Genome-wide analysis of salinity-stress induced DNA methylation alterations in cotton (Gossypium hirsutum L.) using the Me-DIP sequencing technology.

Cytosine DNA methylation is a significant form of DNA modification closely associated with gene expression in eukaryotes, fungi, animals, and plants. Although the reference genomes of cotton (Gossypium hirsutum L.) have been publically available, the salinity-stress-induced DNA methylome alterations in cotton are not well understood. Here, we constructed a map of genome-wide DNA methylation characteristics of cotton leaves under salt stress using the methylated DNA immunoprecipitation sequencing method. The results showed that the methylation reads on chromosome 9 were most comparable with those on the other chromosomes, but the greatest changes occurred on chromosome 8 under salt stress. The DNA methylation pattern analysis indicated that a relatively higher methylation density was found in the upstream2k and downstream2k elements of the CDS region and CG-islands. Almost 94% of the reads belonged to LTR-gspsy and LTR-copia, and the number of methylation reads in LTR-gypsy was four times greater than that in LTR-copia in both control and stressed samples. The analysis of differentially methylated regions (DMRs) showed that the gene elements upstream2k, intron, and downstream2k were hypomethylated, but the CDS regions were hypermethylated. The GO (Gene Ontology) analysis suggested that the methylated genes were most enriched in cellular processes, metabolic processes, cell parts and catalytic activities, which might be closely correlated with response to NaCl stress. In this study, we completed a genomic DNA methylation profile and conducted a DMR analysis under salt stress, which provided valuable information for the better understanding of epigenetics in response to salt stress in cotton.

Genome-wide identification and expression analysis of CIPK genes in diploid cottons.

Calcineurin B-like protein-interacting protein kinase (CIPK) plays a key regulatory role in the growth, development, and stress resistance of plants by combining with phosphatase B subunit-like protein. In the present study, CIPK genes were identified in the whole genomes of diploid cottons and their sequences were subjected to bioinformatic analyses. The results demonstrated that the CIPK gene family was unevenly distributed in two diploid cotton genomes. Forty-one CIPKs were identified in the D genome, mainly located on chromosomes 9 and 10, whereas thirty-nine CIPKs were identified in the A genome, mainly located on chromosomes 8 and 11. Based on the gene structures, CIPKs in cotton could be classified into two types: one that is intron-rich and the other that has few introns. Phylogenetic analysis revealed that the CIPK gene family members in cotton had close evolutionary relationships with those of the dicotyledonous plants, such as Arabidopsis thaliana and poplar. The analysis of transcriptome sequence data demonstrated that there were differences in gene expression in different tissues, indicating that the expression of the CIPKs in cotton had spatio-temporal specificity. The expression analysis of CIPKs under abiotic stresses (drought, salt, and low temperature) in different tissues at trefoil stage demonstrated that these stresses induced the expression of CIPKs.

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.

Germline mutations of DICER1 in Chinese women with BRCA1/BRCA2-negative familial breast cancer.

Germline mutations in identified breast cancer susceptibility genes account for less than 20% of Chinese familial breast cancers. Dicer is an essential component of the microRNA-producing machinery; germline mutations of DICER1 have been confirmed in familial pleuropulmonary blastoma, ovarian sex cord-stromal tumors, and other cancers. Low expression of DICER1 is frequently detected in breast cancer. However, whether germline mutations of DICER1 occur in familial breast cancers remain unknown. Sixty-five breast cancer probands from BRCA1/BRCA2-negative Chinese breast cancer families were screened for germline mutations in DICER1. In addition, 100 unrelated healthy females were enrolled as controls. A polymerase chain reaction sequencing assay was used to screen for mutations in coding regions and at the exon-intron boundaries of DICER1. All variants in introns were evaluated using the NNSplice software to determine the potential splicing effect. A total of 12 germline variants were found, including 11 variants in introns and 1 variant in the 3'-non-coding region. Four variants (IVS8-205 C>T, IVS11+131 delGAAA, IVS16+42 delTA, and IVS19+160 T>C) were novel. Three variants (IVS11+105 C>T, IVS16+42 delTA, and 6095 T>A) may affect splice sites. None of the observed variants appeared to be disease-related, suggesting that germline mutations in DICER1 are rare or absent in familial breast cancer patients.

Association between a single nucleotide polymorphism of the XRCC1 gene and hepatocellular carcinoma susceptibility in the Chinese Han population.

The human X-ray repair cross-complementing protein 1 (XRCC1) gene is a potentially gene determining hepatocellular carcinoma (HCC) susceptibility. The purpose of this study was to evaluate the association between XRCC1 and susceptibility to HCC. The association of XRCC1 polymorphisms with HCC susceptibility was investigated in 460 HCC patients and 463 controls using the created restriction site-polymerase chain reaction method. Our results indicate that the c.1471G>A variant could be detected and that the allele and genotype frequencies were statistically different between cases and controls. The AA genotype was strongly associated with increased HCC susceptibility as compared with the GG wild genotype (OR = 2.214, 95%CI = 1.493-3.283, χ(2) = 15.97, P < 0.0001). In addition, significantly increased HCC susceptibility was also found in a dominant and recessive model (P < 0.01). The allele A could contribute to HCC susceptibility compared with the G allele (OR = 1.480, 95%CI = 1.224-1.789, χ(2) = 16.44, P = 0.0001). Results from this study indicate that the XRCC1 c.1471G>A polymorphism is associated with HCC susceptibility in the Chinese Han population. Future studies on larger populations are essential to confirm this association.

Right ventricular and septal anomalies complicated by subacute bacterial endocarditis.

We report the case of a 31-year-old woman with no history of heart disease. She came to the hospital with fever, dyspnea, palpitation, and edema of the lower extremities. She was found to have aortic, mitral, and pulmonary valve insufficiency, and the initial diagnosis was subacute bacterial endocarditis. At surgery, we replaced the aortic and mitral valves with mechanical prostheses and the pulmonary valve with a bioprosthesis. The prostheses were soaked intraoperatively with fluconazole and the heart chambers were irrigated with povidone-iodine to prevent infection by bacteria and fungi. We also found 2 previously unsuspected anomalies: 1 was a muscular bundle that divided the right ventricle into 2 chambers, and the other was a ventricular septal defect, 1.0 cm in diameter. We resected the muscular bundle and patched the septal defect. The patient had an uneventful postoperative course and was in New York Heart Association functional class I at the 15-month follow-up visit. We speculate that this patient's congenital anomalies made the heart more susceptible to damage from the endocarditis. Therefore, any patient who has infective endocarditis should also be examined closely for congenital defects.

Open-heart surgery in 48 patients via a small right anterolateral thoracotomy.

To limit the trauma to the chest and to achieve a pleasing cosmetic result, we used 2 types of right anterolateral thoracotomy in 48 patients who required open-heart surgery: 1 was a curved incision along the lower edge of the right breast in women with developed breasts; the other was a slanted incision for men and children. These surgical procedures took place between July 1996 and November 1997. Intraoperatively, a right atriotomy was used to repair 11 atrial septal defects and 11 ventricular septal defects, 2 combined atrial and ventricular septal defects, 1 case of a single atrium, and 1 partial atrioventricular canal. A right ventricular outflow tract incision was used to repair 7 ventricular septal defects and 7 ruptured aortic sinus aneurysm. A combination of a right atriotomy and right ventricular outflow tract incision was used for 2 repairs of combined atrial and ventricular septal defects, 3 radical corrections of tetralogy of Fallot, and 2 radical corrections of trilogy of Fallot. A combined right and interatrial septal incision was used for 6 mitral valve replacements and 1 mitral valvuloplasty. Smooth bypass cannulation and satisfactory intracardiac exposure were achieved with the right anterolateral thoracotomy. There was no complication or mortality directly related to the incision. We believe that the right anterolateral thoracotomy is safer and more effective than the median sternotomy for many common congenital and acquired heart diseases. The thoracotomy causes less trauma and results in a cosmetic appearance that is more acceptable to the patient.

Co-expression of hepatitis B virus antigens by a non-defective adenovirus vaccine vector.

Adenovirus type 7 vaccine strain was engineered to express foreign antigens from both the E3 early promoter in the E3 region and the major late promoter inserted between the E4 region and the right inverted terminal repeat. This multiple expression vector was used to express hepatitis B core antigen (HBcAg), hepatitis B e antigen (HBeAg), and hepatitis B surface antigen (HBsAg). The gene inserted in the E3 region was derived from the core gene of the hepatitis B virus genome. When the precore region was present, an immunoreactive group of proteins with molecular weights ranging from 15,000 to 19,000 was secreted into the media. Velocity sedimentation centrifugation of media and lysates from cells infected with recombinants containing the core gene with the precore region resulted in peaks of HBeAg at the top of the gradient where authentic HBeAg should be found. In addition to the core gene in the E3 region, the surface antigen gene of hepatitis B virus was inserted behind the major late promoter in the E4 region resulting in an adeno-hepatitis recombinant virus capable of expressing both the core gene and the HBsAg cells. Cells infected with the adeno-hepatitis recombinants could also be stained with peroxidase-conjugates after reacting to antibody against HBcAg. Inoculation of dogs with the recombinant viruses which contained the core gene, with and without the precore sequence, resulted in a significant antibody response to HBcAg/HBeAg. The dogs also produced a significant antibody response to HBsAg as well as neutralizing antibody to adenovirus.

Seroepidemiology of adult diarrhea rotavirus in China, 1977 to 1987.

In 1982, large outbreaks of diarrhea that were caused by group B adult diarrhea rotavirus (ADRV) occurred throughout the People's Republic of China. Until 1982, group B rotavirus had never been associated with disease in humans. To determine whether ADRV was a new virus introduced in 1982 or had been present before that time, we examined antibody titers of ADRV in gamma globulin (pooled immunoglobulin) pools that were prepared during 1977 to 1987 in four cities in the People's Republic of China (Shanghai, Lanzhou, Wuhan, and Chandu). ADRV antibodies were assayed by using a blocking enzyme-linked immunosorbent assay. Antibodies were present in most Chinese gamma globulins tested, including those collected in Shanghai before the 1982 epidemic, and absent from American reference pools. The highest titers of antibody to ADRV (3,200) were found in gamma globulins collected in 1983 in Shanghai just after the epidemic, and these were fourfold higher than titers present in the preceding years. The quality of the gamma globulins stored for up to 12 years was tested by measuring levels of immunoglobulin G to group A rotavirus; these were equally high in gamma globulin pools prepared in the United States and in all samples from the People's Republic of China. Serum samples from patients from an outbreak of ADRV had elevated titers to ADRV 3 and 16 months after the onset of symptoms. These findings, as well as other epidemiologic findings on ADRV, suggest that the organism is an important and continuing cause of diarrhea in the People's Republic of China, was present before the first epidemic in 1982, and represents a risk to surrounding populations in Asia.

Morphological evidence for identifying the viruses of hemorrhagic fever with renal syndrome as candidate members of the Bunyaviridae family. Brief report.

Thin section immuno-electron microscopy has been successfully applied to investigate and identify the classical and mild form of HFRS viruses isolated in the People's Republic of China. The results showed that all the 8 strains studied (derived from different parts of China, adapted in different cell lines) share a common morphology and morphogenesis. Essentially, the viruses possess characteristics of members of the Bunyaviridae Family, however, differing by a larger size and size variation and formation of cytoplasmic viral inclusions.