Aisa Zulibiya^1,2,#, Jing Wen^3,#, Huiqing Yu^3,#, Xiaoming Chen³, Lei Xu³, Xiao Ma^1,2, Baojian Zhang^1,2,*

Congenital Heart Disease, Vol.18, No.6, pp. 611-625, 2023, DOI:10.32604/chd.2023.047689

Abstract Background: Tetralogy of Fallot (TOF) is a very common cyanotic congenital heart disease. Endothelial-to-mesenchymal transition (EndoMT) is recognized as a physiological mechanism involved in embryonic heart development and endothelial formation. However, there is still a gap in the reports related to the mechanism of EndoMT development in TOF. Methods: First, transcriptomic data of single cell nuclei of TOF and Donor were obtained based on the Gene Expression Omnibus (GEO) database, and the data were normalized and clustered by dimensionality reduction using the Seurat package. Subsequently, differentially expressed genes (DEGs) between TOF and Donor were screened using the “FindMarkers” function, and… More >

GERWIN HELLER^1,*, THORSTEN FUEREDER¹, ALEXANDER MICHAEL GRANDITS¹, ROTRAUD WIESER^1,2,*

Oncology Research, Vol.32, No.1, pp. 1-17, 2024, DOI:10.32604/or.2023.044774

Abstract Head and neck squamous cell carcinoma (HNSCC) is one of the most frequent cancers worldwide. The main risk factors are consumption of tobacco products and alcohol, as well as infection with human papilloma virus. Approved therapeutic options comprise surgery, radiation, chemotherapy, targeted therapy through epidermal growth factor receptor inhibition, and immunotherapy, but outcome has remained unsatisfactory due to recurrence rates of ~50% and the frequent occurrence of second primaries. The availability of the human genome sequence at the beginning of the millennium heralded the omics era, in which rapid technological progress has advanced our knowledge of the molecular biology of… 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 >

TINGTING SUN, XUE SUN, XIN WANG, RUI GUO, YUANHUA YU^*, LE GAO^*

BIOCELL, Vol.47, No.4, pp. 879-889, 2023, DOI:10.32604/biocell.2023.026229

Abstract Background: Aldo-keto oxidoreductase (AKR) inhibitors could reverse the resistance of several cancer cells to cis-platin, but their role in resistance remains unclear.Methods: We verified the difference of AKR1Cs expression by Western blot, RNA sequencing and qRT-PCR. The differences of AKR1Cs expression were analyzed and inferred. Use Assay of NADH and NAD⁺ content to verify the inference. The Docking experience was used to verify the affinity between MPA, MCFLA, MLS and AKR1C3.Results: Our RNA-seq results showed de novo NAD biosynthesis-related genes and NAD(P)H-dependent oxidoreductases were significantly upregulated in cis-platin-resistant HepG2 hepatic cancer cells (HepG2-RC cells) compared with HepG2 cells. At least… More >

Lina Tang^1,2, Haiyan Hu², Yan Zhou², Yujing Huang², Yonggang Wang², Yawen Zhang², Jinrong Liang², Zhenxin Wang^1,*

Oncologie, Vol.24, No.4, pp. 913-925, 2022, DOI:10.32604/oncologie.2022.026296

Abstract Objective: To investigate the expression of alpha–smooth muscle actin (ACTA2) in osteosarcoma tissues and its relationship with prognosis. Methods: Prognostic analysis of lung metastasis–related genes in osteosarcoma using the TCGA database. Single-cell sequencing detected the expression of ACTA2 in 11 osteosarcoma tissues. Paraf- fin-embedded tissues of 74 osteosarcoma patients treated at the Sixth People’s Hospital of Shanghai Jiao Tong University from 2014 to 2019 were collected, and tissue microarrays were prepared. ACTA2 expression was detected and scored by immunohistochemistry. According to the median value of the ACTA2 histochemical score, 74 patients were divided into two groups, the high-expression group and… More >

Ting Zhang^1,2, Ping Li^3,*, Jiali Wei^3,*

Phyton-International Journal of Experimental Botany, Vol.91, No.11, pp. 2403-2417, 2022, DOI:10.32604/phyton.2022.022421

Abstract Hedera helix is an evergreen ornamental plant that is resistant to cool but not high temperature and deserves to be further researched for improving its adaptability to heat stress. Two Hedera helix cultivars, heat-tolerant (HT) ‘Jessica’ and heat-sensitive (HS) ‘Shamrock’, were used for differences analyses of transcriptome. We detected 6179 differentially expressed genes (DEGs) and 5992 DEGs in ‘Jessica’ and ‘Shamrock’ to heat stress, respectively. Among these, 1983 upregulated DEGs and 1400 downregulated DEGs were shared between both varieties, resulting in enhancement of various pathways such as biosynthesis of secondary metabolites, glyoxylate dicarboxylate metabolism, and protein processing in endoplasmic reticulum… More >

JIABAO WU^1,2,#, XIAOHUA LIU^1,2,#, LU HAN^1,2, HUA NIE^1,2, YUAN TANG^1,2, YUNGE TANG^1,3, GE SONG^1,5, LIXIN ZHENG^1,4, WEIBING QIN^1,2,*

BIOCELL, Vol.46, No.4, pp. 1013-1023, 2022, DOI:10.32604/biocell.2022.016744

Abstract Piwi-interacting RNAs (piRNAs) is a novel class of non-coding RNAs. However, changes in piRNA expression profiles in recurrent spontaneous abortion (RSA) have not yet been investigated. The aim of this study was to identify differentially expressed piRNAs in deciduas of RSA patients. Decidua tissues were collected by curettage from recruited RSA patients and normal early pregnant (NEP) women with their informed consent. Small RNA sequencing was used to evaluate the differences in piRNA expression profiles between RSA and NEP. The present results demonstrated that the counts of total piRNA reads in RSA samples were increased compared with those in NEP… More >

JIRUI WEN^1,#, WENCHAO WU^2,#, MIN TANG¹, MINGYUE BAO¹, XUELING HE³, XINGHONG YAO¹, LIANG LI^1,*

BIOCELL, Vol.46, No.3, pp. 655-665, 2022, DOI:10.32604/biocell.2022.016915

Abstract To dissect which subset of bone marrow monocyte is the major precursor of osteoclast, 3-month-old rat bone marrow was obtained for single-cell RNA sequencing. A total of 6091 cells were acquired for detailed analysis, with a median number of 1206 genes detected per cell and 17,959 genes detected in total. A total of 19 cell clusters were recognized, with the main lineages identified as B cells, Granulocytes, Monocytes, T cells, Erythrocytes and Macrophages. Monocytes were further divided into classical monocytes and non-classical monocytes. Compared with non-classical monocytes, classical monocytes highly expressed osteoclast differentiation related genes Mitf, Spi1, Fos and Csf1r.… More >

Ping Zhang¹, Zhiyou Kong², Junna Liu¹, Yongjiang Liu¹, Qianchao Wang¹, Xiuju Huan¹, Li Li¹, Yunfeng Jiang³, Peng Qin^1,*

Phyton-International Journal of Experimental Botany, Vol.91, No.2, pp. 375-394, 2022, DOI:10.32604/phyton.2022.016358

Abstract Drought is the main abiotic stress that restricts wheat production. The rapid development of sequencing technology and its widespread application to various fields have revealed the structural characteristics and regulation of related genes through gene expression analysis. Here, we studied responses of wheat plants under drought and re-watering conditions, using morphological and physiological indicators. Moreover, a transcriptome analysis was conducted on Jingmai 12, a drought-resistant wheat strain, to explore the mechanism underlying the response of drought-resistant wheat seedlings to drought stress at the transcriptome level. Drought stress caused morphological and physiological changes in both drought-resistant and -sensitive varieties, but to… More >

JOE R. DELANEY^*

BIOCELL, Vol.45, No.5, pp. 1167-1170, 2021, DOI:10.32604/biocell.2021.017296

Abstract Single-cell sequencing data has transformed the understanding of biological heterogeneity. While many flavors of single-cell sequencing have been developed, single-cell RNA sequencing (scRNA-seq) is currently the most prolific form in published literature. Bioinformatic analysis of differential biology within the population of cells studied relies on inferences and grouping of cells due to the spotty nature of data within individual cell scRNA-seq gene counts. One biologically relevant variable is readily inferred from scRNA-seq gene count tables regardless of individual gene representation within single cells: aneuploidy. Since hundreds of genes are present on chromosome arms, high-quality inferences of aneuploidy can be made… More >