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.

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.

Use of recombinant Lactobacillus sakei for the prevention and treatment of radiation-induced enteritis.

Radiation-induced enteritis is one of the most common complications in patients under radiotherapy at abdominal or pelvic cavity. Up to 50% of patients treated with pelvic radiotherapy has been reported radiation-induced acute enteritis, and half of them developed chronic enteritis. Overproduction of free radicals, activation of inflammatory pathways and vascular endothelial dysfunction were considered as the primary mechanisms of radiation-induced enteritis. Because probiotics have been demonstrated as a promising potential candidate for treating intestinal diseases, it may be a safer and more effective radioprotector for the enteritis compared to conventional chemical agents with inherent toxicities. Here, we propose that a recombinant Lactobacillus sakei would decrease the complications or symptoms significantly through against different pathogenic mechanisms simultaneously. Therefore, application of higher radiation dose for tumor control would be feasible when co-treating with recombinant Lactobacillus sakei.

MicroRNA-24 aggravates atherosclerosis by inhibiting selective lipid uptake from HDL cholesterol via the post-transcriptional repression of scavenger receptor class B type I.

BACKGROUND AND AIMS: Liver scavenger receptor class B type I (SR-BI) exerts atheroprotective effects through selective lipid uptake (SLU) from high-density lipoprotein cholesterol (HDL-C). Low hepatic SR-BI expression leads to high HDL-C levels in the circulation and an increased risk of atherosclerosis. Furthermore, macrophage SR-BI mediates bidirectional cholesterol flux and may protect against atherogenesis. Previous studies have revealed that miR-24 is closely related to cardiovascular disease (CVD) progression. We aimed to investigate the molecular mechanisms by which miR-24 participates in SR-BI-mediated selective HDL cholesteryl ester (HDL-CE) uptake and further atherogenesis in apoE-/- mice. METHODS: Bioinformatic predictions and luciferase reporter assays were utilized to detect the association between miR-24 and the SR-BI 3' untranslated region (3' UTR), and RT-PCR and western blotting were used to evaluate SR-BI mRNA and protein expression, respectively. The effects of miR-24 on Dil-HDL uptake were determined by flow cytometry assay. Double-radiolabeled HDL (125I-TC-/[3H] CEt-HDL) was utilized to measure the effects of miR-24 on HDL and CE binding and SLU in HepG2 and PMA-treated THP-1 cells. In addition, total cholesterol (TC) levels in HepG2 cells were analyzed using enzymatic methods, and macrophage lipid content was evaluated by high-performance liquid chromatography (HPLC) assay. Small interfering RNA (siRNA) and pcDNA3.1(-)-hSR-BI plasmid transfection procedures were utilized to confirm the role of SR-BI in the effects of miR-24 on Dil-HDL uptake, SLU and cholesterol levels in both cell types. Hepatic SR-BI level in apoE-/- mice was measured by western blotting. Liver TC, FC and CE levels and plasma triglycerides (TG), TC and HDL-C levels were evaluated enzymatically using commercial test kits. Atherosclerotic lesion sizes were measured using Oil Red O and hematoxylin-eosin staining. RESULTS: miR-24 directly repressed SR-BI expression by targeting its 3'UTR. In addition, miR-24 decreased Dil-HDL uptake and SLU in HepG2 and THP-1 macrophages. In the presence of HDL, miR-24 decreased TC levels in HepG2 cells and TC, free cholesterol (FC) and CE levels in macrophages. Overexpression and down-regulation assays showed that SR-BI mediated the effects of miR-24 on Dil-HDL uptake, SLU and cholesterol levels. Lastly, miR-24 administration decreased hepatic SR-BI expression and promoted atheromatous plaque formation in apoE-/- mice, findings in line with those of our in vitro studies. CONCLUSIONS: These findings indicate that miR-24 accelerates atherogenesis by repressing SR-BI-mediated SLU from HDL-C.

Prevalence and diversity of norovirus genogroups I and II in Hong Kong marine waters and detection by real-time PCR.

Marine waters from six sites around Hong Kong with varying levels of sewage pollution were examined for noroviruses (NoVs) by PCR cloning and sequencing of a highly-variable N-terminal region of the VP1 capsid gene, at the ORF1-ORF2 junction of NoV. Phylogenetic analysis of genogroups GI- and GII-specific PCR clones obtained from different marine sites indicated that human NoV GI.1 and GII.4 strains are the most prevalent genotypes circulating in Hong Kong waters. GI- and GII-specific TaqMan-based real-time PCR assays targeting the ORF1-ORF2 junction of NoVs were used to quantify NoV particles in marine water samples in parallel with total Escherichia coli counts which were enumerated on TBX medium. No correlation of any significance between NoV and E. coli counts was observed which highlighted the inadequacy in using E. coli as a fecal indicator to predict the level of NoVs in marine waters to protect public health.

Major human Hepatitis A virus genotype in Hong Kong marine waters and detection by real-time PCR.

Marine waters from seven sites around Hong Kong with varying levels of sewage pollution were analyzed for Hepatitis A virus (HAV) by PCR cloning and DNA sequencing of the highly variable VP1/2A junction of the HAV genome. Phylogenetic analysis of 10 PCR clones from each of the HAV-positive marine sites indicated that human HAV genotype IB is the most widely distributed type in Hong Kong waters. A sensitive and quantitative TaqMan-based PCR method targeting the 5'-noncoding region (5'-NCR) of HAV was used to quantify HAV particles in marine water samples along with the total Escherichia coli counts being enumerated on TBX medium for comparison. Our results showed that no correlation of any significance between HAV and E. coli counts was observed which underscores the inadequacy in using E. coli as a sanitary standard to predict the levels of HAV in marine waters.

Identification of differentially expressed genes in Sulfobacillus sp. TPY grown on either elemental sulphur or Fe(2+).

Sulfobacillus sp. TPY is a moderately thermophilic and acidophilic bacterium found in hydrothermal vents in the Pacific Ocean. This bacterium can oxidize ferrous sulfate (Fe(2+)) and elemental sulfur (S(0)) under separate conditions. We used random arbitrarily primed polymerase chain reaction (RAP-PCR) to screen and identify differentially expressed genes from bacteria grown on Fe(2+) or S(0) as the energy source. Fifty-five differential cDNA fragments were isolated and subjected to single-pass sequencing. Thirty-five fragments were identified as orthologs of known genes in the GenBank databases, of which 19 were confirmed to be differentially expressed at the transcriptional level by Northern blot analysis. Among these 19 genes, 14 genes, including isocitrate dehydrogenase, formyltetrahydrofolate deformylase, 3-hydroxybutyryl-CoA dehydrogenase, and GTP-binding protein, were upregulated in TPY grown on Fe(2+) or downregulated in TPY grown on S(0), while five genes such as the outer membrane adhesion-like protein, phosphomannomutase, and cysteine desulfurase sufS were upregulated in TPY strain grown on S(0) or downregulated in TPY grown on Fe(2+). These altered genes are involved in metabolism, osmotic stress, cell membrane alterations, oxidative stress, and the regulatory adaptive response. These results will aid our understanding of the molecular basis of Fe(2+) or S(0) oxidation by the moderately thermophilic and acidophilic bacteria.