Multiple copies of 16s rRNA gene affect the restriction patterns and DGGE profile as revealed by analysis of genome database

The use of 16S rRNA gene has been a "golden" method to determine the diversity of microbial communities in environmental samples, phylogenetic relationships of prokaryotes and taxonomic position of newly isolated organisms. However due to the presence of multiple heterogeneous 16S rRNA gene copies in many strains, the interpretation of microbial ecology via 16S rRNA sequences is complicated. Purpose of present paper is to demonstrate the extent to which the multiple heterogeneous 16S rRNA gene copies affect RFLP patterns and DGG E profiles by using the genome database. In present genome database, there are 782 bacterial strains in total whose genomes have been completely sequenced and annotated. Among the total strains, 639 strains (82%) possess multiple 16S rRNA gene copies, 415 strains (53%) whose multiple copies are heterogeneous in sequences as revealed by alignment, 236 strains (30%) whose multiple copies show different restrict patterns by CSP61 + Hinfl, MspI + Rsal or HhaI as analyzed in silico. Polymorphisms of the multiple copies in certain strains were further characterized by G + C% and phylogentic distances based on the sequences of V3 region, which are linked to DGGE patters. Polymorphisms of a few strains were shown as examples. Using artificial communities, it is demonstrated that the presence of multiple heterogeneous 16S rRNA gene copies potentially leads to over-estimation of the diversity of a community. It is suggested that care must be taken when interpreting 16S rRNA-based RFLP and DGGE data and profiling an environmental community.     

Alpneumines A–H,new anti-melanogenic indole alkaloids from Alstonia pneumatophora

Eight new indole alkaloids, alpneumines A–H (1–8) were isolated from the Malaysian Alstonia pneumatophora (Apocynaceae) and their structures were determined by MS and 2D NMR spectroscopic methods. Alpneumines E and G (5 and 7), vincamine, and apovincamine showed anti-melanogenesis in B16 mouse melanoma cells.     

Effects of organic matter incorporation on nitrous oxide emissions from rice-wheat rotation ecosystems in China

Organic matter addition is thought to be an important regulator of nitrous oxide (N₂O) emissions from croplands. Contradictory effects, however, were reported in previous studies. To investigate the effects of crop residue management on N₂O emissions from rice-wheat rotation ecosystems, we conducted field experiments at three sites (Suzhou, Wuxi and Jiangdu) in the Yangtze River Delta, using static chamber and gas chromatography methods. Our data show that N₂O emissions throughout the rice season from plots treated with wheat straw application at a high rate (WS) prior to rice transplanting (1.1–2.0 kg N ha^?1) were significantly lower (P?<?0.05) than those from the control plots without organic matter addition or added with wheat straw at a moderate rate (1.6–2.9 kg N ha^?1). Furthermore, the WS treatments had a residual inhibitory effect on N₂O emissions in the following non-rice season, which consistently resulted in significantly lower emissions (P?<?0.05) compared to the control treatments (2.2–3.1 vs. 3.9–5.6 kg N ha^?1). In comparison to the control treatments, the WS treatments reduced both the seasonal and annual direct emission factors of the applied nitrogen (EF_d) by 50–68% (mean: 57%). The addition of compost (aerobically composted rice or wheat straw harvested in the last rotation) reduced the seasonal and annual EF_ds by 29–32%. Over the entire rice-wheat rotation cycle, annual N₂O emissions from the fertilized fields at the three sites ranged from 3.3?±?0.3 to 16.8?±?0.6 kg N ha^?1, with a coefficient of variation (CV) of 61%. Similarly, the EF_ds during the rice-wheat rotation cycle ranged from 0.4% to 2.5%, with a CV of 67%. These high spatial variations might have been related to: variations in soil properties, such as texture and soil organic carbon; management practices, such as straw treatments (i.e., compost versus fresh straw) and weather conditions, such as precipitation and rainfall distribution. Our results indicate that the incorporation of fresh wheat straw at a high rate during the rice season is an effective management practice for the mitigation of N₂O emissions in rice-wheat rotation systems. Whether this practice is also effective in reducing the overall global warming potential of net N₂O, CH₄ and CO₂ emissions needs to be seen through further studies.     

The crystal structure of a TIR domain from Arabidopsis thaliana reveals a conserved helical region unique to plants

Plants use a highly evolved immune system to exhibit defense response against microbial infections. The plant TIR domain, together with the nucleotide‐binding (NB) domain and/or a LRR region, forms a type of molecule, named resistance (R) proteins, that interact with microbial effector proteins and elicit hypersensitive responses against infection. Here, we report the first crystal structure of a plant TIR domain from Arabidopsis thaliana (AtTIR) solved at a resolution of 2.0 Å. The structure consists of five β‐strands forming a parallel β‐sheet at the core of the protein. The β‐strands are connected by a series of α‐helices and the overall fold mimics closely that of other mammalian and bacterial TIR domains. However, the region of the αD‐helix reveals significant differences when compared with other TIR structures, especially the αD3‐helix that corresponds to an insertion only present in plant TIR domains. Available mutagenesis data suggest that several conserved and exposed residues in this region are involved in the plant TIR signaling function.     

53BP1 promotes ATM activity through direct interactions with the MRN complex

The Mre11/Rad50/Nbs1 (MRN) complex has a central function in facilitating activation of the ATM protein kinase at sites of DNA double‐strand breaks (DSBs). However, several other factors are also required in human cells for efficient signalling through MRN and ATM, including the tumour suppressor proteins p53‐binding protein 1 (53BP1) and BRCA1. In this study, we investigate the functions of these mediator proteins in ATM activation and find that the presence of 53BP1 and BRCA1 can amplify the effects of MRN when interactions between MRN and ATM are compromised. This effect is dependent on a direct interaction between MRN and the tandem breast cancer carboxy‐terminal (BRCT) repeats in 53BP1, and is accompanied by hyper‐phosphorylation of both Nbs1 and 53BP1. We also find that the BRCT domains of 53BP1 affect the overall structure of 53BP1 multimers and that this structure is important for promoting ATM phosphorylation of substrates as well as for the repair of DNA DSBs in mammalian cells.     

汉滩病毒膜蛋白重组腺病毒的构建表达及免疫效果研究

探讨利用腺病毒载体作为汉滩病毒基因工程疫苗载体的可行性。通过PCR扩增,得到完整的汉滩病毒76-118株M片段编码区,将该片段克隆入质粒pAdTrackCMV的CMV启动子下游,得到阳性克隆pAdTrackCMV—M。Pmel线性化的阳性克隆与腺病毒骨架载体pAdEasy—1共转化大肠杆菌BJ5183,经同源重组后得到重组病毒pAdEasy—M。pAdEasy—M经PacI线性化后,脂质体介导转染293细胞,经Western—blot检测表明,G1、G2基因在293细胞中得到表达。重组病毒免疫BALB／c小鼠,产生了具有一定中和活性的抗体。该研究为进一步研制以腺病毒为活载体的工程疫苗奠定了基础。     

吸水链霉菌NND-52-C基因工程宿主载体系统的构建

吸水链霉菌NND-52-C菌株是大环内酯类抗生素-阿扎霉素B的高产菌株。采用原生质体转化技术,将来自变铅青链霉菌TK24菌株的pU702质粒转化吸水链霉菌NND-52-C菌株的原生质体,建立了吸水链霉菌NND-52-C菌株的基因工程宿主载体系统。确定了NND-52-C菌株原生质体制备和再生的条件,其原生质体形成率达到10^8／mL,再生率约为0．2％,转化率为10^2-10^3个转化子／μg质粒DNA。     

动态检测血管紧张素Ⅱ刺激后STAT3信号核转位及其与衰老的关系

为了动态观察复制性衰老细胞中血管紧张素Ⅱ(AngⅡ)激活人信号转导与转录活化因子3(hSTAT3)信号转导途径的核转位情况及该途径在细胞衰老过程中的变化。将载体pMS1-hSTAT3上的目的基因STAT3序列亚克隆到pEGFP-C3报告载体中,构建出pEGFP-hSTAT3质粒选择人胚肺二倍体成纤维细胞WI-38细胞株进行细胞培养,通过脂质体(Effectene)转染的方法,将pEGFP-STAT3质粒分别转染至19代,42代WI-38细胞中;在激光共聚焦显微镜下动态观察血管紧张素Ⅱ激活STAT3的核转位的变化及不同代数的差别．结果显示AngⅡ刺激细胞后,出现活化的STAT3在胞核内聚集现象,并且在19代细胞中15分钟开始出现,30—45分钟左右时达到高峰;42代细胞中30分钟左右开始出现,50—60分钟左右达到高峰。因此我们认为AngⅡ刺激WI-38细胞,能出现hSTAT3信号转导的核内集聚现象;并且随着WI-38细胞传代数的增加,STAT3信号转导入核时间延迟。说明随着细胞的复制性衰老,通过STAT3通路转导的信号活性逐渐降低,最终影响细胞的增殖,可能是促进细胞衰老的原因之一。     

Dendritic cells: sentinels against pathogens

Dendritic cells (DCs) are the most potent antigen-presenting cells, and are regarded as "natural adjuvants" for the induction of primary T or T-dependent immunity. DCs in the peripheral sites capture and process antigens. Encounter of exogenous or endogenous stimuli mature the function of DCs, and they thus acquire T-cell stimulatory capacity and distinct chemotactic behavior which enables them to migrate to lymphoid tissue. In the secondary lymphoid organs, they present antigens to T- and B-cells and stimulate their proliferation. Dendritic cells are also involved in tolerance induction, in particular, to self antigens. DCs also play a key role in the transmission of many pathogens, and therefore may become targets for designing new therapies. DCs have been manipulated in vitro and in vivo for cancer immunotherapy. In this article, we provide a concise overview of DC biology and its current and future role in clinical settings.     

Photoaffinity labeling identifies the substrate-binding site of mammalian squalene epoxidase

Squalene epoxidase (SE) catalyzes the conversion of squalene to (3S)-2,3-oxidosqualene. Photolabeling and site-directed mutagenesis were performed on recombinant rat SE (rrSE) in order to identify the location of the substrate-binding site and the roles of key residues in catalysis. Truncated 50-kDa rrSE was purified and photoaffinity labeled by competitive SE inhibitor (Ki=18.4 microM), [(3)H]TNSA-Dza. An 8-kDa CNBr/BNPS-skatole peptide was purified and the first 24 amino acids were sequenced by Edman degradation. The sequence PASFLPPSSVNKRGVLLLGDAYNL corresponded to residues 388-411 of the full-length rat SE. Three nucleophilic residues (Lys-399, Arg-400, and Asp-407) were labeled by [(3)H]TNSA-Dza. Triple mutants were prepared in which bulky groups were used to replace the labeled charged residues. Purified mutant enzymes showed lower enzymatic activity and reduced photoaffinity labeling by [(3)H]TNSA-Dza. This constitutes the first evidence as to the identity of the substrate-binding site of SE.