Progress of uranium-contaminated soil bioremediation technology.

With the extensive exploitation of nuclear energy and uranium, the problem of uranium-contaminated soil is becoming increasingly prominent. In recent years, various technologies for remediation of uranium-contaminated soil have emerged, such as bioremediation, physical remediation and chemical remediation. Bioremediation technology has the widespread attention because of its environmental friendliness, low cost and high economic benefits. This paper mainly reviews the evaluation index of uranium-contaminated soil, soil remediation technology and its advantages and disadvantages, introduces especially the research status of soil bioremediation technology in detail, and puts forward some suggestions and prospects for bioremediation of uranium-contaminated soil.

Application Progress of Deinococcus radiodurans in Biological Treatment of Radioactive Uranium-Containing Wastewater.

Radioactive uranium wastewater contains a large amount of radionuclide uranium and other heavy metal ions. The radioactive uranium wastewater discharged into the environment will not only pollute the natural environment, but also threat human health. Therefore, the treatment of radioactive uranium wastewater is a current research focus for many researchers. The treatment in radioactive uranium wastewater mainly includes physical, chemical and biological methods. At present, the using of biological treatment to treat uranium in radioactive uranium wastewater has been gradually shown its superiority and advantages. Deinococcus radiodurans is a famous microorganism with the most radiation resistant to ionizing radiation in the world, and can also resist various other extreme pressures. D. radiodurans can be directly used for the adsorption of uranium in radioactive waste water, and it can also transform other functional genes into D. radiodurans to construct genetically engineered bacteria, and then applied to the treatment of radioactive uranium containing wastewater. Radionuclides uranium in radioactive uranium-containing wastewater treated by D. radiodurans involves a lot of mechanisms. This article reviews currently the application of D. radiodurans that directly or construct genetically engineered bacteria in the treatment of radioactive uranium wastewater and discusses the mechanism of D. radiodurans in bioremediation of uranium. The application of constructing an engineered bacteria of D. radiodurans with powerful functions in uranium-containing wastewater is prospected.

Mechanism of recombinant bacteria adsorb UO22+ under culture condition.

Research on the ability and mechanism of genetically recombinant E. coli DH5α containing DSR A gene to enrich uranium under culture conditions provides a theoretical basis for the application of the bacteria in the treatment of uranium pollution. By exploring the influence of factors such as the initial concentration of uranium, culture time, and inoculation amount on the characteristics of uranium enrichment in genetically recombinant E. coli, using FTIR, SEM-EDS, XPS and XRD explore the mechanism of uranium-enriched bacteria. The results showed that when initial UO22+ concentration reach 600 mg/L, E. Coli D1 could not survived, indicated that the maximum tolerance concentration is lower than 600 mg/L. While concentration between 0∼500 mg/L, strains D1 can grow normally and has the ability to enrich uranium. In the prime stage, strains D1 resist toxics through release inorganic phosphates to precipitate UO22+ on cell wall, after 96 h, most UO22+ were transferred into cytoplasm and metabolized into U(IV) which is less toxic. In the metabolize process, all groups involved in metabolizing UO22+, especially protein contain groups like hydroxyl, amine and carboxyl paly a huge role. It shows that within a certain concentration rage, strains D1 has a good enrichment effect on uranium under culture conditions.

Kinetics model of DNA double-strand break repair in eukaryotes.

This manuscript outlines the kinetics of two main repair pathways of DNA double-strand break (DSB) in eukaryotes: non-homologous end joining (NHEJ) and homologous recombination repair (HRR). In this review, we discuss the precise study of recruitment kinetics of repair proteins based on the latest technologies in the past two decades. Then we simulate the theoretical description of the DNA repair process by mathematical models. In our study, the consecutive reactions chain (CRC) model and continuous-time random walk (CTRW) model have been unified by us, so that we can obtain the function of the number of intermediates with time in the same framework of equations, overcome the incompatibility between the two models. On this basis, we propose a data fitting workflow using these both models. Finally, we give an overview of different real-time quantitative methods and the new mechanism complexity that can be found from the corresponding dynamic models.

Identification of circRNA-associated ceRNA network in BMSCs of OVX models for postmenopausal osteoporosis.

Circular RNAs (circRNAs) serve as competing endogenous RNAs (ceRNAs) and indirectly regulate gene expression through shared microRNAs (miRNAs). However, the potential circRNAs functioning as ceRNAs in osteoporosis remain unclear. The bone marrow mesenchymal stem cells (BMSCs) were isolated from ovariectomy (OVX) mice and controls. We systematically analyzed RNA-seq and miRNA-microarray data, miRNA-target interactions, and prominently coexpressed gene pairs to identify aberrantly expressed circRNAs, miRNAs, and messenger RNAs (mRNAs) between the OVX mice and controls. A total of 45 circRNAs, 22 miRNAs, and 548 mRNAs were significantly dysregulated (fold change > 1.5; p < 0.05). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were conducted for differentially expressed mRNAs, and subsequently a circRNA-associated ceRNA network involved in osteoporosis was constructed. We identified two ceRNA regulatory pathways in this osteoporosis mouse model-novel circRNA 0020/miR-206-3p/Nnmt and circRNA 3832/miR-3473e/Runx3, which were validated by real-time PCR. This is the first study to elucidate the circRNA-associated ceRNA network in OVX and control mice using deep RNA-seq and RNA-microarray analysis. The data further expanded the understanding of circRNA-associated ceRNA networks, and the regulatory functions of circRNAs, miRNAs and mRNAs in the pathogenesis and pathology of osteoporosis.

MiR-1-3p regulates the differentiation of mesenchymal stem cells to prevent osteoporosis by targeting secreted frizzled-related protein 1.

Osteoporosis (OP) is a systemic skeletal disorder with the characteristics of bone mass reduction and microarchitecture deterioration, resulting in bone fragility and increased fracture risk. A reduction in the osteoblast-differentiation of bone marrow mesenchymal stem cells (BMSCs) is considered as a basic pathogenesis of osteoporosis. miRNAs play a substantial role in the development and differentiation of BMSCs. In the present study, we found that miR-1-3p was significantly downregulated in the bones of Chinese osteoporotic patients (n = 29). Secreted frizzled-related protein 1 (SFRP1) was predicted as a target gene of miR-1-3p via the TargetScan and PicTar softwares and validated by dual-luciferase reporter assays. The findings revealed that the expression of SFRP1 was inversely correlated with miR-1-3p in osteoporotic patients. We induced mouse MSCs (mMSCs) to osteogenesis or adipogenesis and found that miR-1-3p was upregulated during osteogenesis but downregulated during adipogenesis. The overexpression of miR-1-3p stimulated osteogenesis and inhibited adipogenesis of mMSCs. In addition, ovariectomized (OVX) mice were tested and the function of miR-1-3p in vivo was explored. Immunohistochemistry and histomorphometric assays showed that in vivo inhibition of miR-1-3p increased the expression level of SFRP1 and reduced bone formation and bone mass. Furthermore, tartrate-resistant acid phosphatase (TRAP) staining indicated that the in vivo suppression of miR-1-3p promoted osteoclast activity, suggesting that miR-1-3p may influence bone mass by regulating bone resorption. It can be concluded that miR-1-3p plays a pivotal role in the pathogenesis of osteoporosis via targeting SFRP1 and may be a potential therapeutic target for osteoporosis.

Antioxidative system of Deinococcus radiodurans.

Deinococcus radiodurans is famous for its extreme resistance to various stresses such as ionizing radiation (IR), desiccation and oxidative stress. The underlying mechanism of exceptional resistance of this robust bacterium still remained unclear. However, the antioxidative system of D. radiodurans has been considered to be the determinant factor for its unparalleled resistance and protects the proteome during stress, then the DNA repair system and metabolic system exert their functions to restore the cell to normal physiological state. The antioxidative system not only equipped with the common reactive oxygen species (ROS) scavenging enzymes (e.g., catalase and superoxide dismutase) but also armed with a variety of non-enzyme antioxidants (e.g., carotenoids and manganese species). And the small manganese complexes play an important role in the antioxidative system of D. radiodurans. Recent studies have characterized several regulators (e.g., PprI and PprM) in D. radiodurans, which play critical roles in the protection of the bacteria from various stresses. In this review, we offer a panorama of the progress regarding the characteristics of the antioxidative system in D. radiodurans and its application in the future.

Gene regulation for the extreme resistance to ionizing radiation of Deinococcus radiodurans.

Deinococcus radiodurans is a model microorganism used for studies on DNA repair and antioxidation due to its extraordinary tolerance to ionizing radiation and other DNA-damaging agents. Various transcriptome analyses have revealed that hundreds of genes are induced and that many other genes are repressed during recovery of D. radiodurans following irradiation, suggesting that gene regulation is of great importance for the extreme resistance of this microorganism to ionizing radiation. In this article, we focus on some reported strategies that are employed by D. radiodurans to regulate the genes implicated in its extreme tolerance to ionizing radiation for a comprehensive understanding of the reasons this bacterium can survive such extraordinary stress. We expect this review to shed light on potential radioprotective agents and applications for use in a range of fields.

RNA-Binding Domain is Necessary for PprM Function in Response to the Extreme Environmental Stress in Deinococcus radiodurans.

Deinococcus radiodurans was considered as one of the most radiation-resistant organisms on Earth because of its strong resistance to the damaging factors of both DNA and protein, including ionizing radiation, ultraviolet radiation, oxidants, and desiccation. PprM, as a bacterial cold shock protein homolog, was involved in the radiation resistance and oxidative stress response of D. radiodurans, but its potential mechanisms are poorly expounded. In this study, we found that PprM was highly conserved with the RNA-binding domain in Deinococcus genus through performing phylogenic analysis. Moreover, the paper presents the analysis on the tolerance of environmental stresses both in the wild-type and the pprM/pprM RBD mutant strains, demonstrating that pprM and RNA-binding domain disruptant strain were with higher sensitivity than the wild-type strain to cold stress, mitomycin C, UV radiation, and hydrogen peroxide. In the following step, the recombinant PprM was purified, with the finding that PprM was bound to the 5'-untranslated region of its own mRNA by gel mobility shift assay in vitro. With all these findings taken into consideration, it was suggested that PprM act as a cold shock protein and its RNA-binding domain may be involved in reaction to the extreme environmental stress in D. radiodurans.

Knockout of pprM Decreases Resistance to Desiccation and Oxidation in Deinococcus radiodurans.

Deinococcus radiodurans has attracted a great interest in the past decades due to its extraordinary resistance to ionizing radiation and highly efficient DNA repair system. Recent studies indicated that pprM is a putative pleiotropic gene in D. radiodurans and plays an important role in radioresistance and antioxidation, but its underlying mechanisms are poorly elucidated. In this study, pprM mutation was generated to investigate resistance to desiccation and oxidative stress. The result showed that the survival of pprM mutant under desiccation was markedly retarded compared to the wild strain from day 7-28. Furthermore, knockout of pprM increases the intercellular accumulation of ROS and the sensibility to H2O2 stress in the bacterial growth inhibition assay. The absorbance spectrum experiment for detecting the carotenoid showed that deinoxanthin, a carotenoid that peculiarly exists in Deinococcus, was reduced in the pprM mutant in the pprM mutant. Quantitative real time PCR showed decreased expression of three genes viz. CrtI (DR0861, 50%),CrtB (DR0862, 40%) and CrtO (DR0093, 50%), which are involved in deinoxanthin synthesis, and of Dps (DNA protection during starving) gene (DRB0092) relevant to ion combining and DNA protection in cells. Our results suggest that pprM may affect antioxidative ability of D. radiodurans by regulating the synthesis of deinoxanthin and the concentration of metal ions. This may provide new clues for the treatment of antioxidants.

Predicting Thermodynamic Properties of PBXTHs with New Quantum Topological Indexes.

Novel group quantitative structure-property relationship (QSPR) models on the thermodynamic properties of PBXTHs were presented, by the multiple linear regression (MLR) analysis method. Four thermodynamic properties were studied: the entropy (Sθ), the standard enthalpy of formation (ΔfHθ), the standard Gibbs energy of formation (ΔfGθ), and the relative standard Gibbs energy of formation (ΔRGθ). The results by the formula indicate that the calculated and predicted data in this study are in good agreement with those in literature and the deviation is within the experimental errors. To validate the estimation reliability for internal samples and the predictive ability for other samples, leave-one-out (LOO) cross validation (CV) and external validation were performed, and the results show that the models are satisfactory.