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 were identified in verruca… More >

Seung Hee Eom, Tae Kyung Hyun^*

Phyton-International Journal of Experimental Botany, Vol.92, No.11, pp. 3077-3090, 2023, DOI:10.32604/phyton.2023.044032

Abstract Heat and drought are prominent abiotic stressors that limit crop productivity and yield, particularly concerning climate change; therefore, understanding the molecular mechanisms underlying plant stress responses is crucial for stress-tolerant crop production. This study conducted a transcriptomic analysis to elucidate how garlic (Allium sativum L.) responds to drought and heat stress conditions. Transcriptome libraries were generated to identify differentially expressed genes (DEGs) induced by drought and heat stresses. Functional classification and clustering analysis of DEGs revealed stress-specific gene expression patterns. Notably, cell wall-related genes were implicated in the drought response, whereas heat stress was associated with heat stress transcription factors… More >

Genhai Hu^1,*, Maoni Chao¹, Xiuren Zhou², Yuanzhi Fu²

Phyton-International Journal of Experimental Botany, Vol.92, No.9, pp. 2535-2554, 2023, DOI:10.32604/phyton.2023.030163

Abstract Gossypium hirsutum L. is an important cash crop native to the subtropics and is widely cultivated around the world. Low temperature is an important stress that seriously affects seed germination and emergence during planting. In this study, transcriptomic profiles of low-temperature- and normal-temperature-germinated seeds of Xinluzao 25, a variety with low-temperature tolerance and high germination rates, were analyzed and compared. The following results were obtained. (1) A total of 81.06 Gb of clean data were obtained after transcriptome sequencing and assembly, and 76,931 non-redundant Unigene sequences were obtained after data consolidation and concatenation; of these, 69,883 Unigene sequences were annotated.… More >

Yanyan Pu^1,#, Liwen Wang^2,#, Leilei Li³, Yujun Si⁴, Shubin Xie², Yunzhe Cong¹, Dong Wang¹, Yongchao Gong¹, Rumei Tian¹, Xue Chen³, Xiaoyan Zhang¹, Min Liu¹, Hanfeng Ding^1,3,*, Nana Li^1,3,*

Phyton-International Journal of Experimental Botany, Vol.92, No.6, pp. 1793-1812, 2023, DOI:10.32604/phyton.2023.026822

Abstract During the life cycle of a plant, seed germination is crucial. Upon ingestion of water, the dry seeds resumed energy metabolism and cellular repair. To dissect the complex mechanisms at the very beginning of seed germination, two approaches including transcriptome and small RNA sequencing were conducted during the water imbibition process of mung bean seeds compared with dry seed. The transcriptome sequencing analysis identified 10,108 differentially expressed genes (DEGs) between dry and imbibed mung bean seeds. KEGG enrichment analyses demonstrated numerous DEGs involved in hormone signaling pathways, carbohydrate, and energy metabolism. Out of the total DEGs, 129 genes were investigated… More >

CAN CHEN^#, RUI FENG^#, ZONGQIONG ZHANG^#, XIUZHONG XIA, BAOXUAN NONG, YU ZENG, HUI GUO, XINGHAI YANG^*, DANTING LI^*

BIOCELL, Vol.47, No.2, pp. 409-421, 2023, DOI:10.32604/biocell.2023.023543

Abstract Plant height (PH) is a complex trait regulated by the environment and multiple genes. PH directly affects crop yield, harvest index, and lodging resistance. From plant dwarf mutants, many genes related to PH have been identified and described. Nonetheless, the molecular mechanism of height regulation in high-culm rice mutants has not been well studied. By using transcriptome and weighted gene co-expression network analysis (WGCNA), we identified the differentially expressed genes (DEGs) between high-culm rice mutants (MUT) and wild-type (WT) and explored the key pathways and potential candidate genes involved in PH regulation. Transcriptome analysis identified a total of 2,184 DEGs,… More >

Liyan Wu¹, Jie Cheng^1,2, Yaju Gong¹, Rui Bao¹, Zhibin Li¹, Min Gui^1,*, Guanghui Du^2,*

Phyton-International Journal of Experimental Botany, Vol.92, No.2, pp. 591-609, 2023, DOI:10.32604/phyton.2022.023481

Abstract In this study, wild eggplant germplasm No. M239, which is highly susceptible to Verticillium wilt, was used as the experimental material. The physiological and biochemical indices (SOD, PAL, MDA and soluble protein) of M239 roots were measured at different times (0, 12, 24, 36, 48, 60 and 72 h) post inoculation with Verticillium dahliae, and the key time points for the M239 response to Verticillium wilt infection were screened. Then, RNA-Seq technology was used to screen the differentially expressed genes (DEGs) in M239 roots at 0, 12 and 48 h post-inoculation (hpi). The transcriptional results of M239 were also compared… More >

Siyan Liu^1,*, Jinfeng Liu¹, Yuzhe Zhang¹, Yushi Jiang¹, Shaowang Hu¹, Andi Shi¹, Qiyao Cong¹, Shuyan Guan^2,*, Jing Qu², Yao Dan¹

Phyton-International Journal of Experimental Botany, Vol.91, No.7, pp. 1465-1482, 2022, DOI:10.32604/phyton.2022.018836

Abstract Exploring the molecular mechanism of soybean response to drought stress, providing a basis for genetic improvement and breeding of heat-resistant varieties, relying on the transcriptome sequencing data of unpollinated ovary at the seven-leaf stage of soybean Jinong 18(JN18) and Jinong 18 mutant (JB18) soybeans, using reverse transcription, one gene in the sHSP family was cloned using PCR (RT-PCR) and it was named sHSP26. In this experiment, the soybean sHSP26 gene was successfully cloned by RT-PCR, the protein encoded by the sHSP26 gene was analyzed by bioinformatics, and the sHSP26 gene overexpression vector and CRISPR/Cas9 gene-editing vector were constructed. The positive… More >

RUI XU¹, QIBIAO WU¹, YUHAN GONG², YONGZHE WU¹, QINGJIA CHI^1,*, DA SUN^3,*

BIOCELL, Vol.46, No.5, pp. 1261-1288, 2022, DOI:10.32604/biocell.2022.018427

Abstract There is currently no effective solution to the problem of poor prognosis and recurrence of HCC. The technology of immunotherapy and prognosis of genetic material has made continuous progress in recent years. In the study, a 5-gene signature was established for the prognosis of HCC through biological information, and the immune infiltration of HCC patients was studied. After studied HCC patients’ immune infiltration, the paper screened the differential target genes of miR-126-3p in HCC downloaded from TCGA database, and uses WGCNA method to select the modular genes highly relevant to M2 macrophage. Then we use LASSO and COX regression analysis… More >

Fan Feng¹, Tingting Xia¹, Runze Zhao¹, Mengyue Wang¹, Li Yang^1,*

Molecular & Cellular Biomechanics, Vol.16, Suppl.2, pp. 131-131, 2019, DOI:10.32604/mcb.2019.07211

Abstract Objective: To study the effects of different substrate stiffness on human hepatocytes using RNA sequencing (RNA-Seq) technology. The stiffness was corresponding to physiology and pathology stiffness of liver tissues.
Results: With the aid of RNA-Seq technology, our study characterizes the transcriptome of hepatocytes cultured on soft, moderate, stiff and plastic substrates. Compared to soft substrate, our RNA-Seq results revealed 1131 genes that were up-regulated and 2534 that were down-regulated on moderate substrate, 1370 genes that were up-regulated and 2677 down-regulated genes on stiff substrate. Functional enrichment analysis indicated that differentially expressed genes were associated with the regulation of actin… More >

Sufang Wang^1,2, Wenjuan Zhao^1,2, Guolin Shi^1,2, Nu Zhang^1,2, Chen Zhang^1,2, Hui Yang^1,2,*

Molecular & Cellular Biomechanics, Vol.16, Suppl.2, pp. 100-100, 2019, DOI:10.32604/mcb.2019.07112

Abstract Long-term space flight will be a major mission for International Space Administration. However, it has been shown that exposure to space flight result in immune system dysfunction. Therefore, understand the mechanism of immune response under microgravity condition is a key topic. Macrophage is one of the most important immune cells in human body, playing key roles in both innate and adaptive immune systems. In this research, we used mouse macrophages (RAW264.7) and collected samples at short-term (8 hour), mediate-term (24 hour) and long-term (48 hour) microgravity treatment. We measured cell proliferation, phagocytosis function and used next-generation sequencing (NGS) to obtain… More >