Long read sequencing of Toona sinensis (A. Juss) Roem: A chromosome-level reference genome for the family Meliaceae.

Chinese mahogany (Toona sinensis) is a woody plant that is widely cultivated in China and Malaysia. Toona sinensis is important economically, including as a nutritious food source, as material for traditional Chinese medicine and as a high-quality hardwood. However, the absence of a reference genome has hindered in-depth molecular and evolutionary studies of this plant. In this study, we report a high-quality T. sinensis genome assembly, with scaffolds anchored to 28 chromosomes and a total assembled length of 596 Mb (contig N50 = 1.5 Mb and scaffold N50 = 21.5 Mb). A total of 34,345 genes were predicted in the genome after homology-based and de novo annotation analyses. Evolutionary analysis showed that the genomes of T. sinensis and Populus trichocarpa diverged ~99.1-103.1 million years ago, and the T. sinensis genome underwent a recent genome-wide duplication event at ~7.8 million years and one more ancient whole genome duplication event at ~71.5 million years. These results provide a high-quality chromosome-level reference genome for T. sinensis and confirm its evolutionary position at the genomic level. Such information will offer genomic resources to study the molecular mechanism of terpenoid biosynthesis and the formation of flavour compounds, which will further facilitate its molecular breeding. As the first chromosome-level genome assembled in the family Meliaceae, it will provide unique insights into the evolution of members of the Meliaceae.

LncRNA MIR4435-2HG inhibits the progression of osteoarthritis through miR-510-3p sponging.

Osteoarthritis (OA) is a disorder of diarthrodial joints that can have multiple causes. Long non-coding RNAs (lncRNAs) participate in multiple diseases, including OA. It has recently been reported that the lncRNA microRNA 4435-2HG (MIR4435-2HG) is downregulated in OA tissues; however, the biological role of MIR4435-2HG during OA progression remains unclear. In the present study, interleukin (IL)-1ß was used to establish an in vitro model of OA. Protein expressions of matrix metallopeptidase (MMP) 1, MMP13, collagen II, interleukin (IL)-17A, p65, phosphorylated (p)-p65, IκB and p-IκB in CHON-001 cells were detected by western blotting. Gene expressions of IL-17A, MIR4435-2HG and miR-510-3p in tissues or CHON-001 cells were measured by reverse transcription-quantitative PCR and western blotting, respectively. Cell Counting Kit-8 assay and immunofluorescence staining were used to investigate cell proliferation, and cell apoptosis was detected by flow cytometry. The association between MIR4435-2HG, miR-510-3p and IL-17A was investigated using the dual luciferase report assay. MIR4435-2HG and miR-510-3p overexpression were transfected into CHON-001 cells. The results demonstrated that miR4435-2HG overexpression significantly increased proliferation and inhibited apoptosis of CHON-001 cells. In addition, miR-510-3p was identified as the downstream target of MIR4435-2HG, and miR-510-3p directly targeted IL-17A. The results from the present study suggested that MIR4435-2HG could mediate the progression of OA by inactivating the NF-κB signaling pathway. In addition, miR4435-2HG overexpression inhibited OA progression, suggesting that miR4435-2HG may be considered as a potential therapeutic target in OA.

Transcriptome changes in the phenylpropanoid pathway in senescing leaves of Toona sinensis.

Toona sinensis is a deciduous tree native to eastern and southeastern Asia that has important culinary and cultural values. To expand current knowledge of the transcriptome and functional genomics in this species, a de novo transcriptome sequence analysis of young and mature leaf tissues of T. sinensis was performed using the Illumina platform. Over 8.1 Gb of data were generated, assembled into 64,541 unigenes, and annotated with known biological functions. Proteins involved in primary metabolite biosynthesis were identified based on similarities to known proteins, including some related to biosynthesis of carbohydrates, amino acids, lipids, and energy. Analysis of unigenes differentially expressed between young and mature leaves (transcriptomic libraries 'YL' and 'ML', respectively) showed that the KEGG pathways of phenylpropanoid, naringenin, lignin, cutin, suberin, and wax biosynthesis were significantly enriched in mature leaves. These results not only expand knowledge of transcriptome characteristics for this valuable species, but also provide a useful transcriptomic dataset to accelerate the researches on its metabolic mechanisms and functional genomics. This study can also further the understanding of unique aromatic metabolism and Chinese medicinal properties of T. sinensis.

Correction: MMP-3 gene polymorphisms are associated with increased risk of osteoarthritis in Chinese men.

[This corrects the article DOI: 10.18632/oncotarget.18493.].

Laboratory Observations of Linkage of Preslip Zones Prior to Stick-Slip Instability.

Field and experimental observations showed that preslip undergoes a transition from multiple to single preslip zones, which implies the existence of linkage of preslip zones before the fault instability. However, the observations of the linkage process, which is significant for understanding the mechanism of earthquake preparation, remains to be implemented due to the limitations of observation methods in previous studies. Detailed spatiotemporal evolutions of preslip were observed via a high-speed camera and a digital image correlation method in our experiments. The normalized length of preslip zones shows an increase trend while the normalized number of preslip zones (NN) shows an increase followed by a decrease trend, which indicate that the expansion of the preslip undergoes a transition from increase to linkage of the isolated preslip zones. The peak NN indicates the initiation of the linkage of preslip zones. Both the linkage of the preslip zones and the decrease in the normalized information entropy of fault displacement direction indicate the reduction of spatial complexity of preslip as the instability approaches. Furthermore, the influences of dynamic adjustment of stress along the fault and the interactions between the asperities and preslip on the spatial complexity of preslip were also observed and analyzed.

MMP-3 gene polymorphisms are associated with increased risk of osteoarthritis in Chinese men.

Osteoarthritis (OA) is the most common late-onset degenerative joint disease., It is characterized by progressive degradation of articular cartilage. We investigated the association between OA occurrence and single nucleotide polymorphisms (SNPs) in the matrix metalloproteinase-3 (MMP-3) gene involved in the breakdown of extra-cellular matrix proteins. The study included 100 male OA patients and 197 healthy men from the north area of China. Eight MMP-3 SNPs were genotyped. Odds ratios (ORs) with 95% confidence intervals (95%CIs) and multivariate logistic regression analysis were used to assess the association. Multivariate logistic regression analysis was used to identify SNPs that correlated with OA susceptibility. We found that rs639752 (dominant, OR = 2.03, 95% CI: 1.03-4.01, P = 0.038; over-dominant, OR = 2.00, 95% CI: 1.03-3.88, P = 0.037); rs520540 (dominant, OR = 2.03, 95% CI: 1.03-4.01, P = 0.038; over-dominant, OR = 2.00, 95% CI: 1.03-3.88, P = 0.037); rs602128 (dominant, OR = 2.03, 95% CI: 1.03-4.01, P = 0.038; over-dominant, OR = 2.01, 95% CI: 1.03-3.89, P = 0.037); and rs679620 (dominant, OR = 2.03, 95% CI: 1.03-4.01, P = 0.038; over-dominant, OR = 2.04, 95% CI: 1.05-3.96, P = 0.033) were associated with the increased risk of OA. Our results suggest that these SNPs may contribute to OA development, and could serve as molecular markers of OA susceptibility.

Rock signaling control PPARγ expression and actin polymerization during adipogenesis.

Aim: Adipogenesis is characterized by a strong interdependence between cell shape, cytoskeletal organization, and the onset of adipogenic gene expression. Here we investigated the role of the RhoA/ROCK pathway in adipogenesis. Result: High RhoA activity in the cell line C3H10T1/2 were generated (Named RhoA14V cells). Treatment of RhoA14V cells with Shield 1 following their differentiation into adipocytes resulted in the appearance of thick cortical actin filaments, and increased mRNA expression levels of RhoA, ROCK, p-MYPT1 and p-MLC, while PPARγ mRNA decreased. This resulted in decreased triglyceride synthesis and reduced expression of the adipogenic transcription factor PPARγ. These molecular changes were accompanied by reorganization of the actin cytoskeleton, during which ROCK signaling suppressed actin polymerization. Conclusion: ROCK signaling suppresses adipogenesis by controlling PPARγ expression and actin organization in adipocytes.

Hypoxia promotes AMP-activated protein kinase (AMPK) and induces apoptosis in mouse osteoblasts.

The hypoxic environment around the fracture site develops post the blood flow disruption and leads to osteoblast cell death and further impairs fracture healing. Hypoxia usually leads to the mitochondrial dysfunction and then results in apoptotic cell death. AMPK is ubiquitously expressed and functions as an intracellular fuel sensor by maintaining energy balance, as is potentially activated by hypoxia, ischemia, and ROS, however, the regulatory role of AMPK in hypoxia-induced apoptosis in osteoblasts and in the fracture healing has not been identified. In present study, we firstly determined the apoptosis induction by hypoxia in mouse osteoblastic MC3T3-E1 cells via examining the apoptotic cells and the activation of apoptosis-related molecules, then investigated the activation of AMPK signaling by hypoxia via analyzing the phosphorylation of AMPKα and ACC1, finally we explored the association of the AMPK activation with the hypoxia-induced apoptosis using loss-of-function strategy. Results demonstrated that hypoxia induced apoptosis in MC3T3-E1 cells and activated the AMPK signaling. And the knockdown of AMPK via chemical treatment or RNA interfering significantly decreased the hypoxia-induced apoptosis in MC3T3-E1 cells. Taken together, present study unveiled the regulatory role of AMPK signaling in the hypoxia-induced osteoblast apoptosis.

An optimal method of DNA silver staining in polyacrylamide gels.

A silver staining technique has widely been used to detect DNA fragments with high sensitivity on polyacrylamide gels. The conventional procedure of the silver staining is tedious, which takes about 40-60 min and needs five or six kinds of chemicals and four kinds of solutions. Although our previous improved method reduced several steps, it still needed six kinds of chemicals. The objective of this study was to improve further the existing procedures and develop an optimal method for DNA silver staining on polyacrylamide gels. The novel procedure could be completed with only four chemicals and two solutions within 20 min. The steps of ethanol, acetic acid, and nitric acid precession before silver impregnation have been eliminated and the minimal AgNO3 dose has been used in this up-to-date method. The polyacrylamide gel of the DNA silver staining displayed a golden yellow and transparent background with high sensitivity. The minimum 0.44 and 3.5 ng of DNA amount could be detected in denaturing and nondenaturing polyacrylamide gel, respectively. This result indicated that our optimal method can save time and cost, and still keep a high sensitivity for DNA staining in polyacrylamide gels.