Community-wide assessment of protein-interface modeling suggests improvements to design methodology

The CAPRI (Critical Assessment of Predicted Interactions) and CASP (Critical Assessment of protein Structure Prediction) experiments have demonstrated the power of community-wide tests of methodology in assessing the current state of the art and spurring progress in the very challenging areas of protein docking and structure prediction. We sought to bring the power of community-wide experiments to bear on a very challenging protein design problem that provides a complementary but equally fundamental test of current understanding of protein-binding thermodynamics. We have generated a number of designed protein-protein interfaces with very favorable computed binding energies but which do not appear to be formed in experiments, suggesting that there may be important physical chemistry missing in the energy calculations. A total of 28 research groups took up the challenge of determining what is missing: we provided structures of 87 designed complexes and 120 naturally occurring complexes and asked participants to identify energetic contributions and/or structural features that distinguish between the two sets. The community found that electrostatics and solvation terms partially distinguish the designs from the natural complexes, largely due to the nonpolar character of the designed interactions. Beyond this polarity difference, the community found that the designed binding surfaces were, on average, structurally less embedded in the designed monomers, suggesting that backbone conformational rigidity at the designed surface is important for realization of the designed function. These results can be used to improve computational design strategies, but there is still much to be learned; for example, one designed complex, which does form in experiments, was classified by all metrics as a nonbinder.     

Preservation effects on stable isotope ratios and consequences for the reconstruction of energetic pathways

Stable isotope analysis provides a powerful tool for describing the energetic pathways in a variety of ecosystems. However, isotope ratios of animal tissues can be altered by preservation methods, potentially leading to biased estimates of energy pathways when they are not taken into account. Here, we investigated the direct preservation effects of formalin, ethanol, NaCl, and drying on the δ¹³C and δ¹⁵N of fish muscle tissues, as well as the ultimate effects on the reconstruction of the energy pathways. All preservation methods, except drying, had significant impacts on δ¹³C and δ¹⁵N values. The effects of preservation appear to be highly taxa-specific and no significant time-dependent variations in nearly 2-year duration of preservation. δ¹³C and δ¹⁵N values were generally changed dramatically within the early stage of the preservation process and became stable over a relatively long-term preservation. Using an isotopic balance mixing model, the isotope-based food web reconstruction reveals that, without preservation correction, the importance of the pelagic energetic pathways for the fishes could be misestimated, except for the drying preservation. These results highlight that preservation can bias the interpretation of food web reconstruction results.     

不同部位喉黏膜间充质细胞的分离培养

目的:探讨不同部位喉黏膜间充质细胞的分离、培养方法,为喉部组织工程提供更多的可供选择的种子细胞。方法:收集临床上喉部手术病人切下的不同部位的喉黏膜,主要是会厌的背侧黏膜和声带的黏膜,各3例,共计6例。对会厌背侧的黏膜采用消化培养的方法,对声带部位的黏膜采用组织块培养法。最后通过免疫荧光染色对两种方法所获得的细胞进行鉴定,确定其来源于喉黏膜的间充质。结果:通过两种方法均可以成功获得相应部位的细胞,免疫荧光染色vimentin均呈阳性表达且CK均呈阴性表达,证明了获得的细胞确实是来源于间充质。结论:本实验成功的培养出了喉部不同部位的间充质细胞,为喉部的组织工程提供了更多的可供选择的种子细胞。     

不结球白菜优异种质对小菜蛾抗性的遗传分析

以不结球白菜抗小菜蛾材料508为母本(P1)、以感虫材料114为父本(P2)构建了包括P1、P2、F1、F2、BC1P1和BC1P2的6个世代群体,通过人工网室鏊定各世代群体的抗虫性,利用主基因+多基因混合遗传模型联合分析法分析了不结球白菜抗虫遗传规律.结果表明:在508×114组合中,感虫对抗虫表现部分显性,抗虫性遗传符合一对加性-显性主基因+加性-显性多基因遗传模型,在BC1P1、BC1P2和F2群体中的主基因遗传率分别为57.21%、25.87%和76.05%,为有效利用抗虫资源和挖掘抗虫基因奠定了基础.     

Knowledge-based virtual screening of HLA-A*0201-restricted CD8+ T-cell epitope peptides from herpes simplex virus genome

A novel knowledge-based method is developed to virtually screen potential HLA-A?0201 binders from large-scale peptide candidates. This method utilizes the information from both the crystal structures and experimental affinities of various peptides bound with HLA-A*0201 to construct a single-position mutation free energy profile for accurately characterizing HLA-A*0201-peptide interaction and for effectively predicting the binding affinities of peptides to HLA-A*0201. We employ this method to analyze physicochemical properties and structural implication underlying the specific recognition and association between the HLA-A*0201 and a large panel of peptide segments generated from the herpes simplex virus type 1 (HSV-1) genome, and to evaluate the binding potencies of these peptide candidates to HLA-A*0201. As a result, 288 out of 38,020 candidates are predicted as the potential high-affinity binders of HLA-A*0201, from which three most promising peptides are picked out for further development of potent vaccines against HSV-1. In addition, we also demonstrate that this newly proposed method can successfully identify 8 known binders and 3 known nonbinders from the glycoproteins D and K of HSV-1.     

Pesticide Residues in Agricultural Produce in Hubei Province,PR China

Pesticide residues in agricultural produce were examined in two villages of Qianjiang municipality, Hubei province, PR China. Six food groups were sampled from the fields prior to harvesting from the farmers' market and from farmers' homes. Organochlorine residues were detected in almost all examined food groups, with residue levels significantly lower than the national tolerances (MRL). Total BHC residues were on average 31.7?µg/kg and DDT 102.5 (µg/kg. Organophosphorus residues were detected in vegetable samples. Mean residue levels of phoxim and methamidophos in vegetables were 89.9?µg/kg and 36.5?µg/kg, respectively, both exceeding the MRL. Estimated daily intakes (EDIs) of pesticide residues per person, based on the six food groups sampled, were 4.88?mg for total DDT, 2.04 (µg for total BHC, and 19.33 (µg for methamidophos. The overall results show that the increased use and misuse of pesticides for crop protection in Qianjiang municipality, notably in vegetable production, have led to worrisome levels of pesticide contamination of agricultural produce that may carry certain risks for human health.     

固氮树种在混交林中的作用研究Ⅲ.固氮树种凋落物分解及N的释放

研究了１１种固氮和非固氮树种凋落物分解及可利用态Ｎ的释放．结果表明,固氮树木凋落物中Ｎ的生物分解系数、落叶分解过程中干重的损失率及有效态氮的释放分别比非固氮树种高出１．３、１．５和８．２倍．     

中微量元素和有益元素对水稻生长和吸收镉的影响

采用盆栽试验,研究了中微量元素和有益元素对水稻生长和吸收镉的影响。结果表明,在所有测试的元素和施用方法中,硅酸钠叶面喷施显著增加稻谷产量,而碳酸钙、硼酸、硅酸钠土施和亚硒酸钠显著降低了稻谷产量。镁、锌、铁的盐酸盐形态对水稻籽粒的增产效果优于硫酸盐形态,而钙、铜的硫酸盐形态增产效果略高于盐酸盐形态。在钙、镁、硫三种中量元素中,钙增加了水稻籽粒中的Cd浓度和吸收量,而镁和硫则降低了籽粒中的Cd浓度和吸收量,以硫磺粉处理为最低。稻草中的Cd浓度和总量均以氯化镁处理为最高,硫磺粉处理最低。镁能有效抑制Cd从秸秆向籽粒的转移,其盐酸盐优于硫酸盐。在微量元素中,锌对水稻Cd的吸收抑制作用最为显著,其次是铜,而有益元素肥料硅酸钠叶面喷施则显著增加了稻谷中的Cd浓度和吸收量。硫酸亚铁、氯化锰、氯化铜、硼酸和硼砂处理都能有效地抑制Cd从秸秆向籽粒的转移,而硅酸钠叶面喷施和锌处理则促进了Cd的转移,表明硅酸钠抑制水稻吸收Cd的机制很可能发生在土壤中,而非在植株体内或地上部分。在Cd污染土壤上选用适宜的中微量和有益元素肥料及其施用方法,能有效降低水稻对镉的吸收和稻米中的Cd含量。     

Upregulation of PHLDA2 in Dicer knockdown HEK293 cells

It has been reported that RNAi-dependent chromatin silencing in vertebrates is not restricted to the centromeres. To address whether RNAi machinery could regulate the chromatin structure of imprinted genes, we knocked down Dicer in HEK293 cells and found that the expression of PHLDA2, one of the several genes in the imprinted gene domain of 11p15.5, was specifically upregulated. This was accompanied by a shift towards more activated chromatin at PHLDA2 locus as indicated by change in H3K9 acetylation, however, the methylation state at this locus was not affected. Furthermore, we found that PHLDA2 was downregulated in growth-arrested HEK293 cells induced by either serum deprivation or contact inhibition. This suggests that PHLDA2 upregulation might be a direct result of Dicer depletion rather than the consequence of growth arrest induced by Dicer knockdown. Considering the reports that there is consistent placental outgrowth in PHLDA2 knockout mice and that PHLDA2 overexpression in mice causes growth inhibition, we speculate that PHLDA2 may be a candidate for contributing to the reduced growth rate of Dicer-deficient cells and the very early embryonic lethality in Dicer knockout mice.     

基于Visual C#语言的DICOM标准医学图像的显示和实现

介绍DICOM3.0医学图像文件的格式和C#语言的特点,首次利用Visual C#语言对该标准的图像进行显示和处理,能够直接读取DICOM格式原始图像数据,并可批量转换成BMP等格式进行处理,此项工作可为医学图像处理研究及相关医学图像软件开发奠定基础。