Failure of DNA barcoding in discriminating Calligonum species

We tested the effectiveness of four DNA barcoding markers (rbcL, matK, ITS and trnLF region) for land plants in identifying Calligonum species. High quality sequences were obtained for rbcL, matK and trnLF with the universal primers whereas ITS sequences were of poor quality. RbcL and matK were highly conservative and failed in species discrimination. When rbcL, matK and trnLF were combined, the species resolution was up to 6.25%. Low sequence variation resulted in poorly resolved tree topologies. Among the sixteen sampled species, only three were recovered as a monophyletic group. Our results show that although DNA barcoding is an important tool for species identification, it fails in discriminating Calligonum species. Further research will be needed to develop markers capable to discriminate species in this taxonomy complicated and recently diverged genus.     

Plasmodium chabaudi AS: Distinct CD4+CD25+Foxp3+ regulatory T cell responses during infection in DBA/2 and BALB/c mice

Malaria infections display variation patterns of clinical course and outcome. Although CD4⁺CD25⁺Foxp3⁺ regulatory T (Treg) cells play an essential role in immune homeostasis, the immune regulatory roles involved in malaria infection remains to be elucidated. Herein, we compared the disparity in Treg cells response during the course of blood stage Plasmodium chabaudi chabaudi AS (P. c chabaudi AS) infection in DBA/2 and BALB/c mice. BALB/c mice initiated a Th1/Th2 profile respond to P. c chabaudi AS infection, but DBA/2 mice failed to control P. c chabaudi AS infection and almost of them died post-peak parasitemia. At the peak parasitemia, we found that higher proportion of Treg cells with elevated Foxp3 expression in DBA/2 than in BALB/c mice. We used anti-CD25 mAb to deplete Treg cells and found that the survival time and rate were prolonged in DBA/2 mice treated with anti-CD25 mAb. Treatment with anti-CD25 mAb in vivo led to enhanced pro-inflammation responses and Foxp3 expression decline on Treg cells. In contrast, after DBA/2 was treatment with anti-IL-10R mAb, IL-10R blockade in vivo caused excessive pro-inflammation responses and Foxp3 expression loss on CD4⁺CD25⁺ T cells. Earlier death was found in all of DBA/2 mice with anti-IL-10R mAb. It suggested that IL-2 and IL-10 signal involved in maintaining Foxp3 expression on Treg cells. In all, the moderate suppressive activity of Treg cells may facilitate resistance to P. c chabaudi AS infection.     

以小时为步长的大兴安岭典型林分地表死可燃物含水率模型预测及外推精度

地表死可燃物含水率是火险天气和火行为预报中的重要指标.本研究基于时滞平衡含水率法(Nelson和Simard方法)及气象要素回归方法,于2010年9—10月对黑龙江省大兴安岭地区盘古林场不同郁闭度的山杨-白桦混交林、红皮云杉纯林,以及采伐迹地(原1∶1樟子松-白桦混交林)地表死可燃物含水率进行以小时为步长的连续测定,建立其预测模型,得到预测误差,并使用相应的模型对其他林分地表死可燃物含水率进行外推精度分析.结果表明:采用Nelson平衡含水率法构建的地表死可燃物含水率变化模型的平均绝对误差、平均相对误差和均方误差根(0.0154、0.104和0.0226)低于Simard法(0.0185、0.117和0.0256)和气象要素回归法(0.0222、0.150和0.0331).在外推效果方面,气象要素回归法的平均绝对误差、平均相对误差和均方误差根(0.0410、0.0300和0.0740)低于Simard法(0.610、0.492和0.846),但前两者均高于Nelson法(0.034、0.021和0.0660),说明以小时为步长的时滞平衡含水率法,尤其是Nelson法适用于大兴安岭地区所测林分.外推虽不能降低误差,但有助于提高现有模型应用至不同林分条件或大尺度范围内的地表死可燃物含水率预测精度和利用率.模型建模和外推误差与不同树种和郁闭度条件差异有关,研究时应根据不同林分和地点选择合适的平衡含水率模型.     

Glucocorticoid receptor and sequential P53 activation by dexamethasone mediates apoptosis and cell cycle arrest of osteoblastic MC3T3-E1 cells

Glucocorticoids play a pivotal role in the proliferation of osteoblasts, but the underlying mechanism has not been successfully elucidated. In this report, we have investigated the molecular mechanism which elucidates the inhibitory effects of dexamethasone on murine osteoblastic MC3T3-E1 cells. It was found that the inhibitory effects were largely attributed to apoptosis and G1 phase arrest. Both the cell cycle arrest and apoptosis were dependent on glucocorticoid receptor (GR), as they were abolished by GR blocker RU486 pre-treatment and GR interference. G1 phase arrest and apoptosis were accompanied with a p53-dependent up-regulation of p21 and pro-apoptotic genes NOXA and PUMA. We also proved that dexamethasone can't induce apoptosis and cell cycle arrest when p53 was inhibited by p53 RNA interference. These data demonstrate that proliferation of MC3T3-E1 cell was significantly and directly inhibited by dexamethasone treatment via aberrant GR activation and subsequently P53 activation.     

The outer membrane usher forms a twin-pore secretion complex

The PapC usher is an outer membrane protein required for assembly and secretion of P pili in uropathogenic Escherichia coli. P pilus biogenesis occurs by the chaperone/usher pathway, a terminal branch of the general secretory pathway. Periplasmic chaperone-subunit complexes target to the PapC usher for fiber assembly and secretion through the usher to the cell surface. The molecular details of pilus biogenesis at the usher, and protein secretion across the outer membrane in general, are unclear. We studied the structure and oligomeric state of PapC by gel filtration, dynamic light scattering, and electron microscopy and image analysis. Two-dimensional crystals of wild-type PapC and a C-terminal deletion mutant of PapC were produced by reconstituting detergent purified usher into E.coli lipids. PapC formed a dimer both in detergent solution and in the phospholipid bilayer. Cryo-electron microscopy revealed that the usher forms a twin-pore complex. Removal of the C-terminal domain did not change the basic shape of the PapC molecule, but altered the dimeric association of the usher, suggesting that the C terminus forms part of the dimerization interface. The overall molecular size (11 nm), pore size (2 nm), and twin-pore configuration of PapC resemble that of the Tom40 complex, a mitochondrial outer membrane protein translocase.     

Two novel loci for pollen sterility in hybrids between the weedy strain Ludao and the Japonica variety Akihikari of rice (Oryza sativa L.)

Partial pollen sterility has been observed in hybrid progeny derived from a japonica cultivar, Akihikari and a weedy strain, Ludao, which naturally grows in Jiangsu province of east China. Cytological and histological analyses revealed that pollen abortion occurred largely at the bicellular pollen stage, primarily due to the gradual disaggregation of generative and vegetative cells. A genome-wide analysis was further carried out in a backcross population of Akihikari //Ludao/Akihikari using a total of 118 simple sequence repeat (SSR) markers and an expressed sequence tag (EST) marker distributed on the entire rice linkage map. Two loci controlling hybrid pollen sterility, designated as S33(t) and S34(t), were located on chromosomes 3 and 11, respectively. Both loci were putatively different from all the previously reported gametophyte genes and hybrid pollen sterility loci. Interaction between the Ludao and Akihikari alleles at each of the two loci resulted in reduction of fertility in the pollens carring the Ludao alleles. To map the precise location of the major locus, S33(t), we selected 165 plants of the backcross population with pollen fertility higher than 80.0%, and assayed the recombinant events surrounding the S33(t) locus using newly developed SSR markers. The S33(t) was delimited to an 86 kb region between SSR markers RM15621 and RM15627. Sequence analysis of this region indicated that there were ten open reading frames. These results will be valuable for cloning this gene and marker-assisted transferring of the corresponding neutral allele in rice breeding programs. Furthermore, the origin of the weedy strain Ludao is discussed.     

vGNM: a better model for understanding the dynamics of proteins in crystals

The dynamics of proteins are important for understanding their functions. In recent years, the simple coarse-grained Gaussian Network Model (GNM) has been fairly successful in interpreting crystallographic B-factors. However, the model clearly ignores the contribution of the rigid body motions and the effect of crystal packing. The model cannot explain the fact that the same protein may have significantly different B-factors under different crystal packing conditions. In this work, we propose a new GNM, called vGNM, which takes into account both the contribution of the rigid body motions and the effect of crystal packing, by allowing the amplitude of the internal modes to be variables. It hypothesizes that the effect of crystal packing should cause some modes to be amplified and others to become less important. In doing so, vGNM is able to resolve the apparent discrepancy in experimental B-factors among structures of the same protein but with different crystal packing conditions, which GNM cannot explain. With a small number of parameters, vGNM is able to reproduce experimental B-factors for a large set of proteins with significantly better correlations (having a mean value of 0.81 as compared to 0.59 by GNM). The results of applying vGNM also show that the rigid body motions account for nearly 60% of the total fluctuations, in good agreement with previous findings.     

荧光假单胞菌香兰素脱氢酶基因功能的验证

验证了荧光假单胞菌(Pseudomonas fluorescensATCC13525)香兰素脱氢酶基因(vanillin dehydrogenasegene,vdh)的功能。基因vdh表达产物(Vdh)的活性测定结果显示Vdh具有很高的活性,而且不经IPTG诱导的Vdh也具有同样高的活性。经过4 h的体外酶促反应,重组蛋白Vdh能把95%以上的香兰素转化为香兰素酸,从而验证了vdh基因的表达产物具有香兰素脱氢酶的功能。同时发现NAD 是从香兰素到香兰素酸体外转化必不可少的因素。     

Gene discovery from an ovary cDNA library of oriental river prawn Macrobrachium nipponense by ESTs annotation

The oriental river prawn, Macrobrachium nipponense, is an important crustacean species in aquaculture. However, early gonad maturity is a ubiquitous problem which devalues the product quality. While husbandry and nutritional management have achieved little success in tackling this issue, a molecular approach may discover the genes involved in reproduction and development, which will provide the basic knowledge on reproductive control. In this study, a high-quality cDNA library of prawn was constructed from the ovary tissue. A total of 3294 successful sequencing reactions yielded 3256 expressed sequence tags (ESTs) longer than 100 bp. The cluster and assembly analyses yielded 1514 unique sequences including 414 contigs and 1168 singletons. About 719 (47.49%) unique sequences were identified as orthologs of genes from other organisms. By sequence comparability analysis, 28 important genes including cathepsin B, chromobox protein, Cdc2, cyclin B, DEAD box protein and ADF/cofilin protein were expressed. These genes may be involved in reproductive and developmental functions in prawn. Peritrophin consisting of cortical rods was also found in this species. The identification of these EST sequences in M. nipponense would improve our understanding on the genes that regulate reproduction and development in prawn species. This study also lays the groundwork for development of molecular markers related to ovary development in other prawn species.     

Seven new dolphin mitochondrial genomes and a time-calibrated phylogeny of whales

Background  

The phylogeny of Cetacea (whales) is not fully resolved with substantial support. The ambiguous and conflicting results of multiple phylogenetic studies may be the result of the use of too little data, phylogenetic methods that do not adequately capture the complex nature of DNA evolution, or both. In addition, there is also evidence that the generic taxonomy of Delphinidae (dolphins) underestimates its diversity. To remedy these problems, we sequenced the complete mitochondrial genomes of seven dolphins and analyzed these data with partitioned Bayesian analyses. Moreover, we incorporate a newly-developed "relaxed" molecular clock to model heterogenous rates of evolution among cetacean lineages.