MiPRIME: An integrated and intelligent platform for mining primer and probe sequences of microbial species.

MOTIVATION: Accurately detecting pathogenic microorganisms requires effective primers and probe designs. Literature-derived primers are a valuable resource as they have been tested and proven effective in previous research. However, manually mining primers from published texts is time-consuming and limited in species scop. RESULTS: To address these challenges, we have developed MiPRIME, a real-time Microbial Primer Mining platform for primer/probe sequences extraction of pathogenic microorganisms with three highlights: i) Comprehensive integration. Covering more than 40 million articles and 548,942 organisms, the platform enables high-frequency microbial gene discovery from a global perspective, facilitating user-defined primer design and advancing microbial research. ii) Employing a BioBERT-based text mining model with 98.02% accuracy, greatly reducing information processing time. iii) using a primer ranking score, PRscore, for intelligent recommendation of species-specific primers. Overall, MiPRIME is a practical tool for primer mining in the pan-microbial field, saving time and cost of trial-and-error experiments. AVAILABILITY: The web is available at {{https://www.ai-bt.com}}. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Narrow Leaf21, encoding ribosomal protein RPS3A, controls leaf development in rice.

Leaf morphology influences photosynthesis, transpiration, and ultimately crop yield. However, the molecular mechanism of leaf development is still not fully understood. Here, we identified and characterized the narrow leaf21 (nal21) mutant in rice (Oryza sativa), showing a significant reduction in leaf width, leaf length and plant height, and increased tiller number. Microscopic observation revealed defects in the vascular system and reduced epidermal cell size and number in the nal21 leaf blade. Map-based cloning revealed that NAL21 encodes a ribosomal small subunit protein RPS3A. Ribosome-targeting antibiotics resistance assay and ribosome profiling showed a significant reduction in the free 40S ribosome subunit in the nal21 mutant. The nal21 mutant showed aberrant auxin responses in which multiple auxin response factors (ARFs) harboring upstream open-reading frames (uORFs) in their 5'-untranslated region were repressed at the translational level. The WUSCHEL-related homeobox 3A (OsWOX3A) gene, a key transcription factor involved in leaf blade lateral outgrowth, is also under the translational regulation by RPS3A. Transformation with modified OsARF11, OsARF16, and OsWOX3A genomic DNA (gDNA) lacking uORFs rescued the narrow leaf phenotype of nal21 to a better extent than transformation with their native gDNA, implying that RPS3A could regulate translation of ARFs and WOX3A through uORFs. Our results demonstrate that proper translational regulation of key factors involved in leaf development is essential to maintain normal leaf morphology.

Study of the mechanism of ultrasound-induced enhanced therapeutic effects of a chitosan-based nanoplatform.

Ultrasound (US) has been used in drug delivery systems for controlling drug release and activation of US-sensitive drugs for sonodynamic therapy of cancer. In our previous work, we found that erlotinib-grafted chitosan nanocomplexes loading perfluorooctyl bromide and hematoporphyrin under US irradiation showed satisfactory therapeutic effects for non-small cell lung cancer treatment. However, the underlying mechanism of US-mediated delivery and therapy has not been fully explored. In this work, the underlying mechanisms of the US-induced effects of the nanocomplexes were evaluated at the physical and biological levels after the chitosan-based nanocomplexes were characterized. The results showed that US could activate the cavitation effects and promote nanocomplexes penetrating into the depth of three-dimensional multicellular tumor spheroids (3D MCTSs) when nanocomplexes were selectively uptaken by targeted cancer cells, but push the extracellular nanocomplexes out of the 3D MCTSs. US demonstrated strong tissue penetration ability to effectively induce obvious reactive oxygen species production deep inside the 3D MCTSs. Under the US condition of 0.1 W cm-2for 1 min, US caused little mechanical damage and weak thermal effect to avoid severe cell necrosis, whereas cell apoptosis could be induced by collapse of mitochondrial membrane potential and the nucleus damage. The present study indicates that US can potentially be used jointly with nanomedicine to improve targeted drug delivery and combination therapy of deep-seated tumors.