Hua Yang^*

Oncologie, Vol.24, No.4, pp. 835-863, 2022, DOI:10.32604/oncologie.2022.026447

Abstract Background: Epithelial ovarian cancer (EOC) is the deadliest malignancy among the gynecologic tumors, and ovarian serous cystadenocarcinoma (OV) is the dominant histological type. Ferroptosis is a novel iron-dependent, programmed form of cell death, and agents that trigger ferroptosis may constitute potential anti-cancer therapies. Materials and Methods: We herein extracted the genes that participate in the process of ferroptosis from the online FerrDb database to create a ferroptosis-related genome (FRG), and then comprehensively analyzed the relationship between the mRNA expression of each gene and the clinicopathologic features of The Cancer Genome Atlas (TCGA)-OV cohort. Results: We found that most of the… More >

Yanhua Li^1,#, Hualei Huang^1,#, Youming Shi¹, Shuqin Huang¹, Tao Liu¹, Changming Xiao¹, Xiaoqing Tian², Ping Zhao¹, Xiaoyan Dai³, Taocui Huang^1,*, Yan Zhou^1,*

Phyton-International Journal of Experimental Botany, Vol.92, No.3, pp. 815-835, 2023, DOI:10.32604/phyton.2023.023928

Abstract Gibberellin 2-oxidases (GA2ox) are important enzymes that maintain the balance of bioactive GAs in plants. GA2ox genes have been identified and characterized in many plants, but these genes were not investigated in Brassica napus. Here, we identified 31 GA2ox genes in B. napus and 15 of these BnaGA2ox genes were distributed in the A and C subgenomes. Subcellular localization predictions suggested that all BnaGA2ox proteins were localized in the cytoplasm, and gene structure analysis showed that the BnaGA2ox genes contained 2–4 exons. Phylogenetic analysis indicated that BnGA2ox family proteins in monocotyledons and dicotyledons can be divided into four groups, including… More >

Noureldin Eissa^1,2,*, Uswah Khairuddin^1,3, Rubiyah Yusof¹, Ahmed Madani²

CMC-Computers, Materials & Continua, Vol.74, No.2, pp. 2817-2838, 2023, DOI:10.32604/cmc.2023.033632

Abstract Epigenetics is the study of phenotypic variations that do not alter DNA sequences. Cancer epigenetics has grown rapidly over the past few years as epigenetic alterations exist in all human cancers. One of these alterations is DNA methylation; an epigenetic process that regulates gene expression and often occurs at tumor suppressor gene loci in cancer. Therefore, studying this methylation process may shed light on different gene functions that cannot otherwise be interpreted using the changes that occur in DNA sequences. Currently, microarray technologies; such as Illumina Infinium BeadChip assays; are used to study DNA methylation at an extremely large number… More >

Lunzeng Huang^1,2,#, Hongsheng Gao^1,#, Ning Jiang^1,2, Yunhong Xu^1,2, Zijian Gong^1,2, Lele Chen^1,2, Shijie Xue^1,2, Xiaoyan Li¹, Ruichao Liu^1,2, Bei Li¹, Hongxia Zhang¹, Chunyan Yu^1,*, Xiaotong Guo^1,2,*

Phyton-International Journal of Experimental Botany, Vol.92, No.2, pp. 349-368, 2023, DOI:10.32604/phyton.2022.025467

Abstract Calcium (Ca²⁺) plays a pivotal role in various signal transduction pathways. Calcineurin B-like proteins (CBLs) are a unique group of Ca²⁺ sensors that decode Ca²⁺ signals by activating the plant specific protein kinase known as the CBL-interacting protein kinase (CIPK). In plants, the CBL-CIPK signaling network regulates multiple signals in response to different extracellular cues including abiotic stress. However, the genome wide annotation and expression patterns of CBLs and CIPKs in woody cutting flower plants are still unclear. In this study, a total number of 7 CBLs (RcCBLs) and 17 CIPKs (RcCIPKs) genes, divided into four and five subfamilies, respectively,… More >

Han Lei^1,#, Junlin Li^2,#, Zhizhong Song^1,3,*

Phyton-International Journal of Experimental Botany, Vol.91, No.11, pp. 2519-2536, 2022, DOI:10.32604/phyton.2022.021268

Abstract Potassium (K⁺) is an essential macronutrient for plants to maintain normal growth and development. Shaker-like K⁺ channels and HAK/KUP/KT transporters are critical components in the K⁺ acquisition and translocation. In this study, we identified 9 Shaker-like K⁺ channel (VvK) and 18 HAK/KUP/KT transporter (VvKUP) genes in grape, which were renamed according to their distributions in the genome and relative linear orders among the distinct chromosomes. Similar structure organizations were found within each group according to the exon/intron structure and protein motif analysis. Chromosomal distribution analysis showed that 9 VvK genes and 18 VvKUP genes were unevenly distributed on 7 or… More >

Bo Ling, Zuliang Huang, Suoyi Huang, Li Qian, Genliang Li, Qianli Tang

Oncology Research, Vol.28, No.6, pp. 561-578, 2020, DOI:10.3727/096504020X15907428281601

Abstract There is growing evidence on the clinical significance of tumor microenvironment (TME) cells in predicting prognosis and therapeutic effects. However, cell interactions in tumor microenvironments have not been thoroughly studied or systematically analyzed so far. In this study, 22 immune cell components in the lung adenocarcinoma (LUAD) TME were analyzed using gene expression profile from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). The TME-based molecular subtypes of LUAD were defined to evaluate further the relationship between molecular subtypes, prognosis, and clinical characteristics. A TME risk score model was constructed by using the differentially expressed genes (DEGs) of… More >

Qianqian Li¹, Qi Zhao^1,2,*, Xinzhuan Yao¹, Baohui Zhang¹, Litang Lu^1,2,*

Phyton-International Journal of Experimental Botany, Vol.91, No.10, pp. 2163-2189, 2022, DOI:10.32604/phyton.2022.021530

Abstract The cellulose synthase gene superfamily, including Cellulose synthase A (CesA) and cellulose synthase-like (Csl) gene families, is responsible for the synthesis of cellulose and hemicellulose, respectively. The CesA/Csl genes are vital for abiotic stress resistance and shoot tenderness regulation of tea plants (Camellia sinensis). However, the CesA/Csl gene family has not been extensively studied in tea plants. Here, we identified 53 CsCesA/Csl genes in tea plants. These genes were grouped into five subfamilies (CsCesA, CsCslB, CsCslD, CsCslE, CsCslG) based on the phylogenetic relationships with Arabidopsis and rice. The analysis of chromosome distribution, gene structure, protein domain and motif revealed that… More >

Pranav Pushkar¹, Christo Ananth², Preeti Nagrath¹, Jehad F. Al-Amri⁵, Vividha¹, Anand Nayyar^3,4,*

CMC-Computers, Materials & Continua, Vol.73, No.1, pp. 1601-1619, 2022, DOI:10.32604/cmc.2022.026205

Abstract The study of viruses and their genetics has been an opportunity as well as a challenge for the scientific community. The recent ongoing SARS-Cov2 (Severe Acute Respiratory Syndrome) pandemic proved the unpreparedness for these situations. Not only the countermeasures for the effect caused by virus need to be tackled but the mutation taking place in the very genome of the virus is needed to be kept in check frequently. One major way to find out more information about such pathogens is by extracting the genetic data of such viruses. Though genetic data of viruses have been cultured and stored as… More >

XIN LI¹, JIANMIN PAN¹, FAISAL ISLAM², JUANJUAN LI¹, ZHUONI HOU¹, ZONGQI YANG¹, LING XU^1,*

BIOCELL, Vol.46, No.8, pp. 1947-1958, 2022, DOI:10.32604/biocell.2022.019806

Abstract NAC (NAM, ATAF, CUC) is a class of transcription factors involved in plant growth regulation, abiotic stress responses, morphogenesis and metabolism. Salvia miltiorrhiza is an important Chinese medicinal herb, but the characterization of NAC genes in this species is limited. In this study, based on the Salvia miltiorrhiza genomic databases, 82 NAC transcription factors were identified, which were divided into 14 groups. Meanwhile, phylogenetic analysis, gene structure, chromosomal localization and potential role of SmNACs in abiotic stress conditions were also studied. The results revealed that some SmNACs had different structures than others, which advised that these genes may have multiple/distinct… More >

MENGMENG WU^1,#, PENG GUO^1,#, YISU SHI^1,#, DANYAN ZHENG¹, QIAONAN ZHANG¹, XIN JIN¹, YUHUA WANG¹, QIANG LIN², RONGJUN FANG^1,*, WEIGUO ZHAO^1,*

BIOCELL, Vol.46, No.8, pp. 1935-1945, 2022, DOI:10.32604/biocell.2022.019223

Abstract A variety of plants were colchicine treated to double their chromosome number. Chromosomes are genetic carriers that determine the individual traits of organisms. The doubling of chromosomes will lead to modifications in plant morphology, physiology and genetics. To determine the response of mulberry trees induced by colchicine, using mulberry variety Yu-711 leaves as research materials, two small RNA libraries (control and experimental groups) were constructed. It was found that 45 known miRNA genes and 78 predicted novel miRNA genes in the sequence results. A comparison of data between the control group and the experimental group revealed 37 differentially expressed miRNA… More >