS: As expected, the mvda morphants showed abnormal morphology of the epidermis. Moreover, we observed ectopic sprouts in trunk angiogenesis and impaired formation of the caudal vein plexus in the mvda-deficient zebrafish. Besides, increased apoptosis was found throughout the tail, heart, and eyes in mvda zebrafish morphants. CONCLUSIONS: These findings indicated the essential role of mvda in the early development of zebrafish. This was the first in vivo knockdown study of the zebrafish mvda gene, which might offer insight into the biological function of the human MVD gene.

Strong Metal-Support Interactions between Pt Single Atoms and TiO2.

Strong metal-support interaction (SMSI) has gained great attention in the field of heterogeneous catalysis. However, whether single-atom catalysts can exhibit SMSI remains unknown. Here, we demonstrate that SMSI can occur on TiO2 -supported Pt single atoms but at a much higher reduction temperature than that for Pt nanoparticles (NPs). Pt single atoms involved in SMSI are not covered by the TiO2 support nor do they sink into its subsurface. The suppression of CO adsorption on Pt single atoms stems from coordination saturation (18-electron rule) rather than the physical coverage of Pt atoms by the support. Based on the new finding it is revealed that single atoms are the true active sites in the hydrogenation of 3-nitrostyrene, while Pt NPs barely contribute to the activity since the NP sites are selectively encapsulated. The findings in this work provide a new approach to study the active sites by tuning SMSI.

Controlling CO2 Hydrogenation Selectivity by Metal-Supported Electron Transfer.

Tuning CO2 hydrogenation selectivity to obtain targeted value-added chemicals and fuels has attracted increasing attention. However, a fundamental understanding of the way to control the selectivity is still lacking, posing a challenge in catalyst design and development. Herein, we report our new discovery in ambient pressure CO2 hydrogenation reaction where selectivity can be completely reversed by simply changing the crystal phases of TiO2 support (anatase- or rutile-TiO2 ) or changing metal loadings on anatase-TiO2 . Operando spectroscopy and NAP-XPS studies reveal that the determining factor is a different electron transfer from metal to the support, most probably as a result of the different extents of hydrogen spillover, which changes the adsorption and activation of the intermediate of CO. Based on this new finding, we can not only regulate CO2 hydrogenation selectivity but also tune catalytic performance in other important reactions, thus opening up a door for efficient catalyst development by rational design.

A SPE Method with Two MIPs in Two Steps for Improving the Selectivity of MIPs.

Molecular imprinted polymers (MIPs) have been widely applied in the separation of compounds in complex matrixes due to the high selectivity for molecular recognition. However, MIPs not only adsorb the targeted molecule but also adsorb structurally similar analogues, which leads to some loss of selectivity. In this work, for improvement of selectivity of MIPs, a novel solid-phase extraction method with two MIPs in two steps (TMIPs-TSPE) was established. As a demonstration, two MIPs were prepared by using quercetin as the template and 4-vinylypyridine (4VP) and acrylamide (AM) as representative functional monomers, respectively. The adsorption properties and kinetic characteristics of the two MIPs showed that they had a distinct adsorption capacity and adsorption mechanism, which is the basis for establishment of TMIPs-TSPE. The TMIPs-TSPE method first used one of the two MIPs as adsorbent to extract molecules from a solution mixture containing quercetin and three analogues. Then the other MIP was used to achieve a second extraction of the extracted molecules from the first step. The results showed that the unique targeted molecule quercetin was extracted, which illustrates that TMIPs-TSPE improved the specificity of the MIPs. The process of molecular recognition can be influenced by the intensity of binding sites between MIPs and molecules. Moreover, it may also depend on the spatial orientation of molecules entering the cavities of MIPs, which deserves more attention as one important property for the development of molecular imprinting. These results demonstrated that the novel TMIPs-TSPE method contributes to the improved selectivity of MIPs.

A Chinese cross-sectional study on depression and anxiety symptoms in patients with psoriasis vulgaris.

Previous studies have reported a higher incidence of depression and anxiety in psoriasis patients compared to the general population, which has important implications for assessment and treatment. In this study, we determined the frequency of depression and anxiety in Chinese patients with psoriasis and its relationship with disease severity and other demographic variables. The study included 208 Chinese patients with psoriasis vulgaris. The Patient Health Questionnaire (PHQ-9) and Generalized Anxiety Disorder scale (GAD-7) were used to screen for depression and anxiety. The Psoriasis Area and Severity Index (PASI) was used to assess the severity of psoriasis. Of the 208 patients included in the study, 29 patients (13.9%) were positive for moderate-to-severe depression (PHQ-9 ≥ 10) and 22 patients (10.6%) were positive for anxiety (GAD-7 ≥ 10) symptoms. Both positive stress reactors who perceived stress as an exacerbating factor of psoriasis and moderate-to-severe psoriasis were found to be positive predictors for the presence of moderate-to-severe depression or anxiety symptoms while longer duration and late onset age played a protective role. In the sample of Chinese patients with psoriasis there was a clinically significant prevalence of depression and anxiety. Our study suggests that Chinese psoriasis patients should be screened for psychiatric comorbidities.

Solvent-Triggered Reversible Phase Changes in Two Manganese-Based Metal-Organic Frameworks and Associated Sensing Events.

A flexible Mn-based MOF, Mn-sdc-1, has been successfully synthesized by using the ligand 4,4'-stilbenedicarboxylic acid (H2 sdc). Attributed to the flexibility of the framework, Mn-sdc-1 can transform into a new phase (Mn-sdc-2) with completely different structural geometry; this is induced by trace levels of H2 O at room temperature. Reversibly, the transformation from Mn-sdc-2 to Mn-sdc-1 can be triggered by DMF upon heating beyond 100 °C. These results inspired a study of the influences of temperature and H2 O volume in the solid-state transformation of two MOF phases and, for the first time, a phase diagram of MOFs has been depicted. This phase diagram reflects the gradual H2 O-/temperature-dependent changes between Mn-sdc-1 and Mn-sdc-2, which is very meaningful in achieving the controllable synthesis of these two MOFs and lead to targeting the desired water-stable structure. As a result, the obtained water-stable Mn-sdc-2 can be developed as an excellent Pb2+ sensor in aqueous solution through the luminescence quenching effect with a limit of detection of 31.4 nm.

A mean-field theory on the differential capacitance of asymmetric ionic liquid electrolytes. II. Accounts of ionic interactions.

A size-asymmetric mean-field theory with ionic interactions is developed for the electric double layer of room temperature ionic liquid (IL) electrolytes, based on the previous work on non-interacting ions (Y. Han et al., J. Phys.: Condens. Matter, 2014, 26, 284103). By solving the modified Poisson-Boltzmann equation with some simplified assumptions following a recent work (Z. A. H. Goodwin et al., Electrochim. Acta, 2017, 225, 190-197), an analytical expression of differential capacitance can be derived, with a scaled electrode potential due to the ionic interactions. Compared with non-interacting ions, the main effect of ionic interactions is the insufficient screening of the electrode potential, and this depresses the differential capacitance compared with the non-interactive case.