大熊猫9个BAC的测序、注释和进化分析

本文构建了相当于大熊猫10倍基因组覆盖度的BAC文库, 并随机挑选了其中9个BAC进行测序和组装, 9个BAC的选择满足更多基因更少重复序列的原则. 这9个BAC的组装将为评估基于新一代Illumina GA测序技术的大熊猫全基因组测序及组装的准确性提供有效资源. 运用同源比对和从头预测的方法, 对9个BAC, 共约878 kb的序列进行了基因和重复序列的注释以及进化分析. 一共预测到12个蛋白编码基因, 其中, 7个基因匹配到同源基因的功能注释. 这7个基因平均大小约41 kb, 编码区平均大小约1.2 kb, 每个基因平均约含6个外显子. 同时预测到7个tRNA基因. 大约27%的序列被注释为重复序列. 同时, 基于邻接法, 构建了包含人、小鼠、狗、猫以及大熊猫5个物种的物种进化树, 结果显示狗的基因与其他4个物种相比距大熊猫最近. 本实验结果提供了大熊猫9个BAC的详细序列及注释信息, 为对大熊猫的研究提供了数据资源.     

Pedogenesis, permafrost, and soil moisture as controlling factors for soil nitrogen and carbon contents across the Tibetan Plateau

We investigated the main parameters [e.g. mean annual air temperature , mean annual soil temperature, mean annual precipitation, soil moisture (SM), soil chemistry, and physics] influencing soil organic carbon (C_org), soil total nitrogen (N_t) as well as plant available nitrogen (N_min) at 47 sites along a 1200 km transect across the high‐altitude and low‐latitude permafrost region of the central‐eastern Tibetan Plateau. This large‐scale survey allows testing the hypothesis that beside commonly used ecological variables, diversity of pedogenesis is another major component for assessing carbon (C) and nitrogen (N) cycling. The aim of the presented research was to evaluate consequences of permafrost degradation for C and N stocks and hence nutrient supply for plants, as the transect covers all types of permafrost including heavily degraded areas and regions without permafrost. Our results show that SM is the dominant parameter explaining 64% of C_org and 60% of N variation. The extent of the effect of SM is determined by permafrost, current aeolian sedimentation occurring mostly on degraded sites, and pedogenesis. Thus, the explanatory power for C and N concentrations is significantly improved by adding CaCO₃ content (P=0.012 for C_org; P=0.006 for N_t) and soil texture (P=0.077 for C_org; P=0.015 for N_t) to the model. For soil temperature, no correlations were detected indicating that in high‐altitude grassland ecosystems influenced by permafrost, SM overrides soil temperature as the main driving parameter at landscape scale. It was concluded from the current study that degradation of permafrost and corresponding changes in soil hydrology combined with a shift from mature stages of pedogenesis to initial stages, have severe impact on soil C and plant available N. This may alter biodiversity patterns as well as the development and functioning of the ecosystems on the Tibetan Plateau.     

Circle of Willis variation in a complex stroke presentation: a case report

Background  

The impact of circle of Willis anatomical variation upon the presentation of stroke is probably underrecognised.     

Transition of healthy to diseased synovial tissue in rheumatoid arthritis is associated with gain of mesenchymal/fibrotic characteristics

The healthy synovial lining layer consists of a single cell layer that regulates the transport between the joint cavity and the surrounding tissue. It has been suggested that abnormalities such as somatic mutations in the p53 tumor-suppressor gene contribute to synovial hyperplasia and invasion in rheumatoid arthritis (RA). In this study, expression of epithelial markers on healthy and diseased synovial lining tissue was examined. In addition, we investigated whether a regulated process, resembling epithelial to mesenchymal transition (EMT)/fibrosis, could be responsible for the altered phenotype of the synovial lining layer in RA. Synovial tissue from healthy subjects and RA patients was obtained during arthroscopy. To detect signs of EMT, expression of E-cadherin (epithelial marker), collagen type IV (indicator of the presence of a basement membrane) and alpha-smooth muscle actin (alpha-sma; a myofibroblast marker) was investigated on frozen tissue sections using immunohistochemistry. Fibroblast-like synoviocytes (FLSs) from healthy subjects were isolated and subjected to stimulation with synovial fluid (SF) from two RA patients and to transforming growth factor (TGF)-beta. To detect whether EMT/fibrotic markers were increased, expression of collagen type I, alpha-sma and telopeptide lysylhydroxylase (TLH) was measured by real time PCR. Expression of E-cadherin and collagen type IV was found in healthy and arthritic synovial tissue. Expression of alpha-sma was only found in the synovial lining layer of RA patients. Stimulation of healthy FLSs with SF resulted in an upregulation of alpha-sma and TLH mRNA. Collagen type I and TLH mRNA were upregulated after stimulation with TGF-beta. Addition of bone morphogenetic protein (BMP)-7 to healthy FLS stimulated with SF inhibited the expression of alpha-sma mRNA. The finding that E-cadherin and collagen type IV are expressed in the lining layer of healthy and arthritic synovium indicates that these lining cells display an epithelial-like phenotype. In addition, the presence of alpha-sma in the synovial lining layer of RA patients and induction of fibrotic markers in healthy FLSs by SF from RA patients indicate that a regulated process comparable to EMT might cause the alteration in phenotype of RA FLSs. Therefore, BMP-7 may represent a promising agent to counteract the transition imposed on synoviocytes in the RA joint.     

利用重组自交系群体对黄瓜侧枝相关性状进行QTL定位分析

侧枝与黄瓜(Cucumis sativus)产量有密切关系. 本实验利用侧枝长势较弱、萌发较早的华北类型品系S94和侧枝长势较强、萌发较晚的欧洲类型品系S06构建的224个F6:7家系进行黄瓜侧枝相关性状的研究. 利用已构建的重组自交系群体遗传图谱, 使用软件WinQTLCart 2.5进行复合区间定位. 在2006年秋和2007年春两季, 共检测到4个侧枝相关性状(侧枝均长LBAL、侧枝总长LBTL、侧枝数目LBN和第一侧枝节位FLBN)的36个QTL, 单个QTL的贡献率在3.1%(lbtl2.1, 春季)~32.3%(lbn2.3, 春季)之间. 结果显示, 4个不同性状的11个QTL (lbal1.1, lbtl1.1, lbn1.2, flbn1.2等)在两季中都聚集在第1连锁群e23m18d~ME23EM6c之间(7.4 cM), 并且在第2连锁群的S94A1~ME4SA4a之间(13.9 cM)也检测到了4个不同性状的15个QTL (lbal2.1, lbtl2.1, lbn2.1和flbn2.1等). 两季共有21个QTL贡献率超过10%, 其中lbn2.3的贡献率(春季32.3%, LOD=18.4)为最大, lbtl1.3(秋季26.2%, LOD=17.4; 春季26.9%, LOD=17.9)在两季的位置和贡献率都稳定. 这些基因座为将来进行QTL精细定位提供了参考, 同时利用其紧密连锁(<10 cM)的特异标记(CMBR40, F, CS30, S94A1, CSWTA11B)可进行黄瓜侧枝性状的分子标记辅助育种.     

DNA methyltransferase homologue TRDMT1 in Plasmodium falciparum specifically methylates endogenous aspartic acid tRNA

In eukaryotes, cytosine methylation regulates diverse biological processes such as gene expression, development and maintenance of genomic integrity. However, cytosine methylation and its functions in pathogenic apicomplexan protozoans remain enigmatic. To address this, here we investigated the presence of cytosine methylation in the nucleic acids of the protozoan Plasmodium falciparum. Interestingly, P. falciparum has TRDMT1, a conserved homologue of DNA methyltransferase DNMT2. However, we found that TRDMT1 did not methylate DNA, in vitro. We demonstrate that TRDMT1 methylates cytosine in the endogenous aspartic acid tRNA of P. falciparum. Through RNA bisulfite sequencing, we mapped the position of 5-methyl cytosine in aspartic acid tRNA and found methylation only at C38 position. P. falciparum proteome has significantly higher aspartic acid content and a higher proportion of proteins with poly aspartic acid repeats than other apicomplexan pathogenic protozoans. Proteins with such repeats are functionally important, with significant roles in host-pathogen interactions. Therefore, TRDMT1 mediated C38 methylation of aspartic acid tRNA might play a critical role by translational regulation of important proteins and modulate the pathogenicity of the malarial parasite.