Advances in understanding cold tolerance in grapevine.

Grapevine (Vitis ssp.) is a deciduous perennial fruit crop, and the canes and buds of grapevine should withstand low temperatures (LTs) annually during winter. However, the widely cultivated Vitis vinifera is cold-sensitive and cannot survive the severe winter in regions with extremely LTs, such as viticulture regions in northern China. By contrast, a few wild Vitis species like V. amurensis and V. riparia exhibit excellent freezing tolerance. However, the mechanisms underlying grapevine cold tolerance remain largely unknown. In recent years, much progress has been made in elucidating the mechanisms, owing to the advances in sequencing and molecular biotechnology. Assembly of grapevine genomes together with resequencing and transcriptome data enable researchers to conduct genomic and transcriptomic analyses in various grapevine genotypes and populations to explore genetic variations involved in cold tolerance. In addition, a number of pivotal genes have been identified and functionally characterized. In this review, we summarize recent major advances in physiological and molecular analyses of cold tolerance in grapevine and put forward questions in this field. We also discuss the strategies for improving the tolerance of grapevine to cold stress. Understanding grapevine cold tolerance will facilitate the development of grapevines for adaption to global climate change.

Synthetic Nuclease-Producing Microbiome Achieves Efficient Removal of Extracellular Antibiotic Resistance Genes from Wastewater Effluent.

Antibiotic resistance gene (ARG) transmission poses significant threats to human health. The effluent of wastewater treatment plants is demonstrated as a hotspot source of ARGs released into the environment. In this study, a synthetic microbiome containing nuclease-producing Deinococcus radiodurans was constructed to remove extracellular ARGs. Results of quantitative polymerase chain reaction (qPCR) showed significant reduction in plasmid RP4-associated ARGs (by more than 3 orders of magnitude) and reduction of indigenous ARG sul1 and mobile genetic element (MGE) intl1 (by more than 1 order of magnitude) in the synthetic microbiome compared to the control without D. radiodurans. Metagenomic analysis revealed a decrease in ARG and MGE diversity in extracellular DNA (eDNA) of the treated group. Notably, whereas eight antibiotic-resistant plasmids with mobility risk were detected in the control, only one was detected in the synthetic microbiome. The abundance of the nuclease encoding gene exeM, quantified by qPCR, indicated its enrichment in the synthetic microbiome, which ensures stable eDNA degradation even when D. radiodurans decreased. Moreover, intracellular ARGs and MGEs and pathogenic ARG hosts in the river receiving treated effluent were lower than those in the river receiving untreated effluent. Overall, this study presents a new approach for removing extracellular ARGs and further reducing the risk of ARG transmission in receiving rivers.

Overexpression of grape ABA receptor gene VaPYL4 enhances tolerance to multiple abiotic stresses in Arabidopsis.

BACKGROUND: Abscisic acid (ABA) plays a crucial role in abiotic stress responses. The pyrabactin resistance (PYR)/PYR-like (PYL)/regulatory component of ABA receptor (RCAR) proteins that have been characterized as ABA receptors function as the core components in ABA signaling pathway. However, the functions of grape PYL genes in response to different abiotic stresses, particularly cold stress, remain less studied. RESULTS: In this study, we investigated the expression profiles of grape PYL genes upon cold treatment and isolated the VaPYL4 gene from Vitis amurensis, a cold-hardy grape species. Overexpression of VaPYL4 gene in grape calli and Arabidopsis resulted in enhanced cold tolerance. Moreover, plant resistance to drought and salt stress was also improved by overexpressing VaPYL4 in Arabidopsis. More importantly, we evaluated the contribution of VaPYL4 to plant growth and development after the treatment with cold, salt and drought stress simultaneously. The transgenic plants showed higher survival rates, earlier flowering phenotype, and heavier fresh weight of seedlings and siliques when compared with wild-type plants. Physiological analyses showed that transgenic plants had much lower content of malondialdehyde (MDA) and higher peroxidase (POD) activity. Stress-responsive genes such as RD29A (Responsive to desiccation 29A), COR15A (Cold responsive 15A) and KIN2 (Kinase 2) were also significantly up-regulated in VaPYL4-overexpressing Arabidopsis plants. CONCLUSIONS: Our results show that overexpression of VaPYL4 could improve plant performance upon different abiotic stresses, which therefore provides a useful strategy for engineering future crops to deal with adverse environments.

GRAS-domain transcription factor PAT1 regulates jasmonic acid biosynthesis in grape cold stress response.

Cultivated grapevine (Vitis) is a highly valued horticultural crop, and cold stress affects its growth and productivity. Wild Amur grape (Vitis amurensis) PAT1 (Phytochrome A signal transduction 1, VaPAT1) is induced by low temperature, and ectopic expression of VaPAT1 enhances cold tolerance in Arabidopsis (Arabidopsis thaliana). However, little is known about the molecular mechanism of VaPAT1 during the cold stress response in grapevine. Here, we confirmed the overexpression of VaPAT1 in transformed grape calli enhanced cold tolerance. Yeast two-hybrid and bimolecular fluorescence complementation assays highlighted an interaction between VaPAT1 with INDETERMINATE-DOMAIN 3 (VaIDD3). A role of VaIDD3 in cold tolerance was also indicated. Transcriptome analysis revealed VaPAT1 and VaIDD3 overexpression and cold treatment coordinately modulate the expression of stress-related genes including lipoxygenase 3 (LOX3), a gene encoding a key jasmonate biosynthesis enzyme. Co-expression network analysis indicated LOX3 might be a downstream target of VaPAT1. Both electrophoretic mobility shift and dual luciferase reporter assays showed the VaPAT1-IDD3 complex binds to the IDD-box (AGACAAA) in the VaLOX3 promoter to activate its expression. Overexpression of both VaPAT1 and VaIDD3 increased the transcription of VaLOX3 and JA levels in transgenic grape calli. Conversely, VaPAT1-SRDX (dominant repression) and CRISPR/Cas9-mediated mutagenesis of PAT1-ED causing the loss of the C-terminus in grape calli dramatically prohibited the accumulation of VaLOX3 and JA levels during cold treatment. Together, these findings point to a pivotal role of VaPAT1 in the cold stress response in grape by regulating JA biosynthesis.

A Carotenoid- and Nuclease-Producing Bacterium Can Mitigate Enterococcus faecalis Transformation by Antibiotic Resistance Genes.

Dissemination of antibiotic resistance genes (ARGs) through natural transformation is facilitated by factors that stabilize extracellular DNA (eDNA) and that induce reactive oxygen species (ROS) that permeabilize receptor cells and upregulate transformation competence genes. In this study, we demonstrate that Deinococcus radiodurans can mitigate this ARG dissemination pathway by removing both eDNA and ROS that make recipient cells more vulnerable to transformation. We used plasmid RP4 as source of extracellular ARGs (tetA, aphA, and blaTEM-2) and the opportunistic pathogen Enterococcus faecalis as receptor. The presence of D. radiodurans significantly reduced the transformation frequency from 2.5 ± 0.7 × 10-6 to 7.4 ± 1.4 × 10-7 (p < 0.05). Based on quantification of intracellular ROS accumulation and superoxide dismutase (SOD) activity, and quantitative polymerase chain reaction (qPCR) and transcriptomic analyses, we propose two mechanisms by which D. radiodurans mitigates E. faecalis transformation by ARGs: (a) residual antibiotics induce D. radiodurans to synthesize liposoluble carotenoids that scavenge ROS and thus mitigate the susceptibility of E. faecalis for eDNA uptake, and (b) eDNA induces D. radiodurans to synthesize extracellular nucleases that degrade eARGs. This mechanistic insight informs biological strategies (including bioaugmentation) to curtail the spread of ARGs through transformation.

Characterization of Chromatin Accessibility and Gene Expression upon Cold Stress Reveals that the RAV1 Transcription Factor Functions in Cold Response in Vitis Amurensis.

Cold tolerance is regulated by a variety of transcription factors (TFs) and their target genes. Except for the well-characterized C-repeat binding factors (CBFs)-dependent transcriptional cascade, the mechanisms of cold tolerance mediated by other transcriptional regulatory networks are still largely unknown. Here, we used the assay for transposase-accessible chromatin with sequencing (ATAC-seq) and RNA-seq to identify cold responsive TFs in Vitis amurensis, a grape species with high cold hardiness. Nine TFs, including CBF4, RAV1 and ERF104, were identified after cold treatment. Weighted gene co-expression network analysis (WGCNA) and gene ontology (GO) analysis revealed that these TFs may regulate cold response through different pathways. As a prime candidate TF, overexpression of VaRAV1 in grape cells improved its cold tolerance. The transgenic cells exhibited low electrolyte leakage and malondialdehyde content and high peroxidase activity. Moreover, the TF gene TCP8 and a gene involving in homogalacturonan biosynthesis were found to be regulated by VaRAV1, suggesting that the contribution of VaRAV1 to cold tolerance may be achieved by enhancing the stability of cell membrane and regulating the expression of target genes involved in plant cell wall composition. Our work provides novel insights into plant response to cold stress and demonstrates the utility of ATAC-seq and RNA-seq for the rapid identification of TFs in response to cold stress in grapevine. VaRAV1 may play an important role in adaption to cold stress.

CHRDL2 promotes osteosarcoma cell proliferation and metastasis through the BMP-9/PI3K/AKT pathway.

Various studies demonstrated that bone morphogenetic proteins (BMPs) and their antagonists contribute to the development of cancers. Chordin-like 2 (CHRDL2) is a member of BMP antagonists. However, the role and its relative mechanism of CHRDL2 in osteosarcoma remains unclear. In the present study, we demonstrated that the expression of CHRDL2 was significantly upregulated in osteosarcoma tissues and cell lines compared with adjacent tissues and human normal osteoblast. Inhibition of CHRDL2 decreased the proliferation and colony formation of osteosarcoma cells in vitro, as well as the migration and invasion. CHRDL2 overexpression induced the opposite effects. CHRDL2 can bind with BMP-9, thus decreasing BMP-9 expression and the combination to its receptor protein kinase ALK1. It was predicted that BMP-9 regulates PI3K/AKT pathways using gene set enrichment analysis. Inhibition of CHRDL2 decreased the activation of PI3K/AKT pathway, while overexpression of CHRDL2 upregulated the activation. Increasing the expression of BMP-9 reversed the effects of CHRDL2 overexpression on the activation of PI3K/AKT pathway, as well as the proliferation and metastasis of osteosarcoma cells. Take together, our present study revealed that CHRDL2 upregulated in osteosarcoma tissues and cell lines, and promoted osteosarcoma cell proliferation and metastasis through the BMP-9/PI3K/AKT pathway. CHRDL2 maybe an oncogene in osteosarcoma, as well as novel biomarker for the diagnosis of osteosarcoma.

Biological Mitigation of Antibiotic Resistance Gene Dissemination by Antioxidant-Producing Microorganisms in Activated Sludge Systems.

Antibiotic resistance is the principal mechanism of an evergrowing bacterial threat. Antibiotic residues in the environment are a major contributor to the spread of antibiotic resistance genes (ARGs). Subinhibitory concentrations of antibiotics cause bacteria to produce reactive oxygen species (ROS), which can lead to mutagenesis and horizontal gene transfer (HGT) of ARGs; however, little is known about the mitigation of ARG dissemination through ROS removal by antioxidants. In this study, we examine how antioxidant-producing microorganisms inoculated in replicate activated sludge systems can biologically mitigate the dissemination of ARGs. Through quantitative polymerase chain reaction (qPCR), we showed that antioxidant-producing microorganisms could decrease the persistence of the RP4 plasmid and alleviate enrichment of ARGs (sul1) and class 1 integrons (intl1). Metagenomic sequencing identified the most diverse resistome and the most mutated Escherichia coli ARGs in the reactor that contained antibiotics but no antioxidant-producing microorganisms, suggesting that antioxidant-producing microorganisms mitigated ARG enrichment and mutation. Host classification revealed that antioxidant-producing microorganisms decreased the diversity of ARG hosts by shaping the microbial community through competition and functional pathway changes. Conjugative experiments demonstrated that conjugative transfer of ARGs could be mitigated by coculture with antioxidant-producing microorganisms. Overall, this is a novel study that shows how ARG enrichment and HGT can be mitigated through bioaugmentation with antioxidant-producing microorganisms.

Treatment of Recurrent Axillary Osmidrosis: Trimming and Electrocoagulation of Apocrine Glands Under Direct Vision Through Double Incisions.

OBJECTIVE: The aim of this study was to explore the clinical effect of treatment for recurrent axillary osmidrosis (AO) after small-incision minimally invasive surgery by trimming and electrocoagulation of apocrine glands under direct vision through double incisions parallel to axillary creases. METHODS: This was a retrospective study. From September 2012 to January 2019, 75 axillae in 48 cases of recurrent AO after small-incision minimally invasive surgery were treated using trimming and electrocoagulation of apocrine glands under direct vision through double incisions parallel to axillary creases. Patient data, such as sex, age, original surgery method, the severity of underarm malodor before and after the operation, and occurrence of complications, were collected and analyzed. RESULTS: For the follow-up of at least 12 months after the surgery, all patients' underarm malodor disappeared or was significantly reduced. Patients with preoperative severity of grade I did not show a recurring AO, whereas the recurrence rate of grade II and grade III AO was 7.9% and 14.3%, respectively. Furthermore, the AO recurrence rate was 9.1% for those younger than 18 years and 6.2% in those 18 years or older. Subcutaneous hematomas appeared on 3 axillae (4.0%), and the contraction of subdermal fibrotic bands appeared on 5 axillae (6.7%). CONCLUSIONS: Patients with recurring AO after small-incision minimally invasive surgery achieved good treatment results by trimming and electrocoagulation of apocrine glands under direct vision through double incisions parallel to axillary creases.

Comparative genomics analysis of c-di-GMP metabolism and regulation in Microcystis aeruginosa.

BACKGROUND: Cyanobacteria are of special concern because they proliferate in eutrophic water bodies worldwide and affect water quality. As an ancient photosynthetic microorganism, cyanobacteria can survive in ecologically diverse habitats because of their capacity to rapidly respond to environmental changes through a web of complex signaling networks, including using second messengers to regulate physiology or metabolism. A ubiquitous second messenger, bis-(3',5')-cyclic-dimeric-guanosine monophosphate (c-di-GMP), has been found to regulate essential behaviors in a few cyanobacteria but not Microcystis, which are the most dominant species in cyanobacterial blooms. In this study, comparative genomics analysis was performed to explore the genomic basis of c-di-GMP signaling in Microcystis aeruginosa. RESULTS: Proteins involved in c-di-GMP metabolism and regulation, such as diguanylate cyclases, phosphodiesterases, and PilZ-containing proteins, were encoded in M. aeruginosa genomes. However, the number of identified protein domains involved in c-di-GMP signaling was not proportional to the size of M. aeruginosa genomes (4.97 Mb in average). Pan-genome analysis showed that genes involved in c-di-GMP metabolism and regulation are conservative in M. aeruginosa strains. Phylogenetic analysis showed good congruence between the two types of phylogenetic trees based on 31 highly conserved protein-coding genes and sensor domain-coding genes. Propensity for gene loss analysis revealed that most of genes involved in c-di-GMP signaling are stable in M. aeruginosa strains. Moreover, bioinformatics and structure analysis of c-di-GMP signal-related GGDEF and EAL domains revealed that they all possess essential conserved amino acid residues that bind the substrate. In addition, it was also found that all selected M. aeruginosa genomes encode PilZ domain containing proteins. CONCLUSIONS: Comparative genomics analysis of c-di-GMP metabolism and regulation in M. aeruginosa strains helped elucidating the genetic basis of c-di-GMP signaling pathways in M. aeruginosa. Knowledge of c-di-GMP metabolism and relevant signal regulatory processes in cyanobacteria can enhance our understanding of their adaptability to various environments and bloom-forming mechanism.

Knockout of VvCCD8 gene in grapevine affects shoot branching.

BACKGROUND: Shoot branching is an important trait of plants that allows them to adapt to environment changes. Strigolactones (SLs) are newly identified plant hormones that inhibit shoot branching in plants. The SL biosynthesis genes CCD7 (carotenoid cleavage dioxygenase 7) and CCD8 have been found to regulate branching in several herbaceous plants by taking advantage of their loss-of-function mutants. However, the role for CCD7 and CCD8 in shoot branching control in grapevine is still unknown due to the lack of corresponding mutants. RESULTS: Here we employed the CRISPR/Cas9 system to edit the VvCCD7 and VvCCD8 genes in the grape hybrid 41B. The 41B embryogenic cells can easily be transformed and used for regeneration of the corresponding transformed plants. Sequencing analysis revealed that gene editing has been used successfully to target both VvCCD genes in 41B embryogenic cells. After regeneration, six 41B plantlets were identified as transgenic plants carrying the CCD8-sgRNA expression cassette. Among these, four plants showed mutation in the target region and were selected as ccd8 mutants. These ccd8 mutants showed increased shoot branching compared to the corresponding wild-type plants. In addition, no off-target mutation was detected in the tested mutants at predicted off-target sites. CONCLUSIONS: Our results underline the key role of VvCCD8 in the control of grapevine shoot branching.

Low-level laser-aided orthodontic treatment of periodontally compromised patients: a randomised controlled trial.

Low-level laser irradiation (LLLI) shows effects in orthodontic pain relief and periodontal inflammation control. The aim of this article is to investigate the analgesic and inflammation-modulatory effects of low-level laser irradiation among orthodontic patients with compromised periodontium. A randomised controlled trial with split-mouth design was conducted in 27 adults with treated and controlled chronic periodontitis over 6 months. One side of the dental arch underwent repeated treatment under a 940-nm diode laser (EZlase; Biolase Technology Inc.) with a beam size of 2.8 cm2 for 60 seconds at 8.6 J/cm2, whilst the other side received pseudo-laser treatment. Laser irradiation was applied repeatedly for 8 times during the first 6 weeks after bracket bonding and monthly thereafter until the end of orthodontic treatment. Subjective pain (assessed by visual analogue scale in pain diary and by chairside archwire activation), periodontal status (assessed by periodontal clinical parameters), cytokines in gingival crevicular fluid (interleukin 1ß, prostaglandin E2, substance P) and periodontopathic bacteria (Porphyromonas gingivalis and Treponema denticola) in supragingival plaque were assessed. The intensity of pain was lower on the laser-irradiated side at multiple follow-up visits (P < 0.05). The pain subsided 1 day earlier on the laser side, with a lower peak value during the first week after initial archwire placement (P < 0.05). The laser side exhibited a smaller reduction in bite force during the first month (mean difference = 3.17, 95% CI: 2.36-3.98, P < 0.05 at 1-week interval; mean difference = 3.09, 95% CI: 1.87-4.32, P < 0.05 at 1-month interval). A smaller increase was observed in the plaque index scores on the laser side at 1-month (mean difference = 0.19, 95% CI: 0.13-0.24, P < 0.05) and in the gingival index scores at the 3-month follow-up visit (mean difference = 0.18, 95% CI: 0.14-0.21, P < 0.05). Laser irradiation inhibited the elevation of interleukin-1ß, prostaglandin E2 and substance P levels during the first month (P < 0.05). However, no intergroup difference was detected in the bacteria levels. Low-level laser irradiation exhibits benefits in pain relief and inflammation control during the early stage of adjunctive orthodontic treatment in periodontally compromised individuals.

N-terminal domain of EcC1INH in Epinephelus coioides can antagonize the LPS-stimulated inflammatory response.

Complement 1 inhibitor (C1INH) serving as a multifunctional factor can participate in the regulation of complement cascades and attenuate the activation of various proteases. In this study, we obtained EcC1INH cDNA and the tissue-specific analysis indicate that the highest expression level of EcC1INH mRNA was detected in liver. Moreover, Vibrio alginolyticus challenge can significantly increase EcC1INH mRNA expression in liver and kidney. N-terminal domain of EcC1INH could decrease LPS binding activity to cell surface, while loss of positively charged residues (PCRs) Arg21, His22, Lys50, Arg61 in N-terminal domain of EcC1INH can significantly reduce its interaction with LPS. Furthermore, LPS injection experiment indicated that the binding of EcC1INH N-terminal domain to LPS can antagonize LPS-induced inflammatory signaling pathway and attenuate the production of proinflammatory cytokines in vivo, indicating that EcC1INH was involved in negative regulation of inflammatory response.

Recovery of the non-functional EGFP-assisted identification of mutants generated by CRISPR/Cas9.

KEY MESSAGE: The recovery of non-functional-enhanced green fluorescence protein can be used as indicator to facilitate the identification of mutants generated by CRISPR/Cas9. The CRISPR/Cas9 system is a powerful tool for genome editing and it has been employed to knock out genes of interest in multiple plant species. Identification of desired mutants from regenerated plants is necessary prior to functional study. Current screening methods work based on the purification of genomic DNA and it would be laborious and time consuming using these methods to screen mutants from a large population of seedlings. Here, we developed the non-functional enhanced green fluorescence protein (nEGFP) reporter gene by inserting a single guide RNA (sgRNA) and the protospacer adjacent motif in the 5' coding region of EGFP, and the activity of nEGFP could be recovered after successful targeted editing. Using the nEGFP as the reporter gene in Nicotiana tabacum, we found that over 94% of the plants exhibiting EGFP fluorescence were confirmed to be desired mutants. The use of this nEGFP reporter construct had limited negative effect on editing efficiency, and the expression of Cas9 and sgRNA was not affected. Moreover, this method was also applied in grape by targeting the phytoene desaturase gene (PDS), and the grape cells with EGFP signal were revealed to contain targeted mutations in VvPDS. Our results show that the nEGFP gene can be used as reporter to help screen mutants according to the recovered EGFP fluorescence during the application of CRISPR/Cas9 in plants.

Tunable plasmonic effects arising from metal-dielectric nanorods.

We have investigated the plasmonic effects in a two-dimensional periodic array of metallodielectric nanorods with and without the rotational angle, in which the integration of the localized surface plasmon resonance (SPR) and hollow plasmon resonance (HPR) properties is performed. Four patterns of nanostructures are investigated. We make use of the three-dimensional finite element method to obtain the simulation results, which demonstrate that the localized SPR and HPR in metallodielectric nanorods enhance the near-field intensity and increase the depth of the transmittance dip, providing an additional degree of freedom in the control of the light wave at the nanoscale. Numerical results show that the depth of the transmittance dip and sensitivity of case 1 and case 2 can be elevated to a value of 83.21% and 6.7 times, respectively, when the rotational angle of metal-dielectric nanorods varies from 0° to 90°. The sensitivity of case 3 and case 4 can be raised to the magnitude of 700-1091 nm/RIU (where RIU is the refractive index unit), and the characteristics enable the extensive applications for nanophotonic devices with high performance in a predictable manner.

Orthodontic Treatment Need and the Psychosocial Impact of Malocclusion in 12-Year-Old Hong Kong Children.

OBJECTIVES: To determine the prevalence of orthodontic treatment need in 12-year-old children in Hong Kong and its relationship with the psychosocial impact of malocclusion and to assess their associations with sociodemographic factors. MATERIALS AND METHODS: A random sample of 687 12-year-old children was recruited from 45 secondary schools in Hong Kong. Orthodontic treatment need was assessed on study models by five indices: the Dental Health Component of the Index of Orthodontic Treatment Need (IOTN-DHC), the Aesthetic Component of the IOTN (IOTN-AC), the Dental Aesthetic Index (DAI), the Index of Complexity Outcome and Need (ICON), and the Peer Assessment Rating (PAR). The psychosocial impact of malocclusion on participants and sociodemographic factors were obtained from a questionnaire. Logistic regression was used to examine the correlations between treatment need and the psychosocial impact of malocclusion as well as their associations with sociodemographic factors. RESULTS: The final number of participants was 667 (339 boys and 328 girls, participation rate 667/687 = 97.1%). The prevalence of orthodontic treatment need varied depending on the indices used (10.9-47.8%), but significant correlations were found among the five indices (p < 0.01). The uptake of treatment among the cohort was 2.3%. Boys had higher IOTN-DHC (p < 0.05), DAI (p < 0.05), and PAR (p = 0.05) scores than girls. IOTN-AC was significantly associated with the psychosocial impact of malocclusion (p < 0.05). Parents' level of education and household income were not significantly associated with either treatment need or the psychosocial impact of malocclusion (p > 0.05). CONCLUSION: The need for orthodontic treatment in 12-year-old children in Hong Kong remained high, and the uptake of treatment was low. Boys had a higher normative treatment need than girls. Among the five indices, IOTN-AC appears to be the best indicator of the psychosocial impact of malocclusion.

Characterization of the GATA gene family in Vitis vinifera: genome-wide analysis, expression profiles, and involvement in light and phytohormone response.

The plant GATA family is one of the most important transcription factors involved in light-responsive development, nitrogen metabolism, phytohormone signaling, and source/sink balance. However, the function of the GATA gene is less known in grape (Vitis vinifera L.). In this study, we comprehensively analyzed the GATA family in grape, particularly the phylogenetic evolution, duplication patterns, conserved motifs, gene structures, cis-elements, tissue expression patterns, and predicted function of VvGATA genes in response to abiotic stress. The potential roles of VvGATA genes in berry development were also investigated. The GATA transcription factors displayed expression diversity among different grape organs and tissues, and some of them showed preferential expression in a specific tissue. Heterotrophic cultured cells were used as model systems for the functional characterization of the VvGATA gene and study of its response to light and phytohormone. Results indicated that some VvGATA genes displayed differential responses to light and phytohormones, suggesting their role in light and hormone signaling pathways. A thorough analysis of GATA transcription factors in grape (V. vinifera L.) presented the characterization and functional prediction of VvGATA genes. The data presented here lay the foundation for further functional studies of grape GATA transcription factors.

Edentulism and associated factors among community-dwelling middle-aged and elderly adults in China.

OBJECTIVE: To investigate the prevalence of self-reported edentulism and its associated risk factors among community-dwelling adults aged 45 years and older in China. MATERIALS AND METHODS: Data from the national baseline survey (2011-2012) of the China Health and Retirement Longitudinal Study (CHARLS) were used for this study (N = 17 167). Bivariate and multivariate logistic regressions were conducted to assess the predictors of edentulism. Models 1 and 2 were based on the whole sample. Models 3 and 4 were based on the subsample (N = 9933) from whom anthropometric and blood biomarker data were available. RESULTS: The prevalence of edentulism was 8.64% among Chinese adults aged 45 and above. As shown by Model 1, older age was a robust predictor for edentulism (odds ratio [OR] = 3.81 for people aged 55-64; OR = 11.22 for people aged 65-74; OR = 24.05 for people aged 75 and above). Other factors positively associated with edentulism included being female (OR = 1.25), rural residence (OR = 1.30), asthma (OR = 1.48), depression (OR = 1.20), reduced physical function (OR = 1.37) and current smoking status (OR = 1.36). People with higher educational levels (OR = 0.75 for people who can read and write; OR = 0.64 for people who obtained a junior high school education or above) and better-off economic status (OR = 0.80) were less likely to be edentate. The association between edentulism and age, educational level, economic status and physical function remained significant in Model 3, and in addition, being underweight appeared as another strong predictor (OR = 1.93). CONCLUSIONS: The estimated prevalence of edentulism and the identified associated factors will provide epidemiologic evidence for future research and interventions in the target population in China.

Genome-wide identification and characterization of the NF-Y gene family in grape (vitis vinifera L.).

BACKGROUND: Nuclear factor Y (NF-Y) transcription factor is composed of three distinct subunits: NF-YA, NF-YB and NF-YC. Many members of NF-Y family have been reported to be key regulators in plant development, phytohormone signaling and drought tolerance. However, the function of the NF-Y family is less known in grape (Vitis vinifera L.). RESULTS: A total of 34 grape NF-Y genes that distributed unevenly on grape (V. vinifera) chromosomes were identified in this study. Phylogenetic analysis was performed to predict functional similarities between Arabidopsis thaliana and grape NF-Y genes. Comparison of the structures of grape NF-Y genes (VvNF-Ys) revealed their functional conservation and alteration. Furthermore, we investigated the expression profiles of VvNF-Ys in response to various stresses, phytohormone treatments, and in leaves and grape berries with various sugar contents at different developmental stages. The relationship between VvNF-Y transcript levels and sugar content was examined to select candidates for exogenous sugar treatments. Quantitative real-time PCR (qPCR) indicated that many VvNF-Ys responded to different sugar stimuli with variations in transcript abundance. qPCR and publicly available microarray data suggest that VvNF-Ys exhibit distinct expression patterns in different grape organs and developmental stages, and a number of VvNF-Ys may participate in responses to multiple abiotic and biotic stresses, phytohormone treatments and sugar accumulation or metabolism. CONCLUSIONS: In this study, we characterized 34 VvNF-Ys based on their distributions on chromosomes, gene structures, phylogenetic relationship with Arabidopsis NF-Y genes, and their expression patterns. The potential roles of VvNF-Ys in sugar accumulation or metabolism were also investigated. Altogether, the data provide significant insights on VvNF-Ys, and lay foundations for further functional studies of NF-Y genes in grape.

Identification of genomic sites for CRISPR/Cas9-based genome editing in the Vitis vinifera genome.

BACKGROUND: CRISPR/Cas9 has been recently demonstrated as an effective and popular genome editing tool for modifying genomes of humans, animals, microorganisms, and plants. Success of such genome editing is highly dependent on the availability of suitable target sites in the genomes to be edited. Many specific target sites for CRISPR/Cas9 have been computationally identified for several annual model and crop species, but such sites have not been reported for perennial, woody fruit species. In this study, we identified and characterized five types of CRISPR/Cas9 target sites in the widely cultivated grape species Vitis vinifera and developed a user-friendly database for editing grape genomes in the future. RESULTS: A total of 35,767,960 potential CRISPR/Cas9 target sites were identified from grape genomes in this study. Among them, 22,597,817 target sites were mapped to specific genomic locations and 7,269,788 were found to be highly specific. Protospacers and PAMs were found to distribute uniformly and abundantly in the grape genomes. They were present in all the structural elements of genes with the coding region having the highest abundance. Five PAM types, TGG, AGG, GGG, CGG and NGG, were observed. With the exception of the NGG type, they were abundantly present in the grape genomes. Synteny analysis of similar genes revealed that the synteny of protospacers matched the synteny of homologous genes. A user-friendly database containing protospacers and detailed information of the sites was developed and is available for public use at the Grape-CRISPR website ( http://biodb.sdau.edu.cn/gc/index.html ). CONCLUSION: Grape genomes harbour millions of potential CRISPR/Cas9 target sites. These sites are widely distributed among and within chromosomes with predominant abundance in the coding regions of genes. We developed a publicly-accessible Grape-CRISPR database for facilitating the use of the CRISPR/Cas9 system as a genome editing tool for functional studies and molecular breeding of grapes. Among other functions, the database allows users to identify and select multi-protospacers for editing similar sequences in grape genomes simultaneously.