Wei Tian¹, Lingdi Liu¹, Zhongxing Song², Zhishu Tang², Chunxiu Wen¹, Tao Jiang^1,*

Phyton-International Journal of Experimental Botany, Vol.92, No.2, pp. 369-382, 2023, DOI:10.32604/phyton.2022.023184 - 12 October 2022

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 >

G. Anurekha^*, P. Geetha

Intelligent Automation & Soft Computing, Vol.35, No.3, pp. 3049-3064, 2023, DOI:10.32604/iasc.2023.029127 - 17 August 2022

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 >

Tyler Overholt^1,2, Robert J. Evans¹, Gopal Badlani¹, Catherine A. Matthews¹, Stephen J. Walker^1,2

Canadian Journal of Urology, Vol.29, No.1, pp. 11012-11019, 2022

Abstract Introduction: To further facilitate understanding of disease pathophysiology and patient stratification in interstitial cystitis/bladder pain syndrome (IC/BPS), we utilized molecular phenotyping to compare three clinically distinct IC/BPS patient subgroups.
Materials and methods: Total RNA (miRNA and mRNA) was isolated via standard protocols from IC/BPS patient bladder biopsies and assayed on whole genome and microRNA expression arrays. Data from three patient subgroups (n = 4 per group): (1) low bladder capacity (BC; ≤ 400 cc) without Hunner’s lesion, (2) low BC with Hunner’s lesion, and (3) non-low BC (> 400 cc) were used in comparative analyses to evaluate… More >

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 - 12 July 2022

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 >

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 - 12 July 2022

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 >

Areej A. Malibari¹, Reem M. Alshehri², Fahd N. Al-Wesabi³, Noha Negm³, Mesfer Al Duhayyim⁴, Anwer Mustafa Hilal^5,*, Ishfaq Yaseen⁵, Abdelwahed Motwakel⁵

CMC-Computers, Materials & Continua, Vol.73, No.2, pp. 4277-4290, 2022, DOI:10.32604/cmc.2022.027030 - 16 June 2022

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 >

LEI WANG^1,#, QIUXIA DU^1,#, YISU SHI^1,#, MICHAEL ACKAH¹, PENG GUO¹, DANYAN ZHENG¹, MENGMENG WU¹, XIN JIN¹, PEILAN LI³, QIAONAN ZHANG¹, RUIXUE LI⁴, ZHI YIN³, MENGDI ZHAO^2,*, WEIGUO ZHAO^1,*

BIOCELL, Vol.46, No.10, pp. 2327-2342, 2022, DOI:10.32604/biocell.2022.021542 - 13 June 2022

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 >

E. Kavitha^1,*, R. Tamilarasan², Arunadevi Baladhandapani³, M. K. Jayanthi Kannan⁴

Computer Systems Science and Engineering, Vol.43, No.3, pp. 871-886, 2022, DOI:10.32604/csse.2022.021215 - 09 May 2022

Abstract Gene expression data represents a condition matrix where each row represents the gene and the column shows the condition. Micro array used to detect gene expression in lab for thousands of gene at a time. Genes encode proteins which in turn will dictate the cell function. The production of messenger RNA along with processing the same are the two main stages involved in the process of gene expression. The biological networks complexity added with the volume of data containing imprecision and outliers increases the challenges in dealing with them. Clustering methods are hence essential to… More >

MING-AO CAO¹, FEI ZHANG², ELSAYED FATHI ABD_ALLAH³, QIANGSHENG WU^1,*

BIOCELL, Vol.46, No.8, pp. 1959-1966, 2022, DOI:10.32604/biocell.2022.020391 - 22 April 2022

Abstract A potted experiment was carried out to study the effect of an arbuscular mycorrhizal fungus (Diversispora versiformis) and arbuscular mycorrhizal like fungus (Piriformospora indica) on antioxidant enzyme defense system of Satsuma orange (Citrus sinensis cv. Oita 4) grafted on Poncirus trifoliata under favourable temperature (25°C) and cold temperature (0°C) for 12 h. Such short-term treatment of cold temperature did not cause any significant change in root fungal colonization and spore density in soil. Under cold stress, D. versiformis inoculation did not change the activity of superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) in leaves and roots, whereas P.… More >

IVANA SAMARŽIJA^1,2,*

BIOCELL, Vol.46, No.7, pp. 1747-1750, 2022, DOI:10.32604/biocell.2022.018784 - 17 March 2022

Abstract Comparisons of gene expression profiles between primary tumors and metastasis have revealed genes that are implicated in metastasis formation. However, gene expression studies conducted on metastasis samples from the same primary site usually do not discriminate between different secondary sites. Although the change in the expression of number of genes is expected to be common to metastasis from the same primary but different secondary sites, herein the data that point to substantial differences are presented. Furthermore, the reciprocal communication between metastatic and host cells that is influencing these differences is outlined to emphasize the need More >