Free PSA performs better than total PSA in predicting prostate volume in Chinese men with PSA levels of 2.5-9.9 ng ml-1.

This study investigated whether free prostate-specific antigen (fPSA) performs better than total PSA (tPSA) in predicting prostate volume (PV) in Chinese men with different PSA levels. A total of 5463 men with PSA levels of <10 ng ml-1 and without prostate cancer diagnosis were included in this study. Patients were classified into four groups: PSA <2.5 ng ml-1, 2.5-3.9 ng ml-1, 4.0-9.9 ng ml-1, and 2.5-9.9 ng ml-1. Pearson/Spearman's correlation coefficient (r) and receiver operating characteristic (ROC) curves were used to evaluate the ability of tPSA and fPSA to predict PV. The correlation coefficient between tPSA and PV in the PSA <2.5 ng ml-1 cohort (r = 0.422; P < 0.001) was markedly higher than those of the cohorts with PSA levels of 2.5-3.9 ng ml-1, 4.0-9.9 ng ml-1, and 2.5-9.9 ng ml-1 (r = 0.114, 0.167, and 0.264, respectively; all P ≤ 0.001), while fPSA levels did not differ significantly among different PSA groups. Area under ROC curve (AUC) analyses revealed that the performance of fPSA in predicting PV ≥40 ml (AUC: 0.694, 0.714, and 0.727) was better than that of tPSA (AUC = 0.545, 0.561, and 0.611) in men with PSA levels of 2.5-3.9 ng ml-1, 4.0-9.9 ng ml-1, and 2.5-9.9 ng ml-1, respectively, but not at PSA levels of <2.5 ng ml-1 (AUC: 0.713 vs 0.720). These findings suggest that the relationship between tPSA and PV may vary with PSA level and that fPSA is more powerful at predicting PV only in the ''gray zone'' (PSA levels of 2.5-9.9 ng ml-1), but its performance was similar to that of tPSA at PSA levels of <2.5 ng ml-1.

Parallel Speciation of Wild Rice Associated with Habitat Shifts.

The occurrence of parallel speciation strongly implies the action of natural selection. However, it is unclear how general a phenomena parallel speciation is since it was only shown in a small number of animal species. In particular, the adaptive process and mechanisms underlying the process of parallel speciation remain elusive. Here, we used an integrative approach incorporating population genomics, common garden, and crossing experiments to investigate parallel speciation of the wild rice species Oryza nivara from O. rufipogon. We demonstrated that O. nivara originated multiple times from different O. rufipogon populations and revealed that different O. nivara populations have evolved similar phenotypes under divergent selection, a reflection of recurrent local adaptation of ancient O. rufipogon populations to dry habitats. Almost completed premating isolation was detected between O. nivara and O. rufipogon in the absence of any postmating barriers between and within these species. These results suggest that flowering time is a "magic" trait that contributes to both local adaptation and reproductive isolation in the origin of wild rice species. Our study thus demonstrates a convincing case of parallel ecological speciation as a consequence of adaptation to new environments.

PGL3 is required for chlorophyll synthesis and impacts leaf senescence in rice.

Rice leaf color mutants play a great role in research about the formation and development of chloroplasts and the genetic mechanism of the chlorophyll (Chl) metabolism pathway. pgl3 is a rice leaf color mutant derived from Xiushui11 (Oryza sativa L. spp. japonica), treated with ethyl methane sulfonate (EMS). The mutant exhibited a pale-green leaf (pgl) phenotype throughout the whole development as well as reduced grain quality. Map-based cloning of PGL3 revealed that it encodes the chloroplast signal recognition particle 43 kDa protein (cpSRP43). PGL3 affected the Chl synthesis by regulating the expression levels of the Chl synthesis-associated genes. Considerable reactive oxygen species were accumulated in the leaves of pgl3, and the transcription levels of its scavenging genes were down-regulated, indicating that pgl3 can accelerate senescence. In addition, high temperatures could inhibit the plant's growth and facilitate the process of senescence in pgl3.

Widespread and Adaptive Alterations in Genome-Wide Gene Expression Associated with Ecological Divergence of Two Oryza Species.

Ecological speciation is a common mechanism by which new species arise. Despite great efforts, the role of gene expression in ecological divergence and speciation is poorly understood. Here, we conducted a genome-wide gene expression investigation of two Oryza species that are evolutionarily young and distinct in ecology and morphology. Using digital gene expression technology and the paired-end RNA sequencing method, we obtained 21,415 expressed genes across three reproduction-related tissues. Of them, approximately 8% (1,717) differed significantly in expression levels between the two species and these differentially expressed genes are randomly distributed across the genome. Moreover, 62% (1,064) of the differentially expressed genes exhibited a signature of directional selection in at least one species. Importantly, the genes with differential expression between species evolved more rapidly at the 5' flanking sequences than the genes without differential expression relative to coding sequences, suggesting that cis-regulatory changes are likely adaptive and play an important role in the ecological divergence of the two species. Finally, we showed evidence of significant differentiation between species in phenotype traits and observed that genes with differential expression were overrepresented with functional terms involving phenotypic and ecological differentiation between the two species, including reproduction- and stress-related characteristics. Our findings demonstrate that ecological speciation is associated with widespread and adaptive alterations in genome-wide gene expression and provide new insights into the importance of regulatory evolution in ecological speciation in plants.

PSA density improves the rate of prostate cancer detection in Chinese men with a PSA between 2.5-10.0 ng ml (-1) and 10.1-20.0 ng ml (-1) : a multicenter study.

Chinese men should have a higher prostate-specific antigen (PSA) "gray zone" than the traditional value of 2.5-10.0 ng ml-1 since the incidence of prostate cancer (PCa) in Chinese men is relative low. We hypothesized that PSA density (PSAD) could improve the rate of PCa detection in Chinese men with a PSA higher than the traditional PSA "gray zone." A total of 461 men with a PSA between 2.5 and 20.0 ng ml-1 , who had undergone prostatic biopsy at two Chinese centers were included in the analysis. The men were then further divided into groups with a PSA between 2.5-10.0 ng ml-1 and 10.1-20.0 ng ml-1 . Receiver operating characteristic (ROC) curve was used to evaluate the efficacy of PSA and PSAD for the diagnosis of PCa. In men with a PSA of 2.5-10.0 ng ml-1 or 10.1-20.0 ng ml-1 , the areas under the ROC curve were higher for PSAD than for PSA. This was consistent across both centers and the cohort overall. When the entire cohort was considered, the optimal PSAD cut-off for predicting PCa in men with a PSA of 2.5-10.0 ng ml-1 was 0.15 ng ml-1 ml-1 , with a sensitivity of 64.4% and specificity of 64.6%. The optimal cut-off for PSAD in men with a PSA of 10.1-20.0 ng ml-1 was 0.33 ng ml-1 ml-1 , with a sensitivity of 60.3% and specificity of 82.7%. PSAD can improve the effectiveness for PCa detection in Chinese men with a PSA of 2.5-10.0 ng ml-1 (traditional Western PSA "gray zone") and 10.1-20.0 ng ml-1 (Chinese PSA "gray zone").

Effectiveness and complication rates of tension-free vaginal tape, transobturator tape, and tension-free vaginal tape-obturator in the treatment of female stress urinary incontinence in a medium- to long-term follow up. Meta-analysis of randomized controlled trials.

OBJECTIVE: To evaluate the effectiveness and complications of tension-free vaginal tape (TVT), transobturator tape (TOT), and tension-free vaginal tape-obturator (TVT-O) in a medium- to long-term follow up. METHODS: We searched PubMed, EMBASE, Cochrane database, ClinicalTrials.gov, Google Scholar, and the International Continence Society (ICS) website from August to December 2012 in Guangzhou First People's Hospital, Guangzhou, China. Randomized controlled trials (RCTs) comparing the effectiveness and complications of TVT, TOT, and TVT-O were selected. RESULTS: Forty RCTs were included. The TVT and TOT had similar subjective (risk ratio [RR]: 0.99; 95% confidence interval [CI]: 0.93-1.04), and objective cure rates (RR: 0.96; 95% CI: 0.70-1.32). However, TVT had a reduced risk of groin/thigh pain (RR: 0.33; 95% CI: 0.18-0.59). The subjective (RR: 1.02; 95% CI: 0.97-1.06) and objective cure rates (RR: 1.02; 95% CI: 0.99-1.06) of TVT-O were similar to TVT, but TVT had a higher risk of bladder perforations (RR: 2.29; 95% CI: 1.18-4.45). The TVT-O and TOT had similar subjective (RR: 0.99; 95% CI: 0.93-1.06), and objective cure rates (RR: 1.01; 95% CI: 0.95-1.07). However, TVT-O had a lower risk of vaginal erosion rates (RR: 0.16; 95% CI: 0.03-0.89). CONCLUSION: The subjective and objective cure rates of stress urinary incontinence were similar among TVT, TOT, and TVT-O in a medium- to long-term follow up. The TVT had a higher risk of bladder perforation than TVT-O, and a lower risk of groin/thigh pain than TOT, and TVT-O had a lower risk of vaginal erosion rates than TOT.

Genome-wide copy number variations in Oryza sativa L.

BACKGROUND: Copy number variation (CNV) can lead to intra-specific genome variations. It is not only part of normal genetic variation, but also is the source of phenotypic differences. Rice (Oryza sativa L.) is a model organism with a well-annotated genome, but investigation of CNVs in rice lags behind its mammalian counterparts. RESULTS: We comprehensively assayed CNVs using high-density array comparative genomic hybridization in a panel of 20 Asian cultivated rice comprising six indica, three aus, two rayada, two aromatic, three tropical japonica, and four temperate japonica varieties. We used a stringent criterion to identify a total of 2886 high-confidence copy number variable regions (CNVRs), which span 10.28 Mb (or 2.69%) of the rice genome, overlapping 1321 genes. These genes were significantly enriched for specific biological functions involved in cell death, protein phosphorylation, and defense response. Transposable elements (TEs) and other repetitive sequences were identified in the majority of CNVRs. Chromosome 11 showed the greatest enrichment for CNVs. Of subspecies-specific CNVRs, 55.75% and 61.96% were observed in only one cultivar of ssp. indica and ssp. japonica, respectively. Some CNVs with high frequency differences among groups resided in genes underlying rice adaptation. CONCLUSIONS: Higher recombination rates and the presence of homologous gene clusters are probably predispositions for generation of the higher number of CNVs on chromosome 11 by non-allelic homologous recombination events. The subspecies-specific variants are enriched for rare alleles, which suggests that CNVs are relatively recent events that have arisen within breeding populations. A number of the CNVs identified in this study are candidates for generation of group-specific phenotypes.

[Difference in P utilization from organic phosphate between two rice genotypes and its relations with root-secreted acid phosphatase activity].

With two rice genotypes (cv. Zhongbu 51 and Azucena) differing in their root-secreted acid phosphatase activity (APA) under low P condition as test materials, an agar culture experiment was conducted to investigate their P utilization from myo-inositol hexaphosphate (IHP) under conditions of sterilization and inoculating with soil microorganisms. Under sterilization, the shoot dry mass, P absorption and P concentration of test genotypes supplied with hexaphosphate (IHP) as the P source were significantly higher than those with no P supply, but significantly lower than those supplied with inorganic P, indicating that rice plants could partly acquire P from IHP under sterilized condition. The root-secreted APA of the two genotypes was significantly higher under low P than under sufficient P supply, and the higher APA of Zhongbu 51 under low P could be one of the mechanisms of higher P utilization capability of Zhongbu 51 than Azucena under deficient P supply. When supplied with high level IHP (0.96 mmol P x L(-1)), the shoot dry mass, P absorption and P concentration of both Zhongbu 51 and Azucena were higher than those when supplied with low level IHP (0.16 mmol P x L(-1)), indicating that substrate availability could be one of the limiting factors to the utilization of phytate by rice. Inoculation with soil microorganisms had no significant effects on the shoot dry mass, P absorption and P concentration of rice plants, regardless of IHP level and rice genotypes, implying that the utilization of IHP by rice could not be improved via inoculation with soil microorganisms.