Whole-Genome Sequencing Of Mesorhizobium huakuii 7653R Provides Molecular Insights into Host Specificity and Symbiosis Island Dynamics

Background Evidence based on genomic sequences is urgently needed to confirm the phylogenetic relationship between Mesorhizobium strain MAFF303099 and M. huakuii. To define underlying causes for the rather striking difference in host specificity between M. huakuii strain 7653R and MAFF303099, several probable determinants also require comparison at the genomic level. An improved understanding of mobile genetic elements that can be integrated into the main chromosomes of Mesorhizobium to form genomic islands would enrich our knowledge of how genome dynamics may contribute to Mesorhizobium evolution in general. Results In this study, we sequenced the complete genome of 7653R and compared it with five other Mesorhizobium genomes. Genomes of 7653R and MAFF303099 were found to share a large set of orthologs and, most importantly, a conserved chromosomal backbone and even larger perfectly conserved synteny blocks. We also identified candidate molecular differences responsible for the different host specificities of these two strains. Finally, we reconstructed an ancestral Mesorhizobium genomic island that has evolved into diverse forms in different Mesorhizobium species. Conclusions Our ortholog and synteny analyses firmly establish MAFF303099 as a strain of M. huakuii. Differences in nodulation factors and secretion systems T3SS, T4SS, and T6SS may be responsible for the unique host specificities of 7653R and MAFF303099 strains. The plasmids of 7653R may have arisen by excision of the original genomic island from the 7653R chromosome

A Genome-Wide Prediction and Identification of Intergenic Small RNAs by Comparative Analysis in Mesorhizobium huakuii 7653R

In bacteria, small non-coding RNAs (sRNAs) are critical regulators of cellular adaptation to changes in metabolism, physiology, or the external environment. In the last decade, more than 2000 of sRNA families have been reported in the Rfam database and have been shown to exert various regulatory functions in bacterial transcription and translation. However, little is known about sRNAs and their functions in Mesorhizobium. Here, we predicted putative sRNAs in the intergenic regions (IGRs) of M. huakuii 7653R by genome-wide comparisons with four related Mesorhizobial strains. The expression and transcribed regions of candidate sRNAs were analyzed using a set of high-throughput RNA deep sequencing data. In all, 39 candidate sRNAs were found, with 5 located in the symbiotic megaplasmids and 34 in the chromosome of M. huakuii 7653R. Of these, 24 were annotated as functional sRNAs in the Rfam database and 15 were recognized as putative novel sRNAs. The expression of nine selected sRNAs was confirmed by Northern blotting, and most of the nine selected sRNAs were highly expressed in 28 dpi nodules and under symbiosis-mimicking conditions. For those putative novel sRNAs, functional categorizations of their target genes were performed by analyzing the enriched GO terms. In addition, MH_s15 was shown to be an abundant and conserved sRNA

Network Pharmacological Study of Achyranthis bidentatae Radix Effect on Bone Trauma

Purpose. Bone trauma is a clinical condition that afflicts the majority of the world’s population. For the management of bone trauma, the underlying mechanisms of the drugs effective for bone healing are deemed necessary. Achyranthis bidentatae Radix (ABR) is a popular alternative medicine recommended in the treatment of bone trauma and injury, yet its mechanism of action persists to be vague. This study was conducted for the evaluation of the mode of action of ABR through network pharmacology in treating bone trauma. Methods. An extensive survey of published works led to the development of a drug-target database, after which multiple protein targets for bone trauma were discerned. The protein-protein interaction network was developed by utilizing the STITCH database and gene ontology (GO) enrichment analysis using Cytoscape and ClueGO. Moreover, docking studies were performed for revealing the affinity of various ingredients with IL6. Results. The extensive literature survey yielded the presence of 176 components in ABR, and 151 potential targets were acquired. Scrutinization of these targets revealed that 21 potential targets were found to be associated with bone trauma. Out of which, some remarkable targets such as IL6, MAPK14, MAPK8, SRC, PTGS2, and MMP2 were observed to be associated in the functional interaction of ABR. According to docking results, several ingredients of ABR such as Baicalien, Copistine, Epiberberine, Kaempferol, and Palmatine have the lowest docking scores (range between -6 and -7). Conclusions. The results of the study elucidated that ABR can positively be utilized for the management of bone trauma, which can be mediated by multiple molecular mechanisms such as ERBB2 signaling pathway, positive regulation of oxidoreductase activity, JNK cascade pathway, multicellular organism metabolic process, T cell costimulation, and the positive regulation of MAPK activity. The findings also suggest that several ingredients of ABR such as Baicalien, Copistine, Epiberberine, Kaempferol, and Palmatine have good affinity with IL6, suggesting the promising potential of ABR in treating bone trauma, likely through IL6

Molecular Insight into the Methane Occurrence inside a Shale Nanochannel with Formation Water

The occurrence status of shale gas inside a nanochannel of a shale reservoir is crucial for shale gas reserve assessment and exploitation. In this work, adopting molecular dynamics simulations, the methane occurrence inside a shale nanochannel was investigated under different formation water saturations. Moreover, employing three common inorganic minerals including of quartz, calcite, and kaolinite, the influence of mineral hydrophilicity on methane occurrence was also examined. The simulations indicate that there are three occurrence statuses of methane inside nanochannels including a free status located in the internal nanochannel, an adsorption status on mineral and water film surfaces, and a dissolution status inside the water phase. Among them, free-status methane is the dominant contribution to the recoverable reserve assessment and could be feasibly exploited. Without formation water, methane gives two occurrence statuses including an adsorption status on mineral surfaces and a free status. Once the formation water emerges, it will preferentially adsorb onto the mineral surface to form a water film. With the increase of formation water saturation, the proportions of free-status and dissolution-status methanes increase, while the proportion of adsorption-status methane decreases. In three mineral nanochannels with hydrophilicity orders of quartz > calcite > kaolinite, the proportion of adsorption-status methane follows the order of kaolinite > calcite > quartz, and free-status methane gives the order of kaolinite ≈ quartz > calcite. The underlying mechanisms of these occurrence features were discussed at length from the view of microscopic interactions among mineral surfaces, water, and methane. Our work presents the methane occurrence structure inside a shale nanochannel, and the discussion of the three methane occurrence statuses could provide fundamental data and theoretical guidance for shale gas reserve assessment and exploitation

Syntheses, Structures, Optical and Magnetic Properties of Ba₂M<i>Ln</i>Se₅ (M = Ga, In; <i>Ln</i> = Y, Nd, Sm, Gd, Dy, Er)

The twelve quaternary rare-earth selenides Ba₂M<i>Ln</i>Se₅ (M = Ga, In; <i>Ln</i> = Y, Nd, Sm, Gd, Dy, Er) have been synthesized for the first time. The compounds Ba₂Ga<i>Ln</i>Se₅ (<i>Ln</i> = Y, Nd, Sm, Gd, Dy, Er) are isostructural and crystallize in a new structure type in the centrosymmetric space group <i>P</i>1̅ of the triclinic system while the isostructural compounds Ba₂In<i>Ln</i>Se₅ (<i>Ln</i> = Y, Nd, Sm, Gd, Dy, Er) belong to the Ba₂BiInS₅ structure type and crystallize in the noncentrosymmetric space group <i>Cmc</i>2₁ of the orthorhombic system. The structures contain infinite one-dimensional anionic chains ₁^∞[Ga<i>Ln</i>Se₅]^4– and ₁^∞[In<i>Ln</i>Se₅]^4–, and both chains are built from <i>Ln</i>Se₆ octahedra and MSe₄ (M = Ga, In) tetrahedra in the corresponding selenides. As deduced from the diffuse reflectance spectra, the band gaps of most Ba₂M<i>Ln</i>Se₅ (M = Ga, In; <i>Ln</i> = Y, Nd, Sm, Gd, Dy, Er) compounds are around 2.2 eV. The magnetic susceptibility measurements on Ba₂GaGdSe₅ and Ba₂In<i>Ln</i>Se₅ (Ln = Nd, Gd, Dy, Er) indicate that they are paramagnetic and obey the Curie–Weiss law, while the magnetic susceptibility of Ba₂InSmSe₅ deviates from the Curie–Weiss law as a result of the crystal field splitting. Furthermore, Ba₂InYSe₅ exhibits a strong second harmonic generation response close to that of AgGaSe₂, when probed with the 2090 nm laser as fundamental wavelength

RNA-Seq and Microarrays Analyses Reveal Global Differential Transcriptomes of <i>Mesorhizobium huakuii</i> 7653R between Bacteroids and Free-Living Cells

<div><p><i>Mesorhizobium huakuii</i> 7653R occurs either in nitrogen-fixing symbiosis with its host plant, <i>Astragalus sinicus</i>, or free-living in the soil. The <i>M. huakuii</i> 7653R genome has recently been sequenced. To better understand the complex biochemical and developmental changes that occur in 7653R during bacteroid development, RNA-Seq and Microarrays were used to investigate the differential transcriptomes of 7653R bacteroids and free-living cells. The two approaches identified several thousand differentially expressed genes. The most prominent up-regulation occurred in the symbiosis plasmids, meanwhile gene expression is concentrated to a set of genes (clusters) in bacteroids to fulfill corresponding functional requirements. The results suggested that the main energy metabolism is active while fatty acid metabolism is inactive in bacteroid and that most of genes relevant to cell cycle are down-regulated accordingly. For a global analysis, we reconstructed a protein-protein interaction (PPI) network for 7653R and integrated gene expression data into the network using Cytoscape. A highly inter-connected subnetwork, with function enrichment for nitrogen fixation, was found, and a set of hubs and previously uncharacterized genes participating in nitrogen fixation were identified. The results described here provide a broader biological landscape and novel insights that elucidate rhizobial bacteroid differentiation, nitrogen fixation and related novel gene functions.</p></div

The putative CtrA regulatory network in <i>M. huakuii</i> 7653R according to the regulation model of cell cycle in <i>C. crescentus</i>.

<p>Blue arrows indicate positive effects and blunt blue lines indicate negative effects. Genes up-regulated were shown in red and down-regulated shown in green in <i>M. huakuii</i> 7653R bacteroids. Phosphorylated CtrA autoregulated its own transcription and CtrA regulated genes associated with DNA replication, DNA methylation, cell division, flagellar assembly, CtrA degradation, cell division, polar morphogenesis and pili biogenesis.</p