Qunlu Liu^1,#, Fiza Liaquat^1,2,#, Qiqi Tang¹, Jun Yang^3,4, Shuai Qiu⁵, Amber Malik², Kang Ye^3,4, Kai Gao⁵, Jun Qin^3,4,*

Phyton-International Journal of Experimental Botany, Vol.94, No.11, pp. 3539-3562, 2025, DOI:10.32604/phyton.2025.071989 - 01 December 2025

Abstract Hydrangea macrophylla is a popular ornamental shrub with a lot of economic and aesthetic value. It is known for its different flower shapes (lacecap and mophead) and the way its flowers change color depending on the pH of the soil. Even though it is important for gardening, we still don’t know much about the molecular processes that lead to flower growth. The purpose of this study was to find and study SNP-related genes and transcription factors that are connected to the growth of H. macrophylla flowers. Genome-wide SNP analysis identified 11 SNPs associated with MYB transcription factors… More >

Rawabi S. Altuwayjiri, Ibtesam S. Almami^*

Oncology Research, Vol.33, No.12, pp. 3923-3943, 2025, DOI:10.32604/or.2025.070104 - 27 November 2025

Abstract Objective: Testicular germ cell tumors (TGCTs) represent the most common malignancy among young men aged 20–40 years. Transglutaminase 7 (TG7), encoded by TGM7, is a poorly characterized enzyme whose function in TGCT remains unknown. This study aimed to assess TG7 expression in clinical specimens and investigate its functional role in a testicular germ cell tumor cell line (NT2/D1). Methods: TG7 protein expression was evaluated in clinical testicular tissue samples via immunohistochemistry (IHC) and immunofluorescence (IF). Functional analysis was conducted in the NT2/D1 human testicular cancer cell line using Dicer-substrate small interfering RNAs (DsiRNAs) targeting TG7. Gene… More >

Abdil Hakan Eren^*

Phyton-International Journal of Experimental Botany, Vol.94, No.10, pp. 3085-3107, 2025, DOI:10.32604/phyton.2025.069506 - 29 October 2025

Abstract The FAR1-related sequence (FAR1) gene family consists of transcription factors that originated from transposases and is crucial for light signaling and stress adaptation in plants. Despite the recognized importance of FAR1 genes in model organisms, their genomic architecture, structural variability, and expression patterns in Phaseolus vulgaris have yet to be investigated. This study offers the inaugural comprehensive genome-wide identification and characterization of the FAR1 gene family in P. vulgaris. A total of 27 PvulFAR1 genes were identified, and their chromosomal distribution, gene structures, conserved domains, and phylogenetic relationships were analyzed systematically. The promoter regions of these genes were discovered… More >

Amber Hassan¹, Badr Hafiz², Taghreed Alsinani³, Rakan Bokhari⁴, Dahlia Mirdad⁵, Awab Tayyib⁵, Alaa Alkhotani⁶, Ahmad Fallata⁷, Iman Mirza⁸, Eyad Faizo^9,10, Saleh Baeesa², Huda Alghefari¹¹, Maher Kurdi^11,*

Oncology Research, Vol.33, No.11, pp. 3293-3325, 2025, DOI:10.32604/or.2025.070031 - 22 October 2025

Abstract Background: Glioblastoma (GBM) remains the most aggressive primary brain tumour in adults, marked by pronounced cellular heterogeneity, diffuse infiltration, and resistance to conventional treatment. In recent years, transcriptomic profiling has provided valuable insights into the molecular mechanisms that govern the progression of glioblastoma. This systematic review aims to synthesise the current literature on dysregulated gene expression in GBM, focusing on gene signatures associated with stemness, immune modulation, extracellular matrix remodelling, metabolic adaptation, and therapeutic resistance. Methods: We conducted a systematic search of PubMed, The Cancer Genome Atlas (TCGA), Chinese Glioma Genome Atlas (CGGA), and the GlioVis… More >

Sae Hee Cheon¹, Sung-Whan Kim^2,3,*

BIOCELL, Vol.49, No.9, pp. 1697-1710, 2025, DOI:10.32604/biocell.2025.068743 - 25 September 2025

Abstract Objectives: Despite the considerable regenerative capacity exhibited by adipose-derived mesenchymal stem cells (ASCs), their genetic and molecular mechanisms remain incompletely understood. Methods: In this study, we analyzed the global gene expression profile of adipose-derived mesenchymal stem cells (ASCs) using microarray analysis and compared it with stromal vascular fraction (SVF) cells. Results: Microarray analysis revealed that ASCs express elevated levels of genes related to the extracellular matrix (ECM; extracellular matrix) and collagen, which are critical components of tissue remodeling and wound healing. Additionally, genes associated with cell growth, differentiation, motility, and plasticity were highly expressed. When compared… More >

JONG-HYUK AHN¹, JIN WOOK YI^2,3,*

Oncology Research, Vol.33, No.8, pp. 1909-1931, 2025, DOI:10.32604/or.2025.065847 - 18 July 2025

Abstract Background: With growing interest in space exploration, understanding microgravity’s impact on human health is essential. This study aims to investigate gene expression changes and migration and invasion potential in five thyroid-related cell lines cultured under simulated microgravity. Methods: Five thyroid-related cell lines—normal thyrocytes (Nthy-ori 3-1), papillary thyroid cancer (PTC) cells (SNU-790, TPC-1), poorly differentiated thyroid cancer cell (BCPAP), and anaplastic thyroid cancer cell (SNU-80)—were cultured under simulated microgravity (10⁻³ g) using a clinostat. Differentially expressed genes (DEGs) were analyzed using cDNA microarray, followed by functional annotation and assessment of aggressiveness via Transwell migration and invasion assays.… More >

Siti Ramadhani^1,2, Lestari Handayani², Theam Foo Ng³, Sumayyah Dzulkifly¹, Roziana Ariffin^4,5, Haldi Budiman⁶, Shir Li Wang^1,7,*

CMES-Computer Modeling in Engineering & Sciences, Vol.143, No.3, pp. 2711-2765, 2025, DOI:10.32604/cmes.2025.062709 - 30 June 2025

Abstract In recent years, feature selection (FS) optimization of high-dimensional gene expression data has become one of the most promising approaches for cancer prediction and classification. This work reviews FS and classification methods that utilize evolutionary algorithms (EAs) for gene expression profiles in cancer or medical applications based on research motivations, challenges, and recommendations. Relevant studies were retrieved from four major academic databases–IEEE, Scopus, Springer, and ScienceDirect–using the keywords ‘cancer classification’, ‘optimization’, ‘FS’, and ‘gene expression profile’. A total of 67 papers were finally selected with key advancements identified as follows: (1) The majority of papers… More > Graphic Abstract

Lucas Leal Lima¹, Angélica Souza Gouveia¹, Analice Martins Duarte¹, Filipe Schitini Salgado², Nathália Silva Oliveira¹, Monique da Silva Bonjour¹, Iana Pedro da Silva Quadros¹, Maria Goreti Almeida Oliveira¹, Flavia Maria Silva Carmo², Elizabeth Pacheco Batista Fontes¹, Humberto Josué de Oliveira Ramos^1,3,*

Phyton-International Journal of Experimental Botany, Vol.94, No.6, pp. 1787-1810, 2025, DOI:10.32604/phyton.2025.064068 - 27 June 2025

Abstract Sound contains mechanical signals that can promote physiological and biochemical changes in plants. Insects produce different sounds in the environment, which may be relevant to plant behavior. Thus, we evaluated whether signaling cascades are regulated differently by ecological sounds and whether they trigger molecular responses following those produced by herbivorous insects. Soybean plants were treated with two different sounds: chewing herbivore and forest ambient. The responses were markedly distinct, indicating that sound signals may also trigger specific cascades. Enzymes involved in oxidative metabolism were responsive to both sounds, while salicylic acid (SA) was responsive only… More >

Zijian Liu¹, Yong Shi², Chuanqi Li¹, Xiliang Zhang^3,*, Jian Zhou¹, Manoj Khandelwal^4,*

CMES-Computer Modeling in Engineering & Sciences, Vol.143, No.1, pp. 153-183, 2025, DOI:10.32604/cmes.2025.062426 - 11 April 2025

Abstract Given the growing concern over global warming and the critical role of carbon dioxide (CO₂) in this phenomenon, the study of CO₂-induced alterations in coal strength has garnered significant attention due to its implications for carbon sequestration. A large number of experiments have proved that CO₂ interaction time (T), saturation pressure (P) and other parameters have significant effects on coal strength. However, accurate evaluation of CO₂-induced alterations in coal strength is still a difficult problem, so it is particularly important to establish accurate and efficient prediction models. This study explored the application of advanced machine learning (ML)… More >

Fayez Althobaiti¹, Hadeer Darwish^1,*, Raghad Alruqayb¹, Saqer S. Alotaibi¹, Fahad E. Alharthi², Ibrahim Jafri¹, Sarah Awwadh Altalhi¹, Ghadi Alsharif^3,4, Hussam Awwadh E Althagafi⁵, Hesham Noureldeen⁶, Sarah Alharthi⁷, Jawaher Albaqami², Najla Amin T. Al Kashgry², Ahmed Noureldeen²

Phyton-International Journal of Experimental Botany, Vol.94, No.1, pp. 181-198, 2025, DOI:10.32604/phyton.2025.059387 - 24 January 2025

Abstract The interest in using the Datura stramonium plant is due to its natural products, which are used in many pharmaceutical industries. The objective of the current study was to assess the therapeutic and cytotoxic effects of the D. stramonium plant on two types of human cancer cell models (MCF7 and HT29) in vitro. A soxhlet apparatus was used to obtain methanolic extract from dried plant leaves. The recovered crude, after the solvent had evaporated, was then dispersed at varied concentrations of extract 100, 50, 20, and 0.0 µg/mL and tested to see how the cells responded. Also,… More >