Differential microRNA expression between shoots and rhizomes in Oryza longistaminata using high-throughput RNA sequencing

AbstractPlant microRNAs (miRNAs) play important roles in biological processes such as development and stress responses. Although the diverse functions of miRNAs in model organisms have been well studied, their function in wild rice is poorly understood. In this study, high-throughput small RNA sequencing was performed to characterize tissue-specific transcriptomes in Oryza longistaminata. A total of 603 miRNAs, 380 known rice miRNAs, 72 conserved plant miRNAs, and 151 predicted novel miRNAs were identified as being expressed in aerial shoots and rhizomes. Additionally, 99 and 79 miRNAs were expressed exclusively or differentially, respectively, in the two tissues, and 144 potential targets were predicted for the differentially expressed miRNAs in the rhizomes. Functional annotation of these targets suggested that transcription factors, including squamosa promoter binding proteins and auxin response factors, function in rhizome growth and development. The expression levels of several miRNAs and target genes in the rhizomes were quantified by RT-PCR, and the results indicated the existence of complex regulatory mechanisms between the miRNAs and their targets. Eight target cleavage sites were verified by RNA ligase-mediated rapid 5′ end amplification. These results provide valuable information on the composition, expression and function of miRNAs in O. longistaminata, and will aid in understanding the molecular mechanisms of rhizome development

Ternary NiCoTi-layered double hydroxide nanosheets as a pH-responsive nanoagent for photodynamic/chemodynamic synergistic therapy

Combining photodynamic therapy (PDT) with chemodynamic therapy (CDT) has been proven to be a promising strategy to improve the treatment efficiency of cancer, because of the synergistic therapeutic effect arising between the two modalities. Herein, we report an inorganic nanoagent based on ternary NiCoTi-layered double hydroxide (NiCoTi-LDH) nanosheets to realize highly efficient photodynamic/chemodynamic synergistic therapy. The NiCoTi-LDH nanosheets exhibit oxygen vacancy-promoted electron-hole separation and photogenerated hole-induced O2-independent reactive oxygen species (ROS) generation under acidic circumstances, realizing in situ pH-responsive PDT. Moreover, due to the effective conversion between Co^{3+} and Co^{2+} caused by photogenerated electrons, the NiCoTi-LDH nanosheets catalyze the release of hydroxyl radicals (∙OH) from H2O2 through Fenton reactions, resulting in CDT. Laser irradiation enhances the catalyzed ability of the NiCoTi-LDH nanosheets to promote the ROS generation, resulting in a better performance than TiO_{2} nanoparticles at pH 6.5. In vitro and in vivo experimental results show conclusively that NiCoTi-LDH nanosheets plus irradiation lead to efficient cell apoptosis and significant inhibition of tumor growth. This study reports a new pH-responsive inorganic nanoagent with oxygen vacancy-promoted photodynamic/chemodynamic synergistic performance, offering a potentially appealing clinical strategy for selective tumor elimination

Identification of rhizome-specific genes by genome-wide differential expression Analysis in Oryza longistaminata

<p>Abstract</p> <p>Background</p> <p>Rhizomatousness is a key component of perenniality of many grasses that contribute to competitiveness and invasiveness of many noxious grass weeds, but can potentially be used to develop perennial cereal crops for sustainable farmers in hilly areas of tropical Asia. <it>Oryza longistaminata</it>, a perennial wild rice with strong rhizomes, has been used as the model species for genetic and molecular dissection of rhizome development and in breeding efforts to transfer rhizome-related traits into annual rice species. In this study, an effort was taken to get insights into the genes and molecular mechanisms underlying the rhizomatous trait in <it>O. longistaminata </it>by comparative analysis of the genome-wide tissue-specific gene expression patterns of five different tissues of <it>O. longistaminata </it>using the Affymetrix GeneChip Rice Genome Array.</p> <p>Results</p> <p>A total of 2,566 tissue-specific genes were identified in five different tissues of <it>O. longistaminata</it>, including 58 and 61 unique genes that were specifically expressed in the rhizome tips (RT) and internodes (RI), respectively. In addition, 162 genes were up-regulated and 261 genes were down-regulated in RT compared to the shoot tips. Six distinct <it>cis</it>-regulatory elements (CGACG, GCCGCC, GAGAC, AACGG, CATGCA, and TAAAG) were found to be significantly more abundant in the promoter regions of genes differentially expressed in RT than in the promoter regions of genes uniformly expressed in all other tissues. Many of the RT and/or RI specifically or differentially expressed genes were located in the QTL regions associated with rhizome expression, rhizome abundance and rhizome growth-related traits in <it>O. longistaminata </it>and thus are good candidate genes for these QTLs.</p> <p>Conclusion</p> <p>The initiation and development of the rhizomatous trait in <it>O. longistaminata </it>are controlled by very complex gene networks involving several plant hormones and regulatory genes, different members of gene families showing tissue specificity and their regulated pathways. Auxin/IAA appears to act as a negative regulator in rhizome development, while GA acts as the activator in rhizome development. Co-localization of the genes specifically expressed in rhizome tips and rhizome internodes with the QTLs for rhizome traits identified a large set of candidate genes for rhizome initiation and development in rice for further confirmation.</p

Tissue-specific transcriptomics reveals a central role of CcNST1 in regulating the fruit lignification pattern in Camellia chekiangoleosa, a woody oil-crop

Fruit lignification is of significant economic importance because it affects the quality of fruit and the production of seed oil. The specified lignification pattern in Camellia chekiangoleosa fruits plays critical roles in its seed oil yield, but little is known about how this lignification process is regulated. Here, we report on a comprehensive tissue-specific transcriptomics analysis conducted for C. chekiangoleosa fruit. By mining the differentially expressed genes, we found that lignin biosynthesis and transcriptional regulation pathways were significantly enriched in the lignified tissues. The homolog of NST-like transcription factor, CcNST1, was highly expressed in lignified seed coat and endocarp tissues; transgenic analyses of CcNST1 in Arabidopsis and hybrid poplar revealed the enhanced lignification levels of various tissues. Gene expression analysis of the transgenic lines uncovered potential downstream genes involved in the regulation of lignin biosynthesis. This work provides a valuable gene expression resource and identified the pivotal role of CcNST1 in regulating the lignin biosynthesis underlying fruit lignification

Antisense oligonucleotide targeting Livin induces apoptosis of human bladder cancer cell via a mechanism involving caspase 3

BACKGROUND AND AIM: in recent years, Livin, a new member of IAPs family, is found to be a key molecule in cancers. Researchers consider Livin may become a new target for tumor therapy; however, the role of it in bladder cancer is still unclear. The purpose of this article is to investigate Antisense Oligonucleotide (ASODN) of Livin on treating bladder cancer cell and underlying mechanisms. METHODS: Phosphorathioate modifying was used to synthesize antisense oligonucleotides targeting Livin, followed by transfection into human bladder cancer cell 5637. After transfection, Livin mRNA and protein level, cell proliferation and apoptosis changes, caspase3 level and its effect on human bladder cancer transplantable tumor in nude mice were measured. RESULT: results showed Livin ASODN effectively inhibited Livin expression and tumor cell proliferation, and these effects probably through enhanced caspase3 activity and apoptosis of tumor cells. In nude mice transplantable tumor model, Livin expressions were inhibited meanwhile caspase3 expression was increased. Tumor growth slowed down and apoptosis was enhanced. CONCLUSION: Our data suggest that Livin plays an important role in inhibiting apoptosis of bladder cancer cells. Livin ASODN may promote cell apoptosis, inhibit bladder cancer growth, and become one of the methods of gene therapy for bladder cancer

Effects of zinc oxide and condensed tannins on the growth performance and intestinal health of weaned piglets in ETEC-challenged environment

This experiment was conducted to evaluate effects of zine oxide (ZnO) and condensed tannins (CT), independently or in combination, on the growth performance and intestinal health of weaned piglets in enterotoxigenic Escherichia coli (ETEC-K88)-challenged environment. Randomly divided 72 weaned piglets into 4 groups. Dietary treatments included the following: basic diet group (CON), 1,500 mg/kg zinc oxide group (ZnO), 1,000 mg/kg condensed tannins group (CT), and 1,500 mg/kg zinc oxide +1,000 mg/kg condensed tannins group (ZnO + CT). Dietary ZnO supplementation decreased diarrhea rate from 0 to 14 days, 15 to 28 days, and 0 to 28 days (p &lt; 0.05) and no significant on growth performance. The effect of CT on reducing diarrhea rate and diarrhea index was similar to the results of ZnO. Compared with the CON group, ZnO increased the ileum villus height and improved intestinal barrier function by increasing the content of mucin 2 (MUC-2) in jejunum and ileum mucosa and the mRNA expression of zonula occludens-1 (ZO-1) in jejunum (p &lt; 0.05) and the expression of Occludin in duodenum and ileum (p &lt; 0.05). The effects of CT on intestinal barrier function genes were similar to that of ZnO. Moreover, the mRNA expression of cystic fibrosis transmembrane conductance regulator (CFTR) in jejunum and ileum was reduced in ZnO group (p &lt; 0.05). And CT was also capable of alleviating diarrhea by decreasing CFTR expression and promote water reabsorption by increasing AQP3 expression (p &lt; 0.05). In addition, pigs receiving ZnO diet had higher abundance of phylum Bacteroidetes, and genera Prevotella, and lower phylum Firmicutes and genera Lactobacillus in colonic contents. These results indicated that ZnO and CT can alleviate diarrhea and improve intestinal barrier function of weaned pigs in ETEC-challenged environment. In addition, the application of ZnO combined with CT did not show synergistic effects on piglet intestinal health and overall performance. This study provides a theoretical basis for the application of ZnO in weaning piglet production practices, we also explored effects of CT on the growth performance and intestinal health of weaned piglets in ETEC-challenged environment

Impaired Delta Np63 Expression is Associated with Poor Tumor Development in Transitional Cell Carcinoma of the Bladder

The oncogenic isoform of the p63 protein, delta Np63 (ΔNp63), plays an important role in the pathogenesis of many epithelial carcinomas, and emerging evidences suggest that ΔNp63 is a promising drug target. However, the functions of ΔNp63 in transitional cell carcinoma of bladder (TCCB) are poorly defined. In this study, a ΔNp63 shRNA expression vector was transfected into TCCB cell line 5637 and cell cycling, cell proliferation and protein expression were assessed by flow cytometry and 3-(4, 5-Dimethylthiazol-2-yl)-2, 5-dimethyl tetrazolium bromide (MTT) assay, and immunohistochemistry, respectively. The ΔNp63 shRNA expression vector was also injected into 5637 cell xenograft tumors in nude mice, and tumor size was measured, tumor tissue morphology was assessed by immunohistopathology and transmission electron microscopy. In the in vitro study, ΔNp63 shRNA transfection caused successful ΔNp63 gene silencing and resulted in significant arrest of cell cycling and cellular proliferation (p<0.05) as well as cyclin D1 expression. In the nude mouse xenograft model, ΔNp63 shRNA greatly inhibited tumor growth, induced tumor cell apoptosis (p<0.05) and resulted in cyclin D1 downregulation. Our data suggest that ΔNp63 may play an oncogenic role in TCCB progression through promoting cell survival and proliferation. Intratumoral administration of ΔNp63-specific shRNA suppressed tumor ΔNp63 expression and cellular proliferation while promoted tumor cellular apoptosis, and therefore inhibited tumor growth and improved survival of xenograft-bearing mice, which was not accompanied by significant signs of systemic toxicity

Deep Link-Prediction Based on the Local Structure of Bipartite Networks

Link prediction based on bipartite networks can not only mine hidden relationships between different types of nodes, but also reveal the inherent law of network evolution. Existing bipartite network link prediction is mainly based on the global structure that cannot analyze the role of the local structure in link prediction. To tackle this problem, this paper proposes a deep link-prediction (DLP) method by leveraging the local structure of bipartite networks. The method first extracts the local structure between target nodes and observes structural information between nodes from a local perspective. Then, representation learning of the local structure is performed on the basis of the graph neural network to extract latent features between target nodes. Lastly, a deep-link prediction model is trained on the basis of latent features between target nodes to achieve link prediction. Experimental results on five datasets showed that DLP achieved significant improvement over existing state-of-the-art link prediction methods. In addition, this paper analyzes the relationship between local structure and link prediction, confirming the effectiveness of a local structure in link prediction

Characterizations of MYB Transcription Factors in Camellia oleifera Reveal the Key Regulators Involved in Oil Biosynthesis

MYB (myeloblastosis) transcription factors plays an important role in various physiological and biochemical processes in plants. However, little is known about the regulatory roles of MYB family genes underlying seed oil biosynthesis in Camellia oleifera. To identify potential regulators, we performed the genome-wide characterizations of the MYB family genes and their expression profiles in C. oleifera. A total of 186 CoMYB genes were identified, including 128 R2R3-type MYB genes that had conserved R2 and R3 domains. Phylogenetic analysis revealed the CoR2R3-MYBs formed 25 subgroups and possessed some highly conserved motifs outside the MYB DNA-binding domain. We investigated the promoter regions of CoR2R3-MYBs and revealed a series of cis-acting elements related to development, hormone response, and environmental stress response, suggesting a diversified regulatory mechanism of gene functions. In addition, we identified four tandem clusters containing eleven CoR2R3-MYBs, which indicated that tandem duplications played an important role in the expansion of the CoR2R3-MYB subfamily. Furthermore, we analyzed the global gene expression profiles at five stages during seed development and revealed seven CoR2R3-MYB genes that potentially regulated lipid metabolism and seed maturation in C. oleifera. These results provide new insights into understanding the function of the MYB genes and the genetic improvement of seed oil

Characterizations of a Class-I BASIC PENTACYSTEINE Gene Reveal Conserved Roles in the Transcriptional Repression of Genes Involved in Seed Development

The developmental regulation of flower organs involves the spatio-temporal regulation of floral homeotic genes. BASIC PENTACYSTEINE genes are plant-specific transcription factors that is involved in many aspects of plant development through gene transcriptional regulation. Although studies have shown that the BPC genes are involved in the developmental regulation of flower organs, little is known about their role in the formation of double-flower due. Here we characterized a Class I BPC gene (CjBPC1) from an ornamental flower&mdash;Camellia japonica. We showed that CjBPC1 is highly expressed in the central whorls of flowers in both single and doubled varieties. Overexpression of CjBPC1 in Arabidopsis thaliana caused severe defects in siliques and seeds. We found that genes involved in ovule and seed development, including SEEDSTICK, LEAFY COTYLEDON2, ABSCISIC ACID INSENSITIVE 3 and FUSCA3, were significantly down-regulated in transgenic lines. We showed that the histone 3 lysine 27 methylation levels of these downstream genes were enhanced in the transgenic plants, indicating conserved roles of CjBPC1 in recruiting the Polycomb Repression Complex for gene suppression