SSR-based association mapping of salt tolerance in cotton (Gossypium hirsutum L.).

The identification of simple sequence repeat (SSR) markers associated with salt tolerance in cotton contributes to molecular assisted selection (MAS), which can improve the efficiency of traditional breeding. In this study, 134 samples of upland cotton cultivars were selected. The seedling emergence rates were tested under 0.3% NaCl stress. A total of 74 SSR markers were used to scan the genomes of these samples. To identify SSR markers associated with salt tolerance, an association analysis was performed between salt tolerance and SSR markers using TASSEL 2.1, based on the analysis of genetic structure using Structure 2.3.4. The results showed that the seedling emergence rates of 134 cultivars were significantly different, and 27 salt-sensitive and 10 salt-tolerant cultivars were identified. A total of 148 loci were found in 74 SSR markers involving 246 allelic variations, which ranged from 2 to 7 with an average of 3.32 per SSR marker. The gene diversity ranged from 0.0295 to 0.4959, with the average being 0.2897. The polymorphic information content ranged from0.0290 to 0.3729, with the average being 0.2381. This natural population was classified into two subgroups by Structure 2.3.4, containing 89 and 45 samples, respectively. Finally, eight SSR sites associated with salt tolerance ware found through an association analysis, with the rate of explanation ranging from 2.91 to 7.82% and an average of 4.32%. These results provide reference data for the use MAS for salt tolerance in cotton.

SET8 expression is associated with overall survival in gastric cancer.

SET8, a member of the SET domain-containing methyl-transferase, has been implicated in various biological processes. In this study, SET8 was immunostained in 100 samples of gastric cancer tissues and semi-quantified using the HSCORE method to determine the predictive value of SET8 expression levels for gastric cancer outcome. The relationship between SET8 expression and the 5-year survival rate of gastric cancer patients was assessed. High expression of SET8 was associated with a shorter survival time in gastric cancer patients, and the level of SET8 expression was found to be an independent predictor of gastric cancer outcome (relative risk = 1.939; 95% confidence interval = 1.025-3.668; P = 0.042). Analysis of SET8 levels may help in the identification of patient subgroups that are at high risk for poor disease outcomes.

Analysis of upland cotton (Gossypium hirsutum) response to Verticillium dahliae inoculation by transcriptome sequencing.

Verticillium wilt is one of the main diseases in cotton (Gossypium hirsutum), severely reduces yield and fiber quality, and is difficult to be con-trolled effectively. At present, the molecular mechanism that confers resistance to this disease is unclear. Transcriptome sequencing is an important method to detect resistance genes, explore metabolic pathways, and study resistance mechanisms. In this study, the transcriptome of a disease-resistant inbred cot-ton line inoculated with Verticillium dahliae was sequenced. A total of 126,402 unigenes were obtained using de novo assembly and data analysis, 99,712 (78.88%) of which were annotated into the Nr, Nt, Swiss-Prot, KEGG, COG, and GO databases. The expression patterns of 16 candidate disease-resis-tance genes showed that some genes were upregulated soon after V. dahliae inoculation and others were upregulated later, which may indicate instanta-neous basal defense and lagged specific defense, respectively. We conducted a preliminary analysis of the transcriptome database, which will contribute to further research regarding the cloning of disease-resistance genes.

Single nucleotide polymorphisms in the mitochondrial displacement loop and age-at-onset of non-small cell lung cancer.

The associations between single nucleotide polymorphisms (SNPs) in the displacement loop (D-loop) of mitochondrial DNA (mtDNA) and cancer risk and disease outcome have been extensively analyzed. We investigated the association between age-at-onset and SNPs in the mitochondrial D-loop using a population-based series of non-small cell lung cancer (NSCLC) patients. The D-loop region of mtDNA from NSCLC patients was amplified and sequenced. The age-at-onset curve of NSCLC patients was calculated using the Kaplan-Meier method at each SNP site and values were compared using the log-rank test. The SNP sites of nucleotides 200G/A and 16362T/C were identified to determine their association with age-at-onset of NSCLC using the log-rank test. The nucleotide 207G/A was identified for its association with age-at-onset at a borderline significance level (P = 0.060). We found that genetic polymorphisms in the D-loop were predictive markers for age-at-onset in NSCLC patients. Accordingly, the analysis of genetic polymorphisms in the mitochondrial D-loop can be used to identify NSCLC patient subgroups at high risk of early onset.

Optimization of chloroplast microsatellite PCR conditions and primer screening for endangered Rheum officinale, Rheum palmatum, and Rheum tanguticum.

Chloroplast microsatellite primers were developed in order to provide more population genetic information of endangered Rheum officinale, R. palmatum, and R. tanguticum for conservation. The dried roots and rhizomes of these plants are important in traditional Chinese medicine. The results showed that the optimum concentrations of Mg(2+), Taq DNA polymerase, dNTPs, template DNA, and primers in a 25-µL reaction system were 2.0 mM, 1.0 U, 0.10 mM, 20 ng, and 0.8 µM, respectively. Fourteen of 53 primer combinations were chosen for their high clarity and repetition in three species, and their annealing temperatures ranged from 56 to 58°C. These primers and the optimized polymerase chain reaction system may provide a tool for understanding the demography and genetic variation of these endangered plants.

Fetal fibronectin detection for preterm birth prediction.

To study preterm birth prediction based on fetal fibronectin (fFN) in pregnant women, we randomly selected 124 patients. Vaginal posterior fornix secretions were analyzed using fFN quick test strips. Leucorrhea routine samples were collected to detect bacterial vaginosis, mycoplasma, and chlamydia. Delivery data at 7 days, 14 days, 34 weeks, and 37 weeks were documented and the sensitivity, specificity, positive predictive value, and negative predictive value were analyzed. Of the 124 cases, we found 2, 4, 10, and 18 cases of maternity within 7 days, 14 days, 34 weeks, and 37 weeks, respectively. The sensitivity, specificity, positive predictive value, and negative predictive value were as follows: 100, 77.8, 6.9, and 100% for 7 days; 75, 78.3, 10.3, and 98.9% for 14 days; 50.0, 78.9, 17.2, and 94.7% for 34 weeks; 33.3, 78.3, 20.7, and 87.4% for 37 weeks, respectively. Except for 18 preterm births, 23 cases were fFN-positive, 17 cases had lower genital tract infection. Eighty-three cases were fFN-negative, of which 18 cases had the lower genital tract infections. This difference was statistically significant (P < 0.05). Eighteen cases (14.5% of the pregnant women) had preterm birth. Ten cases delivered within 34 weeks. The negative predictive value and recent predictive value of fFN testing were higher; the positive predictive value was limited due to the impact of lower genital tract infection. The fFN-positive patients need timely clinical processing. During the pregnancy, monitoring of fFN changes and early detection of abnormalities help to reduce perinatal morbidity and mortality.