EndoQuad: a comprehensive genome-wide experimentally validated endogenous G-quadruplex database.

G-quadruplexes (G4s) are non-canonical four-stranded structures and are emerging as novel genetic regulatory elements. However, a comprehensive genomic annotation of endogenous G4s (eG4s) and systematic characterization of their regulatory network are still lacking, posing major challenges for eG4 research. Here, we present EndoQuad (https://EndoQuad.chenzxlab.cn/) to address these pressing issues by integrating high-throughput experimental data. First, based on high-quality genome-wide eG4s mapping datasets (human: 1181; mouse: 24; chicken: 2) generated by G4 ChIP-seq/CUT&Tag, we generate a reference set of genome-wide eG4s. Our multi-omics analyses show that most eG4s are identified in one or a few cell types. The eG4s with higher occurrences across samples are more structurally stable, evolutionarily conserved, enriched in promoter regions, mark highly expressed genes and associate with complex regulatory programs, demonstrating higher confidence level for further experiments. Finally, we integrate millions of functional genomic variants and prioritize eG4s with regulatory functions in disease and cancer contexts. These efforts have culminated in the comprehensive and interactive database of experimentally validated DNA eG4s. As such, EndoQuad enables users to easily access, download and repurpose these data for their own research. EndoQuad will become a one-stop resource for eG4 research and lay the foundation for future functional studies.

[Temporal-spatial distribution of functional feeding groups of macroinvertebrate and biological evaluation of water quality in Xinyang section of the Huaihe River main stream]. / æ·®æ²³å¹²æµä¿¡é˜³æ®µå¤§åž‹åº•æ –åŠ¨ç‰©åŠŸèƒ½æ‘„é£Ÿç±»ç¾¤æ—¶ç©ºåˆ†å¸ƒåŠæ°´è´¨è¯„ä»·.

From November 2021 to September 2022, we conducted four field surveys on macroinvertebrates and water environmental factors in Xinyang section of the Huaihe River main stream. We analyzed the structure and spatiotemporal distribution characteristics of the functional feeding groups of macroinvertebrates, and evaluated river water quality. A total of 73 macroinvertebrate species were collected in the basin, belonging to 42 families, 7 classes, and 3 phyla. The dominant species of macroinvertebrates changed significantly in different months, with Exopalaemon modestus being the absolute advantage species in the basin in July and September 2022. In different sampling months, the functional feeding group of macroinvertebrates was mainly dominated by shredders, accounting for 35.9%. The results of redundancy analysis showed that the main environmental factors affecting the distribution of functional feeding groups of macroinvertebrates varied across different months, with conductivity in February, temperature in July, and oxidation-reduction potential in September and November. The evaluation based on the biolo-gical index and Shannon index of macroinvertebrates indicated that water quality in the investigated section was at a light pollution level.

In vivo dynamics and regulation of DNA G-quadruplex structures in mammals.

G-quadruplex (G4) is a four-stranded helical DNA secondary structure formed by guanine-rich sequence folding, and G4 has been computationally predicted to exist in a wide range of species. Substantial evidence has supported the formation of endogenous G4 (eG4) in living cells and revealed its regulatory dynamics and critical roles in several important biological processes, making eG4 a regulator of gene expression perturbation and a promising therapeutic target in disease biology. Here, we reviewed the methods for prediction of potential G4 sequences (PQS) and detection of eG4s. We also highlighted the factors affecting the dynamics of eG4s and the effects of eG4 dynamics. Finally, we discussed the future applications of eG4 dynamics in disease therapy.

[Risk Factors of Rapidly Progressive Interstitial Lung Disease in Patients With Anti-Melanoma Differentiation-Associated Gene 5 Antibody-Positive Dermatomyositis].

Objective: To investigate the conditions of patients with anti-melanoma differentiation-associated gene 5 (MDA5) antibody-positive dermatomyositis combined with rapidly progressive interstitial lung disease (RPILD), and to analyze the risk factors. Methods: A total of 145 patients diagnosed with anti-MDA5 antibody-positive dermatomyositis at West China Hospital, Sichuan University between January 2018 and September 2021 were selected, and their general and clinical data were collected. The patients were divided into two groups, a RPILD group of patients with comorbid RPILD and a non-RPILD group of those who did not have comorbid RPILD. Factors that might affect whether patients with anti-MDA5 antibody-positive dermatomyositis also had comorbid RPILD were screened out and binary logistic regression analysis was performed. Results: Among the 145 patients with anti-MDA5 antibody-positive dermatomyositis, 32 (22.07%) patients had comorbid RPILD, while the remaining 113 (77.93%) did not have comorbid RPILD. Binary logistic regression analysis showed that lactate dehydrogenase≥370 IU/L (compared with <370 IU/L, OR=4.066, 95% CI: 1.616-10.230) and carcinoembryo antigen≥5 ng/mL (compared with <5 ng/mL, OR=6.070, 95% CI: 2.013-18.303) were risk factors for comorbid RPILD in patients with anti-MDA5 antibody-positive dermatomyositis ( ß>0, OR>1, P<0.05). Conclusion: It is recommended that close attention be given to changes in high-resolution chest CT and pulmonary functions in patients with lactate dehydrogenase≥370 IU/L and carcinoembryo antigen≥5 ng/mL. If rapid progression of lung disease is detected, it is necessary to strengthen the treatment of the lung disease, thereby improving the prognosis of patients.

Photolysis of a calixpyridinium-based supramolecular amphiphilic assembly and its selective turn-on fluorescence recognition of lysine in water.

A new calixpyridinium-based light-responsive host-guest recognition motif was found in this work. This host-guest recognition motif was further discovered to be applied as a selective turn-on fluorescent sensor for lysine over other natural amino acids.

Supramolecular Amphiphilic Assembly Formed by the Complexation of Calixpyridinium with Alimta.

In this work, the host-guest interaction between calixpyridinium and anionic anticancer drug Alimta was studied in aqueous media. Spherical supramolecular amphiphilic assembly rather than simple complex was accidentally fabricated by the complexation of calixpyridinium with Alimta. It is the third kind of anionic guest to be discovered to form the higher-order assembly by the complexation of calixpyridinium besides polyanionic guest and anionic gemini surfactant guest. The finding of this assembly approach supplies a new idea to construct various self-assembly architectures in water via the complexation of calixpyridinium with anionic drugs. The resulting calixpyridinium-drug assemblies may also have the potential to adjust the effects of drugs.