Article
Cell Biology
Lina Wu, Qingzhu Wang, Feng Guo, Xiaojun Ma, Jiao Wang, Yanyan Zhao, Yushan Yan, Guijun Qin
Summary: The study reveals that the miR-27a-3p-prohibitin/TMBIM6 signaling axis plays a crucial role in the progression of diabetic nephropathy. Silencing miR-27a-3p can improve kidney function, alleviate renal fibrosis, mitigate mitochondrial dysfunction, and attenuate endoplasmic reticulum stress. Prohibitin and TMBIM6 are identified as direct targets of miR-27a-3p, and inhibition of miR-27a-3p protects against various pathological changes in kidney cells induced by high glucose.
JOURNAL OF CELLULAR PHYSIOLOGY
(2021)
Article
Oncology
Jia Liu, Xiaoyu Li, Shan Lu, Xiao Zheng, Xiaohui Zhang, Wei Zhao
Summary: MiR-27a plays a crucial regulatory role in diabetic pulmonary fibrosis, and GLP-1 can down-regulate its expression level by activating AMPK. Furthermore, the target gene PPAR gamma is up-regulated, resulting in improved extracellular matrix proliferation in MRC-5 cells.
ANNALS OF TRANSLATIONAL MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Xinzhu Yuan, Wenwu Tang, Changwei Lin, Hongni He, Lingqin Li
Summary: This study found that chrysophanol (Chr) has beneficial effects on renal injury, oxidative stress, and pyroptosis in mice with diabetic nephropathy (DN). Chr improves renal function, reduces glomerular thylakoid and basement membrane thickening, and decreases fibrous tissue proliferation and inflammatory cell infiltration. Additionally, Chr increases antioxidant enzyme levels, decreases oxidative stress markers, and suppresses pyroptosis-related proteins, while activating the Keap1/Nrf2 pathway.
ACTA BIOCHIMICA POLONICA
(2023)
Article
Immunology
Wenting Jian, Huigai Ma, Dingming Wang, Peng Yang, Mengbi Jiang, Yu Zhong, Xiang Long, Jingjing Jiang, Yuan Gong
Summary: This study demonstrates that omaveloxolone exerts significant cardioprotective effects in treating sepsis-induced cardiomyopathy by activating the Nrf2 signaling pathway.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2022)
Article
Gastroenterology & Hepatology
Shuang Zhao, Tianyu Song, Yue Gu, Yihua Zhang, Siyi Cao, Qing Miao, Xiyue Zhang, Hongshan Chen, Yuanqing Gao, Lei Zhang, Yi Han, Hong Wang, Jun Pu, Liping Xie, Yong Ji
Summary: The study suggests that H2S alleviates liver damage by activating Keap1 S-sulfhydration and promoting the activation of Nrf2, leading to increased expression of antioxidant proteins, which may have potential therapeutic benefits for liver diseases.
Review
Medicine, Research & Experimental
Xia Wu, Leitao Huang, Jichun Liu
Summary: Diabetic cardiomyopathy is a major cause of death worldwide, with oxidative stress playing a key role in its pathophysiology. NRF2 is a transcription factor that regulates antioxidant gene expression and detoxifying enzymes, helping to maintain cardiac homeostasis and counteract oxidative stress. Targeting the NRF2 signaling pathway may be a potential strategy for preventing and treating DCM and other cardiac diseases.
EXPERIMENTAL AND THERAPEUTIC MEDICINE
(2021)
Article
Neurosciences
Mingming Wang, Jiaoyan Yu, Qi Yang, Chao Guo, Wei Zhang, Weiwei Li, Yan Weng, Yi Ding, Jingwen Wang
Summary: This study demonstrated that beta-BA exerts neuroprotective effects against cerebral I/R injury by activating the PRKCE/NFE2L2/HMOX1 pathway, improving neurological deficits in animals and protecting neurons in in vitro experiments.
MOLECULAR NEUROBIOLOGY
(2022)
Article
Integrative & Complementary Medicine
Rong Zheng, Weijie Zhang, Jufang Song, Yifei Zhong, Rong Zhu
Summary: The study found that cordycepin produced by Cordyceps militaris can alleviate oxidative stress and inflammation in diabetic nephropathy by regulating the expression of the miR-193b-5p/MCL-1 axis.
Article
Cell Biology
David Rysanek, Pavla Vasicova, Jayaprakash Narayana Kolla, David Sedlak, Ladislav Andera, Jiri Bartek, Zdenek Hodny
Summary: The accumulation of senescent cells in aging tissues contributes to age-associated diseases. Inhibiting the anti-apoptotic machinery of senescent cells through BCL-2 protein family inhibitors can eliminate these cells. Combination therapy with BCL-2 inhibitors shows synergistic effects in eliminating senescent cells and overcoming resistance to monotherapy.
Article
Biochemistry & Molecular Biology
Li-Rong Ren, Ru-Bin Yao, Shi-Yong Wang, Xiang-Dong Gong, Ji-Tao Xu, Kai-Shun Yang
Summary: It was found that miR-27a-3p promotes osteoblast differentiation by mediating the CRY2/ERK1/2 axis, suggesting it could be a new target for treating osteoporosis.
MOLECULAR MEDICINE
(2021)
Article
Medicine, Research & Experimental
Nada H. Eisa, Ahmed E. Khodir, Mohamed El-Sherbiny, Nehal M. Elsherbiny, Eman Said
Summary: PEITC showed renal protective effects against DN in rats induced by STZ, improving kidney and liver functions, histopathological features, tissue fibrosis, macrophage infiltration, and blood glucose levels. The mechanisms involved modulation of glycation, oxidative stress, and inflammatory response, including activation of GLO1 and Nrf2 pathways and suppression of NLRP3 inflammasome activation.
BIOMEDICINE & PHARMACOTHERAPY
(2021)
Article
Food Science & Technology
Tong Jin, Cheng Chen
Summary: The findings suggest that umbelliferone has a protective effect on diabetic nephropathy by activating the Nrf2/HO-1 pathway and attenuating high glucose-induced ferroptosis.
FOOD AND CHEMICAL TOXICOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Reza Noei Razliqi, Akram Ahangarpour, Seyyed Ali Mard, Layasadat Khorsandi
Summary: Oxidative stress and inflammation are important factors in the development of diabetic nephropathy (DN), and the local renin-angiotensin system (RAS) aggravates these processes. Gentisic acid (GA), a phenolic compound and metabolite of aspirin, has been found to have antioxidant and anti-inflammatory properties. However, the protective effects of GA against DN are still unknown.
CHEMICO-BIOLOGICAL INTERACTIONS
(2023)
Article
Urology & Nephrology
Guibao Ke, Xueqin Chen, Ruyi Liao, Lixia Xu, Li Zhang, Hong Zhang, Sujuan Kuang, Yue Du, Juan Hu, Zhiwen Lian, Caoshuai Dou, Qianmei Zhang, Xingchen Zhao, Fengxia Zhang, Shuangshuang Zhu, Jianchao Ma, Zhuo Li, Sijia Li, Chaosheng He, Xia Chen, Yingzhen Wen, Zhonglin Feng, Minghao Zheng, Ting Lin, Ruizhao Li, Bohou Li, Wei Dong, Yuanhan Chen, Wenjian Wang, Zhiming Ye, Chunyu Deng, Houqin Xiao, Jie Xiao, Xinling Liang, Wei Shi, Shuangxin Liu
Summary: The expression of Receptor activator of NF-kappa B (RANK) is increased in podocytes of patients with diabetic nephropathy. Mouse models of podocyte-specific RANK depletion and overexpression showed that RANK depletion alleviated the development of kidney diseases, while RANK overexpression aggravated the condition. The findings suggest that RANK mediates the development of diabetic nephropathy by promoting glomerular oxidative stress and proinflammatory cytokine production.
KIDNEY INTERNATIONAL
(2021)
Article
Biochemistry & Molecular Biology
Jeeyoun Jung, Woo Yeong Park, Yun Jin Kim, Mikyung Kim, Misun Choe, Kyubok Jin, Ji Hae Seo, Eunyoung Ha
Summary: This study demonstrates that 3-OHB delays the progression of diabetic nephropathy (DN) by enhancing autophagy and inhibiting oxidative stress, as observed in both in vivo and in vitro models.
Article
Biochemical Research Methods
Jing-Zhe Jiang, Wen-Guang Yuan, Jiayu Shang, Ying-Hui Shi, Li-Ling Yang, Min Liu, Peng Zhu, Tao Jin, Yanni Sun, Li-Hong Yuan
Summary: The paper presents PhaGCN2, a tool that rapidly classifies viral sequences at the family level and improves the precision and recall of virus classification. It allows for high-throughput processing of viral sequences and supports visualization.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Agronomy
Ping Liao, Stephen M. Bell, Le Chen, Shan Huang, Haiyuan Wang, Jiahui Miao, Yiming Qi, Yanni Sun, Bin Liao, Yongjun Zeng, Haiyan Wei, Hui Gao, Qigen Dai, Hongcheng Zhang
Summary: Smart agronomic management practices can reduce lodging risk in rice paddies. This includes employing lodging-resistant cultivars, appropriate fertilization, and applying plant growth regulators (PGRs). Additionally, the application of silicon, potassium, prohexadione calcium, and uniconazole can improve rice yield and reduce lodging risk.
EUROPEAN JOURNAL OF AGRONOMY
(2023)
Article
Virology
Fan Zhang, Andrew Gia, Guowei Chen, Lan Gong, Jason Behary, Georgina L. Hold, Amany Zekry, Xubo Tang, Yanni Sun, Emad El-Omar, Xiao-Tao Jiang
Summary: Viruses are abundant and important in ecosystems, and the two methods of whole genome shotgun metagenome and viral-like particle enriched metagenome sequencing are commonly used for comparing viruses in different environments. In this study, both methods were applied to investigate the stool virome in HCC patients and healthy controls, and they both successfully identified altered viral profiles in HCC patients. Ultra-deep sequencing recovered more viruses, and VLPM method can detect RNA viruses. Using both methods would capture different parts of the total virome and identify shared and specific viral signatures.
Article
Multidisciplinary Sciences
Zhixin Ma, Yifeng Liu, Lin Chai, Guochen Jin, Yanni Sun, Shaomin Zhou, Peiyuan Yin, Siwen Wang, Yuning Zhu, Dan Zhang, Shiming Lu, Bo Zhu
Summary: Intrahepatic cholestasis of pregnancy (ICP) is a rare liver disease characterized by disordered bile acid metabolism during pregnancy. Different types of ICP show distinct bile acid metabolism profiles. Elevated levels of total bile acids and glycocholic acid are associated with preterm birth in early-onset ICP (EICP), while increased levels of total bile acids and taurocholic acid are predictive of preterm birth in late-onset ICP (LICP). This study highlights the importance of assessing bile acid metabolism in ICP patients to predict perinatal complications.
SCIENTIFIC REPORTS
(2023)
Article
Agriculture, Multidisciplinary
Ping Liao, Lei Liu, Stephen M. Bell, Jinsong Liu, Yanni Sun, Yongjun Zeng, Hongcheng Zhang, Shan Huang
Summary: Ammonia (NH3) emissions are a significant source of nitrogen (N) losses in rice paddies. Lime application and straw retention are commonly used practices to improve soil fertility in acidic soils. However, the interaction between lime and straw application on NH3 emissions from rice paddies is still unclear.
AGRICULTURE ECOSYSTEMS & ENVIRONMENT
(2023)
Article
Biochemical Research Methods
Yongxin Ji, Jiayu Shang, Xubo Tang, Yanni Sun
Summary: Understanding the host range of plasmids is essential for studying their roles in bacterial evolution and adaptation. Existing tools for predicting plasmid hosts face challenges in sensitivity and precision. This study presents a hierarchical classification tool called HOTSPOT, which uses a state-of-the-art language model, Transformer, to accurately predict the host taxonomy of input plasmid contigs.
Article
Medicine, General & Internal
Jonathan Daniel Ip, Allen Wing-Ho Chu, Wan-Mui Chan, Rhoda Cheuk-Ying Leung, Syed Muhammad Umer Abdullah, Yanni Sun, Kelvin Kai -Wang To
Summary: This study aimed to estimate the global prevalence of 3CLpro inhibitor-resistant SARS-CoV-2 strains. Analysis of 13.4 million sequences revealed that 0.5% of the sequences contained mutations associated with resistance to nirmatrelvir or ensitrelvir. However, resistance to 3CLpro inhibitors is currently rare.
Article
Materials Science, Multidisciplinary
Huiqiang Hu, Zheng Zhao, Yanni Sun, Jiawei Zhao, Zhengqian Chen, Jianyi Li, Weiqing Kong, Yukun Du, Jiale Shao, Xiaoyang Zhu, Hongbo Lan, Yongming Xi
Summary: This study utilized melt-extrusion 3D printing to prepare biodegradable composite scaffolds, containing bioactive glass, calcium sulfate hemihydrate, and polylactic acid. The compressive strength of scaffolds was comparable to that of human bone tissue, and in vitro and in vivo experiments demonstrated good biocompatibility. The scaffold maintained biomechanical stability of bone defects for 20 weeks without causing liver or kidney damage in animal experiments. Scaffold degradation was accompanied by trabecular bone and vessel neogenesis. The PLA-CSH-BAG group exhibited satisfactory bone defect repair effect compared to the PLA and control groups. In conclusion, the biodegradable porous scaffold is proposed as a safe and effective approach for bone defect repair.
ADVANCED MATERIALS TECHNOLOGIES
(2023)
Article
Chemistry, Multidisciplinary
Qing Feng, Xianchao Chen, Ning Zhang, Xiaonan Li, Jingchao Zhou, Shengsheng Li, Xiaorong Zhang, Yanni Sun, Yuehui She
Summary: Bohai Oilfield has developed a bio-nano-depressurization and injection-increasing composite system solution to address the high injection pressure and insufficient injection volume in offshore oilfields. The new technology has the advantages of efficient decompression, long-term injection, and wide adaptation. However, there is a need for optimization schemes and application effect prediction methods to further promote and apply the bio-nano-composite system solution. This paper optimizes the injection volume, concentration, and speed of the bio-nano-augmentation fluid and evaluates the application effect using well testing, water absorption index, and numerical simulation methods.
Article
Biochemistry & Molecular Biology
Xubo Tang, Jiayu Shang, Yongxin Ji, Yanni Sun
Summary: In this study, a plasmid detection tool called PLASMe was developed, which combines alignment and learning-based methods to effectively identify closely related and diverged plasmids. By encoding plasmid sequences as a language defined on the protein cluster-based token set, the Transformer model in PLASMe can learn the importance of proteins and their correlation. Comparative analysis showed that PLASMe achieved the highest F1-score in detecting complete plasmids, plasmid contigs, and contigs assembled from CAMI2 simulated data, and exhibited more reliable performance than other tools.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Yu-an Li, Yanni Sun, Yuqin Zhang, Quan Li, Shifeng Wang, Roy Curtiss, Huoying Shi
Summary: The development of a Salmonella mRNA interferase regulation vector (SIRV) system is reported in this study, which overcomes the challenge of effective release strategies in engineered vector-based in vivo protein delivery platforms. The SIRV system induces self-lysis for the release of foreign antigens and activates the cytosolic surveillance cGAS-STING axis. It shows improved safety and immunogenicity in mouse and pig models, leading to better survival rates against Streptococcus suis.
Article
Microbiology
Herui Liao, Yongxin Ji, Yanni Sun
Summary: In this study, a new strain-level composition analysis tool named StrainScan is introduced, which employs a novel tree-based k-mers indexing structure to strike a balance between strain identification accuracy and computational complexity. Extensive testing on simulated and real sequencing data shows that StrainScan outperforms popular strain-level analysis tools in terms of accuracy and resolution. It provides more informative strain composition analysis in one sample or across multiple samples.
Article
Biochemical Research Methods
Jiayu Shang, Xubo Tang, Yanni Sun
Summary: Researchers have developed a tool called PhaTYP that accurately predicts the lifestyle of bacteriophages, especially for short contigs. Experimental results show that PhaTYP outperforms other existing methods and achieves more stable performance on short contigs. Additionally, the utility of PhaTYP for analyzing phage lifestyle in human neonates' gut data has been demonstrated, which helps extend our understanding of microbial communities.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Runzhou Yu, Dehan Cai, Yanni Sun
Summary: RNA viruses mutate constantly, but accurate assembly of viral genomes is crucial for studying virus evolution and understanding the relationship between genotypes and virus properties. A new tool called AccuVIR has been developed for viral genome assembly and polishing using error-prone long reads. It can distinguish sequencing errors from true variants, resulting in more accurate viral genomes compared to other tools.
Article
Soil Science
Ping Liao, Lei Liu, Jin Chen, Yanni Sun, Shan Huang, Yongjun Zeng, Kees Jan van Groenigen
Summary: Liming materials can increase rice yield and nitrogen uptake, but decrease the efficiency of fertilizer nitrogen and promote nitrogen losses. Long-term studies on the impact of liming on nitrogen dynamics in paddy soils are necessary.
SOIL & TILLAGE RESEARCH
(2024)
Review
Medicine, Research & Experimental
Weizhuo Lu, Zhiwu Chen, Jiyue Wen
Summary: Ischemic stroke is a common and serious disease, and neuroinflammation plays a crucial role in its progression. Microglia, astrocytes, and infiltrating immune cells are involved in the complicated neuroinflammation cascade, releasing different molecules that affect inflammation. Flavonoids, plant-specific compounds, have shown protective effects against cerebral ischemia injury by modulating the inflammatory responses.
BIOMEDICINE & PHARMACOTHERAPY
(2024)
