Xiubin Liu

MN-Suite is an open-source, locally deployable molecular networking toolkit developed through LLM-assisted software engineering to provide a flexible, server-independent workflow for natural product MS/MS analysis. The toolkit integrates six similarity algorithms and three spectral modes (MS2, neutral loss (NL), and hybrid MS2+NL), offering a customizable GUI-based framework for local preprocessing, network construction, and visualization. In the Aconitum data set examined here, the neutral-loss entropy-similarity strategy (NL-ES) produced the highest internal RCF score among the tested algorithm–data combinations (RCF = 0.537). By combining diagnostic-ion/neutral-loss filtering with a seed-neighborhood strategy, the MN-Suite prioritized 26 putative alkaloid analogues for further structural confirmation. These results support MN-Suite as a practical local workflow for configurable molecular networking and illustrate how domain experts can use LLM-assisted software engineering under human oversight to develop specialized computational tools.

Improving meat quality using safe phytogenic feed additives is of practical interest in yellow-feathered broiler production. This study aimed to evaluate the effects of dietary Stevia rebaudiana Bertoni extract (SBE) supplementation on meat quality traits. A total of 510 one-day-old, female yellow-feathered broilers were randomly allocated to six dietary treatments (0, 50, 100, 200, 300, and 400 mg/kg SBE) for 63 days. Meat sensory attributes, routine physicochemical characteristics, amino acid and fatty acid composition, electronic-nose profiles, and total volatile basic nitrogen (TVB–N) during refrigerated storage were assessed. Overall, the results provide evidence that dietary SBE supplementation is associated with changes in multiple meat quality-related parameters, supporting further evaluation of SBE as a phytogenic feed additive in yellow-feathered broilers.

Iron is an essential nutrient for all organisms. Feruloyl-COA 6-hydroxylase 1 (F6′H1) plays a pivotal role in iron uptake in plant roots by catalyzing the biosynthesis of iron-mobilizing scopoletin, a secondary metabolite also possessing antimicrobial activity. However, it remains unclear whether F6′H1-mediated iron uptake affects plant resistance to foliar pathogens and how such a process might be regulated. Here, we show that enhanced expression of 2-oxoglutarate-dependent dioxygenases 2 (CmOGD2), a homolog of F6′H1 in Citron C-05 (Citrus medica L.), confers resistance to citrus canker caused by Xanthomonas citri subsp. citri (Xcc). CmOGD2-mediated pathogen resistance is achieved by promoting iron uptake and the accumulation of reactive oxygen species (ROS), which likely results in ferroptosis. Furthermore, CmOGD2 interacts with the enolase CmENO2 to destabilize CmZAT10.1, a transcriptional activator of CmOGD2, thereby forming a negative feedback loop that limits CmOGD2 expression. Notably, the Xcc effector pthA4 interferes with the CmOGD2–CmENO2 interaction, likely via a decoy mechanism, leading to CmZAT10.1 accumulation. These findings reveal complex regulatory mechanisms underlying the critical role of CmOGD2 in mediating Xcc resistance through iron- and ROS-dependent ferroptosis.

Based on network pharmacological analysis and molecular docking techniques, the main components of M. cordata for the treatment of bovine relevant active compounds in M. cordata were searched for through previous research bases and literature databases, and then screened to identify candidate compounds based on physicochemical properties, pharmacokinetic parameters, bioavailability, and drug-like criteria. Target genes associated with hoof disease were obtained from the GeneCards database. Compound−target, compound−target−pathway−disease visualization networks, and protein−protein interaction (PPI) networks were constructed by Cytoscape. Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed in R language. Molecular docking analysis was done using AutoDockTools. The visual network analysis showed that four active compounds, sanguinarine, chelerythrine, allocryptopine and protopine, were associated with the 10 target genes/proteins (SRC, MAPK3, MTOR, ESR1, PIK3CA, BCL2L1, JAK2, GSK3B, MAPK1, and AR) obtained from the screen. The enrichment analysis indicated that the cAMP, PI3K-Akt, and ErbB signaling pathways may be key signaling pathways in network pharmacology. The molecular docking results showed that sanguinarine, chelerythrine, allocryptopine, and protopine bound well to MAPK3 and JAK2. A comprehensive bioinformatics-based network topology strategy and molecular docking study has elucidated the multi-component synergistic mechanism of action of M. cordata in the treatment of bovine hoof disease, offering the possibility of developing M. cordata as a new source of drugs for hoof disease treatment.

Using antibiotics as feed additives have been successively banned worldwide from 1986; therefore, it is an urgent task to finding safe and effective alternatives. As natural products of plant origin, essential oils (EOs) are an outstanding option due to their reported bioactivity. In this research, ten EOs of Labiatae species were extracted by steam distillation and its chemical constituents were identified by gas chromatography-mass spectrometry (GC-MS). A total of 123 chemical compounds, including alkenes, phenols, aldehydes and ketones, were identified. The results of antioxidant activity carried out through DPPH free radical scavenging (DPPH) and ferric reducing antioxidant power (FRAP), showing that EOs of Ocimum basilicum Linn. (ObEO), Thymus mongolicus Ronn. (TmEO), Origanum vulgare Linn. (OvEO) and Mosla chinensis Maxim. (McEO) have strong antioxidant activities. Their 50%-inhibitory concentration (IC₅₀) value was Staphylococcus aureus (S. aureus) and their minimal inhibitory concentrations (MIC) value was 1 μL/mL, 2 μL/mL, and 2 μL/mL, respectively. In conclusion, the results in this work demonstrate the possibility for development and application of EOs as potential feed additives.