The red bayberry genome and genetic basis of sex determination.

Morella rubra, red bayberry, is an economically important fruit tree in south China. Here, we assembled the first high-quality genome for both a female and a male individual of red bayberry. The genome size was 313-Mb, and 90% sequences were assembled into eight pseudo chromosome molecules, with 32 493 predicted genes. By whole-genome comparison between the female and male and association analysis with sequences of bulked and individual DNA samples from female and male, a 59-Kb region determining female was identified and located on distal end of pseudochromosome 8, which contains abundant transposable element and seven putative genes, four of them are related to sex floral development. This 59-Kb female-specific region was likely to be derived from duplication and rearrangement of paralogous genes and retained non-recombinant in the female-specific region. Sex-specific molecular markers developed from candidate genes co-segregated with sex in a genetically diverse female and male germplasm. We propose sex determination follow the ZW model of female heterogamety. The genome sequence of red bayberry provides a valuable resource for plant sex chromosome evolution and also provides important insights for molecular biology, genetics and modern breeding in Myricaceae family.

Incorporating adipose tissue into a CT-based deep learning nomogram to differentiate granulomas from lung adenocarcinomas.

We aimed to build and validate a computed tomography (CT)-based deep learning nomogram for discriminating granulomas from lung adenocarcinomas. A retrospective study of 1,159 patients with solitary lung nodules from three institutions in China who underwent pre-operative lung CT scans was performed. The patients were divided into one training, one validation, one test, and two external validation cohorts. Deep learning features were extracted from CT images. The least absolute shrinkage and selection operator (LASSO) regression model was used for dimension reduction and feature selection. Logistic regression analysis showed that age, gender, intranodular and perinodular (IPN) features, and adipose features were the significant predictors of malignancy presence (all p < 0.05). The nomogram was built by incorporating these four factors and achieved better diagnostic accuracy than the single-factor model. The nomogram demonstrates satisfactory discrimination and calibration. In addition, decision curve analysis revealed the considerable clinical usefulness of the nomogram.

A study on the inhibitory effect of polysaccharides from Radix ranunculus ternati on human breast cancer MCF-7 cell lines.

The objective of this paper was to study the in vitro anti-breast cancer activity of polysaccharides from Radix ranunculus ternati. Different concentrations of polysaccharide extracts were selected, and MTT assay and flow cytometry (FCM) were used to investigate their growth-inhibitory and apoptosis-inducing effects on human breast cancer MCF-7 cell lines. Radix ranunculus ternati polysaccharides had varying degrees of effects on the growth of human breast cancer MCF-7 cell lines, and the differences were significant compared with the blank control group. FCM showed that the polysaccharides can induce apoptosis. In addition, it can also enhance NK cell activity. Radix ranunculus ternati polysaccharides have a relatively good in-vitro anti-breast cancer activity.

Association of Wnt3A gene variants with non-syndromic cleft lip with or without cleft palate in Chinese population.

OBJECTIVE: non-syndromic cleft lip with or without cleft palate (NSCLP) is one of the most common birth defects all over the world. Both genetic and environmental factors may contribute to NSCLP. Recent studies have demonstrated that Wnt/ß-catenin signalling pathway is required for lip and palate formation. WNT family may play an important role in the development of NSCLP. This study aimed to evaluate the association between Wnt3A gene polymorphisms and NSCLP in Chinese population from Northwest China. DESIGN: 216 patients with NSCLP and 233 normal controls were genotyped for two SNPs of Wnt3A by PCR-RFLP. Both SNPs genotype frequencies were analysed between cases group and controls group. RESULTS: the frequencies of rs752107 TT and rs3121310 AA were significantly higher in NSCLP cases group (7.4%, 15.3%) than that in controls group (2.1%, 9.5%) with p-value=0.013, 0.014, corrected p value (p-corr) <0.05 and with odds ratio (OR)=3.49, 95% confidence interval [CI]: 1.244-9.79, OR=2.27, 95% CI: 1.17-4.38, respectively; the frequency of rs3121310 GA was also higher in NSCLP cases group (57.4%) than in controls group (52.0%) with p-value=0.042 and OR=1.56 (95% CI: 1.02-2.39). And the frequency of rs752107 TT of Wnt3A showed higher risk in female patients, while the frequency of A allele of rs3121310 showed stronger association in male patients. CONCLUSIONS: this is the first report that two SNPs of Wnt3A (rs752107 and rs3121310) are significantly associated with NSCLP in Chinese population. These findings provide a context for understanding the genetic aetiology of NSCLP.

Association of mtDNA D-loop polymorphisms with risk of gastric cancer in Chinese population.

The aim of present study was to evaluate the association of common polymorphisms detected in mitochondrial DNA (mtDNA) D-loop region (mononucleotide repetitive D310, single nucleotide polymorphism (SNP) D16521) with susceptibility to gastric cancer (GC) in northwestern Chinese population. A total of 180 GC patients and 218 healthy controls were investigated by using PCR- denaturing high performance liquid chromatography (DHPLC) assay. Genotype and allele distributions and haplotype construction were analyzed in case-control study. We found D310 and D16521 heteroplasmy were significantly different between GC cases and controls (p < 0.05), and D16521 homoplasmy showed association with histological grade of GC (p < 0.05). Haplotype 7C/T, 8C/C and 9C/C had significant association with GC risk implied from analysis of D310 and D16521. Taken together, these findings suggested that mtDNA D-Loop polymorphisms and haplotypes may contribute to genetic susceptibility to GC in Chinese population.