Transcription activation is tightly associated with the openness of chromatin and allows direct contact between transcriptional regulators and their targeted DNA for gene expression. However, there are limited studies on the annotation of open chromatin regions (OCRs) in rice (Oryza sativa), especially those in reproductive organs. Here, we characterized OCRs in rice pistils and anthers with an assay for transposase-accessible chromatin using sequencing. Despite a large overlap, we found more OCRs in pistils than in anthers. These OCRs were enriched in gene transcription start sites (TSSs) and showed tight associations with gene expression. Transcription factor (TF) binding motifs were enriched at these OCRs as validated by TF chromatin immunoprecipitation followed by sequencing. Pistil-specific OCRs provided potential regulatory networks by binding directly to the targets, indicating that pistil-specific OCRs may be indicators of cis-regulatory elements in regulating pistil development, which are absent in anthers. We also found that open chromatin of pistils and anthers responded differently to low temperature (LT). These data offer a comprehensive overview of OCRs regulating reproductive organ development and LT responses in rice.

The role of plastocyanin in regulating photosynthetic and high light response remains unclear. Here we found that a larger PC pool effectively increased the linear electron flow while lowering the reduction state of plastoquinone (PQ) and ferredoxin (Fd), subsequently decreasing ROS formation. The biomass yield was increased in PC-rich cells, which, along with a decrease in intracellular starch content, up-regulated the RuBisCO activity, thereby enhancing carbon fixation. Meanwhile, we observed that ADP-glucose pyrophosphorylase activity was down-regulated, probably due to a lower Fd reduction state leading to reduced starch synthesis. During the transition from low to high light, PC accumulates to a substantial level, effectively reducing the reduction state of PQ and restoring Fv/Fm. These findings highlight the critical function of PC as a redox capacitor in affecting PET, CO₂ fixation, and high light acclimation by modulating the redox states of the electron transport chain (ETC) and its potential for optimizing photosynthetic processes.

In the contemporary field of life sciences, researchers have gradually recognized the critical role of microbes in maintaining human health. However, traditional biological experimental methods for validating the association between microbes and diseases are both time-consuming and costly. Therefore, developing effective computational methods to predict potential associations between microbes and diseases is an important and urgent task. In this study, we propose a novel computational framework, called GCATCMDA, for forecasting potential associations between microbes and diseases. Firstly, we construct Gaussian kernel similarity networks for microbes and diseases using known microbe-disease association data. Then, we design a feature encoder that combines graph convolutional network and graph attention mechanism to learn the node features of networks, and propose a feature dual-fusion module to effectively integrate node features from each layer's output. Next, we apply the feature encoder separately to the microbe similarity network, disease similarity network, and microbe-disease association network, and enhance the consistency of features for the same nodes across different association networks through contrastive learning. Finally, we pass the microbe and disease features into an inner product decoder to obtain the association scores between them. Experimental results demonstrate that the GCATCMDA model achieves superior predictive performance compared to previous methods. Furthermore, case studies confirm that GCATCMDA is an effective tool for predicting microbe-disease associations in real situations.

Chlamydomonas reinhardtii (C. reinhardtii) is a single-cell green alga that can be easily genetically manipulated. With its favorable characteristics of rapid growth, low cost, non-toxicity, and the ability for post-translational protein modification, C. reinhardtii has emerged as an attractive option for the biosynthesis of various valuable products. To enhance the expression level of exogenous genes and overcome the silencing of foreign genes by C. reinhardtii, synthetic promoters such as the chimeric promoter AR have been constructed and evaluated. In this study, a synthetic promoter GA was constructed by hybridizing core fragments from the natural promoters of the acyl carrier protein gene (ACP2) and the glutamate dehydrogenase gene (GDH2). The GA promoter exhibited a significant increase (7 times) in expressing GUS, over the AR promoter as positive control. The GA promoter also displayed a strong responsiveness to blue light (BL), where the GUS expression was doubled compared to the white light (WL) condition. The ability of the GA promoter was further tested in the expression of another exogenous cadA gene, responsible for catalyzing the decarboxylation of lysine to produce cadaverine. The cadaverine yield driven by the GA promoter was increased by 1–2 times under WL and 2–3 times under BL as compared to the AR promoter. This study obtained, for the first time, a blue light-responsive GDH2 minimal fragment in C. reinhardtii, which delivered a doubling effect under BL when used alone or in hybrid. Together with the strong GA synthetic promoter, this study offered useful tools of synthetic biology to the algal biotechnology field.