Long Non-coding RNA DLEU1 Promotes Progression of Osteoarthritis via miR-492/TLR8 Axis.

BACKGROUND: Long non-coding RNAs (LncRNAs) are generally reported to participate in the development of Osteoarthritis (OA) by acting as competing endogenous RNAs (ceRNAs). However, the molecular mechanism is largely unknown. This study aimed to investigate the possible mechanisms contributing to osteoarthritis (OA). METHODS: Four gene expression profiles from patients with OA were downloaded from a public database and integrated to screen important RNAs associated with OA. Differentially expressed (DE) lncRNAs, microRNAs (miRNAs), and mRNAs were filtered, and a ceRNA network was constructed. An in vitro OA model was established by treating chondrocytes with IL-1ß. The expression levels of MMP-13, COL2A1, aggrecan, and RUNX2 were detected by qRT-PCR and western blot. Cell proliferation ability was detected by CCK-8 assay. Flow cytometry was used for apoptosis assay. A dual luciferase reporter gene was used to confirm the relationship between DLEU1, miR-492, and TLR8. RESULTS: An OA-related ceRNA network, including 11 pathways, 3 miRNAs, 7 lncRNAs, and 16 mRNAs, was constructed. DLEU1 and TLR8 were upregulated, and miR-492 was downregulated in IL-1ß-induced chondrocytes. Overexpression of DLEU1 suppressed viability and promoted apoptosis and extracellular matrix (ECM) degradation in IL-1ß induced chondrocytes. Luciferase reporter assay validated the regulatory relations among DLEU1, miR-492, and TLR8. Further study revealed that the effects of DLEU1 on chondrocytes could be reversed by miR-492. CONCLUSION: DLEU1 may be responsible for the viability, apoptosis, and ECM degradation in OA via miR-492/TLR8 axis.

Susceptibility of Flordaguard peach rootstock to a resistant-breaking population of Meloidogyne floridensis and two populations of Meloidogyne arenaria.

Cultivar Flordaguard is suggested as a root-knot nematode (RKN) resistant rootstock for Florida peaches, however, RKN disease has been observed on this rootstock in peach orchards. Our goal was to confirm whether the RKN resistance breaking isolates of M. floridensis and M. arenaria indeed could infect and reproduce on the peach rootstock cv. Flordaguard in both laboratory and field studies. Root galling occurred on all peach cultivars evaluated including Flordaguard, Flordaglo, Okinawa, and Lovell, in the presence of the RKN resistance-breaking isolates of M. floridensis (MfGnv14) and two M. arenaria isolates (Ma1 and Ma2). These rootstocks showed varying degrees of susceptibility (to a lesser extent in Okinawa) to these three RKN resistance-breaking isolates. The importance of nematode inoculum concentrations in differentiating between resistance and susceptible plants was demonstrated, and thus are an important factor to consider in nematode resistance breeding programs. In host differential tests the peach-originated isolates of M. floridensis and M. arenaria behaved similarly with the vegetable-originated isolates of M. floridensis on tomato, peanut, watermelon, and tobacco, but showed variable host responses on cotton and pepper. The two M. arenaria isolates from peach reproduced on pepper but not on peanut. To our knowledge this is the first report of M. arenaria race 3 infecting Flordaguard and pepper in Florida. Soil and root samples collected from cv. Flordaguard infected trees at two commercial peach orchards showed that M. floridensis and M. arenaria were established on the rootstock.

Phylogenomic analysis of the genus Ralstonia based on 686 single-copy genes.

The genus Ralstonia contains species that are devastating plant pathogens, opportunistic human pathogens, and/or important degraders of xenobiotic and recalcitrant compounds. However, significant nomenclature problems exist, especially for the Ralstonia solanacearum species complex which consists of four phylotypes. Phylogenomics of the Ralstonia genus was investigated via a comprehensive analysis of 39 Ralstonia genomes as well as four genomes of Cupriavidus necator (more commonly known by its previous name Ralstonia eutropha). These data revealed 686 single-copy orthologs that could be extracted from the Ralstonia core-genome and used to reconstruct the phylogeny of the genus Ralstonia. The generated tree has strong bootstrap support for almost all branches. We also estimated the in silico DNA-DNA hybridization (isDDH) and the average nucleotide identity (ANI) values between each genome. Our data confirmed that whole genome sequence data provides a powerful tool to resolve the complex taxonomic questions of the genus Ralstonia, e.g. strains of Ralstonia solanacearum phylotype IIA and IIB may represent two subspecies of R. solanacearum, and strains of R. solanacearum phylotype I and III may be classified into two subspecies of Ralstonia pseudosolanacearum. Recently, strains of R. solanacearum phylotype IV were proposed to be reclassified into different subspecies of Ralstonia syzygii; our study, however, showed that phylotype IV strains had high isDDH values (83.8-96.1 %), indicating it may be not appropriate to classify these closely related strains into different subspecies. We also evaluated the performance of six chromosomal housekeeping genes (gdhA, mutS, adk, leuS, rplB and gyrB) used in Ralstonia phylogenetic inference. The multilocus sequence analysis of these six marker genes was able to reliably infer the phylogenetic relationships of the genus Ralstonia.

Examining phylogenetic relationships of Erwinia and Pantoea species using whole genome sequence data.

The genera Erwinia and Pantoea contain species that are devastating plant pathogens, non-pathogen epiphytes, and opportunistic human pathogens. However, some controversies persist in the taxonomic classification of these two closely related genera. The phylogenomic analysis of these two genera was investigated via a comprehensive analysis of 25 Erwinia genomes and 23 Pantoea genomes. Single-copy orthologs could be extracted from the Erwinia/Pantoea core-genome to reconstruct the Erwinia/Pantoea phylogeny. This tree has strong bootstrap support for almost all branches. We also estimated the in silico DNA-DNA hybridization (isDDH) and the average nucleotide identity (ANI) values between each genome; strains from the same species showed ANI values ≥96% and isDDH values >70%. These data confirm that whole genome sequence data provides a powerful tool to resolve the complex taxonomic questions of Erwinia/Pantoea, e.g. Pantoea agglomerans 299R was not clustered into a single group with other P. agglomerans strains, and the ANI values and isDDH values between them were <91% and around 43.8%, respectively. These data indicate P. agglomerans 299R should not be classified into the P. agglomerans species. In addition, another strain (Pantoea sp. At_9b) was identified that may represent a novel Pantoea species. We also evaluated the performance of six commonly used housekeeping genes (atpD, carA, gyrB, infB, recA, and rpoB) in phylogenetic inference. A single gene was not enough to obtain a reliable species tree, and it was necessary to use the multilocus sequence analysis of the six marker genes to recover the Erwinia/Pantoea phylogeny.