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991.
Renying Wang Peijing Zhang Jingjing Wang Lifeng Ma Weigao E Shengbao Suo Mengmeng Jiang Jiaqi Li Haide Chen Huiyu Sun Lijiang Fei Ziming Zhou Yincong Zhou Yao Chen Weiqi Zhang Xinru Wang Yuqing Mei Zhongyi Sun Chengxuan Yu Jikai Shao Yuting Fu Yanyu Xiao Fang Ye Xing Fang Hanyu Wu Qile Guo Xiunan Fang Xia Li Xianzhi Gao Dan Wang Peng-Fei Xu Rui Zeng Gang Xu Lijun Zhu Lie Wang Jing Qu Dan Zhang Hongwei Ouyang He Huang Ming Chen Shyh-Chang NG Guang-Hui Liu Guo-Cheng Yuan Guoji Guo Xiaoping Han 《Nucleic acids research》2023,51(2):501
Individual cells are basic units of life. Despite extensive efforts to characterize the cellular heterogeneity of different organisms, cross-species comparisons of landscape dynamics have not been achieved. Here, we applied single-cell RNA sequencing (scRNA-seq) to map organism-level cell landscapes at multiple life stages for mice, zebrafish and Drosophila. By integrating the comprehensive dataset of > 2.6 million single cells, we constructed a cross-species cell landscape and identified signatures and common pathways that changed throughout the life span. We identified structural inflammation and mitochondrial dysfunction as the most common hallmarks of organism aging, and found that pharmacological activation of mitochondrial metabolism alleviated aging phenotypes in mice. The cross-species cell landscape with other published datasets were stored in an integrated online portal—Cell Landscape. Our work provides a valuable resource for studying lineage development, maturation and aging. 相似文献
992.
Liu He Rebecca Lever Andrew Cubbon Muhammad Tehseen Tabitha Jenkins Alice
O Nottingham Anya Horton Hannah Betts Martin Fisher Samir
M Hamdan Panos Soultanas Edward
L Bolt 《Nucleic acids research》2023,51(4):1740
DNA strand breaks are repaired by DNA synthesis from an exposed DNA end paired with a homologous DNA template. DNA polymerase delta (Pol δ) catalyses DNA synthesis in multiple eukaryotic DNA break repair pathways but triggers genome instability unless its activity is restrained. We show that human HelQ halts DNA synthesis by isolated Pol δ and Pol δ-PCNA-RPA holoenzyme. Using novel HelQ mutant proteins we identify that inhibition of Pol δ is independent of DNA binding, and maps to a 70 amino acid intrinsically disordered region of HelQ. Pol δ and its POLD3 subunit robustly stimulated DNA single-strand annealing by HelQ, and POLD3 and HelQ interact physically via the intrinsically disordered HelQ region. This data, and inability of HelQ to inhibit DNA synthesis by the POLD1 catalytic subunit of Pol δ, reveal a mechanism for limiting DNA synthesis and promoting DNA strand annealing during human DNA break repair, which centres on POLD3. 相似文献
993.
994.
995.
Xiaowei Wei Wei Ma Hui Gu Dan Liu Wenting Luo Songying Cao Shanshan Jia Tianchu Huang Yiwen He Yuzuo Bai Weilin Wang Zhengwei Yuan 《Cell proliferation》2023,56(2)
ObjectivesSpina bifida aperta (SBA) is one of the most common neural tube defects. Neural injury in SBA occurs in two stages involving failed neural tube closure and progressive degeneration through contact with the amniotic fluid. We previously suggested that intra‐amniotic bone marrow‐derived mesenchymal stem cell (BMSC) therapy for fetal rat SBA could achieve beneficial functional recovery through lesion‐specific differentiation. The aim of this study is to examine whether the amniotic fluid microenvironment can be improved by intra‐amniotic BMSC transplantation.MethodsThe intra‐amniotic BMSC injection was performed using in vivo rat fetal SBA models. The various cytokine expressions in rat amniotic fluid were screened by protein microassays. Intervention experiments were used to study the function of differentially expressed cytokines.ResultsA total of 32 cytokines showed significant upregulated expression in the BMSC‐injected amniotic fluid. We focused on Activin A, NGF, BDNF, CNTF, and CXCR4. Intervention experiments showed that the upregulated Activin A, NGF, BDNF, and CNTF could inhibit apoptosis and promote synaptic development in fetal spinal cords. Inhibiting the activity of these factors weakened the anti‐apoptotic and pro‐differentiation effects of transplanted BMSCs. Inhibition of CXCR4 activity reduced the engraftment rate of BMSCs in SBA fetuses.ConclusionBMSC transplantation can improve the amniotic fluid environment, and this is beneficial for SBA repair.In utero intra‐amniotic BMSC or PBS microinjection in the E15 fetuses was performed in E15 rat fetuses with spina bifida aperta, and amniotic fluid was collected at E21 for protein array detection. Venn diagram shows the relationship of three biological processes (GO: 0030335, 0048699, and 0043524) and the attribution of differentially expressed proteins. Comparative analysis of five proteins with the largest fold changes in the process of generation of neurons. 相似文献
996.
Rongjie Cheng Fanying Li Maolei Zhang Xin Xia Jianzhuang Wu Xinya Gao Huangkai Zhou Zhi Zhang Nunu Huang Xuesong Yang Yaliang Zhang Shunli Shen Tiebang Kang Zexian Liu Feizhe Xiao Hongwei Yao Jianbo Xu Chao Yan Nu Zhang 《Cell research》2023,33(1):30
Mutations of the RAS oncogene are found in around 30% of all human cancers yet direct targeting of RAS is still considered clinically impractical except for the KRASG12C mutant. Here we report that RAS-ON (RASON), a novel protein encoded by the long intergenic non-protein coding RNA 00673 (LINC00673), is a positive regulator of oncogenic RAS signaling. RASON is aberrantly overexpressed in pancreatic ductal adenocarcinoma (PDAC) patients, and it promotes proliferation of human PDAC cell lines in vitro and tumor growth in vivo. CRISPR/Cas9-mediated knockout of Rason in mouse embryonic fibroblasts inhibits KRAS-mediated tumor transformation. Genetic deletion of Rason abolishes oncogenic KRAS-driven pancreatic and lung cancer tumorigenesis in LSL-KrasG12D; Trp53R172H/+ mice. Mechanistically, RASON directly binds to KRASG12D/V and inhibits both intrinsic and GTPase activating protein (GAP)-mediated GTP hydrolysis, thus sustaining KRASG12D/V in the GTP-bound hyperactive state. Therapeutically, deprivation of RASON sensitizes KRAS mutant pancreatic cancer cells and patient-derived organoids to EGFR inhibitors. Our findings identify RASON as a critical regulator of oncogenic KRAS signaling and a promising therapeutic target for KRAS mutant cancers.Subject terms: Gastrointestinal cancer, Cancer therapy 相似文献
997.
998.
Junyu Liu Michael Maxwell Thom Cuddihy Theo Crawford Madeline Bassetti Cameron Hyde Steve Peigneur Jan Tytgat Eivind A. B. Undheim Mehdi Mobli 《Protein science : a publication of the Protein Society》2023,32(2)
Receptor avidity through multivalency is a highly sought‐after property of ligands. While readily available in nature in the form of bivalent antibodies, this property remains challenging to engineer in synthetic molecules. The discovery of several bivalent venom peptides containing two homologous and independently folded domains (in a tandem repeat arrangement) has provided a unique opportunity to better understand the underpinning design of multivalency in multimeric biomolecules, as well as how naturally occurring multivalent ligands can be identified. In previous work, we classified these molecules as a larger class termed secreted cysteine‐rich repeat‐proteins (SCREPs). Here, we present an online resource; ScrepYard, designed to assist researchers in identification of SCREP sequences of interest and to aid in characterizing this emerging class of biomolecules. Analysis of sequences within the ScrepYard reveals that two‐domain tandem repeats constitute the most abundant SCREP domain architecture, while the interdomain “linker” regions connecting the functional domains are found to be abundant in amino acids with short or polar sidechains and contain an unusually high abundance of proline residues. Finally, we demonstrate the utility of ScrepYard as a virtual screening tool for discovery of putatively multivalent peptides, by using it as a resource to identify a previously uncharacterized serine protease inhibitor and confirm its predicted activity using an enzyme assay. 相似文献
999.
Karyotype evolution of the Asterids insights from the first genome sequences of the family Cornaceae
Cornaceae is a core representative family in Cornales, the earliest branching lineage in the Asterids on the life tree of angiosperms. This family includes the only genus Cornus, a group of ~55 species. These species occur widely in Northern Hemisphere and have been used as resources for horticultural ornaments, medicinal and industrial manufacturing. However, no any genome sequences are available for this family. Here, we reported a chromosomelevel genome for Cornus controversa. This was generated using high-fidelity plus Hi–C sequencing, and totally ~771.80 Mb assembled sequences and 39,886 protein-coding genes were obtained. We provided evidence for a whole-genome duplication event (WGD) unique to C. controversa. The evolutionary features of this genome indicated that the expanded and unique genes might have contributed to response to stress, stimulus and defense. By using chromosome-level syntenic blocks shared between eight living genomes, we found high degrees of genomic diversification from the ancestral core-eudicot genome to the present-day genomes, suggesting an important role of WGD in genomic plasticity that leads to speciation and diversification. These results provide foundational insights on the evolutionary history of Cornaceae, as well as on the Asterids diversification. 相似文献
1000.
Rui-zhi Tan Jian-chun Li Bing-wen Zhu Xiao-ru Huang Hong-lian Wang Jian Jia Xia Zhong Jian Liu Li Wang Hui-yao Lan 《International journal of biological sciences》2023,19(2):521
Neuropeptide Y (NPY) is produced by the nerve system and may contribute to the progression of CKD. The present study found the new protective role for NPY in AKI in both patients and animal models. Interestingly, NPY was constitutively expressed in blood and resident kidney macrophages by co-expressing NPY and CD68+ markers, which was lost in patients and mice with AKI-induced by cisplatin. Unexpectedly, NPY was renoprotective in AKI as mice lacking NPY developed worse renal necroinflammation and renal dysfunction in cisplatin and ischemic-induced AKI. Importantly, NPY was also a therapeutic agent for AKI because treatment with exogenous NPY dose-dependently inhibited cisplatin-induced AKI. Mechanistically, NPY protected kidney from AKI by inactivating M1 macrophages via the Y1R-NF-κB-Mincle-dependent mechanism as deleting or silencing NPY decreased Y1R but increased NF-κB-Mincle-mediated M1macrophage activation and renal necroinflammation, which were reversed by addition of NPY or by silencing Mincle but promoted by blocking Y1R with BIBP 3226. Thus, NPY is renoprotective and may be a novel therapeutic agent for AKI. NPY may act via Y1R to protect kidney from AKI by blocking NF-κB-Mincle-mediated M1 macrophage activation and renal necroinflammation. 相似文献