5 results on '"Peng, Jun"'
Search Results
2. Excessive and asymmetrical removal of heterozygous sites by maxSH biases downstream population genetic inference: Implications for hybridization between two primroses.
- Author
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Zhang, Jie, Pina‐Martins, Francisco, Jin, Zu‐Shi, Cha, Yong‐Peng, Liu, Zu‐Yao, Peng, Jun‐Chu, Zhao, Jian‐Li, and Li, Qing‐Jun
- Subjects
PRIMROSES ,OUTLIER detection ,HETEROZYGOSITY ,GENOMICS - Abstract
Techniques of reduced‐representation sequencing (RRS) have revolutionized ecological and evolutionary genomics studies. Precise establishment of orthologs is a critical challenge for RRS, especially when a reference genome is absent. The proportion of shared heterozygous sites across samples is an alternative criterion for filtering paralogs. In the prevailing pipeline for variant calling of RRS data – PYRAD/IPYRAD, maxSH is an often overlooked parameter with implications to detecting and filtering paralogs according to shared heterozygosity. Using empirical genotyping by sequencing data of two primroses (Primula alpicola Stapf and Primula florindae Ward) and their putative hybrids, and extra data sets of Californian golden cup oaks, we explore the impact of maxSH on filtering paralogs and further downstream analyses. Our study sheds light on the simultaneous validity and risk of filtering paralogs using maxSH, and its significant effects on downstream analyses of outlier detection, population assignment, and demographic modeling, emphasizing the importance of attention to detail during bioinformatic processes. The mutual confirmation between results of population assignment and demographic modeling in this study suggested maxSH = 0.10 has a potentially excessive and asymmetrical effect on the removal of truly shared heterozygous sites as paralogs. These results indicate that hybridization origin hypotheses of putative hybrids represented by results with maxSH = 0.25 and 0.50 are more credible. In conclusion, we revealed the critical hazard of paralogs filtration according to sharing heterozygosity at first, so that we propose to use specific protocols, rather than maxSH, to filter potential paralogs for closely related lineages. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
3. Genetic analysis of potential biomarkers and therapeutic targets in ferroptosis from coronary artery disease.
- Author
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Wu, Xun, Qin, Kele, Iroegbu, Chukwuemeka Daniel, Xiang, Kun, Peng, Jun, Guo, Jianjun, Yang, Jinfu, and Fan, Chengming
- Subjects
CORONARY artery disease ,DRUG target ,IMMUNOREGULATION ,BIOMARKERS ,CELL death ,HEART diseases ,AMINO acid metabolism ,CORONARY arteries - Abstract
Ferroptosis plays a key role in the death of cells including cardiomyocytes, and it is related to a variety of cardiac diseases. However, the role of ferroptosis‐related genes (FRGs) in coronary artery disease (CAD) is not well characterized. We downloaded CAD‐related information and FRGs from the gene expression omnibus (GEO) database and Ferroptosis Database (FerrDb) respectively. A total of 10 CAD‐related DE‐FRGs were obtained, which were closely linked to autophagy regulation and immune response. Subsequently, CA9, CBS, CEBPG, HSPB1, SLC1A4, STMN1 and TRIB3 among the 10 DE‐FRGs were identified as marker genes by LASSO and SVM‐RFE algorithms, which had tolerable diagnostic capabilities. Subsequent functional enrichment analysis showed that these marker genes may play a corresponding role in CAD by participating in the regulation of immune response, amino acid metabolism, cell cycle and multiple pathways related to the pathogenesis of CAD. Furthermore, a total of 58 drugs targeting 7 marker genes had been obtained. On the contrary, the ceRNA network revealed a complex regulatory relationship based on the marker genes. Also, CIBERSORT analysis showed that the changes in the immune microenvironment of CAD patients may be related to CBS, HSPB1 and CEBPG. We developed a diagnostic potency and provided an insight for exploring the mechanism for CAD. Before clinical application, further research is needed to test its diagnostic value for CAD. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
4. Spica Prunellae Extract Enhances Fluorouracil Sensitivity of 5-Fluorouracil-Resistant Human Colon Carcinoma HCT-8/5-FU Cells via TOP2α and miR-494.
- Author
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Fang, Yi, Yang, Chi, Zhang, Ling, Wei, Lihui, Lin, Jiumao, Zhao, Jinyan, and Peng, Jun
- Subjects
FLUOROURACIL ,APOPTOSIS ,CARRIER proteins ,CELL death ,CELL lines ,CELL physiology ,COMBINATION drug therapy ,COLON tumors ,DRUG resistance in cancer cells ,DRUG synergism ,ETHANOL ,GENE expression ,HERBAL medicine ,CHINESE medicine ,METABOLISM ,RNA ,BIOINFORMATICS ,GENE expression profiling ,MICRORNA ,RNA-binding proteins - Abstract
The use of 5-fluorouracil (5-FU) has been proven benefits, but it also has adverse events in colorectal cancer (CRC) chemotherapy. In this study, we explored the mechanism of 5-FU resistance by bioinformatics analysis of the NCBI public dataset series GSE81005. Fifteen hub genes were screened out of 582 different expressed genes. Modules of the hub genes in protein-protein interaction networks gathered to TOP2α showed a decrease in HCT-8 cells but an increase in 5-FU-resistant HCT-8/5-FU cells with 5-FU exposure. Downregulation of TOP2α with siRNA or miR-494 transfection resulted in an increase of cytotoxicity and decrease of cell colonies to 5-FU for HCT-8/5-FU cells. Moreover, we found that an ethanol extract of Spica Prunellae (EESP), which is a traditional Chinese medicine with clinically beneficial effects in various cancers, was able to enhance the sensitivity of 5-FU in HCT-8/5-FU cells and partly reverse the 5-FU resistance effect. It significantly helped suppress cell growth and induced cell apoptosis in HCT-8/5-FU cells with the expression of TOP2α being significantly suppressed, which increased by 5-FU. Consistently, miR-494, which reportedly regulates TOP2α, exhibited reverse trends in EESP/5-FU combination treatment. These results suggested that Spica Prunellae may be beneficial in the treatment of 5-FU-resistant CRC patients. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
5. Characterization and Identification of novel serum microRNAs in sepsis patients with different outcomes
- Author
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Hui-juan Wang, Lixin Xie, Deng Jie, Feng Dan, Weijun Chen, Peng-jun Zhang, and Yan-hong Jia
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Oncology ,Adult ,Male ,medicine.medical_specialty ,Critical Care and Intensive Care Medicine ,Bioinformatics ,Severity of Illness Index ,law.invention ,Sepsis ,Young Adult ,law ,Internal medicine ,Severity of illness ,medicine ,Humans ,Young adult ,Aged ,Gene Library ,Aged, 80 and over ,Receiver operating characteristic ,business.industry ,Reverse Transcriptase Polymerase Chain Reaction ,Case-control study ,Computational Biology ,Middle Aged ,medicine.disease ,Prognosis ,Intensive care unit ,Confidence interval ,MicroRNAs ,Case-Control Studies ,Emergency Medicine ,Biomarker (medicine) ,Female ,business ,Biomarkers - Abstract
Circulating microRNAs (miRNAs) are an emerging biomarker for sepsis patients. The purpose of this study was to identify novel miRNAs in the sera of sepsis patients and determine their prognostic value. Ninety-four serum samples were collected from sepsis patients within 24 h of intensive care unit admission. Solexa sequencing followed by bioinformatics analysis was used to predict novel miRNAs in survivors (n = 9) and nonsurvivors (n = 9). A total of 650 novel miRNAs were predicted by bioinformatics analysis after Solexa sequencing, and 41 novel miRNAs were validated in 10 survivors, 10 nonsurvivors, and 10 healthy controls by quantitative reverse transcriptase-polymerase chain reaction. Among these 41 miRNAs, 18 were present in both survivors and nonsurvivors, and nine were differentially expressed between the two groups. The expression levels of the nine miRNAs were determined by quantitative reverse transcriptase-polymerase chain reaction in 24 nonsurvivors and 32 survivors, and six were differentially expressed. Conjoint analysis of the six miRNAs and severity scores (Acute Physiology and Chronic Health Evaluation II score and Sequential Organ Failure Assessment score) showed that the area under the receiver operating characteristic curve for the predictive value of the six miRNAs was 0.969 (95% confidence interval, 0.930-1.000). When the cutoff point was set at 0.714, the six miRNAs and severity score provided a sensitivity of 100% and a specificity of 82.6%. In conclusion, 41 novel miRNAs were detectable in the sera of sepsis patients, and six of them might be related to sepsis outcome.
- Published
- 2013
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