Genetic variants modify the effect of age on APOE methylation in the Genetics of Lipid Lowering Drugs and Diet Network study

Although apolipoprotein E (APOE) variants are associated with age-related diseases, the underlying mechanism is unknown and DNA methylation may be a potential one. With methylation data, measured by the Infinium Human Methylation 450 array, from 993 participants (age ranging from 18 to 87 years) in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) study, and from Encyclopedia of DNA Elements (ENCODE) consortium, combined with published methylation datasets, we described the methylation pattern of 13 CpG sites within APOE locus, their correlations with gene expression across cell types, and their relationships with age, plasma lipids, and sequence variants. Based on methylation levels and the genetic regions, we categorized the 13 APOE CpG sites into three groups: Group 1 showed hypermethylation (> 50%) and were located in the promoter region, Group 2 exhibited hypomethylation (< 50%) and were located in the first two exons and introns, and Group 3 showed hypermethylation (> 50%) and were located in the exon 4. APOE methylation was negatively correlated with gene expression (minimum r = −0.66, P = 0.004). APOE methylation was significantly associated with age (minimum P = 2.06E-08) and plasma total cholesterol (minimum P = 3.53E-03). Finally, APOE methylation patterns differed across APOE ε variants (minimum P = 3.51E-05) and the promoter variant rs405509 (minimum P = 0.01), which further showed a significant interaction with age (P = 0.03). These findings suggest that methylation may be a potential mechanistic explanation for APOE functions related to aging and call for further molecular mechanistic studies.     

LTR retrotransposon dynamics in the evolution of the olive (Olea europaea) genome

Improved knowledge of genome composition, especially of its repetitive component, generates important information for both theoretical and applied research. The olive repetitive component is made up of two main classes of sequences: tandem repeats and retrotransposons (REs). In this study, we provide characterization of a sample of 254 unique full-length long terminal repeat (LTR) REs. In the sample, Ty1-Copia elements were more numerous than Ty3-Gypsy elements. Mapping a large set of Illumina whole-genome shotgun reads onto the identified retroelement set revealed that Gypsy elements are more redundant than Copia elements. The insertion time of intact retroelements was estimated based on sister LTR’s divergence. Although some elements inserted relatively recently, the mean insertion age of the isolated retroelements is around 18 million yrs. Gypsy and Copia retroelements showed different waves of transposition, with Gypsy elements especially active between 10 and 25 million yrs ago and nearly inactive in the last 7 million yrs. The occurrence of numerous solo-LTRs related to isolated full-length retroelements was ascertained for two Gypsy elements and one Copia element. Overall, the results reported in this study show that RE activity (both retrotransposition and DNA loss) has impacted the olive genome structure in more ancient times than in other angiosperms.     

Life history strategy and adult and larval behavior of Macrodiplosis selenis (Diptera: Cecidomyiidae), a species that induces leaf‐margin fold galls on deciduous Quercus (Fagaceae)

Life historical, behavioral and ecological traits of Macrodiplosis selenis, which induces leaf‐margin fold galls on Quercus serrata, Q. mongolica and Q. dentata (Fagaceae) in Japan and South Korea, were studied. Daily activity and larval development indicate that M. selenis is a diurnal and univoltine gall midge. In April, females lay their eggs both on upper and under surfaces of fresh leaves. The duration of the egg stage varies from 5 to 9 days, depending on daily temperatures. Hatched larvae crawl to the upper surface of the leaf margin, where they start to induce galls. Larvae become full‐grown in October, drop to the ground in November and overwinter in cocoons on the ground, while larvae of congeners mature in May and drop to the ground in June. A relatively long period of the second larval stadium from July to October on the host trees seems to be effective for M. selenis in avoiding summer mortalities caused by predation and aridity on the ground and by ectoparasitoids that attack mature larvae or pupae on the host leaves. The spatial distribution pattern of M. selenis leaf galls is contagious and the mean gall density per leaf is significantly correlated with the mean crowding. This study adds new insights of life history strategy and adult and larval behavioral pattern to the ecological knowledge of gall midges, and these kinds of information are essential for further studies of M. selenis population dynamics and interactions with other Quercus‐associated herbivores.     

兴安落叶松天然林碳储量及其碳库分配特征

兴安落叶松天然林作为大兴安岭林区的主要植被类型,在森林生态系统碳循环中具有重要的作用。在大兴安岭林区选择不同林龄的兴安落叶松天然林,调查其乔木、灌草、枯落物和土壤,并结合已建立的单木异速生长方程分别计算其碳储量,以期为明确该地区碳库动态及其碳库分配特征提供参考。结果表明,兴安落叶松天然林总碳储量随林龄的增加逐渐增大,由幼龄林到过熟林分别为140.46、186.63、208.64、308.62和341.03 Mg C/hm2,整体表现为碳汇,这主要与乔木碳储量随林龄的增加逐渐增大有关;乔木碳库的变化范围为45.44—212.67 Mg C/hm2,且其占总碳储量的比例也随林龄的增加逐渐增大,由幼龄林的32.60%到过熟林的62.36%;灌草碳储量占总碳储量的比例较小,仅为0.48%—0.93%;枯落物碳库在过熟林中较多,为26.11Mg C/hm2,这与过熟林较少的人为干扰有关;土壤碳储量以幼龄林最小,成熟林最高,分别为78.06和131.93 Mg C/hm2,但这与我国其他地区天然林相比均较低,这与该地区较浅的土壤发生层有关;土壤碳储量随林龄的变化并不明显,但其占总碳储量的比例却随林龄的增加逐渐减小,由幼龄林的56.01%减小到过熟林的29.35%。     

采伐对红松种群结构与动态的影响

红松是我国长白山阔叶红松林的主要建群种,受森林采伐的影响,种群数量急剧下降,现已被列为国家二级保护植物。通过绘制种群静态生命表、生存函数、存活曲线和径级分布图,研究原始林,15%择伐、40%择伐和皆伐后恢复的天然次生林内,红松种群结构和动态的变化规律。结果表明:(1)采伐干扰对红松种群的波动周期影响不大,15%的择伐强度可以提高红松种群的生存期望。(2)原始林和15%择伐林内红松种群存活曲线均为DeeveyⅡ型,种群处于稳定期;40%择伐林内存活曲线介于DeeveyⅡ型和DeeveyⅢ型之间,种群由稳定期向成熟期过渡;皆伐林内存活曲线为DeeveyⅠ型,种群处在增长期。(3)原始阔叶红松林林、15%择伐林和40%择伐林内,红松种群径级结构均呈稳定的倒J型,且在幼树阶段均存在生长更新的停滞现象;与原始林相比,15%择伐林内幼树比例略有下降;40%择伐林和皆伐迹地,随采伐强度的增加,幼树比例明显增大。(4)方差分析表明,4个种群的生存过程差异较大,采伐干扰对红松种群生存过程的影响达到显著水平。