Mesoporous Vinylene-Linked Covalent Organic Frameworks with Heteroatom-Tuned Crystallinity and Photocatalytic Behaviors.

Owing to its prominent π-delocalization and stability, vinylene linkage holds great merits in the construction of covalent organic frameworks (COFs) with promising semiconducting properties. However, carbon-carbon double bond formation reaction always exhibits relatively low reversibility, unfavorable for the formation of high crystalline frameworks through self-error correction and assembling processes. In this work, we report a heteroatom-tuned strategy to build up a series of two-dimensional (2D) vinylene-linked COFs by Knoevenagel condensation of an electron-deficient methylthiazolyl-based monomer with different triformyl substituted (hetero-)aromatic derivatives. The resulting COFs show high-quality periodic mesoporous structures with high surface areas. Embedding heteroatoms into the backbones enables significantly improving their crystallinity, and finely tailoring their semiconducting structures. Upon visible light stimulation, one of the as-prepared COFs with donor-π-acceptor structure could deliver a nearly seven-fold increase in the catalytic activity of hydrogen generation as compared with the other two. Meanwhile, in combination with high crystallinity and the matched conduction band energy level, such kind of COFs can be able to selectively generate singlet oxygen and superoxide radicals in a high ratio of up to 30:1, allowing for catalyzing aerobic thioanisole oxidation in distinctly tunable activities through the substituent electronic effect of the substrates.

Structure-Property Relationship of Cyano-Functionalized Conjugated Polymers for Photocatalytic Hydrogen Production.

Conjugated polymers (CPs) have garnered increasing attention in the field of photocatalysis due to their stability and molecular tunability. Understanding the structure-property relationship in CPs and addressing appropriate molecular design strategies are pivotal to improving the photocatalytic performance of CPs. Herein, a new efficient cyano (CN) engineering approach was proposed to promote the photocatalytic performance of CPs, and three representative CP-based photocatalysts with different CN contents were tailor-made to investigate the relationship between CN functionalization and photocatalytic activity. A series of systematically experimental and theoretical studies reveal that CN functionalization contributes to strengthening the donor-acceptor (D-A) interaction, enhancing the light absorption ability, charge separation/transfer efficiency, and hydrophilicity of CPs, and also facilitating the output of separated photoinduced electrons from CPs to Pt cocatalyst. Thus, the dicyano-functionalized polymer (P-2CN) manifests an attractive photocatalytic performance in hydrogen production. This study provides a facile strategy to develop excellent CP-based photocatalysts for solar fuel production.

Electronic Transmission Channels Promoting Charge Separation of Conjugated Polymers for Photocatalytic CO2 Reduction with Controllable Selectivity.

Conjugated polymers (CPs) represent a promising platform for photocatalytic CO2 fixation owing to their suitable band structures that meet the requirements of the reduction potential of CO2 to value-added fuels. However, the photocatalytic performance of CPs is rather restrained by the low charge transfer efficiency. Herein, we rationally designed three CPs with a more delocalized electronic transmission channel and planar molecular structure, which are regarded to evidently reduce the exciton binding energy (Eb ) and accelerate the internal charge transfer process. Besides, the assembly of suitable electron-output "tentacles" and cocatalysts on the surface of CPs could effectively facilitate interfacial electron delivery. Accordingly, the optimal P-2CN exhibits an apparent quantum yield of 4.6 % at 420 nm for photocatalytic CO2 to CO. Further adjusting the amounts of cyano groups and cocatalysts, the CO selectivity could be obtained in the range of 0-80.5 %.

Molecular Design of Covalent Triazine Frameworks with Anisotropic Charge Migration for Photocatalytic Hydrogen Production.

Covalent triazine frameworks (CTFs) represent promising polymeric photocatalysts for photocatalytic hydrogen production with visible light. However, the separation and transfer of charges in CTFs are isotropic because of the uniform distribution of donor-acceptor motifs in the skeleton. Herein, to achieve the anisotropic charge carrier separation and migration, thiophene (Th) or benzothiadiazole (BT) unit is selected as the dopant to modify the molecular structure of CTF-based photocatalysts. Both theoretical and experimental studies reveal that the incorporation of Th or BT units induces the anisotropic charge carrier separation and migration at the interface of CTFs. The optimized polymer manifests a much enhanced photocatalytic activity for photocatalytic hydrogen production with visible light, and thus this study provides a useful tool to design conjugated polymer photocatalysts at the molecular level for solar energy conversion.

Universal concept signature analysis: genome-wide quantification of new biological and pathological functions of genes and pathways.

Identifying new gene functions and pathways underlying diseases and biological processes are major challenges in genomics research. Particularly, most methods for interpreting the pathways characteristic of an experimental gene list defined by genomic data are limited by their dependence on assessing the overlapping genes or their interactome topology, which cannot account for the variety of functional relations. This is particularly problematic for pathway discovery from single-cell genomics with low gene coverage or interpreting complex pathway changes such as during change of cell states. Here, we exploited the comprehensive sets of molecular concepts that combine ontologies, pathways, interactions and domains to help inform the functional relations. We first developed a universal concept signature (uniConSig) analysis for genome-wide quantification of new gene functions underlying biological or pathological processes based on the signature molecular concepts computed from known functional gene lists. We then further developed a novel concept signature enrichment analysis (CSEA) for deep functional assessment of the pathways enriched in an experimental gene list. This method is grounded on the framework of shared concept signatures between gene sets at multiple functional levels, thus overcoming the limitations of the current methods. Through meta-analysis of transcriptomic data sets of cancer cell line models and single hematopoietic stem cells, we demonstrate the broad applications of CSEA on pathway discovery from gene expression and single-cell transcriptomic data sets for genetic perturbations and change of cell states, which complements the current modalities. The R modules for uniConSig analysis and CSEA are available through https://github.com/wangxlab/uniConSig.

A Fully Coplanar Donor-Acceptor Polymeric Semiconductor with Promoted Charge Separation Kinetics for Photochemistry.

Charge generation and separation are regarded as the major constraints limiting the photocatalytic activity of polymeric photocatalysts. Herein, two new linear polyarylether-based polymers (PAE-CPs) with distinct linking patterns between their donor and acceptor motifs were tailor-made to investigate the influence of different linking patterns on the charge generation and separation process. Theoretical and experimental results revealed that compared to the traditional single-stranded linker, the double-stranded linking pattern strengthens donor-acceptor interactions in PAE-CPs and generates a coplanar structure, facilitating charge generation and separation, and enabling red-shifted light absorption. With these prominent advantages, the PAE-CP interlinked with a double-stranded linker exhibits markedly enhanced photocatalytic activity compared to that of its single-strand-linked analogue. Such findings can facilitate the rational design and modification of organic semiconductors for charge-induced reactions.

Analysing the meta-interaction between pathways by gene set topological impact analysis.

BACKGROUND: Pathway analysis is widely applied in transcriptome analysis. Given certain transcriptomic changes, current pathway analysis tools tend to search for the most impacted pathways, which provides insight into underlying biological mechanisms. Further refining of the enriched pathways and extracting functional modules by "crosstalk" analysis have been proposed. However, the upstream/downstream relationships between the modules, which may provide extra biological insights such as the coordination of different functional modules and the signal transduction flow have been ignored. RESULTS: To quantitatively analyse the upstream/downstream relationships between functional modules, we developed a novel GEne Set Topological Impact Analysis (GESTIA), which could be used to assemble the enriched pathways and functional modules into a super-module with a topological structure. We showed the advantages of this analysis in the exploration of extra biological insight in addition to the individual enriched pathways and functional modules. CONCLUSIONS: GESTIA can be applied to a broad range of pathway/module analysis result. We hope that GESTIA may help researchers to get one additional step closer to understanding the molecular mechanism from the pathway/module analysis results.

Associations of P2X7 Polymorphisms with the Odds of Tuberculosis: A Meta-Analysis.

BACKGROUND: Recently, the roles of purinergic receptor P2X ligand-gated ion channel 7 (P2X7) polymorphisms in tuberculosis (TB) were analyzed by some pilot studies, but the results of these studies were inconsistent. We performed this study to better assess the relationship between P2X7 polymorphisms and the odds of TB. METHODS: Eligible studies were searched in PubMed, MEDLINE, and Embase. Odds ratios and 95% confidence intervals were calculated. RESULTS: A total of 21 studies were included for analyses. Significant associations with the odds of TB were detected for rs3751143 polymorphism in dominant (p = 0.01), recessive (p < 0.0001), additive (p = 0.0002), and allele models (p < 0.0001) in overall analyses. Further subgroup analyses based on the ethnicity of participants revealed that the rs1718119 polymorphism is significantly associated with the odds of TB in Asians and the rs3751143 polymorphism with the odds of TB in Caucasians. CONCLUSION: Our findings indicate that rs1718119 polymorphism may serve as a potential biological marker of TB in Asians and the rs3751143 polymorphism as a potential biological marker of TB in Caucasians.

Discovery of rare mutations in extensively pooled DNA samples using multiple target enrichment.

Chemical mutagenesis is routinely used to create large numbers of rare mutations in plant and animal populations, which can be subsequently subjected to selection for beneficial traits and phenotypes that enable the characterization of gene functions. Several next-generation sequencing (NGS)-based target enrichment methods have been developed for the detection of mutations in target DNA regions. However, most of these methods aim to sequence a large number of target regions from a small number of individuals. Here, we demonstrate an effective and affordable strategy for the discovery of rare mutations in a large sodium azide-induced mutant rice population (F2 ). The integration of multiplex, semi-nested PCR combined with NGS library construction allowed for the amplification of multiple target DNA fragments for sequencing. The 8 × 8 × 8 tridimensional DNA sample pooling strategy enabled us to obtain DNA sequences of 512 individuals while only sequencing 24 samples. A stepwise filtering procedure was then elaborated to eliminate most of the false positives expected to arise through sequencing error, and the application of a simple Student's t-test against position-prone error allowed for the discovery of 16 mutations from 36 enriched targeted DNA fragments of 1024 mutagenized rice plants, all without any false calls.

GINv2.0: a comprehensive topological network integrating molecular interactions from multiple knowledge bases.

Knowledge bases have been instrumental in advancing biological research, facilitating pathway analysis and data visualization, which are now widely employed in the scientific community. Despite the establishment of several prominent knowledge bases focusing on signaling, metabolic networks, or both, integrating these networks into a unified topological network has proven to be challenging. The intricacy of molecular interactions and the diverse formats employed to store and display them contribute to the complexity of this task. In a prior study, we addressed this challenge by introducing a "meta-pathway" structure that integrated the advantages of the Simple Interaction Format (SIF) while accommodating reaction information. Nevertheless, the earlier Global Integrative Network (GIN) was limited to reliance on KEGG alone. Here, we present GIN version 2.0, which incorporates human molecular interaction data from ten distinct knowledge bases, including KEGG, Reactome, and HumanCyc, among others. We standardized the data structure, gene IDs, and chemical IDs, and conducted a comprehensive analysis of the consistency among the ten knowledge bases before combining all unified interactions into GINv2.0. Utilizing GINv2.0, we investigated the glycolysis process and its regulatory proteins, revealing coordinated regulations on glycolysis and autophagy, particularly under glucose starvation. The expanded scope and enhanced capabilities of GINv2.0 provide a valuable resource for comprehensive systems-level analyses in the field of biological research. GINv2.0 can be accessed at: https://github.com/BIGchix/GINv2.0 .

Decoding Aging Hallmarks at the Single-Cell Level.

Organismal aging exhibits wide-ranging hallmarks in divergent cell types across tissues, organs, and systems. The advancement of single-cell technologies and generation of rich datasets have afforded the scientific community the opportunity to decode these hallmarks of aging at an unprecedented scope and resolution. In this review, we describe the technological advancements and bioinformatic methodologies enabling data interpretation at the cellular level. Then, we outline the application of such technologies for decoding aging hallmarks and potential intervention targets and summarize common themes and context-specific molecular features in representative organ systems across the body. Finally, we provide a brief summary of available databases relevant for aging research and present an outlook on the opportunities in this emerging field.

Does the Presence of Type 2 Diabetes or Metabolic Syndrome Impact Reduction in Waist Circumference During Weight Loss?

OBJECTIVES: Our aim in this study was to compare the change in waist circumference given the same degree of weight loss in patients who meet the criteria for metabolic syndrome or type 2 diabetes and those who do not meet these criteria. Because visceral adiposity is a key feature of both conditions and intra-abdominal adipocytes show higher lipolytic activity, we sought to determine whether changes in waist circumference differed in individuals with and without these conditions. METHODS: The Ottawa Hospital Weight Management Clinic offers a course in lifestyle modification and uses 12 weeks of total meal replacement. We compared the decrease in waist circumference between patients with metabolic syndrome or diabetes and those without these conditions who had lost a similar amount of weight using measurements from the first 6 weeks of meal replacement. RESULTS: We evaluated 3,559 patients who attended the program between September 1992 and April 2015. The patient population was largely Caucasian and of European descent and all meetings were face to face. The mean weight loss for men was 15.1±20.2 kg, and the mean weight loss for women was 9.7±2.4 kg. There were no significant differences in decrease in waist circumference between those with and without metabolic syndrome in both men (11.7±3.9 cm vs 11.4±3.8 cm, p=0.48) and women (9.0±3.6 cm vs 9.1±3.7 cm, p=0.26). CONCLUSIONS: Our results show that, given the same degree of weight loss, patients with and without diabetes or metabolic syndrome experience a similar change in waist circumference.

The global integrative network: integration of signaling and metabolic pathways.

The crosstalk between signaling and metabolic pathways has been known to play key roles in human diseases and plant biological processes. The integration of signaling and metabolic pathways can provide an essential reference framework for crosstalk analysis. However, current databases use distinct structures to present signaling and metabolic pathways, which leads to the chaos in the integrated networks. Moreover, for the metabolic pathways, the metabolic enzymes and the reactions are disconnected by the current widely accepted layout of edges and nodes, which hinders the topological analysis of the integrated networks. Here, we propose a novel "meta-pathway" structure, which uses the uniformed structure to display the signaling and metabolic pathways, and resolves the difficulty in linking the metabolic enzymes to the reactions topologically. We compiled a comprehensive collection of global integrative networks (GINs) by merging the meta-pathways of 7077 species. We demonstrated the assembly of the signaling and metabolic pathways using the GINs of four species-human, mouse, Arabidopsis, and rice. Almost all of the nodes were assembled into one major network for each of the four species, which provided opportunities for robust crosstalk and topological analysis, and knowledge graph construction. Supplementary Information: The online version contains supplementary material available at 10.1007/s42994-022-00078-1.

Dynamic DNA 5-hydroxylmethylcytosine and RNA 5-methycytosine Reprogramming During Early Human Development.

After implantation, complex and highly specialized molecular events render functionally distinct organ formation, whereas how the epigenome shapes organ-specific development remains to be fully elucidated. Here, nano-hmC-Seal, RNA bisulfite sequencing (RNA-BisSeq), and RNA sequencing (RNA-Seq) were performed, and the first multilayer landscapes of DNA 5-hydroxymethylcytosine (5hmC) and RNA 5-methylcytosine (m5C) epigenomes were obtained in the heart, kidney, liver, and lung of the human foetuses at 13-28 weeks with 123 samples in total. We identified 70,091 and 503 organ- and stage-specific differentially hydroxymethylated regions (DhMRs) and m5C-modified mRNAs, respectively. The key transcription factors (TFs), T-box transcription factor 20 (TBX20), paired box 8 (PAX8), krueppel-like factor 1 (KLF1), transcription factor 21 (TCF21), and CCAAT enhancer binding protein beta (CEBPB), specifically contribute to the formation of distinct organs at different stages. Additionally, 5hmC-enriched Alu elements may participate in the regulation of expression of TF-targeted genes. Our integrated studies reveal a putative essential link between DNA modification and RNA methylation, and illustrate the epigenetic maps during human foetal organogenesis, which provide a foundation for understanding the in-depth epigenetic mechanisms for early development and birth defects.

Applications of Oxford Nanopore Sequencing in Schizosaccharomyces pombe.

Recent years have seen great progresses in third-generation sequencing. New commercial platforms from Oxford Nanopore Technologies (ONT) can generate ultra-long reads from single-molecule nucleic acid fragments of kilobases up to megabases, exceeding the limitation of short reads and dependency on template amplification suffered by the previous generation of sequencing technologies. Moreover, it can detect epigenetic modifications directly, as well as providing all-around field usage, being pocket-sized and low cost. It has already been applied to yeast research in many aspects, such as complete de novo genome assemblies, the phylogeny of large-brewing yeasts, gene isoform identification, and base modification detection. These applications have delivered novel insights into yeast genomic and transcriptomic analysis.

Forty cases of insomnia treated by suspended moxibustion at Baihui (GV 20).

OBJECTIVE: To observe the therapeutic effect of suspended moxibustion at Baihui (GV 20) for insomnia. METHODS: 75 cases were divided randomly into two groups, with 40 cases in the treatment group treated by suspended moxibustion over Baihui (GV 20) and 35 cases in the control group treated by oral administration of Estazolam. RESULTS: The difference in therapeutic effect between the two groups was not statistically significant (P > 0.1). CONCLUSION: It was concluded that suspended moxibustion at Baihui (GV 20) is as effective as Estazolam for insomnia.

Improvement of multiplex semi-nested PCR system for screening of rare mutations by high-throughput sequencing.

The CRISPR/Cas9 system is an efficient gene-editing method, but it is difficult to obtain mutants for some specific species and special genome structures. A previously reported multiplexed, semi-nested PCR target-enrichment approach, which does not rely on transgenic technology, has been shown to be an effective and affordable strategy for the discovery of rare mutations in a large sodium azide-induced rice population. However, this strategy has the potential for further optimization. Here, we describe an improved multiplex semi-nested PCR target-enrichment strategy with simplified processing procedures, reduced false-positive rates and increased mutation detection frequency (1 mutation/73 Kb).

Effects of auricular stimulation in the cavum conchae on glucometabolism in patients with type 2 diabetes mellitus.

OBJECTIVE: To investigate the effect of auricular stimulation in cavum conchae on the glycemic control for patients with type 2 diabetes mellitus. METHODS: Seventy-one cases were treated with auricular electrical stimulator in the cavum choncha for 30 min, once daily for consecutive 3 months. The changes on the fasting plasma glucose (FBG), 2-h postprandial blood glucose after a 75 g oral glucose load (P2BG), glycated hemoglobin (HbA1c), blood urea nitrogen (BUN), serum creatinine (SCr), total cholesterol (TC) and aspartate transaminase (AST) were compared before and after the treatment. RESULTS: The level of the HbA1c was significantly decreased (P<0.05), and there were also statistically significant decreases in BUN, SCr, TC and AST after the treatment (P<0.05). A few patients (n=7) reduced the dose of the hypoglycemic agents in response to repeated hypoglycemia during the treatment. CONCLUSION: The stimulation in the cavum conchae of patients with types 2 diabetes mellitus may help decrease HbA1c, BUN, SCr, TC and AST, and may be an effective treatment for type 2 diabetes mellitus.

[Effects of stimulating in the cavum concha on glucometabolism in patients with diabetes].

OBJECTIVE: To explore the intervention effect of the auricular stimulator in the cavum concha for diabetes. METHODS: Forty-five cases were treated with auricular simulator in the cavum concha for 30 min, once daily for consecutive 3 months. The changes of the fasting plasma glucose (FBG), blood glucose load after 2-hour 75 g oral glucose tolerance test (P2 BG)and glycosylated hemoglobin (HbA1c) were compared before and after treatment. RESULTS: The level of the HbA1c was obviously decreased (P < 0.05, P < 0.01), and there were also statistically significant differences in FBG and P2 BG after the treatment (P < 0.05, P < 0.01). CONCLUSION: With the auricular stimulator, the stimulation in the cavum concha is benefit for the improvement of HbA1c of the diabetes.