Divergent DNA methylation contributes to duplicated gene evolution and chilling response in tea plants

The tea plant (Camellia sinensis) is a thermophilic cash crop and contains a highly duplicated and repeat-rich genome. It is still unclear how DNA methylation regulates the evolution of duplicated genes and chilling stress in tea plants. We therefore generated a single-base-resolution DNA methylation map of tea plants under chilling stress. We found that, compared with other plants, the tea plant genome is highly methylated in all three sequence contexts, including CG, CHG and CHH (where H = A, T, or C), which is further proven to be correlated with its repeat content and genome size. We show that DNA methylation in the gene body negatively regulates the gene expression of tea plants, whereas non-CG methylation in the flanking region enables a positive regulation of gene expression. We demonstrate that transposable element-mediated methylation dynamics significantly drives the expression divergence of duplicated genes in tea plants. The DNA methylation and expression divergence of duplicated genes in the tea plant increases with evolutionary age and selective pressure. Moreover, we detect thousands of differentially methylated genes, some of which are functionally associated with chilling stress. We also experimentally reveal that DNA methyltransferase genes of tea plants are significantly downregulated, whereas demethylase genes are upregulated at the initial stage of chilling stress, which is in line with the significant loss of DNA methylation of three well-known cold-responsive genes at their promoter and gene body regions. Overall, our findings underscore the importance of DNA methylation regulation and offer new insights into duplicated gene evolution and chilling tolerance in tea plants.     

LRRC4 inhibits glioblastoma cell proliferation, migration, and angiogenesis by downregulating pleiotropic cytokine expression and responses

Leucine-rich repeat C4 (LRRC4) has been shown to inhibit glioma cell proliferation, however, little is known about the mechanism(s) underlying the action of LRRC4. Here, we show that two glioblstoma U251 cell clones stably expressing LRRC4 were established. LRRC4 expression significantly inhibited the expression of some cytokines and their receptors determined by microarray and Western blot assays, and dramatically reduced cytokine-induced AP-1, NF-kB, and CyclinD1 activation in glioma cells. Furthermore, LRRC4 expression in glioma cells significantly downregulated spontaneous and cytokine-induced expression of K-RAS and phosphorylation of c-Raf, ERK, AKT, NF-kBp65, p70S6K, and PKC, suggesting that LRRC4 inhibited receptor tyrosine kinase (RTK) signaling pathways. Moreover, treatment with bFGF, IGF1, or IGF2 stimulated LRRC4(-/-), but not the LRRC4(+), glioma cell proliferation, indicating that LRRC4 mitigated cytokine-stimulated proliferation in glioma cells. In addition, treatment of LRRC4(-/-) glioma cells with EGF, IGF2, or PDGF promoted long distance mobilization, but induced little migration in LRRC4(+) glioma cells, suggesting that LRRC4 retarded cytokine-promoted glioma cell migration in vitro. Finally, human vessel endothelial cells (ECV304) treated with VEGF grew, aligned and formed hollow tube-like structures in vitro. In contrast, LRRC4(+) ECV304 treated with VEGF failed to form vessel-tube structures. Collectively, LRRC4 expression inhibited the expression of some growth factors, cytokines and their receptors, and the capacity of glioma cells responding to cytokine stimulation, leading to inhibition of glioma cell proliferation. Conceivably, induction of LRRC4 expression may provide new intervention for human glioma in the clinic.     

Diterpenoids from the Whole Plants of Ajuga nipponensis and Their Inhibition of RANKL-Induced Osteoclastogenesis

Two new diterpenoids, ajudecunoid A ( 1 ) and ajudecunoid B ( 14 ), along with thirteen known diterpenoids, were isolated from the whole plants of Ajuga nipponensis Makino. Their structures were elucidated by the extensive spectroscopic analysis (UV, IR, MS, and NMR). The absolute configurations of ajudecunoid A ( 1 ) and ajudecunoid B ( 14 ) were defined through analysis of X-ray crystallography. Fifteen compounds were evaluated for inhibition of the formation of osteoclasts in bone marrow-derived macrophages (BMM) cells. Two neo-clerodane diterpenoids ajuganipponin B ( 5 ) and (12S)-6α,19-diacetoxy-18-chloro-4α-hydroxy-12-tigloyloxy-neo-clerod-13-en-15,16-olide ( 12 ) showed significant inhibition of osteoclastogenesis with IC₅₀ values of 0.88 and 0.79 μM, respectively. Here we firstly reported diterpenoids with anti-osteoclastogenesis activity from A. nipponensis.     

芒颖大麦草对菱镁矿粉尘污染的生态适应性

采用盆栽试验,向土壤表面投加不同量(0、1％、5％、10％、15％、20％、30％)的菱镁矿粉尘,研究土壤理化性质和芒颖大麦草对镁的耐性.结果表明:菱镁矿粉尘施加到土壤表面时,可快速形成结皮.当菱镁粉尘比例超过20％时,土壤理化性质发生明显变化,表现为pH显著升高,电导率逐渐降低,有机质含量先降低后升高;芒颖大麦草的叶绿素含量随着镁粉尘含量的增加呈现先增加后降低的趋势,而可溶性蛋白含量随着镁粉尘含量的增加呈现先增加后降低再升高的趋势;芒颖大麦草具有较强的耐镁特性,土壤中镁浓度达到4.61 g·kg-1时,芒颖大麦草仍生长良好.芒颖大麦草适宜作为菱镁矿区撂荒地生态恢复的植物种.     

长江三峡库区蝶类群落的物种获得率、小生境占有率及相对多度

研究于 1998～ 2 0 0 3年在库区 10个区县 ,35个调查点进行。研究时 ,库区蝴蝶的生活环境被划分为 80个小生境 ,设置样带6 6 1条 ;调查期间获得 (Sampled)蝴蝶 331种 ,10 780只个体。报道三峡库区蝴蝶群落的部分参数 :2 5 3种蝴蝶的小生境占有率低于 10 % ,占有 4 0 %以上小生境的蝴蝶只有 7种 ;在 6 0条以上样带都获得的蝴蝶有 16种 ,而在 10条以下样带内获得的蝴蝶 2 19种 ,占总数的 6 6 .2 % ;优势种 2 1个 (6 .3% ) ,常见种 12 5个 (37.8% ) ,少见种 10 3个 (31.1% ) ,罕见种 82个 (2 4 .8% ) ;相对多度高于 1%的种类 2 2个 ,仅占总数的 6 .6 % ;个体数分布的规律接近对数级数法则。三峡库区蝶类现在的分布反映了库区生境破碎化的结果 ,意味着适宜的生境斑块周围分布不适宜生境 ,种群受到面积、隔离、边缘等多种效应的影响 ,形成了现有的物种多样性及其空间格局     

超连续谱激光可见谱段致人眼眩目效应研究

本文采用超连续谱激光光源滤除其红外部分仅输出可见谱段部分,在不超过国家安全标准允许的最大辐照量条件下,以正入射方式照射人眼后,记录并分析在明、暗适应条件下中心极限视力恢复时间、中心近极限视力恢复时间和视觉后像持续时间,明确超连续谱激光可见谱段对人眼的眩目效果。明适应下激光照射0.1 s导致人眼中心极限视力恢复时间为31~119 s,中心近极限视力恢复时间为19~76 s;暗适应下激光照射0.1 s导致人眼中心极限视力恢复时间为26~223 s,中心近极限视力恢复时间为13~123 s;明、暗适应下导致人眼眩目效应的最小功率密度值分别为0.055 mW/cm^2和0.005 mW/cm^2。结果表明,超连续谱激光可见谱段对人眼有良好的眩目效果,可导致数十秒至数百秒的中心视力下降,随着照射功率密度增高,眩目效应增强,显示出较好的量效关系,且相同功率密度时暗适应下人眼的眩目效果优于明适应。该研究探究了明、暗适应条件下超连续谱激光对人眼眩目效应,明确了超连续谱激光与人眼眩目的量效关系。     

拉萨河谷上段江孜沙棘Hippophea gyantsensis(Rousi) Lian种群的海拔梯度性变异

江孜沙棘[Hippophea gyantsensis(Rousi)Lian]是青藏高原特有的一种广生态幅的小乔木,在拉萨河谷地区的海拔3500~4200m范围内均有分布。前人工作多集中在江孜沙棘果实的开发利用方面,对其基础生态学研究较少。本研究旨在探讨江孜沙棘沿海拔梯度的群落组成和表型变异的规律。为此,在拉萨河谷上段沿海拔梯度由东向西设置了4个样带:3850m、3950m、4050m和4200m,每个样带设置2至3个10m×10m的样方进行研究。首先,详细记录了每个样方内林下维管植物的物种组成、样方内的沙棘盖度、海拔、样方与河岸的实际距离,并用DCA[detrended correspondence analysis(去势对应分析)]排序方法对群落及其组成物种进行排序分析。随机抽取了每个样方内的20个江孜沙棘植株个体,测定其胸径、基径、株高和叶片长度,用回归分析法分析这些变量和海拔之间的关系。研究结果表明,江孜沙棘在拉萨河谷内的主要生境分为4种类型,即:河边砾石滩地、河阶草滩、河边草甸和河边林缘,样方排序结果主要受海拔的影响;同时,江孜沙棘植株的基径、胸径和高度都随着海拔的升高而显著减小,而叶片长度与海拔之间无显著相关。本文研究结果表明,对江孜沙棘而言,海拔所代表的综合环境因子对其分布和表型有显著的影响,而局部光照可能也是影响其表型特征的重要生态因子。     

Genetic associations with coronary heart disease: Meta-analyses of 12 candidate genetic variants

Aims

The aim of this study was to evaluate the combined contribution of 12 genetic variants to the risk of coronary heart disease (CHD).

Methods

Through a comprehensive literature search for genetic variants involved in the CHD association study, we harvested a total of 10 genes (12 variants) for the current meta-analyses. These genes consisted of GPX1 (rs1050450), PPARD (rs2016520), ALOX15 (rs34210653), SELPLG (rs2228315), FCGR2A (rs1801274), CCL5 (rs2107538), CYP1A1 (rs4646903), TP53 (rs1042522), CX37 (rs1764391), and PECAM1 (rs668, rs12953, and rs1131012).

Results

A total of 45 studies among 23,314 cases and 28,430 controls were retrieved for the meta-analyses of 12 genetic variants. The results showed a significant association between the GPX1 rs1050450 polymorphism and CHD (odd ratio (OR) = 1.61, 95% confidence interval (CI) = 1.25–2.07, P = 0.0002). Other meta-analyses of the rest 11 variants suggested a lack of association with the risk of CHD.

Conclusion

Our results confirmed that GPX1 rs1050450 was associated with susceptibility to CHD in Chinese and Indian populations.     

两种色型黄粉虫酚氧化酶原的cDNA克隆、生物信息学分析及表达水平检测

酚氧化酶是黑色素合成和昆虫免疫的关键酶, 通常以无活性的酚氧化酶原形式存在。为给黄粉虫Tenebrio molitor遗传分化和免疫防御研究提供参考, 本研究采用PCR和RACE技术克隆了黄、 黑两种色型黄粉虫幼虫的酚氧化酶原基因Tm-ppo, 对其cDNA序列及其推导的氨基酸序列进行生物信息学分析, 采用实时荧光定量PCR检测其在两种色型黄粉虫不同发育阶段mRNA表达水平上的动态变化。结果表明： 从黄、 黑两种色型黄粉虫幼虫中克隆出的两个Tm-ppo cDNA序列全长均为2 199 bp, 碱基序列一致性为99%, 包含一个2 055 bp的开放阅读框, 编码684个氨基酸, 它们的编码蛋白有3个氨基酸差异： 第176位（P→A）、 256位（V→A）和648位（I→M）。这两个基因分别被命名为Tm-ppo-1和Tm-ppo-2 （GenBank登录号分别为JX987235和JX987234）。 Tm-ppo-1和Tm-ppo-2编码的酚氧化酶原异构体蛋白（分别为Tm-PPO-1和Tm-PPO-2）存在一个可能的酚氧化酶原水解活化位点（R50~F51残基之间）和一个双铜结合中心（第196~239位残基和第344~411位残基）; 同时含有一个类似巯基酯区域的序列（第579~588位残基）及一个C 末端保守基序（第634~645位残基）; 但它们无氨基端疏水信号肽序列, 也不存在跨膜区域。Tm-PPO-1和Tm-PPO-2的二级结构由大量的α 螺旋、 β-折叠和无规则卷曲组成; 三级结构分为前导域（第16~66位残基）、 不相邻的功能域Ⅰ（第3~15位残基和第67~181位残基）、 功能域Ⅱ（第182~419位残基）和功能域Ⅲ（第420~679位残基）4部分。此外, Tm-ppo-1和Tm-ppo-2在黄、 黑两种色型黄粉虫的各发育期均有表达, 并且不同发育阶段的mRNA表达水平呈现明显的变化规律： 幼虫期﹥成虫期﹥蛹期。同时, 环境温度对Tm-ppo-1和Tm-ppo-2的mRNA表达具有显著影响： 与常温对照组（25~30℃）相比, 42℃暴露24 h和48 h的两种色型黄粉虫幼虫、 蛹和成虫的mRNA表达量明显下调。相同试验条件下, 黑色型黄粉虫幼虫和成虫的Tm-ppo-2 mRNA表达量明显高于黄色型幼虫和成虫的Tm-ppo-1 mRNA表达量, 但两种色型黄粉虫蛹的Tm-ppo异构体表达量无显著差异。本研究为进一步探讨黄粉虫的遗传分化和免疫防御提供了有益参考。     

A genome-wide association study on growth traits in orange-spotted grouper (<Emphasis Type="Italic">Epinephelus coioides</Emphasis>) with RAD-seq genotyping

The orange-spotted grouper, Epinephelus coioides, is one of the most popular fish in China and Southeast Asian countries because of its important economic value. However, molecular mechanism underlying the growth of orange-spotted grouper has never been fully understood. Herein, we performed a genome-wide association study (GWAS) on a natural population of 198 individuals aiming to screen the whole genome of orange-spotted grouper for identification of growth-related loci by restrictionsite associated DNA sequencing. In this research, 261,366 single nucleotide polymorphisms (SNPs) were developed, in which 110 SNPs were identified to be correlated with growth and 20 SNPs were further confirmed to be associated with both body weight and total length. From these identified SNPs, we annotated a total of 34 genes, including adgrb2, csnkza1, cers5, col22a1, creb5, dnd1, dzank1, dnai1, npy2r, fat3, lrrk2, lrp5, map3k9, and so on. Among these candidate genes, npy2r (neuropeptide Y receptor Y2) was reported to play a critical role in growth of the orange-spotted grouper. In addition, population structure, principal component analysis, kinship matrix and linkage disequilibrium were examined to verify the accuracy and reliability of our GWAS results. Our data will also provide a valuable genetic resource for further marker-assisted selection program to improve growth quality in groupers.