Regulation of Retinoic Acid Inducible Gene-I (RIG-I) Activation by the Histone Deacetylase 6

Retinoic acid inducible gene-I (RIG-I) is a cytosolic pathogen recognition receptor that initiates the immune response against many RNA viruses. Upon RNA ligand binding, RIG-I undergoes a conformational change facilitating its homo-oligomerization and activation that results in its translocation from the cytosol to intracellular membranes to bind its signaling adaptor protein, mitochondrial antiviral-signaling protein (MAVS). Here we show that RIG-I activation is regulated by reversible acetylation. Acetyl-mimetic mutants of RIG-I do not form virus-induced homo-oligomers, revealing that acetyl-lysine residues of the RIG-I repressor domain prevent assembly to active homo-oligomers. During acute infection, deacetylation of RIG-I promotes its oligomerization upon ligand binding. We identify histone deacetylase 6 (HDAC6) as the deacetylase that promotes RIG-I activation and innate antiviral immunity to recognize and restrict RNA virus infection.

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RIG-I undergoes reversible deacetylation during acute virus infection.

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Acetylation of RIG-I Repressor domain controls RIG-I activation by restricting dimerization.

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HDAC6 is the cellular deacetylase essential for RIG-I deacetylation to induce antiviral innate immunity.

RIG-I is a cytosolic pathogen recognition receptor at the frontline of immune response against RNA virus infection. RIG-I is expressed in most cells of the body and becomes activated after sensing and binding to pathogen associated molecular pattern (PAMP) RNA motifs within products of virus infection. The RIG-I activation process involves multiple regulatory events including PAMP binding and ATP hydrolysis, protein conformational change and intracellular redistribution, and specific post-translational modifications. Our results define reversible acetylation of RIG-I and its deacetylation by HDAC6 as key to controlling innate antiviral immune induction in response to RNA virus infection.

Nucleosome breathing and remodeling constrain CRISPR-Cas9 function

The CRISPR-Cas9 bacterial surveillance system has become a versatile tool for genome editing and gene regulation in eukaryotic cells, yet how CRISPR-Cas9 contends with the barriers presented by eukaryotic chromatin is poorly understood. Here we investigate how the smallest unit of chromatin, a nucleosome, constrains the activity of the CRISPR-Cas9 system. We find that nucleosomes assembled on native DNA sequences are permissive to Cas9 action. However, the accessibility of nucleosomal DNA to Cas9 is variable over several orders of magnitude depending on dynamic properties of the DNA sequence and the distance of the PAM site from the nucleosome dyad. We further find that chromatin remodeling enzymes stimulate Cas9 activity on nucleosomal templates. Our findings imply that the spontaneous breathing of nucleosomal DNA together with the action of chromatin remodelers allow Cas9 to effectively act on chromatin in vivo.

DOI:http://dx.doi.org/10.7554/eLife.13450.001

CRISPR is a method of editing the genetic material inside living cells and has enabled dramatic advances in a broad variety of research fields in recent years. The method relies on a bacterial enzyme called Cas9 that can be programmed, via short guide molecules made from RNA, to target specific sites in the cell’s DNA. Once bound to its target, the Cas9 enzyme cuts the DNA molecule; this often leads to changes in the DNA sequence. In nature, bacteria use the CRISPR-Cas9 system to defend themselves against viruses. However, this system also works in other cell types and can be reprogrammed to target almost any site in the DNA.

To date, the CRISPR-Cas9 system has been used in fungi, worms, flies, plants, mammals and other eukaryotes. Yet, unlike in bacteria, much of the DNA in eukaryotes is wrapped around proteins called histones to form units referred to as nucleosomes. This means eukaryotic DNA is often tightly packaged, which makes it less accessible to other proteins. Nevertheless, eukaryotic DNA will spontaneously detach and reattach to the histones – a phenomenon that is commonly known as DNA “breathing”. Also, protein machines known as chromatin remodelers can move, assemble and take apart the nucleosomes in eukaryotic cells. However, because there is much still to learn about how CRISPR-Cas9 works in eukaryotic cells, it is not clear how nucleosomes affect this system’s activity.

Isaac et al. have now used a simplified biochemical system to test how nucleosomes and chromatin remodelers affect CRISP-Cas9 activity. The system comprised purified Cas9 enzymes, short guide RNA molecules and nucleosomes. The experiments revealed that the Cas9 enzyme was able to cut DNA on nucleosomes when the DNA sequence allowed more spontaneous breathing or when chromatin remodelers were present to destabilize or move the nucleosome out of the way.

These results suggest that by taking the placement of the nucleosomes into account, researchers can better predict how effective the CRISPR-Cas9 system will be at targeting a specific DNA sequence in a eukaryotic cell. The findings also suggest ways to make genome editing with CRISPR-Cas9 even more efficient.

DOI:http://dx.doi.org/10.7554/eLife.13450.002

[The study of atmospheric particulate matters and IFN-γDNA methylation in CD4⁺ T cells from patients with AR children]

Objective:To investigate the possible effects of meteorological and environmental factors on AR of children and IFN-γgene specific DNA methylation levels in CD4⁺ T cells of patients with AR. Method:Undergoing follow-up on 35 pediatric AR patients (6-12 years). Data on daily sulfur dioxide (SO₂), nitrogen dioxide (NO₂), particulate matter of diameter smaller than 10 micrometer (PM-10) and particulate matter of diameter smaller than 2.5 micrometer (PM2.5), the average of ozone (O₃) per 8 hours was available as average values derived from the data of 6 state controlled monitoring stations distributed across Pudong district, Shanghai. We quantified IFN-γ (interferon-γ) gene specific DNA methylation levels in CD4⁺ T cells from 35 patients with AR and 30 healthy controls. mRNA levels of IFN-γ gene were measured by real-time reverse transcriptase-PCR. Methods of personal exposure assessment of PM2.5 and PM10 were measured. Result:Compared with control, IFN-γ promoter region was hypermethylated in AR CD4⁺ T cells (P<0.05). Of all observed CpG sites in IFN-γ promoter region, there were significant differences in CpG⁻²⁹⁹, CpG⁺¹¹⁹, CpG⁺¹⁶⁸ (P=0.004, P=0.029, P=0.035). IFN-γ mRNA expression was significantly increase in CD4⁺ T cells (P<0.05). The level of IFN-γ mRNA expression was negatively correlated to mean level of methylation in IFN-γ promoter region. After adjusting, level of long exposure PM2.5 was positively correlated with level of methylation in IFN-γ promoter region. Conclusion:Level of methylation in IFN-γ promoter region may be affected by long exposure PM2.5.

G protein-coupled estrogen receptor is involved in modulating colonic motor function via nitric oxide release in C57BL/6 female mice

BACKGROUND

Estrogen may regulate gastrointestinal motor functions, but the mechanism(s) is not totally understood. Here, we investigated whether G protein-coupled estrogen receptor (GPER/GPR30) was involved in regulating colonic motor functions and explored the underlying physiological mechanisms.

METHODS

Adult female C57BL/6 mice were used. The expression and localization of GPER were examined by RT-PCR, western blot, and immuno-labeling. The role of GPER in modulating colonic motor functions was assessed by the bead propulsion test in vivo and organ bath experiments in vitro.

KEY RESULTS

GPER was expressed in colonic myenteric neurons. The colonic transit time (CTT) in proestrus and estrus was significantly longer than that in diestrus. In vivo treatment with the selective GPER blocker G15 significantly shortened CTT in proestrus and estrus. In ovariectomized mice, acute estrogen supplementation increased CTT, which could be abolished by G15 co-administration. The GPER agonist G-1 caused a concentration-dependent inhibition of carbachol -induced circular muscle strips contraction, which was abolished by tetrodotoxin and the neuronal nitric oxide synthase (nNOS) inhibitor N-propyl-l-arginine. G-1 stimulated NO production in isolated longitudinal muscle myenteric plexus and cultured myenteric neurons, which was dependent on nNOS. Immunofluorescence labeling showed co-localization of GPER with nNOS in the myenteric plexus.

CONCLUSIONS & INFERENCES

We suggest that activation of GPER exerts an inhibitory effect on colonic motility by promoting NO release from myenteric nitrergic nerves. These results raise a possibility that GPER may be involved in mediating the inhibitory effect of estrogen on colonic motor functions, via a non-genomic, neurogenic mechanism.

Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage

Bacterial adaptive immunity and genome engineering involving the CRISPR (clustered regularly interspaced short palindromic repeats)-associated (Cas) protein Cas9 begin with RNA-guided DNA unwinding to form an RNA-DNA hybrid and a displaced DNA strand inside the protein. The role of this R-loop structure in positioning each DNA strand for cleavage by the two Cas9 nuclease domains is unknown. We determine molecular structures of the catalytically active Streptococcus pyogenes Cas9 R-loop that show the displaced DNA strand located near the RuvC nuclease domain active site. These protein-DNA interactions, in turn, position the HNH nuclease domain adjacent to the target DNA strand cleavage site in a conformation essential for concerted DNA cutting. Cas9 bends the DNA helix by 30°, providing the structural distortion needed for R-loop formation.

The autoinhibitory CARD2-Hel2i Interface of RIG-I governs RNA selection

RIG-I (Retinoic Acid Inducible Gene-I) is a cytosolic innate immune receptor that detects atypical features in viral RNAs as foreign to initiate a Type I interferon signaling response. RIG-I is present in an autoinhibited state in the cytoplasm and activated by blunt-ended double-stranded (ds)RNAs carrying a 5' triphosphate (ppp) moiety. These features found in many pathogenic RNAs are absent in cellular RNAs due to post-transcriptional modifications of RNA ends. Although RIG-I is structurally well characterized, the mechanistic basis for RIG-I's remarkable ability to discriminate between cellular and pathogenic RNAs is not completely understood. We show that RIG-I's selectivity for blunt-ended 5'-ppp dsRNAs is ≈3000 times higher than non-blunt ended dsRNAs commonly found in cellular RNAs. Discrimination occurs at multiple stages and signaling RNAs have high affinity and ATPase turnover rate and thus a high katpase/Kd. We show that RIG-I uses its autoinhibitory CARD2-Hel2i (second CARD-helicase insertion domain) interface as a barrier to select against non-blunt ended dsRNAs. Accordingly, deletion of CARDs or point mutations in the CARD2-Hel2i interface decreases the selectivity from ≈3000 to 150 and 750, respectively. We propose that the CARD2-Hel2i interface is a 'gate' that prevents cellular RNAs from generating productive complexes that can signal.

Acetals from primary alcohols with the use of tridentate proton responsive phosphinepyridonate iridium catalysts

The association of the new phosphinepyridonate ligands along with an iridium metallic precursor resulted in the selective acetalization of various primary alcohols via a formal dehydrogenative coupling reaction.

Exceptional material requirement for reproduction in mouse oocytes

Limited information on oocytes and fertilization prevents the efficient therapy of patients with infertility. The most important reason for this lack of understanding is a deficiency in research dedicated to oocytes and fertilization. Currently, we are concerned with the role of nutrition in the process of oocyte development to better understand the relationship between nutrition and infertility. The aim of this study was to explore the relationship between some exceptional materials and infertility to elucidate the role of these materials in oocyte development. We used proteomic analysis to identify numerous nutrition-related proteins in three developmental stages: the germinal vesicle stage, the metaphase II-arrested stage, and the fertilized oocyte-zygote stage. Specific proteins were abundantly expressed during the three stages. These proteins included astacin-like metalloendopeptidase, selenium-binding proteins, and other proteins involved in metabolic and signaling pathways. Other proteins were involved in the citrate cycle, the electron transport chain, the urea cycle, fatty acid metabolism, and the insulin signaling pathway. Almost all these proteins exhibited different expression levels in the three stages. The results of the present study provide a better understanding of the molecular mechanisms of early embryonic development and suggest new treatment methods for infertility.

Effects and mechanism of lipoic acid on beta-amyloid-intoxicated C6 glioma cells

β-amyloid peptides (Aβs) can exert neurotoxic effects through induction of oxidative damage, whereas lipoic acid (LA), a powerful antioxidant, can alleviate oxidative damage. In this study, we explored the effect and mechanism of action of LA on beta-amyloid-intoxicated C6 glioma cells. Cells were randomly divided into three groups: control (vehicle), Aβ, and LA + Aβ. The LA + Aβ group was treated with LA for 2 h, then both the Aβ-only and the LA + Aβ groups were incubated with 25 μM Aβ for 24 h. Cell viability was measured by the MTT method. Mitochondrial reduced glutathione (GSH) and oxidized glutathione (GSSG) levels were detected by enzyme-linked immunosorbent assay (ELISA), and the GSH to GSSG ratio calculated. Real-time polymerase chain reaction and western blot analyses were used to detect MnSOD mRNA and protein, respectively. Aβ significantly inhibited C6 cell proliferation compared with the control group (P < 0.05). LA markedly increased cell viability compared with the Aβ group (P < 0.05). The increased GSSH and decreased GSH mitochondrial accumulation induced by Aβ was profoundly reversed by treatment with LA (P < 0.05). Aβ significantly reduced MnSOD expression compared to controls (P < 0.05), whereas LA pretreatment increased MnSOD expression compared with the Aβ-only group (P < 0.05); MnSOD protein levels showed similar patterns. These results suggest that LA might protect Aβ-intoxicated C6 glioma cells by alleviating oxidative damage, providing a new treatment strategy for neurodegenerative diseases.

A meta-analysis of limb-salvage versus amputation in the treatment of patients with Enneking‡U pathologic fracture osteosarcoma

INTRODUCTION

The aim of this meta-analysis was to further explore whether the relapse, 5-year survival and metastasis the same or not between limb-salvage and amputation in the treatment of patients with limited stage Enneking II pathologic fracture osteosarcoma.

MATERIALS AND METHODS

An electronic search of the Medline, EMBASE and CNKI was done on October 2014. The clinical studies about amputation or limb-salvage surgery in the treatment of patients with limited stage Enneking II pathologic fracture osteosarcoma were searched and reviewed. The effect size of relapse, 5-year survival and metastasis between the amputation and limb-salvage surgery were pooled by stata11.0 software (Stata Corporation, College Station, TX, USA, http://www.stata.com;) using random or fixed effect model. The funnel plot and Egger's line regression test were used for evaluation of publication bias.

RESULTS

A total of 89 studies were identified and seven articles with 200 cases in the limb-salvage surgery group and 84 subjects in the amputation group were finally included in the meta-analysis. The pooled data indicated that no statistical different of risk for developing relapse between limb-salvage and amputation was found relative risk (RR) =1.40, 95% confidence interval (CI): 0.71-2.79, (P = 0.33). The 5-year survival rate of patients underwent limb-salvage surgery was smaller than patients received amputation RR = 1.86, 95%CI: 1.19-2.89, (P = 0.01); the metastasis rate of patients underwent limb-salvage surgery was significant decreased compared with patients received amputation RR = 0.56, 95% CI: 0.34-0.94, (P = 0.03). No publication bias was existed in this meta-analysis.

CONCLUSION

Limb-salvage surgery does not increased the risk of relapse compared with amputation in the treatment of patients with limited stage Enneking II pathologic fracture osteosarcoma.

Randomized phase II study evaluating veliparib (ABT-888) with temozolomide in patients with metastatic melanoma

BACKGROUND

Veliparib (ABT-888) is a potent, orally bioavailable, small-molecule inhibitor of the DNA repair enzymes poly ADP-ribose polymerase-1 and -2. Veliparib enhances the efficacy of temozolomide (TMZ) and other cytotoxic agents in preclinical tumor models.

PATIENTS AND METHODS

In this multicenter, double-blind trial, adults with unresectable stage III or IV metastatic melanoma were randomized 1:1:1 to TMZ plus veliparib 20 or 40 mg, or placebo twice daily. Efficacy end points included progression-free survival (PFS), overall survival (OS), and objective response rate (ORR).

RESULTS

Patients (N = 346) were randomized between February 2009 and January 2010. Median [95% confidence interval (CI)] PFS was 3.7 (3.0-5.5), 3.6 (1.9-4.1), and 2 (1.9-3.7) months in the 20-mg, 40-mg, and placebo arms, respectively. Median (95% CI) OS was 10.8 (9.0-13.1), 13.6 (11.4-15.9), and 12.9 (9.8-14.3) months, respectively; ORR was 10.3%, 8.7%, and 7.0%. Exploratory analyses showed patients with low ERCC1 expression had longer PFS when TMZ was combined with veliparib. Toxicities were as expected for TMZ. The frequencies of thrombocytopenia, neutropenia, and leukopenia were significantly increased in the veliparib groups. Grade 3 or 4 adverse events, mainly hematologic toxicities, were seen in 55%, 63%, and 41% of patients in the 20-mg, 40-mg, and placebo arms, respectively.

CONCLUSIONS

Median PFS with 20 and 40 mg veliparib almost doubled numerically compared with placebo, but the improvements did not reach statistical significance. OS was not increased with veliparib. Toxicities were similar to TMZ monotherapy, but with increased frequency.

Shear stress regulates endothelial cell autophagy via redox regulation and Sirt1 expression

Disturbed cell autophagy is found in various cardiovascular disease conditions. Biomechanical stimuli induced by laminar blood flow have important protective actions against the development of various vascular diseases. However, the impacts and underlying mechanisms of shear stress on the autophagic process in vascular endothelial cells (ECs) are not entirely understood. Here we investigated the impacts of shear stress on autophagy in human vascular ECs. We found that shear stress induced by laminar flow, but not that by oscillatory or low-magnitude flow, promoted autophagy. Time-course analysis and flow cessation experiments confirmed that this effect was not a transient adaptive stress response but appeared to be a sustained physiological action. Flow had no effect on the mammalian target of rapamycin-ULK pathway, whereas it significantly upregulated Sirt1 expression. Inhibition of Sirt1 blunted shear stress-induced autophagy. Overexpression of wild-type Sirt1, but not the deacetylase-dead mutant, was sufficient to induce autophagy in ECs. Using both of gain- and loss-of-function experiments, we showed that Sirt1-dependent activation of FoxO1 was critical in mediating shear stress-induced autophagy. Shear stress also induced deacetylation of Atg5 and Atg7. Moreover, shear stress-induced Sirt1 expression and autophagy were redox dependent, whereas Sirt1 might act as a redox-sensitive transducer mediating reactive oxygen species-elicited autophagy. Functionally, we demonstrated that flow-conditioned cells are more resistant to oxidant-induced cell injury, and this cytoprotective effect was abolished after inhibition of autophagy. In summary, these results suggest that Sirt1-mediated autophagy in ECs may be a novel mechanism by which laminar flow produces its vascular-protective actions.

STRUCTURAL BIOLOGY. A Cas9-guide RNA complex preorganized for target DNA recognition

Bacterial adaptive immunity uses CRISPR (clustered regularly interspaced short palindromic repeats)-associated (Cas) proteins together with CRISPR transcripts for foreign DNA degradation. In type II CRISPR-Cas systems, activation of Cas9 endonuclease for DNA recognition upon guide RNA binding occurs by an unknown mechanism. Crystal structures of Cas9 bound to single-guide RNA reveal a conformation distinct from both the apo and DNA-bound states, in which the 10-nucleotide RNA "seed" sequence required for initial DNA interrogation is preordered in an A-form conformation. This segment of the guide RNA is essential for Cas9 to form a DNA recognition-competent structure that is poised to engage double-stranded DNA target sequences. We construe this as convergent evolution of a "seed" mechanism reminiscent of that used by Argonaute proteins during RNA interference in eukaryotes.

Association of the interleukin-6 polymorphisms with systemic lupus erythematosus: a meta-analysis

BACKGROUND

Interleukin (IL)-6, an important proinflammatory cytokine, plays a potential pathological role in systemic lupus erythematosus (SLE). Studies on the relationship of IL-6 gene polymorphisms with SLE are inconclusive. The aim of this study was to estimate the relationship more precisely.

METHODS

The databases of PubMed and Web of Science updated to 30 August 2014 were retrieved. Meta-analysis was conducted using allelic contrast, dominant, recessive and homozygote contrast models. Fifteen studies were included in this study and ethnicity-specific meta-analysis was performed on European, Iranian and Asian populations.

RESULTS

Analysis for the IL-6-174 G/C polymorphism under all models except the homozygote contrast model indicated an association in the overall population (allelic contrast model: odds ratio (OR) 1.428, 95% confidence interval (CI) 1.124-1.812, dominant model: OR 1.382, 95% CI 1.037-1.842, recessive model: OR 1.610, 95% CI 1.158-2.240, homozygote contrast model: OR 1.759, 95% CI 0.989-3.127), as well as in European individuals under all four genetic models (allelic contrast model: OR 1.557, 95% CI 1.155-2.098, dominant model: OR 1.699, 95% CI 1.203-2.400, recessive model: OR 1.506, 95% CI 1.176-1.930, homozygote contrast model: OR 2.118, 95% CI 1.103-4.065). Analysis for the IL-6-572 G/C polymorphism indicated significant association in overall ethnicities under the recessive model (OR 1.491, 95% CI 1.104-2.014), but not under other models or in Asian individuals. In addition, significant association between the IL-6-174 G/C polymorphism and discoid skin lesions and antinuclear antibodies (ANAs) were found under the allelic contrast model and recessive model, respectively (discoid skin lesions: OR 2.271, 95% CI 1.053-4.895; ANAs: OR 2.244, 95% CI 1.141-4.416).

CONCLUSION

This meta-analysis provides evidence of the association between the IL-6 polymorphism and the risk of SLE, hinting that the IL-6-174 G/C and IL-6-572 G/C polymorphisms may play a role in SLE susceptibility.

Non-invasive prenatal testing for trisomies 21, 18 and 13: clinical experience from 146,958 pregnancies

OBJECTIVES

To report the clinical performance of massively parallel sequencing-based non-invasive prenatal testing (NIPT) in detecting trisomies 21, 18 and 13 in over 140,000 clinical samples and to compare its performance in low-risk and high-risk pregnancies.

METHODS

Between 1 January 2012 and 31 August 2013, 147,314 NIPT requests to screen for fetal trisomies 21, 18 and 13 using low-coverage whole-genome sequencing of plasma cell-free DNA were received. The results were validated by karyotyping or follow-up of clinical outcomes.

RESULTS

NIPT was performed and results obtained in 146,958 samples, for which outcome data were available in 112,669 (76.7%). Repeat blood sampling was required in 3213 cases and 145 had test failure. Aneuploidy was confirmed in 720/781 cases positive for trisomy 21, 167/218 cases positive for trisomy 18 and 22/67 cases positive for trisomy 13 on NIPT. Nine false negatives were identified, including six cases of trisomy 21 and three of trisomy 18. The overall sensitivity of NIPT was 99.17%, 98.24% and 100% for trisomies 21, 18 and 13, respectively, and specificity was 99.95%, 99.95% and 99.96% for trisomies 21, 18 and 13, respectively. There was no significant difference in test performance between the 72,382 high-risk and 40,287 low-risk subjects (sensitivity, 99.21% vs. 98.97% (P = 0.82); specificity, 99.95% vs. 99.95% (P = 0.98)). The major factors contributing to false-positive and false-negative NIPT results were maternal copy number variant and fetal/placental mosaicism, but fetal fraction had no effect.

CONCLUSIONS

Using a stringent protocol, the good performance of NIPT shown by early validation studies can be maintained in large clinical samples. This technique can provide equally high sensitivity and specificity in screening for trisomy 21 in a low-risk, as compared to high-risk, population.

Caffeic acid improves cell viability and protects against DNA damage: involvement of reactive oxygen species and extracellular signal-regulated kinase

Hormesis is an adaptive response to a variety of oxidative stresses that renders cells resistant to harmful doses of stressing agents. Caffeic acid (CaA) is an important antioxidant that has protective effects against DNA damage caused by reactive oxygen species (ROS). However, whether CaA-induced protection is a hormetic effect remains unknown, as is the molecular mechanism that is involved. We found that a low concentration (10 μM) of CaA increased human liver L-02 cell viability, attenuated hydrogen peroxide (H₂O₂)-mediated decreases in cell viability, and decreased the extent of H₂O₂-induced DNA double-strand breaks (DSBs). In L-02 cells exposed to H₂O₂, CaA treatment reduced ROS levels, which might have played a protective role. CaA also activated the extracellular signal-regulated kinase (ERK) signal pathway in a time-dependent manner. Inhibition of ERK by its inhibitor U0126 or by its specific small interfering RNA (siRNA) blocked the CaA-induced improvement in cell viability and the protective effects against H₂O₂-mediated DNA damage. This study adds to the understanding of the antioxidant effects of CaA by identifying a novel molecular mechanism of enhanced cell viability and protection against DNA damage.

The structural biology of CRISPR-Cas systems

Prokaryotic CRISPR-Cas genomic loci encode RNA-mediated adaptive immune systems that bear some functional similarities with eukaryotic RNA interference. Acquired and heritable immunity against bacteriophage and plasmids begins with integration of ∼30 base pair foreign DNA sequences into the host genome. CRISPR-derived transcripts assemble with CRISPR-associated (Cas) proteins to target complementary nucleic acids for degradation. Here we review recent advances in the structural biology of these targeting complexes, with a focus on structural studies of the multisubunit Type I CRISPR RNA-guided surveillance and the Cas9 DNA endonuclease found in Type II CRISPR-Cas systems. These complexes have distinct structures that are each capable of site-specific double-stranded DNA binding and local helix unwinding.

Simulation of ozone formation at different elevations in mountainous area of Hong Kong using WRF-CMAQ model

Field measurements were simultaneously conducted at a mountain (Mt.) site (Tai Mao Shan, TMS) and an urban site (Tsuen Wan, TW) at the foot of the Mt. TMS in Hong Kong. An interesting event with consecutive high-ozone (O₃) days from 08:00 on 28 Oct. to 23:00 on 03 Nov., 2010 was observed at Mt. TMS, while no such polluted event was found at the foot of the mountain. The Weather Research and Forecasting (WRF)-Community Multiscale Air Quality (CMAQ) models were used to understand this event. Model performance evaluation showed that the simulated meteorological parameters and air pollutants were well in agreement with the observations. The index of agreement (IOA) of temperature, relative humidity, wind direction and wind speed were 0.93, 0.83, 0.46 and 0.60, respectively. The multi-day high O₃ episode at Mt. TMS was also reasonably reproduced (IOA=0.68). Horizontally, the photochemical processes determined the O₃ levels in southwestern Pearl River Delta (PRD) and the Pearl River Estuary (PRE), while in eastern and northern PRD, the O₃ destruction was over the production during the event. Vertically, higher O₃ values at higher levels were found at both Mt. TMS and TW, indicating a vertical O₃ gradient over Hong Kong. With the aid of the process analysis module, we found positive contribution of vertical transport including advection and diffusion to O₃ mixing ratios at the two sites, suggesting that O₃ values at lower locations could be affected by O₃ at higher locations via vertical advection and diffusion over Hong Kong.

Genetic variants of PLA2G6 are associated with Type 2 diabetes mellitus and triglyceride levels in a Chinese population

AIM

To test the association of PLA2G6 variants with Type 2 diabetes and clinical characteristics in large Chinese population-based samples.

METHODS

A total of 6822 people were recruited. In the first stage, 15 single nucleotide polymorphisms within the PLA2G6 region were selected and genotyped in 3700 Chinese Han people. In the second stage, the single nucleotide polymorphisms that showed a significant association were genotyped in an additional 3122 samples for replication. Genotype-phenotype association studies and meta-analyses were performed after combining data from the two stages.

RESULTS

In the first stage, we detected rs132984 and rs2284060 as significantly associated with Type 2 diabetes with odds ratios of 1.247 (95% CI 1.074-1.449, P = 0.004, empirical P = 0.047) and 1.173 (95% CI 1.059-1.299, P = 0.002, empirical P = 0.029), respectively. In the second stage, a similar effect of rs132984 on Type 2 diabetes was observed (odds ratio 1.280, 95% CI 1.094-1.497, P = 0.002). The meta-analysis showed a significant effect of the two single nucleotide polymorphisms on Type 2 diabetes (odds ratio 1.254, 95% CI 1.104-1.451, P = 4.85 × 10⁻⁵ for rs132984; odds ratio 1.120, 95% CI 1.046-1.195, P = 0.003 for rs2284060). Moreover, genotype-phenotype association analysis showed that rs132984 was associated with triglyceride levels (P = 0.022, empirical P = 0.044) and area under the curve for glucose (P = 0.015, empirical P = 0.030).

CONCLUSIONS

Our data imply that common single nucleotide polymorphisms within the PLA2G6 region are associated with Type 2 diabetes and triglyceride levels in the Chinese population.