YUSEN ZHANG^1,2,3, LIPING LIU^1,2,3, BIWEI LUO^1,2,3, HONGGUI TANG^1,2,3, XIAOFANG YU^1,2,3, SHIYUN BAO^1,2,3,*

Oncology Research, Vol.31, No.3, pp. 317-331, 2023, DOI:10.32604/or.2023.028418

Abstract Background: Cholangiocarcinoma (CCA) represents the epithelial cell cancer with high aggressiveness whose five-year survival rate is poor with standard treatment. Calcyclin-binding protein (CACYBP) shows aberrant expression within several malignant tumors, but the role of CACYBP in CCA remains unknown. Methods: Immunohistochemical (IHC) analysis was used to identify CACYBP overexpression in clinical samples of CCA patients. Moreover, its correlation with clinical outcome was revealed. Furthermore, CACYBP’s effect on CCA cell growth and invasion was investigated in vitro and in vivo using loss-of-function experiments. Results: CACYBP showed up-regulation in CCA, which predicts the dismal prognostic outcome. CACYBP had an important effect on… More >

RYAN STARK^*

BIOCELL, Vol.47, No.6, pp. 1191-1198, 2023, DOI:10.32604/biocell.2023.027838

Abstract Protein-mediated interactions are the fundamental mechanism through which cells regulate health and disease. These interactions require physical contact between proteins and their respective targets of interest. These targets include not only other proteins but also nucleic acids and other important molecules as well. These proteins are often involved in multibody complexes that work dynamically to regulate cellular health and function. Various techniques have been adapted to study these important interactions, such as affinity-based assays, mass spectrometry, and fluorescent detection. The application of these techniques has led to a greater understanding of how protein interactions are responsible for both the instigation… More >

Yeyao Du^1,#, Ye Zhang^2,#, Yang Song¹, Zhuo Zhang¹, Sujie Fan¹, Hanzhu Zhang¹, Piwu Wang^1,*

Phyton-International Journal of Experimental Botany, Vol.92, No.6, pp. 1907-1920, 2023, DOI:10.32604/phyton.2023.027607

Abstract Soybean (Glycine max (Linn.) Merr.) annual leguminous crop is cultivated all over the world. The occurrence of diseases has a great impact on the yield and quality of soybean. In this study, based on the RNA-seq of soybean variety M18, a complete CDS (Coding sequence) GmPR1L of the pathogenesis-related protein 1 family was obtained, which has the ability to resist fungal diseases. The overexpression vector and interference expression vector were transferred into tobacco NC89, and the resistance of transgenic tobacco (Nicotiana tabacum L.) to Botrytis cinerea infection was identified. The results show that: Compared with the control, the activities of… More >

Minmin Xiao¹, Moxiang Cheng¹, Shuangquan Xie¹, Xiushuang Wang¹, Xingming Hao², Li Zhuang^1,*

Phyton-International Journal of Experimental Botany, Vol.92, No.6, pp. 1841-1857, 2023, DOI:10.32604/phyton.2023.027369

Abstract To clarify the characteristics of photoinhibition and the primary defense mechanisms of ephemeral plant leaves against photodestruction under high temperature stress, inhibitors and the technology to determine chlorophyll fluorescence were used to explore the protective effects of D1 protein turnover and the lutein cycle in the high temperature stress of the leaves of three ephemeral plants. The results showed that the maximum light conversion efficiency (Fv/Fm) of the ephemeral plant leaves decreased, and the initial fluorescence (Fo) increased under 35°C ± 1°C heat stress for 1–4 h or on sunny days in the summer. Both Fv/Fm and Fo could be… More >

Xiaotian Liang^1,#, Qi Wen^1,#, Rui Luo¹, Yanxin Zhang¹, Mingda Yin¹, Yanpeng Wen¹, Xuemei Hu¹, Zhiyan Wang¹, Yumiao Huo¹, Fenglan Huang^{1,2,3,4,5,6,*}

Phyton-International Journal of Experimental Botany, Vol.92, No.6, pp. 1765-1792, 2023, DOI:10.32604/phyton.2023.026935

Abstract Castor bean (Ricinus communis L.), is one of the top 10 oilseed crops in the world and, therefore, of high economic value. Hybridization is one of the most effective ways to breed new varieties with high yield, high oil content, and better stress resistance. Therefore, prediction of desired traits in castor hybrid offspring is particularly important. In this study, proteomic analysis was performed to identify differentially expressed proteins (DEPs) in seeds between castor hybrid offspring and their female (Lm female line aLmAB₂) and male parents (CSR·181). Among the DEPs upregulated in the seeds of hybrid offspring, the majority were related… More >

QINGCHEN LUO^1,#,*, JIALU FENG^2,#, XIUQI DENG¹

BIOCELL, Vol.47, No.5, pp. 1145-1158, 2023, DOI:10.32604/biocell.2023.027847

Abstract As sessile organisms, plants possess a complex system to cope with environmental changes. Ca²⁺ functions as a vital second messenger in the stress signaling of plants, and the CBL-interacting protein kinases (CIPKs) serve as essential elements in the plant Ca²⁺ signaling pathway. In this study, calcineurin B-like protein-interacting protein kinase 26 (BdCIPK26) from Brachypodium distachyon was characterized. Overexpression of BdCIPK26 enhanced tolerance to drought and salt stress of transgenic plants. Further investigations revealed that BdCIPK26 participated in abscisic acid (ABA) signaling, conferred hypersensitivity to exogenous ABA in transgenic plants, and promoted endogenous ABA biosynthesis. Moreover, BdCIPK26 was found to maintain… More >

Fahriye Gemci^1,*, Turgay Ibrikci², Ulus Cevik³

Computer Systems Science and Engineering, Vol.46, No.3, pp. 3703-3713, 2023, DOI:10.32604/csse.2023.032706

Abstract The study aims to find a successful solution by using computer algorithms to detect remote homologous proteins, which is a significant problem in the bioinformatics field. In this experimental study, structural classification of proteins (SCOP) 1.53, SCOP benchmark, and the newly created SCOP protein database from the structural classification of proteins—extended (SCOPe) 2.07 were used to detect remote homolog proteins. N-gram method and then Term Frequency-Inverse Document Frequency (TF-IDF) weighting were performed to extract features of the protein sequences taken from these databases. Next, a smoothing process on the obtained features was performed to avoid misclassification. Finally, the proteins with… More >

Isam Abu-Qasmieh, Amjed Al Fahoum^*, Hiam Alquran, Ala’a Zyout

CMC-Computers, Materials & Continua, Vol.75, No.2, pp. 3971-3991, 2023, DOI:10.32604/cmc.2023.037431

Abstract Proteins are essential for many biological functions. For example, folding amino acid chains reveals their functionalities by maintaining tissue structure, physiology, and homeostasis. Note that quantifiable protein characteristics are vital for improving therapies and precision medicine. The automatic inference of a protein’s properties from its amino acid sequence is called “basic structure”. Nevertheless, it remains a critical unsolved challenge in bioinformatics, although with recent technological advances and the investigation of protein sequence data. Inferring protein function from amino acid sequences is crucial in biology. This study considers using raw sequencing to explain biological facts using a large corpus of protein… More >

Mortaza Hajyzadeh^*

Phyton-International Journal of Experimental Botany, Vol.92, No.5, pp. 1649-1664, 2023, DOI:10.32604/phyton.2023.028028

Abstract Abiotic stresses at different growth stages in the life of plants negatively affect yield productivity. Therefore, plants, including Amaranthus hypochondriacus, develop adaptive strategies to face the stresses and expand functional diversification. In plants, the mitochondrial transcription termination factors (mTERF) are essential functions in regulation, and organelles (mitochondria and chloroplasts) control gene expression (OGE) under several stress conditions. Based on the in-silico-wide genome and transcriptome analysis, twenty-four mTERF genes were detected in the main targeted mitochondria organelles clustered into three different main groups. The chromosomal location and gene duplication analysis indicated one segmental and one tandem duplication in the genome. The… More >

JULIANA A. PORTES¹, ROSSIANE C. VOMMARO¹, LUCIO AYRES CALDAS², ERICA S. MARTINS-DUARTE^3,*

BIOCELL, Vol.47, No.4, pp. 929-950, 2023, DOI:10.32604/biocell.2023.026629

Abstract Toxoplasma gondii is a protozoan of worldwide distribution and the agent of toxoplasmosis. It is estimated that 30%–50% of the world population could be infected with this parasite. Although the infection in immunocompetent individuals is mostly asymptomatic, the disease in immunosuppressed and pregnant is a risk condition. As a member of the phylum Apicomplexa, T. gondii has an obligatory intracellular lifestyle; therefore, invading a host cell and establishing it inside a parasitophorous vacuole (PV) are mandatories for the survival of this parasite. The construction of a perfect intracellular niche for T. gondii requires the secretion of an arsenal of proteins… More >