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  • Open Access

    REVIEW

    A Survey on Acute Leukemia Expression Data Classification Using Ensembles

    Abdel Nasser H. Zaied1, Ehab Rushdy2, Mona Gamal3,*

    Computer Systems Science and Engineering, Vol.47, No.2, pp. 1349-1364, 2023, DOI:10.32604/csse.2023.033596

    Abstract Acute leukemia is an aggressive disease that has high mortality rates worldwide. The error rate can be as high as 40% when classifying acute leukemia into its subtypes. So, there is an urgent need to support hematologists during the classification process. More than two decades ago, researchers used microarray gene expression data to classify cancer and adopted acute leukemia as a test case. The high classification accuracy they achieved confirmed that it is possible to classify cancer subtypes using microarray gene expression data. Ensemble machine learning is an effective method that combines individual classifiers to classify new samples. Ensemble classifiers… More >

  • Open Access

    ARTICLE

    Genome-Wide Analysis of the F3′5′H Gene Family in Blueberry (Vaccinium corymbosum L.) Provides Insights into the Regulation of Anthocyanin Biosynthesis

    Xiaolan Guo1,2, Jinbin Hu3, Shimei Yang4, Delu Wang2,*, Jianbing Wang1

    Phyton-International Journal of Experimental Botany, Vol.92, No.9, pp. 2683-2697, 2023, DOI:10.32604/phyton.2023.029820

    Abstract The F3′5′H gene family plays an important role in regulating anthocyanin biosynthesis, abiotic stress, and hormone signaling. In this study, 14 F3′5′H genes were identified from the blueberry genome. The chromosomal distribution, physicochemical properties, F3′5′H domain, conserved motifs, cis-acting elements, and intron/exon compositions were analyzed. The functional prediction analysis of these VcF3′5′Hs indicated that their biological functions included light response and other secondary metabolites. The results of qRT-PCR showed that VcF3′5′Hs (especially VcF3′5′H4) were highly expressed at the ripening stage. Subcellular localization revealed that VcF3′5′H4 may be located in the endoplasmic reticulum. Co-expression analysis showed that the VcF3′5′H gene family… More >

  • Open Access

    ARTICLE

    Identification of the SERK Gene Family in Paulownia fortunei and Its Involvement in the Response to Biotic and Abiotic Stresses

    Tongman Zhao1,2,#, Yujie Fan1,2,#, Yabing Cao1,2, Xiaogai Zhao1,2, Guoqiang Fan1,2,*

    Phyton-International Journal of Experimental Botany, Vol.92, No.9, pp. 2473-2488, 2023, DOI:10.32604/phyton.2023.029469

    Abstract Somatic embryogenesis receptor-like kinases (SERKs) are receptor-like proteins that contain leucine-rich repeats and are involved in various signaling pathways. This study identified SERK family members in the Paulownia fortunei genome and analyzed their characteristics and expression profiles using bioinformatics methods. We identified 12 SERK genes with relatively conserved gene structures and motifs that were distributed unevenly on eight Paulownia chromosomes. The gene promoters contained various cis-acting elements that regulated the expression of the PfSERK genes in response to hormones and abiotic stresses. Synteny analysis indicated that 10 segmental duplication events had occurred during evolution of the PfSERK family. The expression… More >

  • Open Access

    ARTICLE

    Effects of Manganese on the Antioxidant System and Related Gene Expression Levels in the “Hong Yang” Kiwifruit Seedlings

    Chongpei Zheng1, Liangliang Li2, Zhencheng Han2, Weijie Li2,*, Xiaopeng Wen1,*

    Phyton-International Journal of Experimental Botany, Vol.92, No.8, pp. 2399-2412, 2023, DOI:10.32604/phyton.2023.029891

    Abstract

    To explore how manganese affects the antioxidant system and the expression levels of related genes of “Hong yang” seedlings, the leaves of its tissue cultured seedlings were taken as test materials, and single factor treatment was performed by changing the manganese chloride (MnCl2.4H2O) solution concentration when spraying the leaves. The expression levels of Mn-SOD, POD64 and POD27 genes in leaves were quantitatively analyzed by real-time quantitative PCR (qRT-PCR) at different determination times. Meanwhile, the contents of malondialdehyde (MDA), hydrogen peroxide (H2O2), the activities of antioxidant enzymes, including catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD). The results showed… More >

  • Open Access

    ARTICLE

    Selenium: A Game Changer in Plant Development, Growth, and Stress Tolerance, via the Modulation in Gene Expression and Secondary Metabolite Biosynthesis

    Ali Bandehagh1,*, Zahra Dehghanian2, Vahideh Gougerdchi1, Mohammad Anwar Hossain3,*

    Phyton-International Journal of Experimental Botany, Vol.92, No.8, pp. 2301-2324, 2023, DOI:10.32604/phyton.2023.028586

    Abstract The presence of selenium (Se) is not widely established as crucial for crops, although it is commonly recognized as an important nutrient for animals as well as humans. Even so, it is inevitably accepted that Se usually contributes positively to the life cycle of plants. Previous findings suggested that small amounts of Se seem to have a productive role in growth and production. As a result, Se is assumed to function in multiple ways, primarily by influencing a variety of biochemical and physiological functions. Also, Se also acts as a plant antioxidant and pro-oxidant and confers tolerance against different abiotic… More >

  • Open Access

    ARTICLE

    Identification and Expression Analysis of Abscisic Acid Signal Transduction Genes in Hemp Seeds

    Cong Hou1, Kang Ning1, Xiuye Wei1, Yufei Cheng1, Huatao Yu1, Haibin Yu2, Xia Liu1,*, Linlin Dong1,*

    Phyton-International Journal of Experimental Botany, Vol.92, No.7, pp. 2087-2103, 2023, DOI:10.32604/phyton.2023.029041

    Abstract Abscisic acid (ABA) is involved in regulating diverse biological processes, but its signal transduction genes and roles in hemp seed germination are not well known. Here, the ABA signaling pathway members, PYL, PP2C and SnRK2 gene families, were identified from the hemp reference genome, including 7 CsPYL (pyrab-actin resistance1-like, ABA receptor), 8 CsPP2CA (group A protein phosphatase 2c), and 7 CsSnRK2 (sucrose nonfermenting1-related protein kinase 2). The content of ABA in hemp seeds in germination stage is lower than that in non-germination stage. Exogenous ABA (1 or 10 μM) treatment had a significant regulatory effect on the selected PYL, PP2C,… More >

  • Open Access

    ARTICLE

    Insecticidal Potential of α-Pinene and β-Caryophyllene against Myzus persicae and Their Impacts on Gene Expression

    Talha Ali Chohan1,*, Tahir Ali Chohan2,*, Muhammad Zahid Mumtaz1, Muhammad Waqar Alam3, Salah ud Din4, Iqra Naseer5, Ayesha Riaz1, Tayyeba Naseem1, Areeba Iftikhar6, Dur E. Najaf Ali1, Mubashir Hassan7, Hayssam M. Ali8

    Phyton-International Journal of Experimental Botany, Vol.92, No.7, pp. 1943-1954, 2023, DOI:10.32604/phyton.2023.026945

    Abstract Myzus persicae (M. persicae) is now considered a threat to agricultural crops due to economic losses. Numerous synthetic insecticides applied every year against M. persicae, are reported to be unsafe for environment, humans, and beneficial insects. Furthermore, several species of Myzus have been found to develop resistance due to over application of these insecticides. Therefore, it is required to find some novel insecticide that would be safe for the environment as well as for humans. In the current study, two major pure constituents α-pinene and β-caryophyllene were evaluated for their insecticidal potential against M. persicae using a fumigant toxicity assay.… More >

  • Open Access

    ARTICLE

    Genome-Wide Identification and Expression Analysis of the Phytocyanin Gene Family in Nicotiana tabacum

    Peiling Wang1,#, Xiaohong Xu2,#, Yong Li2, Hecui Zhang1, Xuejie Zhang3, Siru Zhou1, Yimei Liu1, Yunyan Feng1, Tonghong Zuo1, Liquan Zhu1,*

    Phyton-International Journal of Experimental Botany, Vol.92, No.5, pp. 1469-1492, 2023, DOI:10.32604/phyton.2023.027133

    Abstract Phytocyanin (PC) is a class of plant-specific blue copper proteins involved in electron transport, plant growth, development, and stress resistance. However, PC proteins have not been systematically evaluated in tobacco plants. We determined the whole-genome sequences of the PC family in the tobacco cultivar ‘K326.’ The transcriptome data were used to analyze the expression of the NtPC family at different development stages and tissue-specific genes. Real-time fluorescence quantitative analysis was used to analyze the expression of the NtPC gene family under low temperature and methyl jasmonate stress. The tobacco NtPC family contained 110 members and was divided into four subfamilies:… More >

  • Open Access

    ARTICLE

    Rules Mining-Based Gene Expression Programming for the Multi-Skill Resource Constrained Project Scheduling Problem

    Min Hu1,2,3, Zhimin Chen4, Yuan Xia4, Liping Zhang1,2,3,*, Qiuhua Tang1,2,3

    CMES-Computer Modeling in Engineering & Sciences, Vol.136, No.3, pp. 2815-2840, 2023, DOI:10.32604/cmes.2023.027146

    Abstract The multi-skill resource-constrained project scheduling problem (MS-RCPSP) is a significant management science problem that extends from the resource-constrained project scheduling problem (RCPSP) and is integrated with a real project and production environment. To solve MS-RCPSP, it is an efficient method to use dispatching rules combined with a parallel scheduling mechanism to generate a scheduling scheme. This paper proposes an improved gene expression programming (IGEP) approach to explore newly dispatching rules that can broadly solve MS-RCPSP. A new backward traversal decoding mechanism, and several neighborhood operators are applied in IGEP. The backward traversal decoding mechanism dramatically reduces the space complexity in… More > Graphic Abstract

    Rules Mining-Based Gene Expression Programming for the Multi-Skill Resource Constrained Project Scheduling Problem

  • Open Access

    ARTICLE

    Selection and Validation of Reference Genes for Normalization of RT-qPCR Analysis in Developing or Abiotic-Stressed Tissues of Loquat (Eriobotrya japonica)

    Shoukai Lin1,2,#, Shichang Xu1,#, Liyan Huang1, Fuxiang Qiu1, Yihong Zheng1, Qionghao Liu1, Shiwei Ma1,2, Bisha Wu1,2, Jincheng Wu1,2,*

    Phyton-International Journal of Experimental Botany, Vol.92, No.4, pp. 1185-1201, 2023, DOI:10.32604/phyton.2023.026752

    Abstract Loquat (Eriobotrya japonica Lindl.) is a subtropical evergreen fruit tree that produces fruits with abundant nutrients and medicinal components. Confirming suitable reference genes for a set of loquat samples before qRT-PCR experiments is essential for the accurate quantification of gene expression. In this study, eight candidate reference genes were selected from our previously published RNA-seq data, and primers for each candidate reference gene were designed and evaluated. The Cq values of the candidate reference genes were calculated by RT-qPCR in 31 different loquat samples, including 12 subgroups of developing or abiotic-stressed tissues. Different combinations of stable reference genes were screened… More >

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