Single-cell RNA sequencing (scRNA-seq) provides unprecedented insights into plant cellular diversity by enabling high-resolution analyses of gene expression at the single-cell level. However, the complexity of scRNA-seq data, including challenges in batch integration, cell type annotation, and gene regulatory network (GRN) inference, demands advanced computational approaches. To address these challenges, we developed scPlantLLM, a Transformer model trained on millions of plant single-cell data points. Using a sequential pretraining strategy incorporating masked language modeling and cell type annotation tasks, scPlantLLM generates robust and interpretable single-cell data embeddings. When applied to Arabidopsis thaliana datasets, scPlantLLM excels in clustering, cell type annotation, and batch integration, achieving an accuracy of up to 0.91 in zero-shot learning scenarios. Furthermore, the model demonstrates an ability to identify biologically meaningful GRNs and subtle cellular subtypes, showcasing its potential to advance plant biology research. Compared to traditional methods, scPlantLLM outperforms in key metrics such as adjusted rand index (ARI), normalized mutual information (NMI), and silhouette score (SIL), highlighting its superior clustering accuracy and biological relevance. scPlantLLM represents a foundation model for exploring plant single-cell expression atlases, offering unprecedented capabilities to resolve cellular heterogeneity and regulatory dynamics across diverse plant systems. The code used in this study is available at https://github.com/compbioNJU/scPlantLLM.

Copper (Cu²⁺) and zinc (Zn²⁺) are two kinds of heavy metals essential to living organisms. Cu²⁺ and Zn²⁺ at excessive concentrations can cause adverse effects on animals, but little is known about the thyroid-disrupting effects of these metals in fish, especially in the early developmental transition stage from embryos to larvae. Wild-type zebrafish embryos were used to expose to Cu²⁺ (0, 1.5, 15, and 150 μg/L) and Zn²⁺ (0, 20, 200, and 2000 μg/L) for 120 h. Thyroid hormone contents and transcriptional changes of the genes connected with the hypothalamic-pituitary-thyroid (HPT) axis were measured. Results showed that zebrafish embryos/larvae malformation rates were significantly increased in the Cu²⁺ and Zn²⁺ groups. Remarkably elevated thyroxine (T4) concentrations and reduced triiodothyronine (T3) concentrations were observed in Cu²⁺ and Zn²⁺ exposure fish. And the expression patterns of genes connected with the HPT axis were changed after Cu²⁺ and Zn²⁺ treatment. Based on principal component analysis (PCA) results, Zn²⁺ caused significant effects on the thyroid endocrine system at 200 μg/L, while Cu²⁺ resulted in thyroid disruption as low as 1.5 μg/L. In short, our study demonstrated that exposure to Cu²⁺ and Zn²⁺ induced developmental toxicity and thyroid disruption to zebrafish embryos/larvae.

In the filamentous cyanobacterium, Anabaena sp. PCC 7120, single heterocysts differentiate at semi-regular intervals in response to nitrogen stepdown. HetR is a principal regulator of heterocyst differentiation, and hetP and hetZ are two genes that are regulated directly by HetR. In a hetR mutant generated from the IHB (Institute of Hydrobiology) substrain of PCC 7120, heterocyst formation can be restored by moderate expression of hetZ and hetP. The resulting heterocysts are located at terminal positions. We used a tandem promoter, P_rbcLP_petE, to express hetZ and hetP strongly in the hetR mutant. Co-expression of hetZ and hetP enabled the hetR mutant to form multiple contiguous heterocysts at both terminal and intercalary positions. Expression of hetZ, alone resulted in terminally located heterocysts, whereas expression of hetP, alone produced enlarged cells in strings. In the absence of HetR, formation of heterocysts was insensitive to the peptide inhibitor, RGSGR.

In the past decades, the taxonomic status of the cyanobacterial family Phormidiaceae has always been chaotic and problematic. In this study, filamentous cyanobacteria were investigated in the east of China, and twenty strains isolated from different locations of Zhejiang Province were characterized. Using the polyphasic approach combining morphological, molecular and phylogenetic features, these strains were grouped within the members of the genera Ancylothrix and Potamolinea, the newly recorded genera of cyanobacteria in China. Based on the collected taxonomic information of the family Phormidiaceae, cyanobacterial systematics at family level were further discussed. This study provided a simple and efficient example to perform the phylogenetic evaluation for the monophyly and rationality of currently used families of cyanobacteria by using the regional strains based on the polyphasic approach.

Fungicides are frequently detected in the water bodies, however, the adverse effects of these fungicides on aquatic lives remain limited. To better understand the adverse effects of amisulbrom (AML) and isoflucypram (ISO) on embryogenesis, zebrafish embryos were exposed to two different fungicides, 0.75 μM amisulbrom (AML) and 2.5 μM isoflucypram (ISO), for 72 h. Transcriptome sequencing was employed to identify differentially expressed genes (DEGs) after AML and ISO exposure. A total of 571 and 3471 DEGs were detected between the libraries of the two fungicides-treated groups and the control, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that PPAR signaling pathway, phototransduction, ribosome and p53 signaling pathway were significantly enriched in response to both AML and ISO stress. Moreover, a number of DEGs involved in tyrosine metabolism, phagosome pathway, cell cycle pathway, extracellular matrix (ECM) receptor interaction pathway, and arginine and proline metabolism were specially enriched after exposure to AML; a number of DEGs involved in notch signaling pathway, drug metabolism, alanine, aspartate and glutamate metabolism, amino-acyl−tRNA biosynthesis, and protein processing in endoplasmic reticulum were significantly enriched after exposure to ISO. These results provide novel insights into the toxicological mechanisms underlying fish’s responses to fungicides.

Microcystis-dominated blooms cause environmental and ecological impacts worldwide. However, it is sometimes challenging to correctly identify Microcystis and its related genera. Radiocystis fernandoi Komárek et Komáková-Legnerová 1993, characterized by large cells and correspondingly large colonies with gas vesicles, has been frequently found in cyanobacterial blooms in Brazil. However, its molecular and phylogenetic identity is unknown because no valuable DNA sequences are available in GenBank. In this study, a strain with R. fernandoi morphology was successfully isolated from a cyanobacterial bloom sample in Lake Erhai, a subtropical plateau lake in China. Molecular characterization and phylogenetic analyses based on 16S rRNA and cpcBA genes revealed that the strain is different from the type species of the genus Radiocystis but formed a well-supported clade with the Microcystis species. The comparative results of the ITS region between 16S–23S rRNA genes also showed that the strain had very similar secondary structures to the species of Microcystis, supporting it as a new member of the genus Microcystis. Therefore, we propose the transfer of Radiocystis fernandoi into Microcystis fernandoi comb. nov. The correct identification and further taxonomic procedure for the bloom-forming cyanobacterial genera, such as Microcystis, Radiocystis, and Sphaerocavum, are also discussed in this study.