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  • Open Access

    ARTICLE

    Integrated Data Reveal the Flavonoid Biosynthesis Metabolic Pathway in Semen Ziziphi Spinosae Using Transcriptomic and Metabolomic

    Wei Tian1, Lingdi Liu1, Zhongxing Song2, Zhishu Tang2, Chunxiu Wen1, Tao Jiang1,*

    Phyton-International Journal of Experimental Botany, Vol.92, No.2, pp. 369-382, 2023, DOI:10.32604/phyton.2022.023184

    Abstract The extract from Semen Ziziphi Spinosae (SZS) contains many secondary metabolites (flavonoids, alkaloids, and terpenoids), widely reported for their high medicinal value. In order to know the number and type of flavonoids and the regulating mechanism of flavonoid biosynthesis during the growth and development of SZS, we identified and analyzed the flavonoid metabolites and genes in SZS using metabolomic and transcriptomic. A total of 13,232 differentially expressed genes and 83 flavonoid metabolites were identified at three different growth and development stages (T1, T2, and T3) of SZS. The main flavonoid metabolic components of SZS were catechin, More >

  • Open Access

    ARTICLE

    An Intelligent Hybrid Ensemble Gene Selection Model for Autism Using DNN

    G. Anurekha*, P. Geetha

    Intelligent Automation & Soft Computing, Vol.35, No.3, pp. 3049-3064, 2023, DOI:10.32604/iasc.2023.029127

    Abstract Autism Spectrum Disorder (ASD) is a complicated neurodevelopmental disorder that is often identified in toddlers. The microarray data is used as a diagnostic tool to identify the genetics of the disorder. However, microarray data is large and has a high volume. Consequently, it suffers from the problem of dimensionality. In microarray data, the sample size and variance of the gene expression will lead to overfitting and misclassification. Identifying the autism gene (feature) subset from microarray data is an important and challenging research area. It has to be efficiently addressed to improve gene feature selection and… More >

  • Open Access

    ARTICLE

    Selection and Verification of Reference Genes for qRT-PCR Analysis in Iris domestica under Drought

    Qiang Ai, Cuijing Liu*, Mei Han*, Limin Yang

    Phyton-International Journal of Experimental Botany, Vol.91, No.11, pp. 2537-2548, 2022, DOI:10.32604/phyton.2022.021889

    Abstract Iris domestica is a plant of the Iridaceae family and is drought-tolerant, but its drought-resistance mechanism is not yet clear. Analysing the gene expression changes of I. domestica by qRT-PCR is an important mean to understand its drought resistance characteristics. Nevertheless, a lack of reference genes greatly hinders investigation and research on the adaptation of I. domestica to drought at the molecular and genetic levels. In this study, we assessed the expression stability of 11 candidate gene in I. domestica under drought stress conditions and different tissues using geNorm, NormFinder, BestKeeper and RefFinder tools. The results showed that EF1β was More >

  • Open Access

    ARTICLE

    Wheat Lysin-Motif-Containing Proteins Characterization and Gene Expression Patterns under Abiotic and Biotic Stress

    Minjie Liu*, Na Gao, Yaqiong Zhao, Yingpeng Wu, Zongying Yuan

    Phyton-International Journal of Experimental Botany, Vol.91, No.11, pp. 2367-2382, 2022, DOI:10.32604/phyton.2022.021406

    Abstract Lysin motif (LysM)-containing proteins (LYPs) are important pattern recognition receptors in plants. However, the evolutionary history and characteristics of LYP genes remain largely unclear in wheat. In this study, 62 LYPs were identified at genome wide in wheat. Based on phylogenetic and domain analysis, wheat LYPs were classified into 6 subgroups (group LysMe, LysMn, LYP, LYK, LysMFbox). Syntenic analysis showed the evolution of LYP genes in wheat. RNA-seq data showed that 22 genes were not expressed at any tissue or stress stimulation period. Some LYP and LYK genes were tissue- or stage- specific. The majority of TaLYK5s, More >

  • Open Access

    ARTICLE

    Anticancer Effects of Gleditsia sinensis Extract in Rats Transplanted With Hepatocellular Carcinoma Cells

    Yue Cai*†‡, Chizhi Zhang*†‡, Lei Zhan*†, Liangbin Cheng*†, Dingbo Lu*†, Xiaodong Wang*†, Hanlin Xu§, Shuxue Wang, Deng Wu*†, Lianguo Ruan#

    Oncology Research, Vol.27, No.8, pp. 889-899, 2019, DOI:10.3727/096504018X15482423944678

    Abstract The thorns of Gleditsia sinensis have been historically used in Chinese medicine and are considered one of the fundamental therapeutic herbs. Its anticancer effects are currently being explored. Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer and still requires the development of new drugs with higher efficiency. By using a rat HCC model implanted with cancerous Walker-256 cells, the therapeutic effects of G. sinensis extract (GSE) were assessed, as well as its regulatory effects on miRNAs. GSE significantly restored liver morphology and dramatically induced cell apoptosis in HCC rats. In addition, miR-21/181b/183 was More >

  • Open Access

    ARTICLE

    Changes in DNA Damage Repair Gene Expression and Cell Cycle Gene Expression Do Not Explain Radioresistance in Tamoxifen-Resistant Breast Cancer

    Annemarie E. M. Post*†, Johan Bussink*, Fred C. G. J. Sweep, Paul N. Span*

    Oncology Research, Vol.28, No.1, pp. 33-40, 2020, DOI:10.3727/096504019X15555794826018

    Abstract Tamoxifen-induced radioresistance, reported in vitro, might pose a problem for patients who receive neoadjuvant tamoxifen treatment and subsequently receive radiotherapy after surgery. Previous studies suggested that DNA damage repair or cell cycle genes are involved, and could therefore be targeted to preclude the occurrence of cross-resistance. We aimed to characterize the observed cross-resistance by investigating gene expression of DNA damage repair genes and cell cycle genes in estrogen receptor-positive MCF-7 breast cancer cells that were cultured to tamoxifen resistance. RNA sequencing was performed, and expression of genes characteristic for several DNA damage repair pathways was… More >

  • Open Access

    ARTICLE

    PNN and KCNQ1OT1 Can Predict the Efficacy of Adjuvant Fluoropyrimidine-Based Chemotherapy in Colorectal Cancer Patients

    Andrea Lapucci*†1, Gabriele Perrone*†1, Antonello Di Paolo‡§, Cristina Napoli*†, Ida Landini*†, Giandomenico Roviello*†, Laura Calosi, Antonio Giuseppe Naccarato#, Alfredo Falcone#, Daniele Bani, Enrico Mini*†§2, Stefania Nobili*†§2,3

    Oncology Research, Vol.28, No.6, pp. 631-644, 2020, DOI:10.3727/096504020X16056983169118

    Abstract The benefit of adjuvant chemotherapy in the early stages of colorectal cancer (CRC) is still disappointing and the prediction of treatment outcome quite difficult. Recently, through a transcriptomic approach, we evidenced a role of PNN and KCNQ1OT1 gene expression in predicting response to fluoropyrimidine-based adjuvant chemotherapy in stage III CRC patients. Thus, the aim of this study was to validate in an independent cohort of stages II–III CRC patients our previous findings. PNN and KCNQ1OT1 mRNA expression levels were evaluated in 74 formalin-fixed paraffin-embedded tumor and matched normal mucosa samples obtained by stages II–III CRC patients treated… More >

  • Open Access

    ARTICLE

    Microenvironment Analysis of Prognosis and Molecular Signature of Immune-Related Genes in Lung Adenocarcinoma

    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 More >

  • Open Access

    ARTICLE

    Deep Learning Enabled Microarray Gene Expression Classification for Data Science Applications

    Areej A. Malibari1, Reem M. Alshehri2, Fahd N. Al-Wesabi3, Noha Negm3, Mesfer Al Duhayyim4, Anwer Mustafa Hilal5,*, Ishfaq Yaseen5, Abdelwahed Motwakel5

    CMC-Computers, Materials & Continua, Vol.73, No.2, pp. 4277-4290, 2022, DOI:10.32604/cmc.2022.027030

    Abstract In bioinformatics applications, examination of microarray data has received significant interest to diagnose diseases. Microarray gene expression data can be defined by a massive searching space that poses a primary challenge in the appropriate selection of genes. Microarray data classification incorporates multiple disciplines such as bioinformatics, machine learning (ML), data science, and pattern classification. This paper designs an optimal deep neural network based microarray gene expression classification (ODNN-MGEC) model for bioinformatics applications. The proposed ODNN-MGEC technique performs data normalization process to normalize the data into a uniform scale. Besides, improved fruit fly optimization (IFFO) based… More >

  • Open Access

    ARTICLE

    Response of MaHMA2 gene expression and stress tolerance to zinc stress in mulberry (Morus alba L.)

    LEI WANG1,#, QIUXIA DU1,#, YISU SHI1,#, MICHAEL ACKAH1, PENG GUO1, DANYAN ZHENG1, MENGMENG WU1, XIN JIN1, PEILAN LI3, QIAONAN ZHANG1, RUIXUE LI4, ZHI YIN3, MENGDI ZHAO2,*, WEIGUO ZHAO1,*

    BIOCELL, Vol.46, No.10, pp. 2327-2342, 2022, DOI:10.32604/biocell.2022.021542

    Abstract HMA2 (heavy metal ATPase 2) plays a crucial role in extracellular and intracellular Zn2+ transport across biomembranes, maintaining ion homeostasis, and playing an important role in the normal physiological metabolism, growth, and development of plants. In our study, a novel HMA2 gene, named MaHMA2, was isolated and cloned from white mulberry (Morus alba L.). The gene sequence obtained was 1,342 bp long, with an open reading frame of 1,194 bp, encoding a protein of 397 amino acids, with a predicted molecular mass of 42.852 kD and an isoelectric point of 7.53. This protein belonged to the PIB-type ATPase… More >

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