The complete mitochondrial genomes of sixteen ardeid birds revealing the evolutionary process of the gene rearrangements

Background

The animal mitochondrial genome is generally considered to be under selection for both compactness and gene order conservation. As more mitochondrial genomes are sequenced, mitochondrial duplications and gene rearrangements have been frequently identified among diverse animal groups. Although several mechanisms of gene rearrangement have been proposed thus far, more observational evidence from major taxa is needed to validate specific mechanisms. In the current study, the complete mitochondrial DNA of sixteen bird species from the family Ardeidae was sequenced and the evolution of mitochondrial gene rearrangements was investigated. The mitochondrial genomes were then used to review the phylogenies of these ardeid birds.

Results

The complete mitochondrial genome sequences of the sixteen ardeid birds exhibited four distinct mitochondrial gene orders in which two of them, named as “duplicate tRNA^Glu–CR” and “duplicate tRNA^Thr–tRNA^Pro and CR”, were newly discovered. These gene rearrangements arose from an evolutionary process consistent with the tandem duplication - random loss model (TDRL). Additionally, duplications in these gene orders were near identical in nucleotide sequences within each individual, suggesting that they evolved in concert. Phylogenetic analyses of the sixteen ardeid species supported the idea that Ardea ibis, Ardea modesta and Ardea intermedia should be classified as genus Ardea, and Ixobrychus flavicollis as genus Ixobrychus, and indicated that within the subfamily Ardeinae, Nycticorax nycticorax is closely related to genus Egretta and that Ardeola bacchus and Butorides striatus are closely related to the genus Ardea.

Conclusions

The duplicate tRNAThr–CR gene order is found in most ardeid lineages, suggesting this gene order is the ancestral pattern within these birds and persisted in most lineages via concerted evolution. In two independent lineages, when the concerted evolution stopped in some subsections due to the accumulation of numerous substitutions and deletions, the duplicate tRNAThr–CR gene order was transformed into three other gene orders. The phylogenetic trees produced from concatenated rRNA and protein coding genes have high support values in most nodes, indicating that the mitochondrial genome sequences are promising markers for resolving the phylogenetic issues of ardeid birds when more taxa are added.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-573) contains supplementary material, which is available to authorized users.     

3种小麦细胞质雄性不育系及其杂种线粒体DNA的RFLP分析

对细胞质分别来源于提莫菲维（Ｔ．ｔｉｍｏｔｈｅｅｖｉｉ）,粘果山羊草（Ａｅ．ｋｏｔｓｃｈｙｉ）,偏凸山羊草（Ａｅ．ｖｅｎｙｒｉｃｏｓａ）的３种普通小麦的雄性不育系,相应保持系和恢复系及其上的ｍｔＤＮＡ用１２个线粒体基因探针进行了ＲＦＬＰ分析,结果为：⑴Ｔ、Ｋ、Ｖ型不育系的ｍｔＤＮＡ在组织结构上存在显著差异;⑵Ｔ、Ｋ、Ｖ不育系的ｍｔＤＮＡ与共同的保持系间显著不同,失测ｍｔＤＮＡ与小麦ｃｍｓ有关;⑶在     

Cohesin结构及功能研究进展

Cohesin是一类在真核生物进化过程中保守的蛋白复合体,由4个重要亚基相互作用形成环状结构,在细胞分裂过程中参与维持染色体的有序排布。在动物中研究发现cohesin还可以作为分子间的连结器介导绝缘子/增强子–启动子间长距离交互,导致基因表达增强或者抑制,但在植物中关于cohesin在调控基因表达和维持染色体构象方面的研究却相对滞后。本文介绍了cohesin的结构特点和主要组成亚基,对调控cohesin在染色质上动态变化的相关因子进行了总结,并结合近年来植物中cohesin的功能研究和动物中cohesin在三维基因组及转录调控中的重要作用,展望了植物中cohesin在转录调控中的潜在功能。     

纳米器件对叶蛋白提取的影响

从植物中提取蛋白质包括机械破碎和离心等一系列步骤,蛋白质在提取液中的溶解度直接影响蛋白提取率和产量.结果表明,用纳米器件处理过的提取液能显著提高叶蛋白的提取率,提升幅度为10％-30％.利用正交试验研究不同提取条件下纳米器件对蛋白可溶性的影响,结果显示浸泡时长(纳米器件浸泡在提取液中的时长)是最关键的已测因素.此外,植物样品的破碎程度也是影响叶蛋白提取率的关键因素之一.     

The spatial and temporal dynamics of rabies in China

Background and Objectives

Recent years have seen a rapid increase in the number of rabies cases in China and an expansion in the geographic distribution of the virus. In spite of the seriousness of the outbreak and increasing number of fatalities, little is known about the phylogeography of the disease in China. In this study, we report an analysis of a set of Nucleocapsid sequences consisting of samples collected through the trial Chinese National Surveillance System as well as publicly available sequences. This sequence set represents the most comprehensive dataset from China to date, comprising 210 sequences (including 57 new samples) from 15 provinces and covering all epidemic regions. Using this dataset we investigated genetic diversity, patterns of distribution, and evolutionary history.

Results

Our analysis indicates that the rabies virus in China is primarily defined by two clades that exhibit distinct population subdivision and translocation patterns and that contributed to the epidemic in different ways. The younger clade originated around 1992 and has properties that closely match the observed spread of the recent epidemic. The older clade originated around 1960 and has a dispersion pattern that suggests it represents a strain associated with a previous outbreak that remained at low levels throughout the country and reemerged in the current epidemic.

Conclusions

Our findings provide new insight into factors associated with the recent epidemic and are relevant to determining an effective policy for controlling the virus.     

基于图像配准分析物种进化关系的新方法

图像配准是图像处理的一个重要技术,可用于分析两幅图像之间的相似度。本文提出了一种基于图像配准分析物种进化关系的新方法:首先利用一阶马尔可夫链方法计算不同基因组序列的寡聚核苷酸转移概率矩阵;然后将转移概率矩阵转换为彩色图像矩阵,并绘制物种两两之间彩色图像矩阵的联合直方图;最后分析联合直方图点集的分布情况,引入直方图点集的散度公式,将其作为相似性测度的标准,从而鉴定物种亲缘关系的远近。100种细菌全基因组的计算结果表明,相较于单基因法或基于基因组寡聚核苷酸频率组分差异信息的方法,本文提出的新方法具有更高的准确度和分辨力,它不仅能够很好地分辨科以下的分类单元,而且对科以上的分类单元同样具有较好的区分效果。该方法有望发展成为物种鉴定及系统发育推断的有效手段。     

Type 2 diabetes caused by reductive redox potential?

<正>Reactive oxygen species arise(ROS)in the mitochondria as byproducts of respiration and oxidase activity and have important roles in many physiological and pathophysiological conditions.The current literature indicate that excessive levels of ROS can cause oxidative stress and that lots of evidences link ROS and oxidative stress to the pathogenesis of type 2 diabetes mellitus(T2DM)and development of complications.Several studies have shown elevated extraand intracellular glucose concentrations result in oxidative stress both in animal models of diabetes and in diabetic patients[1].And ROS can contribute to the development and progression of diabetes and related complications by directly damaging DNA,proteins,and lipids or indirectly activating a number of cellular stress-sensitive pathways to induce damage to tissues such as isletβcells[2].     

Study on genetic variations of PPARα gene and its effects on thermal tolerance in Chinese Holstein

Peroxisome proliferator-activated receptor alpha (PPARα) regulates responses to chemical or physical stress in part by altering expression of genes involved in proteome maintenance. In this research, polymerase chain reaction (PCR) technique was used to amplify 766 and 589 bp fragments of intron 3 and 7 of PPARα gene in Chinese Holstein (n = 771). Sequencing results showed that three novel single nucleotide polymorphisms (SNPs) were identified at position 44087 (G/A), 65550 (G/A), and 65676(G/A) in the PPARα gene. PCR–restriction fragment length polymorphism technology was used to genotype the three SNPs. Association analysis showed that cows with H1H8 (P < 0.05), H2H8 (P < 0.01), H5H7 (P < 0.05), H5H8 (P < 0.05), and H8H8 (P < 0.05) haplotype combinations had lower potassium content in erythrocytes than those with H2H6 haplotype combination. Cows with H1H8, and H8H8 haplotype combinations had lower decrease rate of milk yield than those with H2H6 and H6H8 haplotype combinations (P < 0.05). Cows with H2H8 and H8H8 haplotype combinations had lower rectal temperature than those with H5H8 and H7H7 haplotype combinations (P < 0.05). In conclusion, H8H8 haplotype combination may be advantageous for heat resistance traits in Chinese Holstein cattle.     

基于GIS和RS的赣江上游流域土地利用动态趋势分析

利用赣江上游流域1990、1995、2000、2005和2010年5期的TM影像以及2010年的SPOT影像资料,通过目视解译方法及GIS软件的空间叠加分析功能,获取了研究区土地利用覆被变化数据。在此基础上,结合1990—2010年赣江上游流域的统计资料利用灰色关联分析和主成分分析法进行分析,找出引起土地利用变化的主导因素。结果表明:研究区20年来林地和建设用地总量增加,耕地、草地、水域和未利用地总量减少。相同时期不同类型的土地利用变化的驱动因子不相同,不同时期同一类型土地利用变化的驱动因子也不相同。再利用GM(1,1)灰色预测模型预测了2015—2030年间研究区驱动因素和土地利用情况,研究表明主导因素对土地利用变化的影响与1990—2010年间变化趋势一致。     

以皮肤受累为首发表现的播散性念珠菌病1例并文献复习

目的：播散性念珠菌病是一种致命性真菌感染性疾病,在免疫缺陷患者中发病率逐年增多,报道1例以双下肢多发皮下结节为首发表现,伴有肺及脑受累的播散性念珠菌病,并文献复习播散性念珠菌病的皮肤受累临床表现。方法患者女,37岁。因双下肢多发皮下结节6个月余就诊。有局灶节段性肾小球硬化病史,口服强的松及他克莫司2a余。取患者皮损组织行病理学检查,皮损组织、脓液、血、痰、尿、粪、脑脊液进行真菌镜检及真菌培养,并文献检索统计播散性念珠菌病皮肤受累患者临床特点。结果皮损组织病理见假菌丝,皮损组织、脓液、痰、尿、粪标本直接涂片均见假菌丝并培养出白念珠菌,CT显示肺受累,诊断为播散性念珠菌病,予抗真菌治疗,患者皮损愈合及肺部病灶部分吸收,但因自行停药,最终出现颅内播散。结论以皮损为首发表现的播散性念珠菌病临床罕见,临床诊疗中应重视应用免疫抑制剂患者皮损的组织病理及微生物检查,及早进行诊断和治疗,防止出现系统性播散,从而降低死亡率。