An acid-responsive DNA hydrogel-mediated cascaded enzymatic nucleic acid amplification system for the sensitive imaging of alkaline phosphatase in living cells.

Alkaline phosphatase (ALP) is a class of hydrolase that catalyzes the dephosphorylation of phosphorylated species in biological tissues, playing an important role in many physiological and pathological processes. Sensitive imaging of ALP activity in living cells is contributory to the research on these processes. Herein, we propose an acid-responsive DNA hydrogel to deliver a cascaded enzymatic nucleic acid amplification system into cells for the sensitive imaging of intracellular ALP activity. The DNA hydrogel is formed by two kinds of Y-shaped DNA monomers and acid-responsive cytosine-rich linkers. The amplification system contained Bst DNA polymerase (Bst DP), Nt.BbvCI endonuclease, a Recognition Probe (RP, containing a DNAzyme sequence, a Nt.BbvCI recognition sequence, and a phosphate group at the 3'-end), and a Signal Probe (SP, containing a cleavage site for DNAzyme, Cy3 and BHQ2 at the two ends). The amplification system was trapped into the DNA hydrogel and taken up by cells, and the cytosine-rich linkers folded into a quadruplex i-motif in the acidic lysosomes, leading to the collapse of the hydrogel and releasing the amplification system. The phosphate groups on RPs were recognized and removed by the target ALP, triggering a polymerization-nicking cycle to produce large numbers of DNAzyme sequences, which then cleaved multiple SPs, restoring Cy3 fluorescence to indicate the ALP activity. This strategy achieved sensitive imaging of ALP in living HeLa, MCF-7, and NCM460 cells, and realized the sensitive detection of ALP in vitro with a detection limit of 2.0 × 10-5 U mL-1, providing a potential tool for the research of ALP-related physiological and pathological processes.

Identification of long non-coding RNAs involved in floral scent of Rosa hybrida.

Long non-coding RNAs (lncRNAs) were found to play important roles in transcriptional, post-transcriptional, and epigenetic gene regulation in various biological processes. However, lncRNAs and their regulatory roles remain poorly studied in horticultural plants. Rose is economically important not only for their wide use as garden and cut flowers but also as important sources of natural fragrance for perfume and cosmetics industry, but presently little was known about the regulatory mechanism of the floral scent production. In this paper, a RNA-Seq analysis with strand-specific libraries, was performed to rose flowers in different flowering stages. The scented variety 'Tianmidemeng' (Rosa hybrida) was used as plant material. A total of 13,957 lncRNAs were identified by mining the RNA-Seq data, including 10,887 annotated lncRNAs and 3070 novel lncRNAs. Among them, 10,075 lncRNAs were predicted to possess a total of 29,622 target genes, including 54 synthase genes and 24 transcription factors related to floral scent synthesis. 425 lncRNAs were differentially expressed during the flowering process, among which 19 were differentially expressed among all the three flowering stages. Using weighted correlation network analysis (WGCNA), we correlate the differentially-expressed lncRNAs to synthesis of individual floral scent compounds. Furthermore, regulatory function of one of candidate lncRNAs for floral scent synthesis was verified using VIGS method in the rose. In this study, we were able to show that lncRNAs may play important roles in floral scent production in the rose. This study also improves our understanding of how plants regulate their secondary metabolism by lncRNAs.

Genetic and Biochemical Aspects of Floral Scents in Roses.

Floral scents possess high ornamental and economic values to rose production in the floricultural industry. In the past two decades, molecular bases of floral scent production have been studied in the rose as well as their genetic inheritance. Some significant achievements have been acquired, such as the comprehensive rose genome and the finding of a novel geraniol synthase in plants. In this review, we summarize the composition of floral scents in modern roses, focusing on the recent advances in the molecular mechanisms of floral scent production and emission, as well as the latest developments in molecular breeding and metabolic engineering of rose scents. It could provide useful information for both studying and improving the floral scent production in the rose.

Comparative RNA-Seq analysis reveals a critical role for brassinosteroids in rose (Rosa hybrida) petal defense against Botrytis cinerea infection.

BACKGROUND: One of the most popular ornamental plants worldwide, roses (Rosa sp.), are very susceptible to Botrytis gray mold disease. The necrotrophic infection of rose petals by B. cinerea causes the collapse and death of these tissues in both the growth and post-harvest stages, resulting in serious economic losses. To understand the molecular basis of rose resistance against B. cinerea, we profiled the petal transcriptome using RNA-Seq technology. RESULTS: We identified differentially transcribed genes (DTGs) in petals during B. cinerea infection at 30 h post inoculation (hpi) and/or 48 hpi. Gene ontology term enrichment and pathway analyses revealed that metabolic, secondary metabolite biosynthesis, plant-pathogen interaction, and plant hormone signal transduction pathways were involved. The expression of 370 cell-surface immune receptors was upregulated during infection. In addition, 188 genes encoding transcription factors were upregulated, particularly in the ERF, WRKY, bHLH, MYB, and NAC families, implying their involvement in resistance against B. cinerea. We further identified 325 upregulated DTGs in the hormone signal transduction pathways. Among them, the brassinosteroid (BR)-related genes were the most significantly enriched. To confirm the role of BR in Botrytis resistance, exogenous BR was applied to rose flowers before the inoculation of B. cinerea, which enhanced the defense response in these petals. CONCLUSIONS: Our global transcriptome profiling provides insights into the complex gene regulatory networks mediating the rose petal response to B. cinerea. We further demonstrated the role of the phytohormone BR in the resistance of petals to necrotrophic fungal pathogens.

Genomic and transcriptomic sequencing of Rosa hybrida provides microsatellite markers for breeding, flower trait improvement and taxonomy studies.

BACKGROUND: Rosa hybrida is a valuable ornamental, food and medicinal crop worldwide, but with relatively limited molecular marker resources, especially for flower-specific markers. In this study, we performed genomic and floral transcriptomic sequencing of modern rose. We obtained comprehensive nucleotide information, from which numerous potential simple sequence repeat (SSR) markers were identified but were found to have high rates of amplification failure and PCR product redundancy. RESULTS: We applied a filtering strategy for BLAST analysis with the assembled genomic sequence and identified 124,591 genomic and 2,292 EST markers with unique annealing sites. These markers had much greater reliability than those obtained before filtering. Additional BLAST analysis against the transcriptomic sequences uncovered 5225 genomic SSRs associated with 4100 transcripts, 2138 of which were associated with functional genes that were annotated against the non-redundant database. More than 90% of these newly developed molecular markers were polymorphic, based on PCR using a subset of SSRs to analyze tetraploid modern rose accessions, diploid Rosa species and one strawberry accession. The relationships among Rosa species determined by cluster analysis (based on these results) were in agreement with modern rose breeding history, whereas strawberry was isolated in a separate cluster, as expected. CONCLUSIONS: Our results provide valuable molecular-genetic tools for rose flower trait improvement, breeding and taxonomy. Importantly, we describe a reproducible organ-specific strategy for molecular marker development and selection in plants, which can be applied to other crops.

Two-dimensional analysis provides molecular insight into flower scent of Lilium 'Siberia'.

Lily is a popular flower around the world not only because of its elegant appearance, but also due to its appealing scent. Little is known about the regulation of the volatile compound biosynthesis in lily flower scent. Here, we conducted an approach combining two-dimensional analysis and weighted gene co-expression network analysis (WGCNA) to explore candidate genes regulating flower scent production. In the approach, changes of flower volatile emissions and corresponding gene expression profiles at four flower developmental stages and four circadian times were both captured by GC-MS and RNA-seq methods. By overlapping differentially-expressed genes (DEGs) that responded to flower scent changes in flower development and circadian rhythm, 3,426 DEGs were initially identified to be candidates for flower scent production, of which 1,270 were predicted as transcriptional factors (TFs). The DEGs were further correlated to individual flower volatiles by WGCNA. Finally, 37, 41 and 90 genes were identified as candidate TFs likely regulating terpenoids, phenylpropanoids and fatty acid derivatives productions, respectively. Moreover, by WGCNA several genes related to auxin, gibberellins and ABC transporter were revealed to be responsible for flower scent production. Thus, this strategy provides an important foundation for future studies on the molecular mechanisms involved in floral scent production.

Graft-accelerated virus-induced gene silencing facilitates functional genomics in rose flowers.

Rose has emerged as a model ornamental plant for studies of flower development, senescence, and morphology, as well as the metabolism of floral fragrances and colors. Virus-induced gene silencing (VIGS) has long been used in functional genomics studies of rose by vacuum infiltration of cuttings or seedlings with an Agrobacterium suspension carrying TRV-derived vectors. However, VIGS in rose flowers remains a challenge because of its low efficiency and long time to establish silencing. Here we present a novel and rapid VIGS method that can be used to analyze gene function in rose, called 'graft-accelerated VIGS', where axillary sprouts are cut from the rose plant and vacuum infiltrated with Agrobacterium. The inoculated scions are then grafted back onto the plants to flower and silencing phenotypes can be observed within 5 weeks, post-infiltration. Using this new method, we successfully silenced expression of the RhDFR1, RhAG, and RhNUDX1 in rose flowers, and affected their color, petal number, as well as fragrance, respectively. This grafting method will facilitate high-throughput functional analysis of genes in rose flowers. Importantly, it may also be applied to other woody species that are not currently amenable to VIGS by conventional leaf or plantlet/seedling infiltration methods.

The adipose triglyceride lipase, adiponectin and visfatin are downregulated by tumor necrosis factor-alpha (TNF-alpha) in vivo.

Inflammatory cytokines have been linked to obesity-related insulin resistance. To investigate the effect of TNF-alpha, an inflammatory cytokine, on insulin action, C57BL/6J mice were treated with TNF-alpha for 7 days after which we examined the in vivo effects of TNF-alpha on glucose tolerance and insulin sensitivity with IV glucose tolerance tests and hyperinsulinemic-euglycemic clamps. In addition, we analyzed the in vivo effect of TNF-alpha on several metabolism-related genes and adipocytokines implicated in the development of insulin resistance. TNF-alpha treatment resulted in markedly increased fasting blood glucose, insulin and free fatty acids (FFA) levels and reduced glucose tolerance. During the clamps, the rates insulin-stimulated whole body (G(Rd)) and skeletal muscle glucose uptake (MGU) and insulin's ability to suppress hepatic glucose production (HGP) were decreased in TNF-alpha treated animals, indicating insulin resistance. In addition, both PPARgamma and ATGL mRNA expression in adipose tissues as well as ATGL protein levels in plasma were downregulated. Moreover, adipose mRNA expression and plasma protein levels of adiponectin and visfatin were significantly down-regulated. We conclude that the alterations of PPARgamma, ATGL, adiponectin and visfatin may contribute to the development of insulin resistance mediated by TNF-alpha.

[Effects of tumor necrosis factor-alpha induced insulin resistance on adipose triglyceride lipase in mice].

OBJECTIVE: To investigate the effects of tumor necrosis factor (TNF)-alpha induced insulin resistance (IR) on glucose and lipid metabolism and adipose triglyceride lipase (ATGL). METHODS: Forty male C57BL/6J mice were randomly divided into 2 equal groups: TNF-alpha group with undergoing intraperitoneal injection of TNF-alpha 6 microg x kg(-1) x d(-1) for 7 days and normal control (NC) group with saline injection. Hyperinsulinemic-euglycemic clamp technique combined with 2-deoxy-[(3)H] glucose as a tracer was used on 20 mice, 10 from each group, to examine the fasting blood glucose (FBG), plasma insulin (INS), total cholesterol (TC), triglyceride (TG), and free fatty acid (FFA). The glucose infusion rate (GIR) was recorded. Other 20 mice, 10 in each group, were killed with their adipose and/or muscle tissues taken out. RT-PCR was used to detect the mRNA expression of ATGL, hormone-sensitive lipase (HSL), carnitine palmitoyl transferase-1 (CPT-1), and peroxisome proliferator activated receptor-gamma (PPARgamma). Western blotting was used to measure the protein expression of ATGL. Muscle glucose uptake (MGU) was measured. RESULTS: After TNF-alpha treatment, the FBG, plasma INS, and FFA were significantly elevated in the TNF group compared with the NC group (all P < 0.05). During the steady-state of clamp test, the plasma INS level of the TNF group was (341.7 +/- 17.7) mU/L, significantly higher than that of the NC group [(84.7 +/- 5.5) mU/L, P < 0.01]. The FFA level of the TNF group was (0.82 +/- 0.03) mmol/L, significantly higher than that of the NC group [(0.43 +/- 0.07) mmol/L, P < 0.01]. The GIR of the TNF group was (39.1 +/- 2.3) mg x kg(-1)x min(-1), significantly lower than that of the NC group [(54.2 +/- 2.2) mg x kg(-1) x min(-1), P < 0.01]. The MGU level of the TNF group was (15.8 +/- 1.7) micromol.100 g(-1) x min(-1), significantly lower than that of the NC group [(20.9 +/- 2.5) micromol.100 g(-1) x min(-1), P < 0.01]. The ATGL mRNA expression level in adipose tissues of the TNF group was (0.85 +/- 0.09), significantly lower than that of the NC group (1.37 +/- 0.12, P < 0.01). The ATGL protein expression level of the TNF group was 0.53 +/- 0.03, significantly lower than that of the NC group (0.65 +/- 0.05, P < 0.05). The PPARgamma mRNA expression level in adipose tissues of the TNF group was 0.83 +/- 0.07, significantly lower than that of the NC group (1.07 +/- 0.07, P < 0.05). CONCLUSION: In TNF-alpha induced insulin resistance, AGTL may be involved in the pathways of lipid metabolism.