Rice transposable elements are characterized by various methylation environments in the genome

<p>Abstract</p> <p>Background</p> <p>Recent studies using high-throughput methods have revealed that transposable elements (TEs) are a comprehensive target for DNA methylation. However, the relationship between TEs and their genomic environment regarding methylation still remains unclear. The rice genome contains representatives of all known TE families with different characteristics of chromosomal distribution, structure, transposition, size, and copy number. Here we studied the DNA methylation state around 12 TEs in nine genomic DNAs from cultivated rice strains and their closely related wild strains.</p> <p>Results</p> <p>We employed a transposon display (TD) method to analyze the methylation environments in the genomes. The 12 TE families, consisting of four class I elements, seven class II elements, and one element of a different class, were differentially distributed in the rice chromosomes: some elements were concentrated in the centromeric or pericentromeric regions, but others were located in euchromatic regions. The TD analyses revealed that the TE families were embedded in flanking sequences with different methylation degrees. Each TE had flanking sequences with similar degrees of methylation among the nine rice strains. The class I elements tended to be present in highly methylated regions, while those of the class II elements showed widely varying degrees of methylation. In some TE families, the degrees of methylation were markedly lower than the average methylation state of the genome. In two families, dramatic changes of the methylation state occurred depending on the distance from the TE.</p> <p>Conclusion</p> <p>Our results demonstrate that the TE families in the rice genomes can be characterized by the methylation states of their surroundings. The copy number and degree of conservation of the TE family are not likely to be correlated with the degree of methylation. We discuss possible relationships between the methylation state of TEs and their surroundings. This is the first report demonstrating that TEs in the genome are associated with a particular methylation environment that is a feature of a given TE.</p

Cardiovascular disease, chronic kidney disease, and diabetes mortality burden of cardiometabolic risk factors from 1980 to 2010: A comparative risk assessment

Background: High blood pressure, blood glucose, serum cholesterol, and BMI are risk factors for cardiovascular diseases and some of these factors also increase the risk of chronic kidney disease and diabetes. We estimated mortality from cardiovascular diseases, chronic kidney disease, and diabetes that was attributable to these four cardiometabolic risk factors for all countries and regions from 1980 to 2010. Methods: We used data for exposure to risk factors by country, age group, and sex from pooled analyses of population-based health surveys. We obtained relative risks for the effects of risk factors on cause-specific mortality from meta-analyses of large prospective studies. We calculated the population attributable fractions for each risk factor alone, and for the combination of all risk factors, accounting for multicausality and for mediation of the effects of BMI by the other three risks. We calculated attributable deaths by multiplying the cause-specific population attributable fractions by the number of disease-specific deaths. We obtained cause-specific mortality from the Global Burden of Diseases, Injuries, and Risk Factors 2010 Study. We propagated the uncertainties of all the inputs to the final estimates. Findings: In 2010, high blood pressure was the leading risk factor for deaths due to cardiovascular diseases, chronic kidney disease, and diabetes in every region, causing more than 40% of worldwide deaths from these diseases; high BMI and glucose were each responsible for about 15% of deaths, and high cholesterol for more than 10%. After accounting for multicausality, 63% (10·8 million deaths, 95% CI 10·1-11·5) of deaths from these diseases in 2010 were attributable to the combined effect of these four metabolic risk factors, compared with 67% (7·1 million deaths, 6·6-7·6) in 1980. The mortality burden of high BMI and glucose nearly doubled from 1980 to 2010. At the country level, age-standardised death rates from these diseases attributable to the combined effects of these four risk factors surpassed 925 deaths per 100 000 for men in Belarus, Kazakhstan, and Mongolia, but were less than 130 deaths per 100 000 for women and less than 200 for men in some high-income countries including Australia, Canada, France, Japan, the Netherlands, Singapore, South Korea, and Spain. Interpretation: The salient features of the cardiometabolic disease and risk factor epidemic at the beginning of the 21st century are high blood pressure and an increasing effect of obesity and diabetes. The mortality burden of cardiometabolic risk factors has shifted from high-income to low-income and middle-income countries. Lowering cardiometabolic risks through dietary, behavioural, and pharmacological interventions should be a part of the global response to non-communicable diseases. Funding: UK Medical Research Council, US National Institutes of Health. © 2014 Elsevier Ltd

Rice transposable elements are characterized by various methylation environments in the genome-3

<p><b>Copyright information:</b></p><p>Taken from "Rice transposable elements are characterized by various methylation environments in the genome"</p><p>http://www.biomedcentral.com/1471-2164/8/469</p><p>BMC Genomics 2007;8():469-469.</p><p>Published online 20 Dec 2007</p><p>PMCID:PMC2222647.</p><p></p>d into two groups: one ranging from 60 to 200 bp and the other ranging from 200 to 500 bp. Methylation degrees were estimated for the fragments in these two ranges and the fragments in the full range from 60 to 500 bp. Within a 500-bp range from the elements, the proximal regions of both and are markedly methylated compared with the distal regions. This tendency was also found in the individual rice strains, as illustrated for Japonica (including A58, T65, and Nipponbare), Indica (IR36, Kasalath, and #108), and (W107, W593, and W630) along with the overall degrees

Rice transposable elements are characterized by various methylation environments in the genome-2

<p><b>Copyright information:</b></p><p>Taken from "Rice transposable elements are characterized by various methylation environments in the genome"</p><p>http://www.biomedcentral.com/1471-2164/8/469</p><p>BMC Genomics 2007;8():469-469.</p><p>Published online 20 Dec 2007</p><p>PMCID:PMC2222647.</p><p></p>h (no. 5), #108 (no. 6), W107 (no. 7), W593 (no. 8), and W630 (no. 9). In each strain, the two TD samples digested with I (M) and II (H) were loaded and electrophoresed in a 50% polyacrylamide gel. Methylated fragments are denoted by the fact that a fragment of the I-digested sample has no corresponding fragment in the II-digested sample. The sizes from 60 bp to 600 bp are indicated by the arrows

Postoperative Concurrent Daily Low-dose Cisplatin-based Chemoradiation Improves the Prognosis of Patients with Pathologic T2b or N1 Cervical Cancer

Aim: To determine the effectiveness of postoperative concurrent daily low-dose cisplatin-based chemoradiation (CCRT) in patients with high-risk cervical cancer. Patients and Methods: Patients with stage IB, IIA, or IIB cervical cancer who were initially treated with radical hysterectomy and pelvic lymphadenectomy, and were proven to have pelvic lymph node metastasis (pN1) or microscopic involvement of the parametrium (pT2b), participated in this study. Thirty-one patients received adjuvant CCRT with daily low-dose (6-8.5 mg/m2) cisplatin (daily CCRT group). A non-randomised control group of 44 patients received adjuvant radiotherapy alone (RT group). Results: Overall survival (OS) at 4 years was 61% in the RT group and 91% in the daily CCRT group (p=0.004). Hazard ratio for poorer recurrence-free survival (RFS) in the RT group vs. the CCRT group was 7.9 (p=0.006). In the daily CCRT group, daily cisplatin chemotherapy was successfully completed in 27 out of 31 patients, although toxicity of grade &#8805;3 was found in 29% for neutropenia and 17% for gastrointestinal tract toxicity. Conclusion: Postoperative adjuvant CCRT with daily low-dose cisplatin improved RFS and OS of pT2b or pN1 patients, with acceptable compliance

Rice transposable elements are characterized by various methylation environments in the genome-0

<p><b>Copyright information:</b></p><p>Taken from "Rice transposable elements are characterized by various methylation environments in the genome"</p><p>http://www.biomedcentral.com/1471-2164/8/469</p><p>BMC Genomics 2007;8():469-469.</p><p>Published online 20 Dec 2007</p><p>PMCID:PMC2222647.</p><p></p>ine cultivated and wild rice strains. The TD bands smaller than 500 bp in the I-digested samples were counted in this study. Standard deviations were calculated from the data from the nine rice strains

Rice transposable elements are characterized by various methylation environments in the genome-1

<p><b>Copyright information:</b></p><p>Taken from "Rice transposable elements are characterized by various methylation environments in the genome"</p><p>http://www.biomedcentral.com/1471-2164/8/469</p><p>BMC Genomics 2007;8():469-469.</p><p>Published online 20 Dec 2007</p><p>PMCID:PMC2222647.</p><p></p>esponding II-digested samples. Methylation degrees are expressed as the proportion of the methylated bands in the total bands of the I-digested samples. The average methylation degree (24.3%) for the whole genomes from the nine strains was estimated by AFLP analyses as described in the Methods, and is indicated by a dotted line. Standard deviations were calculated with the data from the nine rice strains