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The high biosynthetic and energetic demands of floral thermogenesis render thermogenic plants the ideal systems to characterize energy metabolism in plants, but real-time tracking of energy metabolism in plant cells remains challenging. In this study, a new method was developed for tracking the mitochondrial energy metabolism at the single mitochondria level by real-time imaging of mitochondrial superoxide production (i.e., mitoflash). Using this method, we observed the increased mitoflash frequencies in the receptacles of Nelumbo nucifera Gaertn. at the thermogenic stages. This increase, combined with the higher expression of antioxidant response-related genes identified through time-series transcriptomics at the same stages, shows us a new regulatory mechanism for plant redox balance. Furthermore, we found that the upregulation of respiratory metabolism-related genes during the thermogenic stages not only correlates with changes in mitoflash frequency but also underscores the critical roles of these pathways in ensuring adequate substrate supply for thermogenesis. Metabolite analysis revealed that sugars are likely one of the substrates for thermogenesis and may be transported over long distances by sugar transporters. Taken together, our findings demonstrate that mitoflash is a reliable tool for tracking energy metabolism in thermogenic plants and contributes to our understanding of the regulatory mechanisms underlying floral thermogenesis., (© 2024 John Wiley & Sons Ltd.)

Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid "84K" (Populus alba × Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists.)

Long non-coding RNAs (lncRNAs) play essential roles in various biological processes, such as chromatin remodeling, post-transcriptional regulation, and epigenetic modifications. Despite their critical functions in regulating plant growth, root development, and seed dormancy, the identification of plant lncRNAs remains a challenge due to the scarcity of specific and extensively tested identification methods. Most mainstream machine learning-based methods used for plant lncRNA identification were initially developed using human or other animal datasets, and their accuracy and effectiveness in predicting plant lncRNAs have not been fully evaluated or exploited. To overcome this limitation, we retrained several models, including CPAT, PLEK, and LncFinder, using plant datasets and compared their performance with mainstream lncRNA prediction tools such as CPC2, CNCI, RNAplonc, and LncADeep. Retraining these models significantly improved their performance, and two of the retrained models, LncFinder-plant and CPAT-plant, alongside their ensemble, emerged as the most suitable tools for plant lncRNA identification. This underscores the importance of model retraining in tackling the challenges associated with plant lncRNA identification. Finally, we developed a pipeline (Plant-LncPipe) that incorporates an ensemble of the two best-performing models and covers the entire data analysis process, including reads mapping, transcript assembly, lncRNA identification, classification, and origin, for the efficient identification of lncRNAs in plants. The pipeline, Plant-LncPipe, is available at: https://github.com/xuechantian/Plant-LncRNA-pipline., Competing Interests: The authors declare no competing interests., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nanjing Agricultural University.)

Xanthoceras sorbifolium (yellowhorn) is a woody oil plant with super stress resistance and excellent oil characteristics. The yellowhorn oil can be used as biofuel and edible oil with high nutritional and medicinal value. However, genetic studies on yellowhorn are just in the beginning, and fundamental biological questions regarding its very long-chain fatty acid (VLCFA) biosynthesis pathway remain largely unknown. In this study, we reconstructed the VLCFA biosynthesis pathway and annotated 137 genes encoding relevant enzymes. We identified four oleosin genes that package triacylglycerols (TAGs) and are specifically expressed in fruits, likely playing key roles in yellowhorn oil production. Especially, by examining time-ordered gene co-expression network (TO-GCN) constructed from fruit and leaf developments, we identified key enzymatic genes and potential regulatory transcription factors involved in VLCFA synthesis. In fruits, we further inferred a hierarchical regulatory network with MYB-related ( XS03G0296800 ) and B3 ( XS02G0057600 ) transcription factors as top-tier regulators, providing clues into factors controlling carbon flux into fatty acids. Our results offer new insights into key genes and transcriptional regulators governing fatty acid production in yellowhorn, laying the foundation for efforts to optimize oil content and fatty acid composition. Moreover, the gene expression patterns and putative regulatory relationships identified here will inform metabolic engineering and molecular breeding approaches tailored to meet biofuel and bioproduct demands., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Shi, Ma, Wang, Liu, Yan, Tian, Li, Bao, Chen, Zhao, Xiang, Jia, Nie, Guan and Mao.)

Background: The lifestyles of preschoolers have become physically inactive and sedentary, their eating habits unhealthy, and their sleep routines increasingly disturbed. Parental involvement appears crucial to combat the unhealthy lifestyle of preschoolers. Because of the recognized barriers to traditional face-to-face interventions, easy access and lower costs make electronic health (eHealth) interventions appealing. However, whether parent-based eHealth intervention may be harnessed to improve the aforementioned lifestyle behaviors of preschoolers is currently unclear, a gap that this systematic review intends to address. This study aims to systematically review the current literature concerning the effectiveness of parent-based eHealth intervention on the physical activity, dietary behaviors, and sleep of preschoolers., Method: This systematic review conforms to the Preferred Reporting Items for Systematic Reviews and Meta-analysis statement. Six databases (EMBASE, PubMed, MEDLINE, Web of Science, SPORTDiscus, and PsycINFO) were retrieved for the period from January 2000 to December 2022. Studies were eligible if 1 they were quantitative study design; 2 eHealth interventions in which parents were the change agents targeted children aged 3-6 years; 3 interventions examined the effectiveness of eHealth or incorporated eHealth as one of the intervention modalities; 4 at least one variable included in either primary or secondary outcome had to concentrate on the physical activity, diet, and sleep of preschoolers; 5 publication type was limited to the English language and peer-reviewed journal articles; 6 study settings were confined to family- or parent-based ones. The risk of bias was assessed, based upon Version 2 of the Cochrane risk-of-tool for randomized trials (RoB2)., Results: Twelve studies were screened. No significant group-by-time improvement in physical activity was found in studies related to physical activity outcomes. Two studies reported a significant difference between groups concerning motor ability, with one study indicating improved object control with the other reporting improvement in both object control and locomotor skills. Of the studies related to dietary behavior outcomes, six studies reported a significant difference at the posttest compared to the control group, in terms of vegetable and fruit intake, sugar-sweetened drinks, reduced candy consumption, and improved non-core food. Three studies reported a significant difference between groups in sleep duration at the end of the posttest, with the result of one study limited to preference-only participants. None of the reviewed studies found a significant difference between groups for sleep problems., Conclusion: Parent-based eHealth interventions were not significantly effective in improving physical activity and reducing sleep problems in preschoolers, but the majority of studies have found that this type of intervention significantly improves the dietary behaviors and sleep duration of preschoolers. High-quality, robustly designed studies to balance the intervention dosage and sequence are needed to investigate the effectiveness of parent-based eHealth intervention on physical activity, dietary behaviors, and sleep in preschoolers, particularly those raised in other cultural background, which may significantly impact their lifestyle., Trial Registration: International Prospective Register of Systematic Review (PROSPERO): CRD42023418861., (© 2023 The Society of Chinese Scholars on Exercise Physiology and Fitness. Published by Elsevier (Singapore) Pte Ltd.)

Terpenes and terpenoids are key natural compounds for plant defense, development, and composition of plant oil. The synthesis and accumulation of a myriad of volatile terpenoid compounds in these plants may dramatically alter the quality and flavor of the oils, which provide great commercial utilization value for oil-producing plants. Terpene synthases ( TPSs ) are important enzymes responsible for terpenic diversity. Investigating the differentiation of the TPS gene family could provide valuable theoretical support for the genetic improvement of oil-producing plants. While the origin and function of TPS genes have been extensively studied, the exact origin of the initial gene fusion event - it occurred in plants or microbes - remains uncertain. Furthermore, a comprehensive exploration of the TPS gene differentiation is still pending. Here, phylogenetic analysis revealed that the fusion of the TPS gene likely occurred in the ancestor of land plants, following the acquisition of individual C- and N- terminal domains. Potential mutual transfer of TPS genes was observed among microbes and plants. Gene synteny analysis disclosed a differential divergence pattern between TPS-c and TPS-e/f subfamilies involved in primary metabolism and those (TPS-a/b/d/g/h subfamilies) crucial for secondary metabolites. Biosynthetic gene clusters (BGCs) analysis suggested a correlation between lineage divergence and potential natural selection in structuring terpene diversities. This study provides fresh perspectives on the origin and evolution of the TPS gene family., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Yan, Zhou, Liu, Zhao, Tian, Shi, Bao, Li, Jia, Nie, Guo, Kong, Porth and Mao.)

In recent years, perovskite has received increasing attention in the medical field. However, there has been a lack of related bibliometric analysis in this research field. This study aims to analyse the research status and hot topics of perovskite in the medical field from a bibliometric perspective and explore the research direction of perovskite. This study collected 1852 records of perovskite research in the medical field from 1983 to 2022 in the Web of Science (WOS) database. The country, institution, journal, cited references, and keywords were analysed using CiteSpace, VOS viewer, and Bibliometrix software. The number of articles related to perovskite research in the medical field has been increasing every year. China and USA have published the most papers and are the main forces in this research field. The University of London Imperial College of Science, Technology, and Medicine is the most active institution and has contributed the most publications. ACS Applied Materials & Interfaces is the most prolific journal in this field. "Medical electronic devices", "X-rays", and "piezoelectric materials" are the most researched directions of perovskite in the medical field. "Performance", "perovskite", and "solar cells" are the most frequently used keywords in this field. Advanced Materials is the most relevant and academically influential journal for perovskite research. Halide perovskites have been a hot topic in this field in recent years and will be a future research trend. X-ray, electronic medical equipment, and medical stents are the main research directions.

Coriaria nepalensis Wall. (Coriariaceae) is a nitrogen-fixing shrub which forms root nodules with the actinomycete Frankia. Oils and extracts of C. nepalensis have been reported to be bacteriostatic and insecticidal, and C. nepalensis bark provides a valuable tannin resource. Here, by combining PacBio HiFi sequencing and Hi-C scaffolding techniques, we generated a haplotype-resolved chromosome-scale genome assembly for C. nepalensis. This genome assembly is approximately 620 Mb in size with a contig N50 of 11 Mb, with 99.9% of the total assembled sequences anchored to 40 pseudochromosomes. We predicted 60,862 protein-coding genes of which 99.5% were annotated from databases. We further identified 939 tRNAs, 7,297 rRNAs, and 982 ncRNAs. The chromosome-scale genome of C. nepalensis is expected to be a significant resource for understanding the genetic basis of root nodulation with Frankia, toxicity, and tannin biosynthesis., (© 2023. The Author(s).)

Wood decay resistance (WDR) is marking the value of wood utilization. Many trees of the Lauraceae have exceptional WDR, as evidenced by their use in ancient royal palace buildings in China. However, the genetics of WDR remain elusive. Here, through comparative genomics, we revealed the unique characteristics related to the high WDR in Lauraceae trees. We present a 1.27-Gb chromosome-level assembly for Lindera megaphylla (Lauraceae). Comparative genomics integrating major groups of angiosperm revealed Lauraceae species have extensively shared gene microsynteny associated with the biosynthesis of specialized metabolites such as isoquinoline alkaloids, flavonoid, lignins and terpenoid, which play significant roles in WDR. In Lauraceae genomes, tandem and proximal duplications (TD/PD) significantly expanded the coding space of key enzymes of biosynthesis pathways related to WDR, which may enhance the decay resistance of wood by increasing the accumulation of these compounds. Among Lauraceae species, genes of WDR-related biosynthesis pathways showed remarkable expansion by TD/PD and conveyed unique and conserved motifs in their promoter and protein sequences, suggesting conserved gene collinearity, gene expansion and gene regulation supporting the high WDR. Our study thus reveals genomic profiles related to biochemical transitions among major plant groups and the genomic basis of WDR in the Lauraceae., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Tian, Guo, Yan, Shi, Nie, Zhao, Bao, Li, Kong, Su, Mao and Lin.)

Objective: To explore the effect of knot-free suture and frenulum positioning combined with application positioning (KFS-FP + AP) in circumcision using a disposable circumcision suture device., Methods: We retrospectively analyzed the clinical data on 160 cases of circumcision for phimosis or redundant prepuce by KFS-FP + AP (the observation group, n = 80) or by routine circumcision (the control group, n = 80) with a disposable circumcision suture device from February 2021 to December 2021. We recorded the operation time, incidence of frenulum breve, incidence of frenulum dislocation, and Visual Analog Scale (VAS) scores at 6 hours after surgery, and compared them between the two groups of patients., Results: The operation time was longer in the observation than in the control group (8.00 ［8.00, 9.00］ min vs 5.00 ［5.00, 5.00］ min), and the incidence rates of frenulum breve (0 vs 8.75%, P < 0.05) and frenulum dislocation (0 vs 7.5%, P < 0.05) significantly lower in the former than in the latter group. There were no statistically significant difference in the VAS scores between the observation and the control groups (2.60 ［2.00, 3.00］ vs 2.55 ［2.00, 3.00］, P > 0.05)., Conclusion: KFS-FP + AP with a disposable circumcision suture device is a safe and effective method of circumcision, with high satisfaction of the patients and worthy of clinical promotion.

The genus Rhododendron (Ericaceae), with more than 1000 species highly diverse in flower color, is providing distinct ornamental values and a model system for flower color studies. Here, we investigated the divergence between two parental species with different flower color widely used for azalea breeding. Gapless genome assembly was generated for the yellow-flowered azalea, Rhododendron molle . Comparative genomics found recent proliferation of long terminal repeat retrotransposons (LTR-RTs), especially Gypsy , has resulted in a 125 Mb (19%) genome size increase in species-specific regions, and a significant amount of dispersed gene duplicates (13 402) and pseudogenes (17 437). Metabolomic assessment revealed that yellow flower coloration is attributed to the dynamic changes of carotenoids/flavonols biosynthesis and chlorophyll degradation. Time-ordered gene co-expression networks (TO-GCNs) and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct flower pigmentation. B3 and ERF TFs were found dominating the gene regulation of carotenoids/flavonols characterized pigmentation in R. molle , while WRKY, ERF, WD40, C2H2, and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-flowered R simsii . This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding., (© The Author(s) 2023. Published by Oxford University Press on behalf of Nanjing Agricultural University.)

Color change during flower opening is common; however, little is understood on the biochemical and molecular basis related. Lilac (Syringa oblata), a well-known woody ornamental plant with obvious petal color changes, is an ideal model. Here, we presented chromosome-scale genome assembly for lilac, resolved the flavonoids metabolism, and identified key genes and potential regulatory networks related to petal color change. The genome assembly is 1.05 Gb anchored onto 23 chromosomes, with a BUSCO score of 96.6%. Whole-genome duplication (WGD) event shared within Oleaceae was revealed. Metabolome quantification identified delphinidin-3-O-rutinoside (Dp3Ru) and cyanidin-3-O-rutinoside (Cy3Ru) as the major pigments; gene co-expression networks indicated WRKY an essential regulation factor at the early flowering stage, ERF more important in the color transition period (from violet to light nearly white), while the MBW complex participated in the entire process. Our results provide a foundation for functional study and molecular breeding in lilac., (© 2022. The Author(s).)

Estrogen related receptors are orphan members of the nuclear receptor superfamily acting as transcription factors (TFs). In contrast to classical nuclear receptors, the activities of the ERRs are not controlled by a natural ligand. Regulation of their activities thus relies on availability of transcriptional co-regulators. In this paper, we focus on ERRα, whose involvement in cancer progression has been broadly demonstrated. We propose a new approach to identify potential co-activators, starting from previously identified ERRα-activated genes in a breast cancer (BC) cell line. Considering mRNA gene expression from two sets of human BC cells as major endpoint, we used sparse partial least squares modeling to uncover new transcriptional regulators associated with ERRα. Among them, DDX21, MYBBP1A, NFKB1, and SETD7 are functionally relevant in MDA-MB-231 cells, specifically activating the expression of subsets of ERRα-activated genes. We studied SET7 in more details and showed its co-localization with ERRα and its ERRα-dependent transcriptional and phenotypic effects. Our results thus demonstrate the ability of a modeling approach to identify new transcriptional partners from gene expression. Finally, experimental results show that ERRα cooperates with distinct co-regulators to control the expression of distinct sets of target genes, thus reinforcing the combinatorial specificity of transcription., (© 2022. The Author(s).)

In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequencing technologies to assemble a highly contiguous genome for yellowhorn ( Xanthoceras sorbifolium ), an oil-producing tree, and conducted extensive comparative analyses to understand centromere structure and evolution, and fatty acid biosynthesis. We produced a reference-level genome of yellowhorn, ∼470 Mb in length with ∼95% of contigs anchored onto 15 chromosomes. Genome annotation identified 22,049 protein-coding genes and 65.7% of the genome sequence as repetitive elements. Long terminal repeat retrotransposons (LTR-RTs) account for ∼30% of the yellowhorn genome, which is maintained by a moderate birth rate and a low removal rate. We identified the centromeric regions on each chromosome and found enrichment of centromere-specific retrotransposons of LINE1 and Gypsy in these regions, which have evolved recently (∼0.7 MYA). We compared the genomes of three cultivars and found frequent inversions. We analyzed the transcriptomes from different tissues and identified the candidate genes involved in very-long-chain fatty acid biosynthesis and their expression profiles. Collinear block analysis showed that yellowhorn shared the gamma (γ) hexaploidy event with Vitis vinifera but did not undergo any further whole-genome duplication. This study provides excellent genomic resources for understanding centromere structure and evolution and for functional studies in this important oil-producing plant., Competing Interests: The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Liu, Yan, Wang, Zhang, Zhou, Shi, Jia, Tian, Zhou, Zhang, Yun, Wang, Xiang, Mannapperuma, Van Zalen, Street, Porth, El-Kassaby, Zhao, Wang, Guan and Mao.)

Polyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the γ event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species., (© 2021. The Author(s).)

Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger., (© 2021. The Author(s).)

Sex determination systems in plants can involve either female or male heterogamety (ZW or XY, respectively). Here we used Illumina short reads, Oxford Nanopore Technologies (ONT) long reads and Hi-C reads to assemble the first chromosome-scale genome of a female willow tree (Salix dunnii), and to predict genes using transcriptome sequences and available databases. The final genome sequence of 328 Mb in total was assembled in 29 scaffolds, and includes 31,501 predicted genes. Analyses of short-read sequence data that included female and male plants suggested a male heterogametic sex-determining factor on chromosome 7, implying that, unlike the female heterogamety of most species in the genus Salix, male heterogamety evolved in the subgenus Salix. The S. dunnii sex-linked region occupies about 3.21 Mb of chromosome 7 in females (representing its position in the X chromosome), probably within a pericentromeric region. Our data suggest that this region is enriched for transposable element insertions, and about one-third of its 124 protein-coding genes were gained via duplications from other genome regions. We detect purifying selection on the genes that were ancestrally present in the region, though some have been lost. Transcriptome data from female and male individuals show more male- than female-biased genes in catkin and leaf tissues, and indicate enrichment for male-biased genes in the pseudo-autosomal regions. Our study provides valuable genomic resources for further studies of sex-determining regions in the family Salicaceae, and sex chromosome evolution., (© 2021 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.)

Objective: This study established an individualized nomogram for predicting the risk of multidrug-resistant bacterial (MDRB) infection in patients with the diabetic foot (DF), and providing a reference for clinical prevention and treatment., Methods: A total of 199 DF patients admitted to the hospital from July 2015 to December 2018 were included in this study. The pathogenic bacteria at the site of infection were detected and the factors affecting the occurrence of MDRB infection in DF patients summarized. The R software was used to draw the nomogram, and the Bootstrap Method used to internally verify the model. The calibration curve and the Harrell's Concordance Index (C-index) were used to evaluate the predictive effect of the nomogram model., Results: Logistic regression analysis showed that age, course of diabetes, previous use of antibacterial drugs, types of antibacterial drugs, and osteoporosis were risk factors for multidrug-resistant infections in DF (P<0.05). The area under the receiver operating characteristic curve (AUC, Area Under Curve) of the nomogram model after internal verification was 0.773 (95% CI: 0.704-0.830). The mean absolute error between the predicted probability of infection in the nomogram and the actual occurrence of MDRB was 0.032, indicating that the nomogram model had good forecasting efficiency and stability., Conclusion: The risk factors for multidrug-resistant infections in DF are age, course of diabetes, previous use of antibacterial drugs, types of antibacterial drugs used, and osteoporosis. The nomogram model drawn on these risk factors has good predictive accuracy and can assist medical staff in formulating targeted infection prevention strategies for patients., Competing Interests: The authors declare no conflicts of interest., (© 2021 Ma et al.)

Objective: To investigate the causes of abnormally short frenulum induced by circumcision with disposable circumcision suture device and the improvement of the surgical method., Methods: We retrospectively analyzed the clinical data on 320 cases of phimosis or redundant prepuce treated from January 2020 to September 2020, including 160 children (group A) and 160 adults (group B), each further divided into an observation group (n = 80, groups A1 and B1) and a control group (n = 80, groups A2 and B2). The patients in groups A1 and B1 underwent circumcision by suture positioning at the frenulum with the disposable circumcision suture device, and those in groups A2 and B2 received conventional circumcision with the disposable circumcision suture device. We compared the operation time, incidence rate of abnormally short frenulum and Visual Analogue Scale (VAS) score at 6 hours after surgery among the four groups of patients., Results: Statistically significant differences were observed between groups A1 and A2 in the operation time (12.00 ［11.00, 13.00］ vs 8.50 ［8.50, 9.00］ min, P < 0.05) and the incidence rate of abnormally short frenulum (0 vs 10%, P < 0.05) but not in the VAS score (3.00 ［3.00, 4.00］ vs 3.00 ［3.00, 3.75］, P > 0.05). Statistically significant differences were also found between groups B1 and B2 in the operation time (12.00 ［11.00, 12.00］ vs 6.25 ［6.00, 7.00］ min, P < 0.05) and the incidence rate of abnormally short frenulum (0 vs 7.5%, P < 0.05) but not in the VAS score (2.00 ［2.00, 3.00］ vs 2.00 ［2.00, 3.00］, P > 0.05)., Conclusions: Abnormally short frenulum induced by circumcision with the disposable circumcision suture device is mainly attributed to ligation and fixation of the prepuce with the fixation band. Circumcision with the disposable circumcision suture device by suture positioning at the frenulum is a safe and effective method worthy of clinical promotion.

Azaleas (Ericaceae) comprise one of the most diverse ornamental plants, renowned for their cultural and economic importance. We present a chromosome-scale genome assembly for Rhododendron simsii, the primary ancestor of azalea cultivars. Genome analyses unveil the remnants of an ancient whole-genome duplication preceding the radiation of most Ericaceae, likely contributing to the genomic architecture of flowering time. Small-scale gene duplications contribute to the expansion of gene families involved in azalea pigment biosynthesis. We reconstruct entire metabolic pathways for anthocyanins and carotenoids and their potential regulatory networks by detailed analysis of time-ordered gene co-expression networks. MYB, bHLH, and WD40 transcription factors may collectively regulate anthocyanin accumulation in R. simsii, particularly at the initial stages of flower coloration, and with WRKY transcription factors controlling progressive flower coloring at later stages. This work provides a cornerstone for understanding the underlying genetics governing flower timing and coloration and could accelerate selective breeding in azalea.

Salvia splendens , scarlet or tropical sage, is a tender perennial herbaceous flowering plant popularly grown in public and private gardens all over the world. In this study, we developed a set of simple sequence repeats (SSRs) from genome-wide sequences to assess the genetic diversity and population structure among 112 cultivars. We obtained 364,379 SSRs by mining scarlet sage's recently published whole genome sequence; 14,545 gene-associated SSR loci were identified in 2 kb gene flanking regions. Among the 768 gene-associated SSR primer sets we screened, 576 loci successfully amplified in DNA pools of 3-4 different cultivars, of which 271 remained polymorphic when tested across eight individual plants. We searched for the related gene functions attributable to these gene-associated SSRs using diverse databases, resulting in 259 Non-redundant matching sequences, 205 individual Gene Ontology (GO) terms, 236 assigned to eukaryotic orthologous groups, and 67 KEGG-annotated (Kyoto Encyclopedia of Genes and Genomes) sequences. We finally selected 41 polymorphic SSR loci to infer genetic diversity and population structure among 112 S. splendens accessions. Based on the developed gene-associated SSRs, clustering analyses consistently revealed two distinct genetic groups within the core collection of S. splendens cultivars. This work developed and characterized an exhaustive set of genome-wide gene-associated SSR markers for scarlet sage. These SSRs can provide species identification, genetic diversity and population structure information for S. splendens , and will therefore be important tools for the management and protection of S. splendens germplasm., (Copyright © 2020 Jiao, Dong, Shi, Liu, Porth, Xin and Mao.)

Objective: To investigate the availability, prices and affordability of essential medicines in pediatric population across China, in the hope of improving rational use of medicines. Methods: A multicenter cross-sectional survey of medicine prices, availability and affordability was conducted in 17 provinces, municipalities and autonomous region across east, south-central part, west and north of China. Data on 42 medicines used in pediatric population, both original and generic, were collected in 55 public hospitals from May 26 to June 2, 2017. Availability was expressed as the percentage of hospitals with stock of the target medicine on the day of data collection,and median price ratio (MPR) was the ratio of price upon investigation to international reference. Based on national minimum daily wage, affordability represents the number of working days needed to earn the expense which covers a standard course using the target medicine. Statistical software SPSS 13.0 was applied for descriptive analysis of availability, MPR and affordability. Results: Mean Availability of original and generic medicine was 33% and 32%, with median MPR being 5.43 and 1.55. Among the 19 medicines with price information for both original and generic product, the median MPR was 7.73 and 2.04 respectively. Regarding the five medicines used to treat four common pediatric diseases (pneumonia,peptic ulcer, congenital hypothyroidism, refractory nephrotic syndrome), the affordability was 0.63 (0.16-6.17) d for generic medicine, and 1.03 (0.16-11.53) d for its original counterpart. Conclusions: The availability to both original and generic products of the 42 medicines used in pediatric population was low in China. The prices of generic medicines seem to be lower and affordability higher than those of original medicines. There is an urgent need to improve the availability and affordability of pediatric medicines.

The large diameter metal shell component (LDMSC) is an important part of gas insulated (metal-enclosed) switchgear (GIS). The LDMSC with multi branches is filled with gas under certain pressure. The plastic forming process is an efficient approach to manufacturing the high reliability LDMSC. The warm flanging process has been widely used to form LDMSC using aluminum alloy. The forming process is characterized by local heating, and the distribution of temperature is strongly inhomogeneous. Although the wall thickness of the shell is 10 mm to 20 mm, the ratio of outer diameter to thickness is more than 40. These present some difficulties in the flanging process and result in some forming defects. Detailed forming characteristics are hard to obtain by analytical and experimental methods. Thus, the through-process finite element (FE) modeling considering heating, forming, unloading, and cooling is one of the key problems to research the manufacturing process of LDMSC. In this study, the through-process FE modeling of the warm flanging process of LDMSC using aluminum alloy was carried out based on the FORGE. The thermo-mechanical coupled finite element method was adopted in the modeling, and the deformation of the workpiece and the die stress were considered together in the modeling. A full three-dimensional (3D) geometry was modeled due to inhomogeneous distribution in all directions for the temperature field. The simulation data of local flame heating could be transferred seamlessly to the simulations of the deforming process, the unloading process, and the cooling process in the through-process FE model. The model was validated by comparison with geometric shapes and forming defects obtained from the experiment. The developed FE model could describe the inhomogeneous temperature field along circumferential, radial, and axial directions for the formed branch as well as the deformation characteristic and the unloading behavior during the warm flanging process. By using the FE model, the forming defects during the flanging process and their controlling characteristics were explored, the evolution of the temperature field through the whole process was studied, and deformation and springback characteristics were analyzed. The results of this study provide a basis for investigating deformation mechanisms, optimizing processes, and determining parameters in the warm flanging process of a large-diameter aluminum alloy shell component., Competing Interests: The authors declare no conflict of interest. The founding sponsors had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, and in the decision to publish the results.

Although published studies have reported the association between MTHFR C677T (rs 1801133), A1298C (rs 1801131), and MTRR A66G (rs1801394) polymorphisms and male infertility in Asian populations, the results are conflicting. In order to accurately evaluate the relevance, a meta-analysis was performed.We searched for potential studies in 4 databases, containing PubMed, ScienceDirect, China National Knowledge Infrastructure (CNKI), and Wanfang database until May 31, 2018. The summarized odds ratio (OR) with 95% confidence intervals (95% CI) were calculated to evaluate the relevance in 5 genetic models. The heterogeneity test, sensitivity analysis, and publication bias test was performed by Review Manager 5.3 software.Overall, 22 case-control studies with 5049 cases and 4157 controls were included in this meta-analysis, which contained 20 studies of MTHFR C677T polymorphism, 12 studies of MTHFR A1298C polymorphism and 4 studies of MTRR A66G polymorphism. The results indicated that MTHFR C677T, A1298C, and MTRR A66G polymorphisms were significantly associated with male infertility in Asian populations (Dominant model: MTHFR CC + CT vs TT: OR = 0.60, 95% CI (0.53, 0.67), P <.00001; MTHFR AA + AC vs CC: OR = 0.62, 95% CI (0.49, 0.79), P = .0001; MTRR AA + AG vs GG: OR = 0.60, 95% CI (0.45, 0.81), P = .001. Recessive model: MTHFR CC vs CT + TT: OR = 0.67, 95% CI (0.61, 0.74), P <.00001; MTHFR AA vs AC + CC: OR = 0.79, 95% CI (0.70, 0.88), P <.0001; MTRR AA vs AG + GG: OR = 0.70, 95% CI (0.56, 0.88), P = .002. Heterozygote model: MTHFR CC vs CT: OR = 0.74, 95% CI (0.67, 0.82), P <.00001; MTHFR AA vs AC: OR = 0.83, 95% CI (0.73, 0.93), P = .002; MTRR AA vs AG: OR = 0.76, 95% CI (0.60, 0.92), P = .02. Homozygote model: MTHFR CC vs TT: OR = 0.48, 95% CI (0.41, 0.56), P <.00001; MTHFR AA vs CC: OR = 0.61, 95% CI (0.39, 0.93), P = .02; MTRR AA vs GG: OR = 0.51, 95% CI (0.36, 0.72), P = .0001. Allele model: MTHFR C vs T: OR = 0.70, 95% CI (0.66, 0.75), P <.00001; MTHFR A vsC: OR = 0.82, 95% CI (0.71, 0.95), P = .01; MTRR A vs G: OR = 0.76, 95% CI (0.66, 0.88), P = .00003). Stratified analyses by geographical location and source of controls showed the same results. Sensitivity analyses indicated that the final consequences of this meta-analysis were stable, and the publication biases test had not found obvious asymmetry.This meta-analysis indicates that MTHFR C677T, A1298C, and MTRR A66G polymorphisms are the risk factors with susceptibility to male infertility in Asians.

Hepatocellular carcinoma (HCC) has high incidence and mortality in patients with chronic liver diseases worldwide. However, there are limited chemotherapeutic agents for HCC in clinic. Xanthatin, a natural sesquiterpene lactone, has significant antitumor activity against a variety of cancers, but little is known about its effects on HCC and the underlying mechanism. Here, we evaluated the antitumor effects of xanthatin on human hepatoma cells. We found that xanthatin caused morphological changes and reduced cell viability in three HCC cell lines in concentration- and time-dependent manners. Xanthatin at 10 μM significantly arrested cell cycle at the G2/M checkpoint, and at 40 μM significantly arrested cell cycle at the S phase in hepatoma cells. Additionally, xanthatin induced apoptosis associated with activation of caspase-3 in hepatoma cells, but did not apparently induce apoptosis in human normal LO2 hepatocytes. We also demonstrated that the three primary signaling pathways of unfolded protein response (UPR) were activated by xanthatin to different extents. Notably, the PERK/eIF-2α/ATF4 axis was most significantly activated by xanthatin. More importantly, both xanthatin and tunicamycin, an endoplasmic reticulum stress (ERS) inducing compound, increased the levels of CHOP and cleaved-caspase-3 in HepG2 cells, but their effects were significantly abolished by siRNA-mediated knockdown of CHOP. Further experiments validated that xanthatin more potently activated ATF4 by promoting its nuclear translocation in hepatoma cells. Taken together, we discovered that xanthatin induced apoptosis in human hepatoma cells by activating ERS. Our current data revealed a novel mechanism for xanthatin as a promising anti-tumor candidate for HCC therapy., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Background and Objectives: Herpes simplex virus (HSV) and human cytomegalovirus (HCMV) are widespread infections in humans, yet their impact on adverse pregnancy outcomes is controversial. The objective of this study was to evaluate the impact of HSV and HCMV infections during pregnancy on adverse pregnancy outcomes., Methods: A systematic literature search was performed using Web of Science, Scopus, Medline, Embase, PubMed, and the Cochrane Library database for relevant publications up to 2nd August 2017. The odds ratio (OR) and relative risk (RR), and their corresponding 95% confidence intervals (CIs) were selected as the effect size. Statistical analysis was conducted using STATA 12.0., Results: In total, 20 eligible studies were identified and included in the meta-analysis. Of these, 13 and 12 studies were related to the impact of HSV and HCMV upon adverse pregnancy outcomes, respectively. Collectively, the results indicated that HSV infection during pregnancy increased the risk of spontaneous abortion, premature birth and stillbirth with an OR of 3.81 (95% CI: 1.96-7.41), 3.83 (95% CI: 1.17-12.54), and 1.78 (95% CI: 1.08-2.95), respectively. HCMV infection during pregnancy also represented a risk factor for spontaneous abortion, premature birth and stillbirth with an OR of 1.61 (95% CI: 1.14-2.27), 1.86 (95% CI: 1.26-2.76) and 5.74 (95% CI: 2.04-16.12), respectively., Conclusions: Maternal HSV and HCMV infection during pregnancy increase the risk of spontaneous abortion, premature birth, and stillbirth., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Backgrounds: Clopidogrel is widely used in Coronary Heart Disease (CHD) patients undergoing percutaneous coronary intervention (PCI) to prevent thrombotic events. However, clopidogrel response variability (CRV) may affect the patients' clinical outcomes. The current data have shown that genetic factors play an important role in CRV. The aim of this research is to investigate the association of pregnane X receptor (PXR, also called NR1I2) genetic polymorphisms with the clinical efficacy of clopidogrel in patients undergoing PCI., Methods: A total of 384 patients undergoing PCI were recruited and treated with dual antiplatelet therapy (DAPT) for 12 months. The plasma concentration of clopidogrel carboxylic acid metabolites (CLPM) was measured by High Performance Liquid Chromatography (HPLC). The maximum aggregation rate (MAR) of platelet were measured by PL-11 analyzer. PXR genetic polymorphisms were determined by Sequenom MassArray system. The clinical outcomes were observed by readmission, outpatient and calling back interview within 12 months after PCI., Results: Among all 384 patients, a total of 153 patients were occurred with major adverse cardiovascular events (MACE), 29 patients were occurred with bleeding events, the other patients had a favorable prognosis. The polymprphisms of PXR rs3814057A > C [OR(95%CI): 0.71(0.527-0.957), P = 0.024], rs3814058T > C [OR (95%CI): 1.395(1.034-1.883), P = 0.029] and rs6785049 A > G [OR(95%CI): 0.724 (0.535-0.979), P = 0.036] were significantly associated with MACE. The haplotype h1 (GCC) was associated with a higher risk of MACE [OR (95%CI): 1.385 (1.028-1.866), P = 0.031]. Whereas, the haplotype h2 (AAT) was associated with a lower risk of MACE [OR (95%CI): 0.711(0.525-0.962), P = 0.027]., Conclusions: The genotypes and haplotypes of PXR rs3814057, rs3814058 and rs6785049 have impact on the MACE in clopidogrel treated patients after PCI., (Copyright © 2018. Published by Elsevier B.V.)

Volatile organic compounds (VOCs) are an important source of industrial stench. This study was aimed at sampling and analyzing the stench source and its impact on the sensitive spot residential areas, concentrating on certain automobile manufacturing enterprise. The odor concentration and VOCs species of each vent stack, plant boundary, and sensitive spot in the enterprise were determined for November 15 and 17, 2016 via qualitative and quantitative analysis using the triangle odor bag method and gas pre-concentration system-gas chromatography-mass spectra. The results show that the odor concentrations of all vent stacks in the original equipment manufacturing plant and the engine plant were below the criterion level, those of the plant boundaries in the engine plant were below the limits, and those of the plant boundaries and sensitive spots in the original equipment manufacturing plant exceeded the allowed standards. A total of 54 VOCs species were identified, including aromatics, halogenated compounds, alkanes, alkene, cycloalkanes, ketones, esters, ethers, alcohols, sulfur compounds, and oxygen ring compounds. Halogenated compounds were the most abundant VOCs species, followed by aromatics. As a result, aromatics and halogenated compounds are the representative odorants in automobile making. 1,3-Butadiene and ethyl toluene were selected to be the typical odorants of sensitive spots according to mass concentration, detector odor threshold, and threshold dilution multiples of characteristic VOCs species in sensitive spots. The results show that the majority of characteristic VOCs species were from paint composition through the qualitative analysis based on paint used in coating shops. 1,3-Butadiene, which contributed the most to odor pollution, excluding the impact of other emission sources on sensitive spots, originates from spraying and drying processes of coating shops in the original equipment manufacturer. It is recommended that the enterprise should adopt environmentally friendly paints with low VOCs components or RTO purification equipment with higher processing efficiency to reduce the impact of stench on the sensitive residential areas from automobile making.

Objective: To evaluate the effect of maternal dengue virus (DENV) infection during pregnancy in premature birth, low birth weight, miscarriage and stillbirth., Methods: Systematic electronic literature searches were conducted including PubMed, Medline, Embase, Web of science, Scopus and the Cochrane Library database, up until July 5, 2017. Effect sizes were estimated by using the relative risk (RR) or odds ratio (OR) with theirs corresponding 95% confidence interval (CI). Subgroup analyses were conducted for study design (prospective or retrospective) and clinical symptom of participants (symptomatic or asymptomatic). Statistical analysis was conducted by STATA 12.0., Results: The initial systematic literature searches identified 1048 studies. After screening, fourteen studies were included. The pooled results did not suggest maternal DENV infection might increase the risk of adverse fetal outcomes with a pooled RR of 0.96 (95% CI: 0.85-1.09, I 2 =49.6%) for premature birth, RR of 0.99 (95%CI: 0.87-1.12, I 2 =35.1%) for low birth weight, OR of 1.77 (95% CI: 0.99-3.15, I 2 =17.5%) for miscarriage and RR of 3.42 (95% CI: 0.76-15.49, I 2 =54.8%) for stillbirth. Subgroup analysis of studies in symptomatic participants still did not indicate DENV infection appeared to be a risk factor for premature birth, low birth weight and miscarriage with pooled effect size of 0.99 (95% CI: 0.87-1.13, I 2 =49.3%), 1.22 (95% CI: 0.827-1.80, I 2 =55.1%) and 1.19 (95% CI: 0.56-2.55, I 2 =4.7%), respectively., Conclusions: Current evidence did not suggest that maternal DENV infection during pregnancy might increase the risk of premature birth, low birth weight, miscarriage and stillbirth., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Objective: To investigate the effects of mitogen-activated protein kinases (MAPKs) inhibitors on glutathione (GSH) metabolism, and to explore the pathway related to GSH metabolism., Methods: BRL rat hepatocytes were treated by c-Jun NH2-terminal kinase (JNK),p38, and extracellular signal-regulated kinase 1/2 (ERK1/2) inhibitors:SP600125, SB203580 and PD98659, respectively, for 24 h. MTT method was used to measure hepatocytes viability. The content of GSH was determined by high performance liquid chromatography. The protein expressions of JNK and phosphorylated JNK (p-JNK) was tested by Luminex method. Activities of GSH metabolic enzymes were detected by commercial kits., Results: Hepatocytes vitality was inhibited when the concentrations of SP600125, SB203580 and PD98659 were higher than 10 μ mol/L, 20 μ mol/L, and 40 μ mol/L, respectively; SP600125 decreased the content of GSH in hepatocytes, while SB203580 and PD98659 had no effect. SP600125 reduced p-JNK protein expression, and enhanced GSH-Px activity significantly., Conclusions: JNK MAPK pathway takes part in the GSH metabolism in hepatocytes.

A reactivity-based anthropogenic volatile organic compounds (VOCs) emission inventory in China in 2010 was developed on the basis of ozone formation potential (OFP), using the latest VOCs emission inventory, source profiles and maximum incremental reactivity (MIR) values. The results showed that the total anthropogenic OFP was 84187.61 kt in China in 2010, of which 6882.53 kt was from alkanes, 41496.92 kt from alkenes/alkynes, 32945.32 kt from aromatic hydrocarbons, 161.45 kt from halocarbons, and 2701.40 kt from oxygenated organics. The top 10 species in terms of OFP consisted of propene, ethene, m/p -xylene, toluene, 1-butene, o -xylene, 1,2,4-trimethyl benzene, 1,3-butadiene, m -ethyl toluene and ethyl benzene, contributing 63.95% to the total OFP but only 31.84% to the mass-based emission. Industrial sources accounted for the largest (49.29%) of the total OFP, followed by transportation sources (28.31%) and agricultural sources (22.40%). The key industrial sources with high reactivity were architectural decoration industry, oil refinery industry, storage and transport, machinery equipment industry, transport equipment industry and printing. Passenger cars, motorcycles and heavy duty vehicles were the major OFP sources of transportation. The two biomass burning sources were both the key OFP sources of agriculture. Shandong, Jiangsu, Guangdong, Zhejiang and Henan were the top five provinces with contributions of 39.65% of the total OFP in China. The reactivity-based emission inventory in this study would be of great significance for the formulation of reactivity-based ozone (O 3 ) control strategies in China.

Several novel adenoviruses (AdVs) have recently been identified in humans and other animal species. In this study, we report the molecular detection of and phylogenetically characterize bat and human AdVs detected in fecal or rectal swab samples collected in southern China. To detect AdVs, a 252-261 bp fragment of the DNA polymerase (DPOL) gene was amplified using nested PCR. A total of 520 rectal swab samples were collected from eight bat species in four geographic regions of southern China (Guangzhou, Yunfu, Huizhou, and Haikou city). Thirty-six (6.9%) samples from the following species tested positive for AdVs: Myotis ricketti, Miniopterus schreibersii, Scotophilus kuhlii, Taphozous melanopogon, Rhinolophus blythi, and Cynopterus sphinx. Eight novel AdVs were detected in 13.3% of the samples from C. sphinx. Of 328 fecal samples from patients with diarrhea, 16 (4.9%) were positive for classical human AdVs. Phylogenetic analysis showed that human AdVs shared low similarity (57.1-69.3%) with bat AdVs in deduced amino acid sequences of the AdV DPOL region. Thus, our study indicated that bat AdVs and human AdVs are species specific. As such, there is no evidence of cross-species transmission of AdV between bats and humans based on current data.

Alzheimer's disease (AD) is a devastating neurodegenerative disease and there is no effective therapy for it. Peroxisome proliferators activated receptor-gamma (PPAR-γ) agonists is a promising therapeutic approach for AD and has been widely studied recently, but no consensus was available up to now. To clarify this point, a meta-analysis was performed. We searched MEDLINE, EMBASE, Cochrane Central database, PUBMED, Springer Link database, SDOS database, CBM, CNKI and Wan fang database by December 2014. Standardized mean difference (SMD), relative risk (RR) and 95% confidence interval (CI) were calculated to assess the strength of the novel therapeutics for AD and mild-to-moderate AD. A total of nine studies comprising 1314 patients and 1311 controls were included in the final meta-analysis. We found the effect of PPAR-γ agonists on Alzheimer's Disease Assessment Scale - Cognitive Subscale (ADAS-cog) scores by using STATA software. There was no evidence for obvious publication bias in the overall meta-analysis. There is insufficient evidence of statistically incognition of AD and mild-to-moderate AD patients have been improved who were treated with PPAR-γ agonists in our research. However, PPAR-γ agonists may be a promising therapeutic approach in future, especially pioglitazone, with large-scale randomized controlled trials to confirm.

MicroRNAs (miRNAs) are endogenous, non-coding, small RNAs, which play a critical role in regulating varieties of the biological and pathologic processes. MiR-196a has been reported to take part in tumorigenic progression of osteosarcoma (OS). However, the effects of miR-196a on OS are still unclear. The objective of this study is to investigate the molecular mechanism of miR-196a in osteosarcoma cells. In the present study, the expression of miR-196a in OS cell lines was detected by real-time PCR. We found that the expression level of miR-196a was markedly up-regulated in osteosarcoma cell lines compared with normal osteoblastic cells. Then, the miR-196a mimic was transiently transfected into MG63 and U2OS cells using Lipofectamine™ 2000 reagent. Subsequently, the MTT and Brdu-ELISA results showed that up-regulation of miR-196a promoted the cell viability and proliferation. Our results also showed that miR-196a mimic accelerated cell cycle progression of MG63 and U2OS cells by down regulation of p21 and p27, and upregulation of cyclin D1. In addition, overexpression of miR-196a suppressed apoptosis of MG63 and U2OS cells due to increasing BCL2L2 and MCL-1 expressions, and then inactivating caspase-3. Eventually, the effect of miR-196a mimic on the PTEN/phosphoinositide 3-kinase (PI3K)/Akt signaling pathway was explored by Western blot. From our results, transfection of miR-196a decreased the expression of PTEN and increased the phosphorylation of PI3K and Akt. Taken together, miR-196a should be an oncogene in osteosarcoma. The possible mechanism was that overexpression of miR-196a promoted proliferation of MG63 and U2OS cells by modulating the PTEN/PI3K/Akt signaling pathway.

Human parechovirus (HPeV), a member of Picornaviridae family, is a widespread pathogen causing a wide spectrum of diseases. Like other picornaviruses, HPeV genome recombination has been detected. A total of 322 fecal samples were collected from children outpatients in Guangzhou, China, including 42 (13.0%, 42/322) HPeV-positive samples detected in most of the infected children less than two years old. Seven HPeV genotypes (HPeV1, HPeV3, HPeV4, HPeV5, HPeV6, HPeV8 and HPeV14) were detected, among which, HPeV14, a rare genotype, was reported for the first time in children with acute gastroenteritis in China. This study revealed recombination events in eight samples. Clinical profiles did not yield statistical significance between children with HPeV infection alone and cases without pathogens detected. In conclusion, this study demonstrated that HPeV circulated in Guangzhou, China is diverse genetically, which provided evidence of recombination in HPeV in China., (© 2014 Wiley Periodicals, Inc.)

Here we investigated the regulation of Pichia pastoris desaturase genes by low temperature and exogenous fatty acids in the late-exponential phase at the transcriptional level. Time-course studies of gene expression showed that mRNA levels of four desaturase genes were rapidly and transiently enhanced by low temperature and suppressed by exogenous oleic acid. Stearic acid showed no obvious repression of mRNA levels of Fad12 and Fad15 and a slight increase in Fad9A and Fad9B mRNA levels. Using a promoter-reporter gene construct, we demonstrated that the pFAD15 promoter activity was induced by low temperature in a time-dependent manner and reduced in a dose- and time-dependent manner by unsaturated fatty acids. Also, there was no absolute correlation between mRNA abundance and production of corresponding fatty acids. Disruption of Spt23 resulted in a decrease in transcript levels of Fad9A and Fad9B, but had little effect on the other desaturase genes. Consistent with these observations, a decrease in the relative amount of oleic acid (OLA) and an increase in the relative content of linoleic acid and ALA with different degrees were clearly observed in the stationary phase cells of ΔSpt23 mutant. Further analysis showed that the effect of low-temperature activation and OLA inhibition on expression of Fad9A and Fad9B seemed to disappear after disruption of the Spt23 gene, which indicated that Spt23p is essential for the expression of two Δ9-desaturase genes internally and probably involved in the regulation of Δ9-desaturase genes transcription in response to external stimuli, and thereby plays a role in the synthesis of OLA.

Objective: From May 2009-January 2010, a total of 3768 biosamples were tested for influenza A (H1N1) infection at Zhengzhou center for disease control and prevention, China. 1452 cases were laboratory confirmed H1N1 infection and 2316 were considered suspected victims. To evaluate the current protocol of influenza A (H1N1) based on the epidemic situations of Zhengzhou, relationships among features were explored and whether additional clinical characteristics should be part of H1N1 diagnosis protocols were determined., Methods: Both clinical and epidemiologic findings as well as statistical analyses were described in this article. Test for independence between features related to the disease diagnosis has been proposed. Furthermore, logistic regression was carried out to measure the association among features and latent class analysis was performed to identify additional crucial features in laboratory confirmed H1N1 by building various latent models with different combinatorial features., Results: The mean generation time for H1N1 was estimated as 3.59 +/- 1.41 days (range = 2.01-7.26). The estimated infection rate was 0.258 +/- 0.088 3, and reproduction number was 1.94 (95% CI = 1.12-3.18). Our results revealed that the six features, including molecular detections using three separate primer/probe sets, gender, age and temperature, are all associated with clinical diagnosis of H1N1, and that three separate primer/probe sets for laboratory confirmed H1N1, age and temperature are associated with each other., Conclusion: Additional clinical features applied into the H1N1 diagnosis with current three primers/probe sets can increase the diagnostic efficiency.

Recent outbreak of H1N1 virus worldwide has caused 16 226 deaths in over 213 countries and districts. Binding between the virus and the receptor on the host cell surface is the key initial event for the infection, which results in the fusion of viral host cell membrane. Hemagglutinin (HA) is the viral protein that mediates the receptor binding and membrane fusion. The receptor binding sites (RBSs) are located at the membrane-distal part of each subunit of the HA trimer and are formed by three secondary structure elements, 190 helix (residues 190 to 198), 130 loop (residues 135 to 138), and 220 loop (residues 221 to 228). HA1 with 327 amino acid sequences in length was collected from 1221 H1N1 viruses between 1918 and 2009, and bioinformatic studies were carried out through sequence comparison, entropy calculation for each amino acid residue, and 3D structure modeling. The results showed that the RBSs of different viruses with different hosts have different entropies, and the RBSs in HA1 with different hosts have different favorite amino acid sequences. The 3D modeling indicates the subtly conformation changes in the 190 helix region between different HA1s in H1N1. This study explores new characters of the RBS structure in different HA1s, and provides new information for the further investigation of the infection mechanism.

Chloroplast is a typical plant cell organelle where photosynthesis takes place. In this study, a total of 1,808 chloroplast core proteins in Arabidopsis thaliana were reliably identified by combining the results of previously published studies and our own predictions. We then constructed a chloroplast protein interaction network primarily based on these core protein interactions. The network had 22,925 protein interaction pairs which involved 2,214 proteins. A total of 160 previously uncharacterized proteins were annotated in this network. The subunits of the photosynthetic complexes were modularized, and the functional relationships among photosystem I (PSI), photosystem II (PSII), light harvesting complex of photosystem I (LHC I) and light harvesting complex of photosystem I (LHC II) could be deduced from the predicted protein interactions in this network. We further confirmed an interaction between an unknown protein AT1G52220 and a photosynthetic subunit PSI-D2 by yeast two-hybrid analysis. Our chloroplast protein interaction network should be useful for functional mining of photosynthetic proteins and investigation of chloroplast-related functions at the systems biology level in Arabidopsis.

Whooping cough (pertussis) caused by B. pertussis (B.p) is still serious public health threat. B. parapertussis (B.pp), closely related to B.p, also causes whooping cough. The incidence of B.pp infections has been increasing over the last decades, partly because pertussis vaccines have low efficiency against B.pp infections. Moreover, because the majority of pertussis patients are infants, common antimicrobial agents producing serious adverse reactions in infants are not fully satisfactory. Therefore, we try to identify potential vaccine candidates and alternative drug targets against both B.p and B.pp. This preliminary work integrates several different kinds of data from in silico analysis, comparative genomic hybridization, global transcriptional profiling, and protein-protein interaction (PPI) network to screen potential vaccine candidates and drug targets against the two species. Finally, 191 potential crossprotective vaccine candidates are identified. They have high transcriptional levels in both species, or are associated with virulence and pathogenesis. Moreover, these proteins are not only potentially surface-exposed in the bacteria, but also well conserved among the 165 B.p and B.pp strains. Among them, 22 candidates with high essentiality in the two PPI networks of B.p and B.pp are regarded as suitable drug targets against the two species. We just selected Bordetella as an example to develop a rapid and reliable approach for screening alternative drug targets that associated with novel protein pathways, complexes, and cellular functions against these antibiotic-resistant pathogens. Further researches focusing on the 191 vaccine candidates could accelerate the development of more effective vaccines and drug therapy against B.p and B.pp infection.

A genomic library enriched with (gT)(n) repeats from tartary buckwheat (Fagopyrum tataricum) was constructed using 5'-anchored PCR for the development of microsattellite markers. Sequencing analysis of 5 clones from the library showed that they all contained microsatellites (totally 10 loci), and each was unique. An additional locus-specific primer was designed according to flanking sequence. Two of the microsatellite loci of 10 tartary buckwheat varieties were amplified using an anchored primer and a locus-specific primer, which revealed a clear polymorphic pattern. The data confirmed that the degenerate primer was reliably anchoring at the 5'-end of the microsatellite, and the primers developed based on this technology could be used for diversity analysis of tartary buckwheat.

Objective: To investigate the polymorphism of DYS287 among 28 ethnic populations in 9 provinces of China., Method: YAP element was detected by Touchdown PCR amplification and 2% agarose gel electrophoresis., Results: YAP+ frequencies in these ethnic populations were as follows: Zang 36.7%, Tu 23.8%, Yi 18.4%, Pumi 11.3%, Tajik 7.4%, Bai 6.7%, Jino 5.1%, Shandong Han 4%, Mulao 2.7%, and Maonan 1.3%. The rest ethnic populations in our study, including Gansu Han, Yunnan Han, Zhuangzu, Daizu, Lizu, Nuzu, Lisu, Naxi, Lahu, Dulong, Hani, Shezu, Weiwuer, Sala, Kerkizi, Dongxiang, Vazu, and Korea didn't carry YAP + element., Conclusions: Zangzu, Tuzu, Yizu, Pumi, Jino, and Baizu, which belong to Sino-Tibetan language family, carry a high YAP + frequency. Sala, Tuzu, and Tajik, regarded as Central Asia by origin in history and linguistics, also have a high YAP + frequency. Mulao and Maonan, which origin from "Baiyue" ancient ethnic groups, also have a considerable YAP + frequency.

Protein-protein interactions play a central role in numerous processes in cell and are one of the main research fields in current functional proteomics. The increase of finished genomic sequences has greatly stimulated the progress for detecting the functions of the genes and their encoded proteins. As complementary ways to the high through-put experimental methods, various methods of bioinformatics have been developed for the study of the protein-protein interaction. These methods range from the sequence homology-based to the genomic-context based. Recently, it tends to integrate the data from different methods to build the protein-protein interaction network, and to predict the protein function from the analysis of the network structure. Efforts are ongoing to improve these methods and to search for novel aspects in genomes that could be exploited for function prediction. This review highlights the recent advances of the bioinformatics methods in protein-protein interaction researches. In the end, the application of the protein-protein interaction has also been discussed.

Single nucleotide polymorphism (SNP) is the most common type of genetic variant in human genome. Haplotype, defined as a specific set of alleles observed on a single chromosome, or a part of a chromosome,has been an integral part of human genetics for decades. The goal of the international HapMap project is to determine the common patterns of DNA sequence variation and find the Tag SNPs representing all SNPs in the human genome. Some studies demonstrated that the analyses of haplotype defined by the grouping and interaction of several variants rather than any individual SNP correlated with complex phenotypes. Here, we describe the definitions of SNPs, genotype, haplotype and some information of the HapMap project. In this review, we summarize the current three haplotype-inference methods, including Clark' method, EM algorithm and Byes approach, and the different defining methods for haplotype block, as well as the methods for choosing tag SNPs and association studies of complex diseases using haplotype. The major public SNP databases and applications of SNPs and haplotype in common complex diseases and drug response are also introduced in the paper.

The spike (S) protein of severe acute respiratory syndrome coronavirus (SARS-CoV) is an important viral structural protein. Based on bioinformatics analysis, 10 antigenic peptides derived from the S protein sequence were selected and synthesized. The antigenicity and immunoreactivity of all the peptides were tested in vivo and in vitro. Four peptides (P6, P8, P9 and P10) which contain B cell epitopes of the S protein were identified, and P8 peptide was confirmed in vivo to have a potential in serological diagnosis. By using a syncytia formation model, we tested the neutralization ability of all 10 peptides and their corresponding antibodies. It is interesting to find that P8 and P9 peptides inhibited syncytia formation, suggesting that the P8 and P9 spanning regions may provide a good target for anti-SARS-CoV drug design. Our data suggest that we have identified peptides derived from the S protein of SARS-CoV, which are useful for SARS treatment and diagnosis.

Psoriasis is a chronic skin disease triggered by genetic, environment or other risk factors such as infection, drugs, stress, moisture, alcohol, and smoking. A major psoriasis susceptibility locus at 6p21.3 has been identified. Further studies found that HLA-DQA1*0201 allele was associated with psoriasis. However, there were few data exploring an association between the environmental factors and susceptibility genes. In this study, the samples of 189 patients with psoriasis and 333 healthy controls were collected with their consent and were carried on analysis through polymerase chain reaction sequence-specific primer (PCR-SSP) method. The proportion of male psoriasis patients engaging in the smoking and alcohol was much higher than that of the control group (P<0.005). The HLA-DQA1*0201 allele was present at significantly higher frequency in the patients with psoriasis (OR=4.25, P<1.0 x 10(-6)). Association was found between smoking, alcohol and HLA-DQA1*0201 in male patients with psoriasis (OR>6.91, P<1.0 x 10(-4)).