A robust CRISPR–Cas9-based fluorescent reporter assay for the detection and quantification of DNA double-strand break repair

DNA double-strand breaks (DSBs) are highly cytotoxic lesions that can lead to chromosome rearrangements, genomic instability and cell death. Consequently, cells have evolved multiple mechanisms to efficiently repair DSBs to preserve genomic integrity. We have developed a DSB repair assay system, designated CDDR (CRISPR–Cas9-based Dual-fluorescent DSB Repair), that enables the detection and quantification of DSB repair outcomes in mammalian cells with high precision. CDDR is based on the introduction and subsequent resolution of one or two DSB(s) in an intrachromosomal fluorescent reporter following the expression of Cas9 and sgRNAs targeting the reporter. CDDR can discriminate between high-fidelity (HF) and error-prone non-homologous end-joining (NHEJ), as well as between proximal and distal NHEJ repair. Furthermore, CDDR can detect homology-directed repair (HDR) with high sensitivity. Using CDDR, we found HF-NHEJ to be strictly dependent on DNA Ligase IV, XRCC4 and XLF, members of the canonical branch of NHEJ pathway (c-NHEJ). Loss of these genes also stimulated HDR, and promoted error-prone distal end-joining. Deletion of the DNA repair kinase ATM, on the other hand, stimulated HF-NHEJ and suppressed HDR. These findings demonstrate the utility of CDDR in characterizing the effect of repair factors and in elucidating the balance between competing DSB repair pathways.     

Angiotensin II‐induced redox‐sensitive SGLT1 and 2 expression promotes high glucose‐induced endothelial cell senescence

High glucose (HG)‐induced endothelial senescence and dysfunction contribute to the increased cardiovascular risk in diabetes. Empagliflozin, a selective sodium glucose co‐transporter2 (SGLT2) inhibitor, reduced the risk of cardiovascular mortality in type 2 diabetic patients but the protective mechanism remains unclear. This study examines the role of SGLT2 in HG‐induced endothelial senescence and dysfunction. Porcine coronary artery cultured endothelial cells (ECs) or segments were exposed to HG (25 mmol/L) before determination of senescence‐associated beta‐galactosidase activity, protein level by Western blot and immunofluorescence staining, mRNA by RT‐PCR, nitric oxide (NO) by electron paramagnetic resonance, oxidative stress using dihydroethidium and glucose uptake using 2‐NBD‐glucose. HG increased ECs senescence markers and oxidative stress, down‐regulated eNOS expression and NO formation, and induced the expression of VCAM‐1, tissue factor, and the local angiotensin system, all these effects were prevented by empagliflozin. Empagliflozin and LX‐4211 (dual SGLT1/2 inhibitor) reduced glucose uptake stimulated by HG and H₂O₂ in ECs. HG increased SGLT1 and 2 protein levels in cultured ECs and native endothelium. Inhibition of the angiotensin system prevented HG‐induced ECs senescence and SGLT1 and 2 expression. Thus, HG‐induced ECs ageing is driven by the local angiotensin system via the redox‐sensitive up‐regulation of SGLT1 and 2, and, in turn, enhanced glucotoxicity.     

Significance of neutrophil microparticles in ischaemia‐reperfusion: Pro‐inflammatory effectors of endothelial senescence and vascular dysfunction

Endothelial senescence is an emerging cause of vascular dysfunction. Because microparticles are effectors of endothelial inflammation and vascular injury after ischaemia‐reperfusion, we examined leucocyte‐derived microparticles of spleen origin as possible contributors. Microparticles were generated from primary rat splenocytes by either lipopolysaccharide or phorbol‐myristate‐acetate/calcium ionophore, under conditions mimicking innate and adaptive immune responses. Incubation of primary porcine coronary endothelial cells with either type of microparticles, but not with those from unstimulated splenocytes, leads to a similar threefold raise in senescence‐associated β‐galactosidase activity within 48 hours, indicating accelerated senescence, to endothelial oxidative stress, and a fivefold and threefold increase in p21 and p16 senescence markers after 24 hours. After 12‐hour incubation, the endothelial‐dependent relaxation of coronary artery rings was reduced by 50%, at distinct optimal microparticle concentration. In vitro, microparticles were pro‐thrombotic by up‐regulating the local angiotensin system, by prompting tissue factor activity and a secondary generation of pro‐coagulant endothelial microparticles. They initiated an early pro‐inflammatory response by inducing phosphorylation of NF‐κB, MAP kinases and Akt after 1 hour, and up‐regulated VCAM‐1 and ICAM‐1 at 24 hours. Accordingly, VCAM‐1 and COX‐2 were also up‐regulated in the coronary artery endothelium and eNOS down‐regulated. Lipopolysaccharide specifically favoured the shedding of neutrophil‐ and monocyte‐derived microparticles. A 80% immuno‐depletion of neutrophil microparticles reduced endothelial senescence by 55%, indicating a key role. Altogether, data suggest that microparticles from activated splenocytes prompt early pro‐inflammatory, pro‐coagulant and pro‐senescent responses in endothelial cells through redox‐sensitive pathways. The control of neutrophil shedding could preserve the endothelium at site of ischaemia‐reperfusion–driven inflammation and delay its dysfunction.     

Multinuclear Yeast Magnusiomyces (Dipodascus,Endomyces) magnusii is a Promising Isobutanol Producer

Higher alcohol isobutanol is a promising liquid fuel. During alcoholic fermentation, Saccharomyces cerevisiae produces only trace amounts of isobutanol. Screening the collection of nonconventional yeasts show that Magnusiomyces magnusii accumulates 440 mg of isobutanol per L in rich YPD medium. Here, the transformation protocol for M. magnusii is adapted based on the use of the dominant markers conferring resistance to nourseothricin or zeocin; the strong constitutive promoter TEF1 is cloned and a reporter system based on LAC4 gene from Kluyveromyces lactis coding for β‐galactosidase is constructed. In order to increase isobutanol production in M. magnusii, the heterologous gene ILV2 from S. cerevisiae is expressed in M. magnusii under control of the TEF1 promoter. The best stabilized transformants produce 620 mg of isobutanol per L in YPD medium and 760 mg L^?1 in the medium with 2‐oxoisovalerate. This suggests that M. magnusii is a promising organism for further development of a robust isobutanol producer.     

The Effect of Synbiotic Supplementation on Growth Parameters in Mild to Moderate FTT Children Aged 2–5 Years

Synbiotic (probiotic bacteria and prebiotic) has beneficial effects on the gastrointestinal tract. This study was designed to investigate the effect of synbiotic supplementation on the growth of mild to moderate failure to thrive (FTT) children. A randomized, triple-blind, placebo-controlled trial was conducted involving 80 children aged 2–5 years with mild to moderate FTT, who were assigned at random to receive synbiotic supplementation (10⁹ colony-forming units) or placebo for 30 days. The weights, height, and BMI were recorded in a structured diary, and the questionnaires were completed to monitor the numbers of infection episodes, gastrointestinal problems, admission to hospital, and appetite improvement during the study. Sixty-nine children completed the study. There were no differences in the demographic characteristic between the two groups. The mean weight was similar at baseline. After 30 days of intervention, the mean weight of the participants in the synbiotic group increased significantly than those in the placebo group (600?±?37 vs. 74?±?32 g/month P 0.000). BMI changes in synbiotic and placebo group were 0.44 and 0.07 kg/m², and that the differences among the two groups were significant.(P 0.045) Furthermore, the height increment in synbiotic and placebo group was 0.41 and 0.37 cm respectively with no significant difference (P 0.761). Administration of 30-day synbiotic supplementation may significantly improve weight and BMI in Iranian children with mild to moderate FTT, but there is no effect on the height in this study. Further studies should be designed to found out the effect of synbiotic on growth parameters in undernourished and well-nourished children.

     

Does Magnesium Supplementation Improve Body Composition and Muscle Strength in Middle-Aged Overweight Women? A Double-Blind, Placebo-Controlled, Randomized Clinical Trial

Muscle strength, an independent predictor of metabolic disorders, disability, and mortality, reduces gradually with advancing age. Little is known about the influence of nutritional intervention on muscle strength in middle-aged. The aim of the present study is to examine whether magnesium could improve body composition and muscle strength in middle-aged overweight women. In this double-blinded, placebo-controlled, randomized trial, a total of 74 healthy middle-aged overweight women (25?≤?BMI?≤?30 kg/m²) received either 250 mg magnesium in the form of magnesium oxide or placebo daily for 8 weeks. Body composition was assessed using Bioelectrical Impedance Analysis (BIA). Handgrip strength and knee extension strength were measured with isometric dynamometry. Functional mobility was assessed using Time Get Up and Go Test (TGUG). A significant increase in mean lean body mass was observed (P?=?0.05) accompanied with a significant decrease in fat mass (P?=?0.02) solely in the magnesium group at the end of 8 weeks compared to baseline values but the changes did not reach significant as compared to placebo group. Handgrip strength and TGUG improved in the magnesium group compared to baseline but they were not significant compared to placebo. There were no significant differences in increasing knee extension strength in the magnesium group as compared with placebo. Baseline values of serum magnesium and muscle strength of participants did not indicate any influences on response to magnesium supplementation. Our findings indicate that magnesium as magnesium oxide, 250 mg/day, for 8 weeks do not lead to a significant greater gain in muscle strength and function compared to placebo.     

Enhancement of biosurfactants and biofilm production after gamma irradiation-induced mutagenesis of Bacillus subtilis UTB1, a biocontrol agent of Aspergillus flavus

Bacillus subtilis UTB1 is known as a biocontrol agent of Aspergillus flavus in pistachio nuts. In order to reduce growth of this fungal pathogen to a greater extent, a random mutagenesis using gamma irradiation was applied in strain UTB1. We studied the effects of different doses of irradiation (from 100 Gray to 3000 Gray) and efficiency of 500 selected colonies was assessed against A. flavus in a plate assay. Forty-five colonies exhibited higher inhibition activity compared to the non-irradiated wild type. Eight mutants out of the 45 were selected based on different polymorphism patterns obtained by rep-PCR (ERIC and BOX). Six mutants demonstrated enhanced production of biosurfactants on blood agar medium and in oil spreading technique and they also revealed more robust biofilm in comparison with the wild type UTB1. These observations showed that the six mutants are more effective biocontrol agents than the parental strain, suggesting that they would be promising biocontrol candidates against A. flavus in pistachio nuts.     

Structural-dynamic insights into the H. pylori cytotoxin-associated gene A (CagA) and its abrogation to interact with the tumor suppressor protein ASPP2 using decoy peptides

Abstract

Helicobacter pylori (H. pylori) is one of the most extensively studied Gram-negative bacteria due to its implication in gastric cancer. The oncogenicity of H. pylori is associated with cytotoxin-associated gene A (CagA), which is injected into epithelial cells lining the stomach. Both the C- and N-termini of CagA are involved in the interaction with several host proteins, thereby disrupting vital cellular functions, such as cell adhesion, cell cycle, intracellular signal transduction, and cytoskeletal structure. The N-terminus of CagA interacts with the tumor-suppressing protein, apoptosis-stimulating protein of p53 (ASPP2), subsequently disrupting the apoptotic function of tumor suppressor gene p53. Here, we present the in-depth molecular dynamic mechanism of the CagA–ASPP2 interaction and highlight hot-spot residues through in silico mutagenesis. Our findings are in agreement with previous studies and further suggest other residues that are crucial for the CagA–ASPP2 interaction. Furthermore, the ASPP2-binding pocket possesses potential druggability and could be engaged by decoy peptides, identified through a machine-learning system and suggested in this study. The binding affinities of these peptides with CagA were monitored through extensive computational procedures and reported herein. While CagA is crucial for the oncogenicity of H. pylori, our designed peptides possess the potential to inhibit CagA and restore the tumor suppressor function of ASPP2.