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Quantitative model for genome-wide cyclic AMP receptor protein binding site identification and characteristic analysis
Brief Bioinform. 2023 Apr 27:bbad138. doi: 10.1093/bib/bbad138. Online ahead of print.ABSTRACTCyclic AMP receptor proteins (CRPs) are important transcription regulators in many species. The prediction of CRP-binding sites was mainly based on position-weighted matrixes (PWMs). Traditional prediction methods only considered known binding motifs, and their ability to discover inflexible binding patterns was limited. Thus, a novel CRP-binding site prediction model called CRPBSFinder was developed in this research, which combined the hidden Markov model, knowledge-based PWMs and structure-based binding affinity matrixes. We tra...
Source: Briefings in Bioinformatics - April 28, 2023 Category: Bioinformatics Authors: Yigang Chen Yang-Chi-Dung Lin Yijun Luo Xiaoxuan Cai Peng Qiu Shidong Cui Zhe Wang Hsi-Yuan Huang Hsien-Da Huang Source Type: research

Proteomic insights of chitosan mediated inhibition of Fusarium oxysporum f. sp. cucumerinum
This study gives a snapshot of the molecular basis of fungal inhibition by chitosan resulting in disease resistance in cucumber plants after inoculation with chitosan-treated FOC by explaining how chitosan restricted disease severity (i.e., down-regulating the plant cell wall degrading enzymes, FOC self-attack, hindering FOC structural and functional protein biosynthesis and DNA biosynthesis and affecting FOC transporter proteins). This study contributes to putting more weight on using the bioactive natural compound chitosan as an antifungal material instead of applying chemical fungicides in agriculture. SIGNIGICANCE: Fus...
Source: Journal of Proteomics - March 22, 2022 Category: Biochemistry Authors: Eman Elagamey Magdi A E Abellatef Md Yasir Arafat Source Type: research

Molecules, Vol. 26, Pages 2294: Physiological and Transcriptomic Analysis Provide Insight into Low Temperature Enhancing Hypericin Biosynthesis in Hypericum perforatum
i Li Jianhe Wei Hypericin (Hyp), well-known as an antidepressant, is mainly extracted from Hypericum perforatum. Although Hyp accumulation and biomass are greater at lower compared to higher temperature, the regulation mechanism has not been reported. Here, the physiological characteristics and transcriptome of H. perforatum grown at 15 and 22 °C were determined and analyzed by HPLC and de novo sequencing. The results showed that the stomatal density and opening percentages were 1.1- and 1.4-fold more, and the Hyp content was 4.5-fold greater at 15 °C compared to 22 °C. A total of 1584 differentially expressed gen...
Source: Molecules - April 15, 2021 Category: Chemistry Authors: Hongyan Su Jie Li Sijin Chen Ping Sun Hua Xing Delong Yang Xiaona Zhang Mengfei Li Jianhe Wei Tags: Article Source Type: research