IF 1.2 4区生物学

Biocell Pub Date : 2023-01-01 DOI: 10.32604/biocell.2023.030191

Xiao-jun Zhou, Yu Tian, Rui Li

{"title":"The whole-genome survey of Acer griseum, its polymorphic simple sequence repeats development and application","authors":"Xiao-jun Zhou, Yu Tian, Rui Li","doi":"10.32604/biocell.2023.030191","DOIUrl":"https://doi.org/10.32604/biocell.2023.030191","url":null,"abstract":"Background: Acer griseum Pax is an endangered species endemic to China with both ornamental and economic value. However, the lack of information on its genome size and characteristics hinders further work at the genome level. Methods: This paper applied bioinformatics methods to predict the characteristics and patterns of the A. griseum genome, providing an important basis for formulating its whole-genome sequencing scheme. This study also characterized the simple sequence repeats (SSRs) of A. griseum, laying the foundation for the development and application of genome-wide SSR markers. In this study, PE150 sequencing was performed by the BGI MGISEQ platform, and the sequence files were analyzed by the K-mer method to estimate the characteristic information by GCE software. Results: The genome size was finally determined to be 739.63 Mb, its heterozygosity ratio was 1.33%, and the repetition ratio was 65.68%. A total of 825,960 SSR loci were identified in the assembled genome sequence, and primers were successfully designed for 526,020 loci. To verify the effectiveness of these primers, 100 pairs of primers were randomly selected and synthesized, and 81 pairs successfully amplified the target fragments. Fourteen pairs of primers with good polymorphism were selected for principal component analysis of 31 A. griseum individuals from two populations, showing favorable heterozygosity and PIC values. According to the findings, these SSRs might identify genetic variations based on geographic areas. Conclusion: It is suggested that Illumina + PacBio assembly strategy should be used for whole-genome sequencing due to the high heterozygosity rate and high repetition rate of the genome. In addition, the SSR primers designed in batches in this study laid a foundation for the in-depth study of population structure and population maintenance mechanism of A. griseum, which is helpful for the effective conservation and sustainable utilization of this germplasm resource.","PeriodicalId":55384,"journal":{"name":"Biocell","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84522032","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A comprehensive analysis of the role of molecular docking in the development of anticancer agents against the cell cycle CDK enzyme 分子对接在抗细胞周期CDK酶抗癌药物开发中的作用综合分析

IF 1.2 4区生物学

Biocell Pub Date : 2023-01-01 DOI: 10.32604/biocell.2023.026615

P. Solanki, Nisarg Rana, Prakash C. JHA, A. Manhas

引用次数: 2

Columbianetin acetate inhibits the occurrence and development of pancreatic cancer cells by down-regulating the expression of Meiotic nuclear divisions 1 乙酸柱莲素通过下调减数分裂核分裂的表达抑制胰腺癌细胞的发生和发展

IF 1.2 4区生物学

Biocell Pub Date : 2023-01-01 DOI: 10.32604/biocell.2023.023553

K. Sun, Dongqin Wang, Zhiqiang Zhang, Yinlong Huang, Xiaofu Lian, Jia Hua, Jing Zhang, Chaoqun Lian

{"title":"Columbianetin acetate inhibits the occurrence and development of pancreatic cancer cells by down-regulating the expression of Meiotic nuclear divisions 1","authors":"K. Sun, Dongqin Wang, Zhiqiang Zhang, Yinlong Huang, Xiaofu Lian, Jia Hua, Jing Zhang, Chaoqun Lian","doi":"10.32604/biocell.2023.023553","DOIUrl":"https://doi.org/10.32604/biocell.2023.023553","url":null,"abstract":"Columbianetin acetate (CE) is one of the effective components of Angelica pubescens. So far, the specific role and molecular mechanism of CE in pancreatic cancer are not clear. Thus, this study aimed to explore the specific mechanism of CE on pancreatic cancer. The target genes combined with CE were predicted through the PharmMapper database and the 3D molecular structure of CE. Then, the Cancer Genome Atlas (TCGA) and Cistrome data browser (DB) databases were used to screen Meiotic nuclear divisions 1 (MND1)-related genes, transcription factors, and transcription factor data sets, and the intersection of the above data sets. The “limma” package in the R and gene expression profiling interactive analysis (GEPIA) databases were used to analyze the correlation and survival difference between the target genes and MND1 to predict the degree of association between CE and MND1. Western blotting and RT-PCR experiments revealed the regulatory relationship among CE, E2F1, and MND1 at the cellular level. The specific effects of CE on pancreatic cancer cells were explored through CCK8, wound healing, migration, and flow cycle experiments. E2F1, also the predictive transcription factor of MND1, was also the predictive target protein of CE. At the same time, E2F1 and MND1 were closely related in pancreatic tissue. In the cell function experiment, CE and interference with E2F1 expression could reduce the gene and protein expression of MND1, which was closely associated with cell proliferation, migration, and cycle development. Similarly, interfering with the expression of mnd1 can also inhibit the further development of tumor cells. CE may inhibit the development of pancreatic cancer cells by reducing the expression of MND1. This implies that CE may be a potential novel agent for the treatment of pancreatic cancer.","PeriodicalId":55384,"journal":{"name":"Biocell","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83348294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genetic algorithm-optimized backpropagation neural network establishes a diagnostic prediction model for diabetic nephropathy: Combined machine learning and experimental validation in mice 遗传算法优化的反向传播神经网络建立糖尿病肾病诊断预测模型:机器学习与小鼠实验验证相结合

IF 1.2 4区生物学

Biocell Pub Date : 2023-01-01 DOI: 10.32604/biocell.2023.027373

Wei Liang, Zongwei Zhang, Keju Yang, Hongtu Hu, Qiang Luo, Ankang Yang, Li-Chiu Chang, Yuanyuan Zeng

引用次数: 0

Analysis of tumor-draining vein secretome: A direct access to tumor-derived extracellular vesicles in surgical lung cancer patients 肿瘤引流静脉分泌组分析:肺癌手术患者肿瘤源性细胞外囊泡的直接通路

IF 1.2 4区生物学

Biocell Pub Date : 2023-01-01 DOI: 10.32604/biocell.2023.027718

引用次数: 0

Role of foliar spray of plant growth regulators in improving photosynthetic pigments and metabolites in Plantago ovata (Psyllium) under salt stress–A field appraisal 盐胁迫下植物生长调节剂叶面喷施对车前草光合色素和代谢产物的影响

IF 1.2 4区生物学