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Essential mineral elements such as zinc and iron play a crucial role in maintaining crop growth and development, as well as ensuring human health. Foxtail millet is an ancient food crop rich in mineral elements and constitutes an important dietary supplement for nutrient-deficient populations. The ZIP (ZRT, IRT-like protein) transporters are primarily responsible for the absorption, transportation and accumulation of Zn, Fe and other metal ions in plants. Here, we identified 14 ZIP transporters in foxtail millet (SiZIP) and systematically characterized their phylogenetic relationships, expression characteristics, sequence variations, and responses to various abiotic stresses. As a result, SiZIPs display rich spatiotemporal expression characteristics in foxtail millet. Multiple SiZIPs demonstrated significant responses to Fe, Cd, Na, and K metal ions, as well as drought and cold stresses. Based on homologous comparisons, expression characteristics and previous studies, the functions of SiZIPs were predicted as being classified into several categories: absorption/efflux, transport/distribution and accumulation of metal ions. Simultaneously, a schematic diagram of SiZIP was drawn. In general, SiZIPs have diverse functions and extensively involve in the transport of metal ions and osmotic regulation under abiotic stresses. This work provides a fundamental framework for the transport and accumulation of mineral elements and will facilitate the quality improvement of foxtail millet. [ABSTRACT FROM AUTHOR]

Golden pompano, Trachinotus ovatus, as a highly nutritious commercially valuable marine fish, has become one of the preferred species for many fish farmers due to its rapid growth, wide adaptability, and ease of feeding and management. However, with the expansion of aquaculture scale, bacterial and parasitic diseases have also become major threats to the golden pompano industry. This study, based on comparative genomics, shows the possibility of preferential evolution of freshwater fish over marine fish by analyzing the phylogenetic relationships and divergence times of 14 marine fish and freshwater fish. Furthermore, we identified antimicrobial peptide genes from 14 species at the genomic level and found that the number of putative antimicrobial peptides may be related to species evolution. Subsequently, we classified the 341 identified AMPs from golden pompano into 38 categories based on the classification provided by the APD3. Among them, TCP represented the highest proportion, accounting for 23.2% of the total, followed by scolopendin, lectin, chemokine, BPTI, and histone-derived peptides. At the same time, the distribution of AMPs in chromosomes varied with type, and covariance analysis showed the frequency of its repeat events. Enrichment analysis and PPI indicated that AMP was mainly concentrated in pathways associated with disease immunity. In addition, our transcriptomic data measured the expression of putative AMPs of golden pompano in 12 normal tissues, as well as in the liver, spleen, and kidney infected with Streptococcus agalactiae and skin infected with Cryptocaryon irritans. As the infection with S. agalactiae and C. irritans progressed, we observed tissue specificity in the number and types of responsive AMPs. Positive selection of AMP genes may participate in the immune response through the MAPK signaling pathway. The genome-wide identification of antimicrobial peptides in the golden pompano provided a complete database of potential AMPs that can contribute to further understanding the immune mechanisms in pathogens. AMPs were expected to replace traditional antibiotics and be developed into targeted drugs against specific bacterial and parasitic pathogens for more precise and effective treatment to improve aquaculture production.

Mitigating the function of acquired transgenes in crop wild/weedy relatives can provide an ideal strategy to reduce the possible undesired environmental impacts of pollen-mediated transgene flow from genetically engineered (GE) crops. To explore a transgene mitigation system in rice, we edited the seed-shattering genes, SH4 and qSH1, using a weedy rice line (“C9”) that originally had strong seed shattering. We also analyzed seed size-related traits, the total genomic transcriptomic data, and RT-qPCR expression of the SH4 or qSH1 gene-edited and SH4/qSH1 gene-edited weedy rice lines. Substantially reduced seed shattering was observed in all gene-edited weedy rice lines. The single gene-edited weedy rice lines, either the SH4 or qSH1 gene, did not show a consistent reduction in their seed size-related traits. In addition, reduced seed shattering was closely linked with the weakness and absence of abscission layers and reduced abscisic acid (ABA). Additionally, the genes closely associated with ABA biosynthesis and signaling transduction, as well as cell-wall hydrolysis, were downregulated in all gene-edited weedy rice lines. These findings facilitate our deep insights into the underlying mechanisms of reduced seed shattering in plants in the rice genus Oryza. In addition, such a mitigating technology also has practical applications for reducing the potential adverse environmental impacts caused by transgene flow and for managing the infestation of weedy rice by acquiring the mitigator from GE rice cultivars through natural gene flow.

Acute myeloid leukemia (AML) is an aging-related and heterogeneous hematopoietic malignancy. In this study, a total of 1,474 newly diagnosed AML patients with RNA sequencing data were enrolled, and targeted or whole exome sequencing data were obtained in 94% cases. The correlation of aging-related factors including age and clonal hematopoiesis (CH), gender, and genomic/transcriptomic profiles (gene fusions, genetic mutations, and gene expression networks or pathways) was systematically analyzed. Overall, AML patients aged 60 y and older showed an apparently dismal prognosis. Alongside age, the frequency of gene fusions defined in the World Health Organization classification decreased, while the positive rate of gene mutations, especially CH-related ones, increased. Additionally, the number of genetic mutations was higher in gene fusion--negative (GF-) patients than those with GF. Based on the status of CH- and myelodysplastic syndromes (MDS)-related mutations, three mutant subgroups were identified among the GF-AML cohort, namely, CH-AML, CH-MDS-AML, and other GF-AML. Notably, CH-MDS-AML demonstrated a predominance of elderly and male cases, cytopenia, and significantly adverse clinical outcomes. Besides, gene expression networks including HOXA/B, platelet factors, and inflammatory responses were most striking features associated with aging and poor prognosis in AML. Our work has thus unraveled the intricate regulatory circuitry of interactions among different age, gender, and molecular groups of AML. [ABSTRACT FROM AUTHOR]

This article discusses a study on gene editing in Salvia miltiorrhiza, a plant used in Eastern medicine to treat cardiovascular diseases. The researchers developed a protoplast regeneration system for S. miltiorrhiza using CRISPR/Cas9 gene editing technology. They targeted seven transcription factor genes involved in the production of bioactive compounds in the plant. The study demonstrated high-efficiency gene editing and the regeneration of knockout plants, which could potentially enhance the contents of active compounds in medicinal plants. [Extracted from the article]

Introduction: Oculomotor nerve palsy (ONP) arises from primary abnormalities in the central neural pathways that control the extraocular muscles (EOMs). Long non-coding RNAs (lncRNAs) have been found to be involved in the pathogenesis of various neuroparalytic diseases. However, little is known about the role of lncRNAs in ONP. Methods: We collected medial rectus muscle tissue from ONP and constant exotropia (CXT) patients during strabismus surgeries for RNA sequencing analysis. Differentially expressed mRNAs and lncRNAs were revealed and included in the functional enrichment analysis. Co-expression analysis was conducted between these differentially expressed mRNAs and lncRNAs, followed by target gene prediction of differentially expressed lncRNAs. In addition, lncRNA-microRNA and lncRNA-transcription factor-mRNA interaction networks were constructed to further elaborate the pathological changes in medial rectus muscle of ONP. Furthermore, RT-qPCR was applied to further validate the expression levels of important lncRNAs and mRNAs, whose clinical significance was examined by receiver operating characteristic (ROC) curve analysis. Results: A total of 618 differentially expressed lncRNAs and 322 differentially expressed mRNAs were identified. The up-regulated mRNAs were significantly related to cholinergic synaptic transmission (such as CHRM3 and CHRND) and the components and metabolism of extracellular matrix (such as CHI3L1 and COL19A1), while the down-regulated mRNAs were significantly correlated with the composition (such as MYH7 and MYL3) and contraction force (such as MYH7 and TNNT1) of muscle fibers. Co-expression analysis and target gene prediction revealed the strong correlation between MYH7 and NR_126491.1 as well as MYOD1 and ENST00000524479. Moreover, the differential expressions of lncRNAs (XR_001739409.1, NR_024160.1 and XR_001738373.1) and mRNAs (CDKN1A, MYOG, MYOD1, MYBPH, TMEM64, STATH, and MYL3) were validated by RT-qPCR. ROC curve analysis showed that lncRNAs (XR_001739409.1, NR_024160.1, and NR_002766.2) and mRNAs (CDKN1A, MYOG, MYOD1, MYBPH, TMEM64, and STATH) might be promising biomarkers of ONP. Conclusions: These results may shed light on the molecular biology of EOMs of ONP, as well as the possible correlation of lncRNAs and mRNAs with clinical practice. [ABSTRACT FROM AUTHOR]

Introduction: The aim of this study was to develop a prognostic model for chronic lymphocytic leukemia (CLL). Methods: GEO2R was used to retrieve the gene expression data of CLL and normal B cells from the Gene Expression Omnibus (GEO; GSE22529 and GSE50006 datasets) database. Practical Extraction and Report Language was used to extract the gene expression and overall survival (OS) data of CLL patients from the Chronic Lymphocytic Leukemia – ES (CLLE-ES) project in the International Cancer Genome Consortium (ICGC) database. Cox regression with Lasso was used to create and validate a prognostic model for CLL. Results: A total of 267 genes exhibited differential expression between CLL and normal B cells. Cox univariate analysis identified 14 DEGs that correlated with OS. Lasso multivariate evaluation demonstrated that AKAP12 and IGFBP4 are independent prognostic factors for CLL. Kaplan-Meier survival analysis revealed a significant association between the estimated risk score and survival. The area under the receiver operating characteristic curve was calculated to be 0.97, indicating high predictive accuracy. In addition, high AKAP12 and IGFBP4 risk scores were associated with the high incidence of trisomy 12q. Conclusion: Taken together, AKAP12 and IGFBP4 are independent prognostic factors for CLL. [ABSTRACT FROM AUTHOR]

The plant architecture of higher plants is regulated through environmental and genetic factors, as well as phytohormones. Phytohormones play a critical role in regulating shoot branching. We determined the branching phenotype of D16 and N99-6, the content of strigolactones, the genetic expression level, and the interaction between auxin and strigolactones. We found that the branching development of the two soybean varieties under shading was significantly slower than that under normal light. The average branch length of N99-6 decreased by 40.9% after shading; however, the branch length of D16 was not significantly affected. Meanwhile, the branch formation rate in D16 was significantly higher than in N99-6. In addition, after shading treatment, the content of strigolactones in D16 and N99-6 axillary buds increased significantly, and the expression of phytochrome genes, PhyA and PhyB, showed opposite changes. However, strigolactone synthesis gene GmMAX4 and signal transduction gene GmMAX2 expression levels of D16 were lower than those of N99-6 after 24 h of shading. In addition, the application of strigolactone inhibitor TIS108 and auxin inhibitor NPA to soybean had no significant effect on the branch phenotype. The expression of the GmMAX2 gene was significantly up-regulated after the external application of the auxin analog, and the expression of auxin transporter gene GmPINI was significantly down-regulated after external application of the strigolactone analog under shade. In this study, we investigated the adverse effect of shade on soybean branching development, which may be due to the interaction of strigolactones with auxins. [ABSTRACT FROM AUTHOR]

Aerobic glycolysis is critical for the energy metabolism of cancer cells. This study focuses on the regulation of forkhead box A2 (FOXA2) on pyruvate kinase M2 (PKM2) and their effects on the glycolytic activity and malignant phenotype of thyroid carcinoma (THCA) cells. By analysing four Gene Expression Omnibus datasets and querying bioinformatics systems, we obtained FOXA2 as a poorly expressed transcription factor in THCA. Later, we validated decreased mRNA and protein levels of FOXA2 in THCA cells by quantitative polymerase chain reaction and western blot assays. FOXA2 upregulation in THCA cells suppressed the glucose uptake and lactate production, and it reduced the extracellular acidification rate, but increased the oxygen consumption rate of cells. Meanwhile, the FOXA2 overexpression blocked the proliferation and mobility, and the tumourigenic activity of cancer cells. The chromatin immunoprecipitation and luciferase assays showed that FOXA2 bound to PKM2 promoter and suppressed the transcription of PKM2, which was highly expressed in THCA cells. Further upregulation of PKM2 elevated the β‐catenin, c‐Myc and cyclin D1 levels and restored the glycolytic activity as well as the malignant properties of cancer cells. Collectively, this work reveals that FOXA2 suppresses aerobic glycolysis and progression of THCA by blocking PKM2 transcription and inactivating the Wnt/β‐catenin pathway. [ABSTRACT FROM AUTHOR]

Background: Microsatellite instability‐high (MSI‐H) subgroup of gastric cancer (GC) is characterized by a high tumor mutational burden, increased lymphocytic infiltration, and enhanced inflammatory cytokines. GC patients with MSI‐H status have a good response to immune checkpoint blockade management. However, heterogeneity within the subtype and the underlying mechanisms of shaping tumor microenvironments remain poorly understood. Methods: RNA expression levels and clinical parameters of GC were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The data were analyzed using single‐sample Gene Set Enrichment Analysis (ssGSEA), univariate Cox regression, multivariate Cox regression, and Least Absolute Shrinkage Selection Operator (LASSO) regression. In addition, multiplex immunohistochemistry (mIHC) was used in our clinical cohort for the tumor microenvironment study. Results: By ssGSEA and survival analysis, the EMT signaling pathway was identified as a representative pathway, which can stratify the patients with MSI‐H GC with significant survival predictive power. Then, a novel representative EMT‐related five‐gene signature (namely CALU, PCOLCE2, PLOD2, SGCD, and THBS2) was established from EMT signaling gene set, which sensitivity and specificity were further validated in the independent GEO database (GSE62254) cohort for disease outcome prediction. Based on public single‐cell data and in situ immunohistochemistry, we found that most of these five genes were abundantly expressed in cancer‐associated fibroblasts. Furthermore, patients with high or low risk divided by this five‐gene signature exhibited a strong correlation of the distinct patterns of tumor immune microenvironment. By mIHC staining of sections from 30 patients with MSI‐H status, we showed that the patients with better prognoses had the increased infiltration of CD8+ cells in the primary tumoral tissue. Conclusion: Our study developed a simple five‐gene signature for stratifying MSI‐H GC patients with survival predictive power. [ABSTRACT FROM AUTHOR]

Simple Summary: Mitigating the possible adverse environmental impacts caused by transgene flow from genetically engineered crops to their wild/weedy relatives is an ideal strategy for resolving biosafety problems. To explore a transgene mitigation system in rice, we edited the seed-shattering genes (SH4 and qSH1) of a weedy rice line with strong seed shattering. The results showed substantially reduced seed shattering in the gene-edited weedy rice lines. The single gene-edited weedy rice lines displayed an inconsistent reduction in seed size-related traits. Reduced seed shattering was closely linked with a lack of abscission layers and reduced abscisic acid (ABA). In addition, most examined genes that were closely associated with ABA biosynthesis, ABA signaling transduction, and cell wall hydrolysis were downregulated in the gene-edited weedy rice lines. These findings can assist in exploring the underlying mechanisms of reduced seed shattering in weedy rice plants, in addition to practical applications for mitigating environmental impacts caused by transgene flow and for controlling the infestation of weedy rice. Mitigating the function of acquired transgenes in crop wild/weedy relatives can provide an ideal strategy to reduce the possible undesired environmental impacts of pollen-mediated transgene flow from genetically engineered (GE) crops. To explore a transgene mitigation system in rice, we edited the seed-shattering genes, SH4 and qSH1, using a weedy rice line ("C9") that originally had strong seed shattering. We also analyzed seed size-related traits, the total genomic transcriptomic data, and RT-qPCR expression of the SH4 or qSH1 gene-edited and SH4/qSH1 gene-edited weedy rice lines. Substantially reduced seed shattering was observed in all gene-edited weedy rice lines. The single gene-edited weedy rice lines, either the SH4 or qSH1 gene, did not show a consistent reduction in their seed size-related traits. In addition, reduced seed shattering was closely linked with the weakness and absence of abscission layers and reduced abscisic acid (ABA). Additionally, the genes closely associated with ABA biosynthesis and signaling transduction, as well as cell-wall hydrolysis, were downregulated in all gene-edited weedy rice lines. These findings facilitate our deep insights into the underlying mechanisms of reduced seed shattering in plants in the rice genus Oryza. In addition, such a mitigating technology also has practical applications for reducing the potential adverse environmental impacts caused by transgene flow and for managing the infestation of weedy rice by acquiring the mitigator from GE rice cultivars through natural gene flow. [ABSTRACT FROM AUTHOR]

In the absence of copper, DsbS acts as a phosphatase toward DsbR, blocking the transcription of Dsb genes. In the presence of copper, the metal ion directly binds to the sensor domain of DsbS, and the Cys82 residue plays a critical role in this process. The copper-binding behavior appears to inhibit the phosphatase activity of DsbS, leading to the activation of DsbR and thus for copper resistance of Pseudomonas aeruginosa, an important human pathogen. [Display omitted] In nature, bacteria must sense copper and tightly regulate gene expression to evade copper toxicity. Here, we identify a new copper-responsive two-component system named DsbRS in the important human pathogen Pseudomonas aeruginosa ; in this system, DsbS is a sensor histidine kinase, and DsbR, its cognate response regulator, directly induces the transcription of genes involved in protein disulfide bond formation (Dsb) (i.e., the dsbDEG operon and dsbB). In the absence of copper, DsbS acts as a phosphatase toward DsbR, thus blocking the transcription of Dsb genes. In the presence of copper, the metal ion directly binds to the sensor domain of DsbS, and the Cys82 residue plays a critical role in this process. The copper-binding behavior appears to inhibit the phosphatase activity of DsbS, leading to the activation of DsbR. The copper resistance of the dsbRS knock-out mutant is restored by the ectopic expression of the dsbDEG operon, which is a DsbRS major target. Strikingly, cognates of the dsbRS - dsbDEG pair are widely distributed across eubacteria. In addition, a DsbR-binding site, which contains the consensus sequence 5′-TTA-N 8 -TTAA-3′, is detected in the promoter region of dsbDEG homologs in these species. These findings suggest that the regulation of Dsb genes by DsbRS represents a novel mechanism by which bacterial cells cope with copper stress. [ABSTRACT FROM AUTHOR]

Small nucleolar RNA H/ACA Box 51 (SNORA51) is involved in progression of multiple cancers. However, its role in hepatocellular carcinoma (HCC) is still unclear. The aim of the present study was to analyze the expression of SNORA51 in HCC and its clinical significance. A total of 136 patients with HCC who underwent surgery from January 1, 2016 to December 31, 2018 were included. The expression of SNORA51 in cancer tissues and adjacent tissues was compared using reverse transcription-quantitative PCR and bioinformatics methods. Methylation of the SNORA51 promoter in cancer and adjacent tissues was compared using bioinformatics. The relationship between SNORA51 expression levels and clinicopathological characteristics of patients with HCC, in addition to prognosis, was analyzed. The expression of SNORA51 in HCC was significantly higher compared with that in adjacent tissues (P<0.05). starBase demonstrated that higher expression levels of SNORA51 were associated with a significantly worse prognosis of patients with HCC compared with those who had lower expression levels of SNORA51 (P<0.05). Bioinformatics analysis using The University of Alabama at Birmingham Cancer Data Analysis Portal demonstrated that methylation of the SNORA51 promoter region in HCC was significantly decreased compared with adjacent tissues (P<0.05). A high expression of SNORA51 was significantly associated with portal vein tumor thrombus, vascular invasion and TNM stage (P<0.05). The median survival time of patients with high SNORA51 expression was significantly lower compared with those who had low SNORA51 expression (P<0.05). Both uni- and multivariate Cox regression analysis demonstrated that SNORA51 expression was an independent risk factor that significantly worsened the prognosis of patients with HCC (P<0.05). The overexpression of SNORA51 in patients with HCC was significantly associated with a poor prognosis and may be related to the reduced methylation of the SNORA51 promoter region. Therefore, SNORA51 may be a promising biomarker for prediction of the prognosis of patients with HCC and may be a therapeutic target for the treatment of HCC in future. [ABSTRACT FROM AUTHOR]

With restricted usage of growth-promoting antibiotics, identifying alternative feed additives that both improve intestinal barrier function and reduce inflammation is the center to improve chickens' health. This study examined the effects of a microencapsulated feed additive containing citric acid, sorbic acids, thymol, and vanillin on intestinal barrier function and inflammation status. A total of 240 birds were assigned to either a commercial control diet or control diet supplemented with 500 g/MT of the microencapsulated additive product. Birds were raised by feeding a 2-phase diet (starter, d 1 to d 21; and grower, d 15 to d 42). Growth performance was recorded weekly. At d 21 and d 42, total gastrointestinal tract permeability was evaluated by FITC-dextran (FD4) oral gavage. Jejunum-specific barrier functions were evaluated by Ussing chamber. Intestinal gene expression of selected epithelial cell markers, tight junction (TJ) proteins, inflammatory cytokines, and endocannabinoid system (ECS) markers were determined by RT-PCR. Statistical analysis was performed using Student t test. Results showed significant improvement of feed efficiency in the birds supplemented with the blend of organic acids and botanicals. At d 21, both oral and jejunal FD4 permeability were lower in the supplemented group. Jejunal transepithelial resistance was higher in the supplemented birds. At d 21, expression of TJs mRNA (CLDN1 and ZO2) was both upregulated in the jejunum and ileum of supplemented birds, while CLDN2 was downregulated in cecum. Proliferating cell marker SOX9 was higher expressed in jejunum and ceca. Goblet cell marker (MUC2) was upregulated, while Paneth cell marker (LYZ) was downregulated in the ileum. Proinflammatory cytokine expressions of IL1B, TNFA , and IFNG were downregulated in jejunum, while anti-inflammatory IL10 expression was higher in jejunum, ileum, cecum, and cecal tonsil. The ECS markers expressions were upregulated in most intestinal regions. Together, these results demonstrated that the blend of organic acids and botanical supplementation reduced inflammation, improved the TJs expression and intestinal barrier function, and thus improved chicken feed efficiency. The activated ECS may play a role in reducing intestinal tissue inflammation. [ABSTRACT FROM AUTHOR]

• A novel computational method identifies enhancers and their strengths at the sequence level. • A light gradient boost machine algorithm is used for feature selection. • In this paper, a new network structure called multiple Laplacian-regularized radial basis function network is proposed. • Compared with the existing methods, this method achieves more excellent performance. An enhancer is a short DNA sequence containing many binding sites of transcription factors that plays a crucial role in the gene expression of major eukaryotes. It is difficult to avoid the time consumption and high cost of experimental methods. Therefore, with the continuous development of genomics, it is an urgent task to identify enhancers and their intensities by computational methods. In this paper, we propose a two-layer model called iEnhancer-MRBF, wherein the first layer is used to identify enhancers, and the identified enhancers are divided into strong enhancers and weak enhancers according to their strength in the second layer. In iEnhancer-MRBF, a new classifier multiple Laplacian-regularized radial basis function network (MLR-RBFN) is proposed, and three feature representation methods, namely, kmer, nucleotide binary profiles (NBP) and ac-cumulated nucleotide frequency (ANF), as well as feature selection, are used to process DNA sequences. The experimental results show that the model is significantly better than the previous prediction models, and the test accuracy rates of the first and second layers of independent datasets are 79.75% and 83.50%, respectively. [ABSTRACT FROM AUTHOR]

Post-stroke depression (PSD) is a serious neuropsychiatric complication post stroke and leads to cognitive deficits. This study was conducted to explore the molecular mechanism of hypoxia-inducible factor-1α (HIF-1A) in cognitive dysfunction in rats with PSD. The rat model of PSD was established by middle cerebral artery occlusion, followed by 3 weeks of treatment with chronic unpredictable mild stress. The levels of miR-582–5p, HIF-1A, and neighbor of Brca1 gene (NBR1) in brain tissues were determined using RT-qPCR. The behaviors and cognitive capacity of rats were evaluated by various behavioral tests. PSD rats were injected with HIF-1A/miR-582–5p lowexpression vectors or NBR1 overexpression vectors via stereotactic method. The binding of HIF-1A to NBR1 or miR-582–5p was analyzed by chromatin immunoprecipitation and dual-luciferase assay. HIF-1A and NBR1 were highly expressed while miR-582–5p was poorly expressed in the brain of PSD rats. HIF-1A inhibition alleviated cognitive dysfunction of PSD rats. miR-582–5p was the upstream miRNA of HIF-1A, and HIF-1A specifically interacted with the NBR1 promoter to enhance NBR1 expression. miR-582–5p downregulation and NBR1 upregulation reversed the alleviative role of HIF-1A inhibition in cognitive dysfunction of PSD rats. In summary, HIF-1A inhibition may be a therapeutic target for cognitive dysfunction post PSD. [ABSTRACT FROM AUTHOR]