Bacillus abyssalis sp. nov., isolated from a sediment of the South China Sea

A Gram-positive bacterium, designated SCSIO 15042^T, was isolated from a sediment of the South China Sea and was subjected to a polyphasic taxonomic study. The isolate grew at 20–60 °C, pH 6.0–10.0 and it could grow with up to 10 % (w/v) NaCl. The cell-wall diamino acid was found to be meso-diaminopimelic acid. Polar lipids were found to be diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine and an unknown polar lipid. The only menaquinone was determined to be MK-7. The major fatty acids were identified as C_16:1 ω7c/C_16:1 ω6c, C_16:0, iso-C_15:0, anteiso-C_15:0, and iso-C_16:0. The DNA G+C content of strain SCSIO 15042^T was determined to be 43.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences affiliated strain SCSIO 15042^T to the genus Bacillus. Levels of 16S rRNA gene sequence similarities between strain SCSIO 15042^T and Bacillus herbersteinensis D-1-5a^T, Bacillus infantis SMC 4352-1^T, Bacillus novalis LMG 21837^T and Bacillus drentensis LMG 21831^T were 96.2, 96.2, 96.1 and 96.1 %, respectively. Based on the evidence of the present polyphasic study, strain SCSIO 15042^T is considered to represent a novel species of the genus Bacillus, for which the name Bacillus abyssalis sp. nov. is proposed. The type strain is SCSIO 15042^T (=DSM 25875^T = CCTCC AB 2012074^T = NBRC 109102^T).     

The identification of candidate radio marker genes using a coexpression network analysis in gamma‐irradiated rice

Plant physiological and biochemical processes are significantly affected by gamma irradiation stress. In addition, gamma‐ray (GA) differentially affects gene expression across the whole genome. In this study, we identified radio marker genes (RMGs) responding only to GA stress compared with six abiotic stresses (chilling, cold, anoxia, heat, drought and salt) in rice. To analyze the expression patterns of differentially expressed genes (DEGs) in gamma‐irradiated rice plants against six abiotic stresses, we conducted a hierarchical clustering analysis by using a complete linkage algorithm. The up‐ and downregulated DEGs were observed against six abiotic stresses in three and four clusters among a total of 31 clusters, respectively. The common gene ontology functions of upregulated DEGs in clusters 9 and 19 are associated with oxidative stress. In a Pearson's correlation coefficient analysis, GA stress showed highly negative correlation with salt stress. On the basis of specific data about the upregulated DEGs, we identified the 40 candidate RMGs that are induced by gamma irradiation. These candidate RMGs, except two genes, were more highly induced in rice roots than in other tissues. In addition, we obtained other 38 root‐induced genes by using a coexpression network analysis of the specific upregulated candidate RMGs in an ARACNE algorithm. Among these genes, we selected 16 RMGs and 11 genes coexpressed with three RMGs to validate coexpression network results. RT‐PCR assay confirmed that these genes were highly upregulated in GA treatment. All 76 genes (38 root‐induced genes and 38 candidate RMGs) might be useful for the detection of GA sensitivity in rice roots.     

Use of a Novel Escherichia coli-Leuconostoc Shuttle Vector for Metabolic Engineering of Leuconostoc citreum To Overproduce d-Lactate

Determination of the complete nucleotide sequence of a cryptic plasmid, pMBLT00, from Leuconostoc mesenteroides subsp. mesenteroides KCTC13302 revealed that it contains 20,721 bp, a G+C content of 38.7%, and 18 open reading frames. Comparative sequence and mung been nuclease analyses of pMBLT00 showed that pMBLT00 replicates via the theta replication mechanism. A new, stable Escherichia coli-Leuconostoc shuttle vector, pMBLT02, which was constructed from a theta-replicating pMBLT00 replicon and an erythromycin resistance gene of pE194, was successfully introduced into Leuconostoc, Lactococcus lactis, and Pediococcus. This shuttle vector was used to engineer Leuconostoc citreum 95 to overproduce d-lactate. The L. citreum 95 strain engineered using plasmid pMBLT02, which overexpresses d-lactate dehydrogenase, exhibited enhanced production of optically pure d-lactate (61 g/liter, which is 6 times greater than the amount produced by the control strain) when cultured in a reactor supplemented with 140 g/liter glucose. Therefore, the shuttle vector pMBLT02 can serve as a useful and stable plasmid vector for further development of a d-lactate overproduction system in other Leuconostoc strains and Lactococcus lactis.     

Recent advances in the metabolic engineering of microorganisms for the production of 3-hydroxypropionic acid as C3 platform chemical

Development of sustainable technologies for the production of 3-hydroxypropionic acid (3HP) as a platform chemical has recently been gaining much attention owing to its versatility in applications for the synthesis of other specialty chemicals. Several proposed biological synthesis routes and strategies for producing 3HP from glucose and glycerol are reviewed presently. Ten proposed routes for 3HP production from glucose are described and one of which was recently constructed successfully in Escherichia coli with malonyl–Coenzyme A as a precursor. This resulted in a yield still far from the required level for industrial application. On the other hand, strategies employing engineered E. coli and Klebsiella pneumoniae capable of producing 3HP from glycerol are also evaluated. The titers produced by these recombinant strains reached around 3 %. At its current state, it is evident that a bulk of engineering works is yet to be done to acquire a biosynthesis route for 3HP that is acceptable for industrial-scale production.     

Engineered fumarate sensing Escherichia coli based on novel chimeric two-component system

DcuS/DcuR two component system (TCS) was firstly employed for the expression of the gfp gene under the dcuB gene promoter in aerobic condition to develop high throughput screening system able to screen microorganisms producing high amount of fumarate. However, the DcuS/DcuR TCS could not produce a signal strong enough to mediate the expression of the gfp gene responding fumarate concentration. Thus, DcuS/DucR TCS was engineered by recruiting the EnvZ/OmpR system, the most-studied TCS in E. coli. A chimeric DcuS/EnvZ (DcuSZ) TCS was constructed by fusing the sensor histidine kinase of DcuS with the cytoplasmic catalytic domain of EnvZ, in which the expression of the gfp gene or the ompC gene was mediated by the ompC gene promoter through the cognate response regulator, OmpR. The output signals produced by the chimeric DcuSZ TCS were enough to detect fumarate concentration quantatively, in which the expressions of the gfp gene and the ompC gene were proportional to the fumarate concentration in the medium. Moreover, principal component analysis of C₄-dicarboxylates showed that DcuSZ chimera was highly specific to fumarate but could also respond to other C₄-dicarboxylates, which strongly suggests that TCS-based high throughput screening system able to screen microorganisms producing target chemicals can be developed.     

A newly updated and annotated checklist of the Anthocerotae and Hepaticae of Qinling Mts., China

An updated checklist of the Anthocerotae and Hepaticae for Qinling (Mts.) recognizes 261 species, 20 varieties, 9 subspecies and 2 forms in 86 genera and 44 families. The distributional ranges are provided for each taxon in Qinling. The information in this paper is based on a review of the previous reports up to 2014 and the specimens held in PE, KUN, HSNU, SDNU, WUK and WNU herbaria. Eight genera, 122 species, 6 varieties and 6 subspecies are new records for Qinling, including two taxa newly recorded for China. Fifteen species, 8 varieties, and 2 forms are endemic to China.     

The effect of Zn2+ on Pelodiscus sinensis creatine kinase: unfolding and aggregation studies

We studied the effects of Zn²⁺ on creatine kinase from the Chinese soft-shelled turtle, Pelodiscus sinensis (PSCK). Zn²⁺ inactivated the activity of PSCK (IC₅₀?=?.079?±?.004?mM) following first-order kinetics consistent with multiple phases. The spectrofluorimetry results showed that Zn²⁺ induced significant tertiary structural changes of PSCK with exposure to hydrophobic surfaces and that Zn²⁺ directly induced PSCK aggregation. The addition of osmolytes such as glycine, proline, and liquaemin successfully blocked PSCK aggregation, recovering the conformation and activity of PSCK. We measured the ORF gene sequence of PSCK by rapid amplification of cDNA end and simulated the 3D structure of PSCK. The results of molecular dynamics simulations showed that eight Zn²⁺ bind to PSCK and one Zn²⁺ is predicted to bind in a plausible active site of creatine and ATP. The interaction of Zn²⁺ with the active site could mostly block the activity of PSCK. Our study provides important insight into the action of Zn²⁺ on PSCK as well as more insights into the PSCK folding and ligand-binding mechanisms, which could provide important insight into the metabolic enzymes of P. sinensis.     

3-D finite element modelling of facial soft tissue and preliminary application in orthodontics

Prediction of soft tissue aesthetics is important for achieving an optimal outcome in orthodontic treatment planning. Previously, applicable procedures were mainly restricted to 2-D profile prediction. In this study, a generic 3-D finite element (FE) model of the craniofacial soft and hard tissue was constructed, and individualisation of the generic model based on cone beam CT data and mathematical transformation was investigated. The result indicated that patient-specific 3-D facial FE model including different layers of soft tissue could be obtained through mathematical model transformation. Average deviation between the transformed model and the real reconstructed one was 0.47 ± 0.77 mm and 0.75 ± 0.84 mm in soft and hard tissue, respectively. With boundary condition defined according to treatment plan, such FE model could be used to predict the result of orthodontic treatment on facial soft tissue.