Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance.

Polyploidy (genome duplication) is a pivotal force in evolution. However, the interactions between parental genomes in a polyploid nucleus, frequently involving subgenome dominance, are poorly understood. Here we showcase analyses of a bamboo system (Poaceae: Bambusoideae) comprising a series of lineages from diploid (herbaceous) to tetraploid and hexaploid (woody), with 11 chromosome-level de novo genome assemblies and 476 transcriptome samples. We find that woody bamboo subgenomes exhibit stunning karyotype stability, with parallel subgenome dominance in the two tetraploid clades and a gradual shift of dominance in the hexaploid clade. Allopolyploidization and subgenome dominance have shaped the evolution of tree-like lignified culms, rapid growth and synchronous flowering characteristic of woody bamboos as large grasses. Our work provides insights into genome dominance in a remarkable polyploid system, including its dependence on genomic context and its ability to switch which subgenomes are dominant over evolutionary time.

Ultrasound features predicting the 3-week outcome of Pavlik harness treatment for developmental hip dysplasia.

BACKGROUND: The treatment protocol for children with developmental dysplasia of the hip (DDH) is routinely adjusted by assessing the hip reduction after 3 weeks of Pavlik harness treatment. However, there is a high risk of failure and complications in the treatment adjustment. The aim of this study was to explore the value of ultrasound features in predicting the treatment outcome of Pavlik harness after 3 weeks in DDH children. METHODS: A total of 215 DDH children were recruited and the demographics and the changes of ultrasound features [α and ß angle and femoral head coverage (FHC)] during the Pavlik harness treatment were recorded. The children were divided into the success group and the failure group according to the reduction outcome after 3 weeks. Univariate and multivariate analyses were performed to analyze the independent predictors for the treatment outcome. Repeated-measures analysis of variance was used to compare the changes of ultrasound features between the two groups during the treatment. Receiver operating characteristic (ROC) curves were plotted to analyze the predictive accuracy of the ultrasound features. RESULTS: Graf type III (P=0.036), bilateral dislocation (P=0.031), and age at diagnosis (P=0.021) were associated with an increased risk of Pavlik harness failure in the multivariate analysis. The changes in α and ß angle and FHC were generally greater in the success group than in the failure group. The α angle and FHC were larger in the success group, while the ß angle was larger in the failure group (P<0.05). Each ultrasound parameter (α and ß angle and FHC) alone could not accurately predict the treatment outcome within 3 weeks. However, the combined ultrasonic features at the second week could accurately predict the outcome of Pavlik harness treatment after the third week. The combination of the ultrasound features at the first week and the influencing factors (Graf classification, age at diagnosis, and side of pathology) could accurately predict the outcome at the first week [area under curve (AUC) =0.931, sensitivity =82.14%, specificity =97.86%]. CONCLUSIONS: The combined model of ultrasonic features at the second week could accurately predict the reduction outcome of Pavlik harness after the third week. The combined model including independent predictors and ultrasonic features could accurately predict the reduction outcome at the first week.

Genome Sequences Provide Insights into the Reticulate Origin and Unique Traits of Woody Bamboos.

Polyploidization is a major driver of speciation and its importance to plant evolution has been well recognized. Bamboos comprise one diploid herbaceous and three polyploid woody lineages, and are members of the only major subfamily in grasses that diversified in forests, with the woody members having a tree-like lignified culm. In this study, we generated four draft genome assemblies of major bamboo lineages with three different ploidy levels (diploid, tetraploid, and hexaploid). We also constructed a high-density genetic linkage map for a hexaploid species of bamboo, and used a linkage-map-based strategy for genome assembly and identification of subgenomes in polyploids. Further phylogenomic analyses using a large dataset of syntenic genes with expected copies based on ploidy levels revealed that woody bamboos originated subsequent to the divergence of the herbaceous bamboo lineage, and experienced complex reticulate evolution through three independent allopolyploid events involving four extinct diploid ancestors. A shared but distinct subgenome was identified in all polyploid forms, and the progenitor of this subgenome could have been critical in ancient polyploidizations and the origin of woody bamboos. Important genetic clues to the unique flowering behavior and woody trait in bamboos were also found. Taken together, our study provides significant insights into ancient reticulate evolution at the subgenome level in the absence of extant donor species, and offers a potential model scenario for broad-scale study of angiosperm origination by allopolyploidization.

Induction of apoptosis and autophagy by calcifying nanoparticles in human bladder cancer cells.

Calcifying nanoparticles have been linked to various types of human disease, but how they contribute to disease processes is unclear. Here, we examined whether and how calcifying nanoparticles isolated from patients with kidney stones are cytotoxic to human bladder cancer cells. Calcifying nanoparticles were isolated from midstream urine of patients with renal calcium oxalate stones and examined by electron microscopy. Human bladder cancer cells (EJ cells) were cultured in the presence of calcifying nanoparticles or nanohydroxyapatites for 12 and 72 h and examined for toxicity using the Cell Counting Kit-8, for autophagy using transmission electron microscopy and confocal microscopy, and for apoptosis using fluorescence microscopy, transmission electron microscopy, and flow cytometry. Changes in protein expression were analyzed by Western blotting. The results showed that the size and shape of the isolated calcifying nanoparticles were as expected. Calcifying nanoparticles were cytotoxic to EJ cells, more so than nanohydroxyapatites, and this was due, at least in part, to the production of intracellular reactive oxygen species. Transmission electron microscopy showed that calcifying nanoparticles were packaged into vesicles and autolysosomes. Calcifying nanoparticles induced greater autophagy and apoptosis than nanohydroxyapatites. Our findings demonstrate that calcifying nanoparticles can trigger bladder cancer cell injury by boosting reactive oxygen species production and stimulating autophagy and apoptosis.

[Factors influencing the postoperative resolution of varicocele-associated scrotal pain].

OBJECTIVE: To investigate the factors influencing the postoperative resolution of varicocele-associated scrotal pain. METHODS: Using the keywords "varicocele", "testicular pain", "scrotal pain", "painful varicocele", "ligation", and "varicocelectomy", we searched the PubMed, Embase, Cochrane Collaboration's Database, CNKI, Wanfang, and VIP Database up to October 2016 for the studies relating to surgical treatment of varicocele-associated scrotal pain. We assessed the quality of the cohort studies included using the Newcastle-Ottawa Scale and that of the randomized controlled trials included with the Cochrane Collaboration's tool. We conducted a meta-analysis using the RevMan software. RESULTS: Finally 14 studies were included in this meta-analysis, of which, 2 involved the history of disease, 8 involved the nature of pain, 2 involved the intensity of pain, 9 involved the grade of varicocele, 3 involved the side of varicocele, 9 involved surgical approaches, 3 involved surgical techniques, and 4 involved postoperative recurrence. The pain resolution rate was significantly higher after subinguinal ligation than after high or inguinal ligation (RR = 0.82, 95% CI: 0.76－0.89, P <0.01; RR = 0.92, 95% CI: 0.86－0.99, P = 0.02), and so was it after microsurgery than after laparoscopic varicocelectomy (RR = 0.77, 95% CI: 0.60－0.99, P = 0.04). CONCLUSIONS: Subinguinal varicocelectomy and microsurgery are more effective options than laparoscopic and high or trans-inguinal ligation of the spermatic vein for resolution of varicocele-associated scrotal pain, while the history of disease, the nature and intensity of pain, the grade and side of varicocele, or postoperative recurrence cannot be regarded as the influencing factors.

The relationship between apolipoprotein E gene ε2/ε3/ε4 polymorphism and breast cancer risk: a systematic review and meta-analysis.

OBJECTIVE: We conducted a systematic review and meta-analysis aiming to assess the relationship between apolipoprotein E (APOE) gene ε2/ε3/ε4 polymorphism and breast cancer risk. METHODS: Yun-Long Liu and Hao-Min Zhang independently completed literature retrieval and data collection, and statistical analyses were performed by Stata. Individual odds ratio (OR) and 95% confidence interval (CI) were pooled in a random-effects model using the DerSimonian-Laird method. Heterogeneity was evaluated by I (2) statistic at a significance level of 50%. Publication bias was assessed by Egger's test. RESULTS: Eleven articles including 2,074 breast cancer patients and 2,372 controls were summarized. Using the most common allele ε3 as a reference, the ε2 (OR =0.87, 95% CI =0.72-1.05, P=0.154, I (2)=0.0%) and ε4 (OR =1.07, 95% CI =0.80-1.42, P=0.654, I (2)=71.8%) alleles were not found to be significantly associated with breast cancer risk in the overall analyses. Subgroup analyses revealed that the comparison of allele ε4 with ε3 was significant in Asians (OR =1.58, 95% CI =1.17-6.32, P=0.003, I (2)=12.1%) and in studies that used the restriction fragment length polymorphism (RFLP) genotyping method (OR =1.27; 95% CI =1.01-1.61, P=0.045, I (2)=34.3%), and was marginally significant in hospital-based studies (OR =1.33; 95% CI =0.98-1.79, P=0.065, I (2)=30.2%), without heterogeneity. Moreover, the presence of the ε2 allele was significantly associated with breast cancer in small studies (total sample size <500) (OR =0.73, 95% CI =0.54-1.00, P=0.052, I (2)=0.0%) without heterogeneity. The Egger's test indicated low probabilities of publication bias. CONCLUSION: We observed a significant association between APOE gene ε4 allele and breast cancer risk in Asian populations. Moreover, the findings of our subgroup analyses suggest that source of controls, genotyping platform, and sample size might be the potential causes of heterogeneity.

Effect of 5-caffeoylquinic acid on the NF-κB signaling pathway, peroxisome proliferator-activated receptor gamma 2, and macrophage infiltration in high-fat diet-fed Sprague-Dawley rat adipose tissue.

Obesity, considered as a consequence of overnutrition, sustains a low-degree inflammatory state and results in insulin-resistance and type 2 diabetes. Here, we investigated the anti-inflammatory effects of 5-caffeoylquinic acid (5-CQA) in high-fat diet-induced obese rats. Serum interleukin (IL)-6, monocyte chemotactic protein 1 (MCP-1), tumor necrosis factor-alpha (TNF-α), total cholesterol (TC), triglyceride (TG), and free fatty acid (FFA) levels were determined. Expression of genes related to TG metabolism, macrophage biomarkers, and inflammation was assessed by real-time PCR. Protein expression of NF-κB, PPARγ2, and phosphorylated IκBα was evaluated by western blotting, and the histology of adipose tissue was examined. Supplementation of the rat diet with 5-CQA reduced obesity development, macrophage infiltration, and steatosis. Additionally, 5-CQA decreased the expression of NF-κB and downstream inflammatory cytokines, but increased the expression of PPARγ2, in a dose-dependent manner. Thus, 5-CQA improved obesity and obesity-related metabolic disturbances via PPARγ2 and the NF-κB signaling pathway.

Clinical impact and reliability of carbonic anhydrase XII in the differentiation of malignant and tuberculous pleural effusions.

OBJECTIVE: To assess the practical utility of pleural fluid carbonic anhydrase XII (CAXII) quantification for differential diagnosis of effusions. MATERIALS AND METHODS: Fluid was collected prospectively from fifty patients presenting with lymphocytic pleural effusions for investigation and CAXII was quantified by ELISA. RESULTS: Pleural fluid CAXII concentrations were significantly higher in lung cancer patients (n=30) than in tuberculous controls (n=20). The sensitivity and specificity of this biomarker were 60%and 75%, respectively. CAXII measurement was not inferior to cytological examination in the diagnosis and exclusion of pleural effusions from lung cancer patients (sensitivity 60% vs. 57%; specificity 75% vs. 100%; positive predictive value 77%; negative predictive value 54%). In patients with negative cytology, it offered a sensitivity of 54%. CONCLUSIONS: Pleural fluid CAXII is elevated in pleural effusions from lung cancer patients. Measurement of CAXII may be used in the future as a valuable adjunct to cytology in the diagnostic assessment of patients with pleural effusions related to lung cancer, especially when cytological examination is inconclusive.

Prevalent role of gene features in determining evolutionary fates of whole-genome duplication duplicated genes in flowering plants.

The evolution of genes and genomes after polyploidization has been the subject of extensive studies in evolutionary biology and plant sciences. While a significant number of duplicated genes are rapidly removed during a process called fractionation, which operates after the whole-genome duplication (WGD), another considerable number of genes are retained preferentially, leading to the phenomenon of biased gene retention. However, the evolutionary mechanisms underlying gene retention after WGD remain largely unknown. Through genome-wide analyses of sequence and functional data, we comprehensively investigated the relationships between gene features and the retention probability of duplicated genes after WGDs in six plant genomes, Arabidopsis (Arabidopsis thaliana), poplar (Populus trichocarpa), soybean (Glycine max), rice (Oryza sativa), sorghum (Sorghum bicolor), and maize (Zea mays). The results showed that multiple gene features were correlated with the probability of gene retention. Using a logistic regression model based on principal component analysis, we resolved evolutionary rate, structural complexity, and GC3 content as the three major contributors to gene retention. Cluster analysis of these features further classified retained genes into three distinct groups in terms of gene features and evolutionary behaviors. Type I genes are more prone to be selected by dosage balance; type II genes are possibly subject to subfunctionalization; and type III genes may serve as potential targets for neofunctionalization. This study highlights that gene features are able to act jointly as primary forces when determining the retention and evolution of WGD-derived duplicated genes in flowering plants. These findings thus may help to provide a resolution to the debate on different evolutionary models of gene fates after WGDs.