YUNBAO GUO^1,#, XU LIU^1,#, QI XU², XIAOTONG ZHOU³, JIAWEI LIU³, YANYAN XU², YAN LU^2,*, HAIYAN LIU^2,*

BIOCELL, Vol.48, No.6, pp. 945-958, 2024, DOI:10.32604/biocell.2024.049748

Abstract Background: Glioma is a kind of tumor that easily deteriorates and originates from glial cells in nerve tissue. Honokiol is a bisphenol compound that is an essential monomeric compound extracted from the roots and bark of Magnoliaceae plants. It also has anti-infection, antitumor, and immunomodulatory effects. In this study, we found that honokiol induces cell apoptosis in the human glioma cell lines U87-MG and U251-MG. However, the mechanism through which honokiol regulates glioma cell apoptosis is still unknown. Methods: We performed RNA-seq analysis of U251-MG cells treated with honokiol and control cells. Protein-protein interaction (PPI)… More > Graphic Abstract

Yong Zhao^1,#, Yaxuan Jiang^3,#, Li Wen¹, Rui Luo², Guorui Li², Jianjun Di², Mingda Yin², Zhiyan Wang², Fenglan Huang^2,4,5,6,7,*, Fanjuan Meng^3,*

Phyton-International Journal of Experimental Botany, Vol.93, No.4, pp. 713-723, 2024, DOI:10.32604/phyton.2024.047657

Abstract The yield of castor is influenced by the type of inflorescence and the proportion of female flowers. However, there are few studies on the genetic mechanism involved in the development and differentiation of castor inflorescences. In this study, we performed transcriptomic analyses of three different phenotypes of inflorescences at the five-leaf stage. In comparison to the MI (complete pistil without willow leaves), 290 and 89 differentially expressed genes (DEGs) were found in the SFI (complete pistil with willow leaves) and the BI (monoecious inflorescence), respectively. Among the DEGs, 104 and 88 were upregulated in the… More >

QINGQING GUO^1,2, JIAYUE QI^1,2, XIAOQIANG LIANG², ZIGANG ZHAO², JIA BAI², FANG XIE^2,#,*, CHENGXIN LI^1,2,#,*

BIOCELL, Vol.47, No.11, pp. 2435-2443, 2023, DOI:10.32604/biocell.2023.043126

Abstract Introduction: Verruca vulgaris is one of the most common low-risk HPV infections and is characterized by excessive proliferation of keratinocytes. Currently, very little genetic information is available regarding verruca vulgaris in the Chinese population. This study aimed to obtain comprehensive transcript information of verruca vulgaris by RNA sequencing. Methods: High-throughput sequencing was performed on three fresh verruca vulgaris samples and adjacent normal skin on the Illumina sequencing platform. The transcriptomes were analyzed using bioinformatics and the differentially expressed genes (DEGs) were verified by immunohistochemistry. Verruca vulgaris exhibited a unique molecular signature. Results: In total, 1,643 DEGs… More >

JUN SHEN^1,#, HONGFANG MA^2,#, YONGXIA CHEN³, JIANGUO SHEN^1,*

Oncology Research, Vol.31, No.6, pp. 955-966, 2023, DOI:10.32604/or.2023.029638

Abstract The process of lymphatic metastasis was proved to be associated with podoplanin-expressing macrophages in breast cancer (BC). This study aimed to investigate the role of the M2 phenotype of tumor-associated macrophages and mine the key M2 macrophages-related genes for lymph node metastasis in BC. We downloaded the GSE158399 dataset from the Gene Expression Omnibus (GEO) database, which includes transcriptomic profiles of individual cells from primary tumors, negative lymph nodes (NLNs), and positive lymph nodes (PLNs) of breast cancer patients. The cell subsets were identified by clustering analysis after quality control of the scRNA-seq using Seurat.… More >

Shaochun Liu, Jiamin Hu, Haohua He, Junru Fu, Xu Jie, Dahu Zhou^*, Haihui Fu^*

Phyton-International Journal of Experimental Botany, Vol.92, No.7, pp. 2035-2049, 2023, DOI:10.32604/phyton.2023.028296

Abstract OsPLS4 encodes a β-ketoacyl carrier protein reductase (KAR). The role of OsPLS4 in rice sheath blight (Rhizoctonia solani) remains unclear. Our preliminary studies showed that premature leaf senescence mutants (pls4) were highly susceptive to sheath blight in the early stage of rice development. To explore the role of this gene in the development of rice sheath blight, the transcriptome profiles of the rice pls4 mutant and wild type were compared by RNA-seq. The results revealed 2,569 differentially expressed genes (DEGs). The down-regulated genes were significantly enriched in the defense response-related biological processes. These down-regulated genes included the chitinase… More >

Xinyi Zhang, Zimeng Yu, Pingfang Yang^*

Phyton-International Journal of Experimental Botany, Vol.92, No.6, pp. 1665-1679, 2023, DOI:10.32604/phyton.2023.029482

Abstract Sacred lotus (Nelumbo nucifera) is a typical aquatic plant, belonging to basal eudicot plant, which is ideal for genome and genetic evolutionary study. Understanding lotus gene diversity is important for the study of molecular genetics and breeding. In this research, public RNA-seq data and the annotated reference genome were used to identify the genes in lotus. A total of 26,819 consensus and 1,081 novel genes were identified. Meanwhile, a comprehensive analysis of gene alternative splicing events was conducted, and a total of 19,983 “internal” alternative splicing (AS) events and 14,070 “complete” AS events were detected in… More >

Shixiang Duan^1,#, Yaomiao Guo^1,#, Yinping Wang¹, Muhammad Jawad Umer², Dongming Liu¹, Sen Yang¹, Huanhuan Niu¹, Shouru Sun¹, Luming Yang¹, Junling Dou^1,*, Huayu Zhu^1,*

Phyton-International Journal of Experimental Botany, Vol.92, No.5, pp. 1311-1328, 2023, DOI:10.32604/phyton.2023.026928

Abstract Leaf is a vital organ of plants that plays an essential role in photosynthesis and respiration. As an important agronomic trait in leaf development, leaf shape is classified into lobed, entire (no-lobed), and serrated in most crops. In this study, two-lobed leaf watermelon inbred lines WT2 and WCZ, and a no-lobed leaf watermelon inbred line WT20 were used to create two F₂ populations. Segregation analysis suggested that lobed leaves were dominant over the no-lobed leaves, and it was controlled by a signal gene. A locus on watermelon chromosome 4 controlling watermelon lobed/no-lobed leaves was identified through… More >

Mortaza Hajyzadeh^*

Phyton-International Journal of Experimental Botany, Vol.92, No.5, pp. 1649-1664, 2023, DOI:10.32604/phyton.2023.028028

Abstract Abiotic stresses at different growth stages in the life of plants negatively affect yield productivity. Therefore, plants, including Amaranthus hypochondriacus, develop adaptive strategies to face the stresses and expand functional diversification. In plants, the mitochondrial transcription termination factors (mTERF) are essential functions in regulation, and organelles (mitochondria and chloroplasts) control gene expression (OGE) under several stress conditions. Based on the in-silico-wide genome and transcriptome analysis, twenty-four mTERF genes were detected in the main targeted mitochondria organelles clustered into three different main groups. The chromosomal location and gene duplication analysis indicated one segmental and one tandem duplication in… More >

Jiayou Liu, Lian Ding, Xue Zhang, Song Li, Yunxiao Guan, Diwen Jia, Aiping Song, Jiafu Jiang, Fadi Chen^*

Phyton-International Journal of Experimental Botany, Vol.92, No.2, pp. 311-331, 2023, DOI:10.32604/phyton.2022.023896

Abstract Chrysanthemum morifolium, an ornamental crop with diverse forms of inflorescence, is a good model for studying flower development in Asteraceae. However, the genetic background is complex and the mechanisms of regulating flower development are still unclear. Here, we identified two natural mutant lines of chrysanthemum and named them M1 and M2 according to the severity of the phenotype. Both lines showed defects in petal identity, and the petals of the M1 line had a mild phenotype: partially loss of petal identity and conversion of petals into green, leaf-like organs. The M2 line had severe phenotypes: in… More >

Rui Song¹, Yan Huang², Xin Ji³, Yunfei Wei³, Qiuyuan Liu³, Shumei Li³, Juan Liu^3,*, Pengfei Dong^1,*

Phyton-International Journal of Experimental Botany, Vol.92, No.1, pp. 237-250, 2023, DOI:10.32604/phyton.2022.023081

Abstract Soil salinity greatly impairs plant growth and crop productivity. Rice (Oryza sativa L.) is a salt-sensitive crop. To better understand the molecular mechanisms of salt tolerance in roots, the BGISEQ-500 sequencing platform was employed to elucidate transcriptome changes in rice roots after 0, 3, 24, and 72 h of salt stress. The results showed that root K+ content decreased and Na+ content increased rapidly after the initial stage of salt stress, but that fresh and dry weight in root did not significantly reduce. Compared to the control (no salt stress), 1,292, 453, and 486 differentially… More >