Jujube (Ziziphus jujuba Mill.) belongs to the Rhamnaceae family and is a popular fruit tree species with immense economic and nutritional value. Here, we report a draft genome of the dry jujube cultivar 'Junzao' and the genome resequencing of 31 geographically diverse accessions of cultivated and wild jujubes (Ziziphus jujuba var. spinosa). Comparative analysis revealed that the genome of 'Dongzao', a fresh jujube, was ~86.5 Mb larger than that of the 'Junzao', partially due to...

Gnetophytes are an enigmatic gymnosperm lineage comprising three genera, Gnetum, Welwitschia and Ephedra, which are morphologically distinct from all other seed plants. Their distinctiveness has triggered much debate as to their origin, evolution and phylogenetic placement among seed plants. To increase our understanding of the evolution of gnetophytes, and their relation to other seed plants, we report here a high-quality draft genome sequence for Gnetum montanum, the first for any gnetophyte. By using a novel...

RNA editing generates genetic diversity in mammals by altering amino acid sequences, miRNA targeting site sequences, influencing the stability of targeted RNAs, and causing changes in gene expression. However, the extent to which RNA editing affect gene expression via modifying miRNA binding site remains unexplored. Here, we first profiled the dynamic A-to-I RNA editome across tissues of Duroc and Luchuan pigs. The RNA editing events at the miRNA binding sites were generated. The biological function...

Additional file 8: Table S4. The summary of imprinted lncRNA identified in 12 DAP sunflower endosperm.

Additional file 10: Table S5. The summary of lncRNAs exhibiting allele-specific expression in cultivated sunflower lines for edible fruit and oil identified in 12 DAP sunflower endosperm.

Additional file 2: Table S2. The genomic information of lncRNAs in sunflower endosperm at 12DAP.

Additional file 4: Table S1. Sample information and alpha diversity indexes.

Additional file 5: Table S2. The OTU table.

Additional file 8: Table S4. The summary of imprinted lncRNA identified in 12 DAP sunflower endosperm.

Supplemental material, sj-xlsx-1-imr-10.1177_03000605221141312 for CCK regulates osteogenic differentiation through TNFα/NF-κB in peri-implantitis by LongHang Chou, YaTing Chang, KaiWen Lan, Meng Liu, YuKun Lu, XiaoLei Li, PeiRu Li and Yue Xu in Journal of International Medical Research

Steroid-induced osteonecrosis of the femoral head (SONFH) is a progressive disease that leads to an increased disability rate. This study aimed to ascertain biomarkers, infiltrating immune cells, and therapeutic drugs for SONFH. The gene expression profile of the GSE123568 dataset was downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified using the NetworkAnalyst platform. Functional enrichment, protein-protein interaction network (PPI), and module analyses were performed using Metascape tools. An...

RNA editing generates genetic diversity in mammals by altering amino acid sequences, miRNA targeting site sequences, influencing the stability of targeted RNAs, and causing changes in gene expression. However, the extent to which RNA editing affect gene expression via modifying miRNA binding site remains unexplored. Here, we first profiled the dynamic A-to-I RNA editome across tissues of Duroc and Luchuan pigs. The RNA editing events at the miRNA binding sites were generated. The biological function...

Oral cancer is a common life-threatening malignancy having high mortality and morbidity rates. During the treatment process, individuals unavoidably experience severe side effects. It is essential to develop safer and more effective strategies. Currently, extracellular vesicles (EVs) and biomimetic nanoparticles are nanomedicines with long-term blood circulation and lower off-target toxicity that orchestrate immune responses and accumulate specifically in tumor sites. EVs create a synergetic effect by encapsulating drugs and collaborating with naturally loaded elements in...

Oral cancer is a common life-threatening malignancy having high mortality and morbidity rates. During the treatment process, individuals unavoidably experience severe side effects. It is essential to develop safer and more effective strategies. Currently, extracellular vesicles (EVs) and biomimetic nanoparticles are nanomedicines with long-term blood circulation and lower off-target toxicity that orchestrate immune responses and accumulate specifically in tumor sites. EVs create a synergetic effect by encapsulating drugs and collaborating with naturally loaded elements in...

Additional file 2.

Additional file 3: Table S3. GO Gene Ontology analysis of co-expressed protein-coding genes with all candidate lncRNAs.

Additional file 2: Table S1. The characteristics of methylation-driven lncRNAs.

Additional file 15. GTF File of candidate lncRNAs identified in sunflower endosperm.

Phytosulfokines (PSKs) are a class of tyrosine-sulfated pentapeptides. PSK-α, PSK-γ, and PSK-δ are three reported PSK members involved in regulating plant growth, development, and resistance to biotic and abiotic stresses. Here, we reported a novel type of PSK, PSK-ε with the sequence YSO3VYSO3TN, and its precursor proteins (MtPSKε, LjPSKε, and GmPSKε), specifically from legume species. PSK-ε peptide differs from PSK-δ by one amino acid and is close to PSK-δ in the phylogenetic relationship. Expression profile...

Phytosulfokines (PSKs) are a class of tyrosine-sulfated pentapeptides. PSK-α, PSK-γ, and PSK-δ are three reported PSK members involved in regulating plant growth, development, and resistance to biotic and abiotic stresses. Here, we reported a novel type of PSK, PSK-ε with the sequence YSO3VYSO3TN, and its precursor proteins (MtPSKε, LjPSKε, and GmPSKε), specifically from legume species. PSK-ε peptide differs from PSK-δ by one amino acid and is close to PSK-δ in the phylogenetic relationship. Expression profile...

Steroid-induced osteonecrosis of the femoral head (SONFH) is a progressive disease that leads to an increased disability rate. This study aimed to ascertain biomarkers, infiltrating immune cells, and therapeutic drugs for SONFH. The gene expression profile of the GSE123568 dataset was downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified using the NetworkAnalyst platform. Functional enrichment, protein-protein interaction network (PPI), and module analyses were performed using Metascape tools. An...

Soft tissue sarcomas (STSs) are rare, heterogeneous mesenchymal neoplasias. Understanding the tumor microenvironment (TME) and identifying potential biomarkers for prognosis associated with the TME of STS might provide effective clues for immune therapy. We evaluated the immune scores and stromal scores of STS patients by using the RNA sequencing dataset from The Cancer Genome Atlas (TCGA) database and the ESTIMATE algorithm. Then, the differentially expressed mRNAs (DEGs), miRNAs (DEMs) and lncRNAs (DELs) were identified after...

Oral cancer is a common life-threatening malignancy having high mortality and morbidity rates. During the treatment process, individuals unavoidably experience severe side effects. It is essential to develop safer and more effective strategies. Currently, extracellular vesicles (EVs) and biomimetic nanoparticles are nanomedicines with long-term blood circulation and lower off-target toxicity that orchestrate immune responses and accumulate specifically in tumor sites. EVs create a synergetic effect by encapsulating drugs and collaborating with naturally loaded elements in...

Additional file 1.

Additional file 4: Table S1. Sample information and alpha diversity indexes.