Molecular characterization of a phenylalanine ammonia-lyase gene (BoPAL1) from Bambusa oldhamii

Phenylalanine ammonia-lyase is the first enzyme of general phenylpropanoid pathway. A PAL gene, designated as BoPAL1, was cloned from a Bambusa oldhamii cDNA library. The open reading frame of BoPAL1 was 2,139 bp in size and predicted to encode a 712-amino acid polypeptide. BoPAL1 was the first intronless PAL gene found in angiosperm plant. Several putative cis-acting elements such as P box, GT-1motif, and SOLIPs involved in light responsiveness were found in the 5??-flanking sequence of BoPAL1 which was obtained by TAIL-PCR method. Recombinant BoPAL1 protein expressed in Pichia pastoris was active. The optimum temperature and pH for BoPAL1 activity was 50°C and 9.0, respectively. The molecular mass of recombinant BoPAL1 was estimated as 323 kDa using gel filtration chromatography and the molecular mass of full-length BoPAL was about 80 kDa, indicating that BoPAL1 presents as a homotetramer. The K _m and k _cat values of BoPAL1 for L-Phe were 1.01 mM and 10.11 s^?1, respectively. The recombinant protein had similar biochemical properties with PALs reported in other plants.     

大连地区岛屿与大陆藜（Chenopodium album L.）种群遗传多样性的ISSR分析

采用ISSR分子标记对分布于大连市周边的4个藜的天然种群100个个体进行了遗传多样性及遗传结构的研究。13个引物共检测了157个位点,多态位点比率为67.52%,Shannon信息指数在物种水平上为0.332 9。根据G_ST值,藜遗传变异有40.03%发生在种群间。遗传距离分析表明,DT种群与MLN种群遗传一致度最高,遗传距离与地理距离之间没有相关性。     

Fluorescent cyclin-dependent kinase inhibitors block the proliferation of human breast cancer cells

Inhibitors of cyclin-dependent kinases (CDKs) are an emerging class of drugs for the treatment of cancers. CDK inhibitors are currently under evaluation in clinical trials as single agents and as sensitizers in combination with radiation therapy and chemotherapies. Drugs that target CDKs could have important inhibitory effects on cancer cell cycle progression, an extremely important mechanism in the control of cancer cell growth. Using rational drug design, we designed and synthesized fluorescent CDK inhibitors (VMY-1-101 and VMY-1-103) based on a purvalanol B scaffold. The new agents demonstrated more potent CDK inhibitory activity, enhanced induction of G2/M arrest and modest apoptosis as compared to purvalanol B. Intracellular imaging of the CDK inhibitor distribution was performed to reveal drug retention in the cytoplasm of treated breast cancer cells. In human breast cancer tissue, the compounds demonstrated increased binding as compared to the fluorophore. The new fluorescent CDK inhibitors showed undiminished activity in multidrug resistance (MDR) positive breast cancer cells, indicating that they are not a substrate for p-glycoprotein. Fluorescent CDK inhibitors offer potential as novel theranostic agents, combining therapeutic and diagnostic properties in the same molecule.     

Prediction of novel pre-microRNAs with high accuracy through boosting and SVM

High-throughput deep-sequencing technology has generated an unprecedented number of expressed short sequence reads, presenting not only an opportunity but also a challenge for prediction of novel microRNAs. To verify the existence of candidate microRNAs, we have to show that these short sequences can be processed from candidate pre-microRNAs. However, it is laborious and time consuming to verify these using existing experimental techniques. Therefore, here, we describe a new method, miRD, which is constructed using two feature selection strategies based on support vector machines (SVMs) and boosting method. It is a high-efficiency tool for novel pre-microRNA prediction with accuracy up to 94.0% among different species. AVAILABILITY: miRD is implemented in PHP/PERL+MySQL+R and can be freely accessed at http://mcg.ustc.edu.cn/rpg/mird/mird.php.     

Proteomannans in biofilm of Helicobacter pylori ATCC 43504

Background: The human bacterial pathogen Helicobacter pylori forms biofilms. However, the constituents of the biofilm have not been extensively investigated. In this study, we analyzed the carbohydrate and protein components of biofilm formed by H. pylori strain ATCC 43504 (NCTC 11637). Materials and Methods: Development of H. pylori biofilm was analyzed using scanning electron microscopy (SEM) and quantified using crystal violet staining. The extracted extracellular polysaccharide (EPS) matrix was analyzed using GC‐MS and nuclear magnetic resonance (NMR) analyses. Proteomic profiles of biofilms were examined by SDS–PAGE while deletion mutants of upregulated biofilm proteins were constructed and characterized. Results: Formation of H. pylori biofilm is time dependent as shown by crystal violet staining assay and SEM. NMR reveals the prevalence of 1,4‐mannosyl linkages in both developing and mature biofilms. Proteomic analysis of the biofilm indicates the upregulation of neutrophil‐activating protein A (NapA) and several stress‐induced proteins. Interestingly, the isogenic mutant napA revealed a different biofilm phenotype that showed reduced aggregated colonial structure when compared to the wild type. Conclusions: This in vitro study shows that mannose‐related proteoglycans (proteomannans) are involved in the process of H. pylori biofilm formation while the presence of upregulated NapA in the biofilm implies the potency to increase adhesiveness of H. pylori biofilm. Being a complex matrix of proteins and carbohydrates, which are probably interdependent, the H. pylori biofilm could possibly offer a protective haven for the survival of this gastric bacterial pathogen in the extragastric environments.     

The structure and evolution of the ribosomal proteins encoded in the spc operon of the archaeon (Crenarchaeota) Sulfolobus acidocaldarius.

The genes for nine ribosomal proteins, L24, L5, S14, S8, L6, L18, S5, L30, and L15, have been isolated and sequenced from the spc operon in the archaeon (Crenarchaeota) Sulfolobus acidocaldarius, and the putative amino acid sequence of the proteins coded by these genes has been determined. In addition, three other genes in the spc operon, coding for ribosomal proteins S4E, L32E, and L19E (equivalent to rat ribosomal proteins S4, L32, and L19), were sequenced and the structure of the putative proteins was determined. The order of the ribosomal protein genes in the spc operon of the Crenarchaeota kingdom of Archaea is identical to that present in the Euryarchaeota kingdom of Archaea and also identical to that found in bacteria, except for the genes for r-proteins S4E, L32E, and L19E, which are absent in bacteria. Although AUG is the initiation codon in most of the spc genes, GUG (val) and UUG (leu) are also used as initiation codons in S. acidocaldarius. Over 70% of the codons in the Sulfolobus spc operon have A or U in the third position, reflecting the low GC content of Sulfolobus DNA. Phylogenetic analysis indicated that the archaeal r-proteins are a sister group of their eucaryotic counterparts but did not resolve the question of whether the Archaea is monophyletic, as suggested by the L6P, L15P, and L18P trees, or the question of whether the Crenarchaeota is separate from the Euryarchaeota and closer to the Eucarya, as suggested by the S8P, S5P, and L24P trees. In the case of the three Sulfolobus r-proteins that do not have a counterpart in the bacterial ribosome (S4E, L32E, and L19E), the archaeal r-proteins showed substantial identity to their eucaryotic equivalents, but in all cases the archaeal proteins formed a separate group from the eucaryotic proteins.     

小麦珠心细胞衰退过程酸性磷酸酶的超微细胞化学定位(英文)

采用磷酸铅盐沉淀技术对小麦（ Ｔｒｉｔｉｃｕｍ ａｅｓｔｉｖｕｍ Ｌ．） 珠心细胞衰退过程进行了酸性磷酸酶的超微细胞化学定位研究。结果显示,在未有明显衰退迹象的一些珠心细胞中,酸性磷酸酶只出现在细胞核轻微凝聚的染色质上。随珠心细胞衰退程度的逐渐增大,其衰退特征越来越明显,酸性磷酸酶依次在细胞质中较小液泡、细胞壁、线粒体、质体以及内质网等结构上出现活性反应。紧连胚囊的珠心细胞衰退程度最大,细胞严重变形,酸性磷酸酶定位于细胞绝大部分结构中,但此时变形的细胞核则无酸性磷酸酶活性反应。研究结果表明,小麦珠心细胞的衰退过程中,酸性磷酸酶存在一个有规律的变化,支持珠心细胞的衰退是属于细胞程序性死亡类型的观点     

安徽黄精属(Polygonatum)植物叶表皮研究

利用光学显微镜及扫描电子显微镜观察了安徽省黄精属９种植物的叶表皮;统计并测量了气孔类型、气孔大小、气孔密度及气孔指数等;描述了表皮角质膜、蜡质纹饰、气孔的形状及气孔外拱盖等有关特征。结果表明：黄精属植物叶表皮气孔器类型属只有２个保卫细胞而无任何副卫细胞的单子叶植物气孔器类型。气孔的某些特征,如气孔器类型、气孔器分布特征、表皮细胞形状及垂周壁式样、角质层及蜡质纹饰等在种间差异不大,可作种间区别的次级特征用。     

DCD不同施用时间对小麦生长期N2O排放的影响

通过田间试验,采用静态箱法研究相同施肥条件下,DCD不同施用时间(基肥配施,追肥配施,基追肥按比例配施)对麦季N2O排放的影响.结果表明,小麦生长期施肥配施DCD减少麦季N2O排放.从小麦整个生长季来看,与尿素处理相比,基肥配施减少N2O排放21％,追肥配施减少N2O排放26％,基追肥按比例配施减少N2O排放35％,方差分析均达显著水平(P＜0.05),其中基肥配施主要减少小麦播种-返青期N2O排放,追肥配施主要减少小麦返青-成熟期N2O排放,而基追肥按比例配施DCD减少整个小麦生长季N2O排放.在小麦的整个生长阶段,施加DCD处理的土壤NH+4-N浓度和表观硝化率均高于未施加DCD的处理,且土壤NH+4-N浓度随时间的延长而降低.在小麦播种-返青期,基肥配施处理和基追肥按比例配施处理土壤NH+4-N浓度和表观硝化率高于追肥配施处理和对照处理;在小麦的返青-成熟期,追肥配施处理和基追肥按比例配施处理土壤NH+4-N浓度和表观硝化率高于基肥配施处理和对照处理.从小麦产量来看,与尿素处理相比,基肥配施和基追肥按比例配施显著增加小麦产量,而追肥配施处理小麦产量无显著性差异.基追肥按比例配施DCD在提高小麦产量的同时显著减少N2O排放,具有大田推广的现实意义;基肥与追肥配施DCD对N2O减排效果除了与施用时间有关外,还应将降雨或灌溉量的年际变化考虑在内.     

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.