拟南芥泛素家族的全基因组分析

泛素家族是一类含有保守性泛素结构域的蛋白质统称,主要通过ATP依赖性的泛素-蛋白水解酶复合体通路选择性降解细胞蛋白的各种生理活动。本研究基于HMM模型,已知泛素氨基酸序列作为训练集,搜索拟南芥信息资源数据库并鉴定AtUBQ家族成员,然后对这些基因编码的蛋白质序列进行基因结构分析、染色体定位、多序列联配、系统发育树构建和组织差异表达分析。结果表明,AtUBQ家族中共有13个推定的AtUBQ基因,命名为AtUBQ01~AtUBQ13,均属无内含子基因且结构基本相同,非均匀分布于拟南芥5条染色体;AtUBQ家族可划分为A、B和C3个亚家族,其中76.92%的基因编码蛋白质属于A亚家族;EST搜索发现除AtUBQ02和AtUBQ07基因无EST数据支持外,余下的AtUBQ基因在拟南芥根、芽和叶等7个组织中呈现差异表达,仅见AtUBQ08和AtUBQ10基因在上述7个组织中均表达,而AtUBQ03基因仅表达于叶中。本研究结果可为进一步开展该家族的生物学功能和分子进化机制的研究提供基础资料。     

An Improved Strategy for Generating Forces in Steered Molecular Dynamics: The Mechanical Unfolding of Titin,e2lip3 and Ubiquitin

One of the applications of Molecular Dynamics (MD) simulations is to explore the energetic barriers to mechanical unfolding of proteins such as occurs in response to the mechanical pulling of single molecules in Atomic Force Microscopy (AFM) experiments. Although Steered Molecular Dynamics simulations have provided microscopic details of the unfolding process during the pulling, the simulated forces required for unfolding are typically far in excess of the measured values. To rectify this, we have developed the Pulsed Unconstrained Fluctuating Forces (PUFF) method, which induces constant-momentum motions by applying forces directly to the instantaneous velocity of selected atoms in a protein system. The driving forces are applied in pulses, which allows the system to relax between pulses, resulting in more accurate unfolding force estimations than in previous methods. In the cases of titin, ubiquitin and e2lip3, the PUFF trajectories produce force fluctuations that agree quantitatively with AFM experiments. Another useful property of PUFF is that simulations get trapped if the target momentum is too low, simplifying the discovery and analysis of unfolding intermediates.     

Ubiquitin metabolism affects cellular response to volatile anesthetics in yeast

To investigate the mechanism of action of volatile anesthetics, we are studying mutants of the yeast Saccharomyces cerevisiae that have altered sensitivity to isoflurane, a widely used clinical anesthetic. Several lines of evidence from these studies implicate a role for ubiquitin metabolism in cellular response to volatile anesthetics: (i) mutations in the ZZZ1 gene render cells resistant to isoflurane, and the ZZZ1 gene is identical to BUL1 (binds ubiquitin ligase), which appears to be involved in the ubiquitination pathway; (ii) ZZZ4, which we previously found is involved in anesthetic response, is identical to the DOA1/UFD3 gene, which was identified based on altered degradation of ubiquitinated proteins; (iii) analysis of zzz1Delta zzz4Delta double mutants suggests that these genes encode products involved in the same pathway for anesthetic response since the double mutant is no more resistant to anesthetic than either of the single mutant parents; (iv) ubiquitin ligase (MDP1/RSP5) mutants are altered in their response to isoflurane; and (v) mutants with decreased proteasome activity are resistant to isoflurane. The ZZZ1 and MDP1/RSP5 gene products appear to play important roles in determining effective anesthetic dose in yeast since increased levels of either gene increases isoflurane sensitivity whereas decreased activity decreases sensitivity. Like zzz4 strains, zzz1 mutants are resistant to all five volatile anesthetics tested, suggesting there are similarities in the mechanisms of action of a variety of volatile anesthetics in yeast and that ubiquitin metabolism affects response to all the agents examined.     

Comparative Analysis of Different Approaches to Investigate Cell Kinetics

Abstract. The potential of different methods to investigate proliferative activity of cell populations was analysed for non-Hodgkin's lymphomas. Cells in S phase and all cycling cells were determined on cell suspensions obtained from fresh lymph node material by [³H]-thymidine autoradiography ([³H]TdR LI), a monoclonal antibody to bromodeoxyuridine (BrdU LI), and the monoclonal antibody Ki67. A good correlation was observed between the values of [³H]TdR LI and BrdU LI ( r _s= 0.90; P < 0.01), [³H]TdR LI and S phase ( r _s= 0.62; P < 0.01) and [³H]TdR LI and Ki67 ( r _s= 0.64; P < 0.01) in individual lymphomas. Using the median values obtained from the different approaches as cut-off points to define slowly and rapidly proliferating tumours, the best agreement was observed between [³H]TdR LI and BrdU LI (91%) and poorer agreements, even though statistically significant, were observed between [³H]TdR LI and S phase (73%) or Ki67 (76%). In conclusion, the kinetic information derived from different approaches was more or less concordant and newly proposed approaches should be directly and carefully verified for their prognostic relevance before using them as alternatives to conventional methods.     

Generalized Exponential Distribution in Flood Frequency Analysis for Polish Rivers

Many distributions have been used in flood frequency analysis (FFA) for fitting the flood extremes data. However, as shown in the paper, the scatter of Polish data plotted on the moment ratio diagram shows that there is still room for a new model. In the paper, we study the usefulness of the generalized exponential (GE) distribution in flood frequency analysis for Polish Rivers. We investigate the fit of GE distribution to the Polish data of the maximum flows in comparison with the inverse Gaussian (IG) distribution, which in our previous studies showed the best fitting among several models commonly used in FFA. Since the use of a discrimination procedure without the knowledge of its performance for the considered probability density functions may lead to erroneous conclusions, we compare the probability of correct selection for the GE and IG distributions along with the analysis of the asymptotic model error in respect to the upper quantile values. As an application, both GE and IG distributions are alternatively assumed for describing the annual peak flows for several gauging stations of Polish Rivers. To find the best fitting model, four discrimination procedures are used. In turn, they are based on the maximized logarithm of the likelihood function (K procedure), on the density function of the scale transformation maximal invariant (QK procedure), on the Kolmogorov-Smirnov statistics (KS procedure) and the fourth procedure based on the differences between the ML estimate of 1% quantile and its value assessed by the method of moments and linear moments, in sequence (R procedure). Due to the uncertainty of choosing the best model, the method of aggregation is applied to estimate of the maximum flow quantiles.     

Analysis of lymphocytes reactive to histocompatibility antigens. II. Exponential alloantigen-dependent lymphocyte growth in vitro

Rat thoracic duct lymphocytes were maintained in continual blast transformation and cell division by repeated in vitro stimulation with allogeneic cells. This resulted in increases in responder cell numbers of up to 10,000-fold in 10-day periods. Growth of responder lymphocyte populations was dependent upon cell density, culture medium nutrients, and the presence of antigen in the form of allogeneic cells. A titration assay for mixed lymphocyte interactions (MLI) was used to relate absolute growth of cells in preparative cultures to [³H]thymidine incorporation in analytical MLI. Growth of lymphocyte populations derived by repeated stimulation with cells bearing a single foreign MHC haplotype was supported to lesser, variable degrees by stimulation with unrelated “third party” stimulator cells. The extent of this operational cross-reactivity was assessed by parallel line analysis of MLI titrations of responder lymphocytes enriched for specific alloreactivity.     

Comparative Analysis of Techniques to Purify Plasma Membrane Proteins

The aim of this project was to identify the best method for the enrichment of plasma membrane (PM) proteins for proteomics experiments. Following tryptic digestion and extended liquid chromatography-tandem mass spectrometry acquisitions, data were processed using MaxQuant and Gene Ontology (GO) terms used to determine protein subcellular localization. The following techniques were examined for the total number and percentage purity of PM proteins identified: (a) whole cell lysate (total number, 84–112; percentage purity, 9–13%); (b) crude membrane preparation (104–111; 17–20%); (c) biotinylation of surface proteins with N-hydroxysulfosuccinimydyl-S,S-biotin and streptavidin pulldown (78–115; 27–31%); (d) biotinylation of surface glycoproteins with biocytin hydrazide and streptavidin pulldown (41–54; 59–85%); or (e) biotinylation of surface glycoproteins with amino-oxy-biotin (which labels the sialylated fraction of PM glycoproteins) and streptavidin pulldown (120; 65%). A two- to threefold increase in the overall number of proteins identified was achieved by using stop and go extraction tip (StageTip)-based anion exchange (SAX) fractionation. Combining technique (e) with SAX fractionation increased the number of proteins identified to 281 (54%). Analysis of GO terms describing these proteins identified a large subset of proteins integral to the membrane with no subcellular assignment. These are likely to be of PM location and bring the total PM protein identifications to 364 (68%). This study suggests that selective biotinylation of the cell surface using amino-oxy-biotin in combination with SAX fractionation is a useful method for identification of sialylated PM proteins.     

The Ubiquitin Receptor DA1 Interacts with the E3 Ubiquitin Ligase DA2 to Regulate Seed and Organ Size in Arabidopsis

Seed size in higher plants is determined by the coordinated growth of the embryo, endosperm, and maternal tissue. Several factors that act maternally to regulate seed size have been identified, such as AUXIN RESPONSE FACTOR2, APETALA2, KLUH, and DA1, but the genetic and molecular mechanisms of these factors in seed size control are almost totally unknown. We previously demonstrated that the ubiquitin receptor DA1 acts synergistically with the E3 ubiquitin ligase ENHANCER1 OF DA1 (EOD1)/BIG BROTHER to regulate the final size of seeds in Arabidopsis thaliana. Here, we describe another RING-type protein with E3 ubiquitin ligase activity, encoded by DA2, which regulates seed size by restricting cell proliferation in the maternal integuments of developing seeds. The da2-1 mutant forms large seeds, while overexpression of DA2 decreases seed size of wild-type plants. Overexpression of rice (Oryza sativa) GRAIN WIDTH AND WEIGHT2, a homolog of DA2, restricts seed growth in Arabidopsis. Genetic analyses show that DA2 functions synergistically with DA1 to regulate seed size, but does so independently of EOD1. Further results reveal that DA2 interacts physically with DA1 in vitro and in vivo. Therefore, our findings define the genetic and molecular mechanisms of three ubiquitin-related proteins DA1, DA2, and EOD1 in seed size control and indicate that they are promising targets for crop improvement.     

Incorrect Citations Give Unfair Credit to Review Authors in Ecology Journals

The number of citations that papers receive has become significant in measuring researchers'' scientific productivity, and such measurements are important when one seeks career opportunities and research funding. Skewed citation practices can thus have profound effects on academic careers. We investigated (i) how frequently authors misinterpret original information and (ii) how frequently authors inappropriately cite reviews instead of the articles upon which the reviews are based. To reach this aim, we carried a survey of ecology journals indexed in the Web of Science and assessed the appropriateness of citations of review papers. Reviews were significantly more often cited than regular articles. In addition, 22% of citations were inaccurate, and another 15% unfairly gave credit to the review authors for other scientists'' ideas. These practices should be stopped, mainly through more open discussion among mentors, researchers and students.     

糖组学研究技术及其进展

多细胞生物机体内,蛋白质糖基化是一个重要后修饰事件 . 蛋白质的糖链不仅仅是区别细胞种类的标志,且与众多的生物现象有关,如细胞发育、分化、形态、肿瘤转移、微生物感染等 . 糖组学的内容主要涉及单个个体的全部糖蛋白结构分析,确定编码糖蛋白的基因和蛋白质糖基化的机制 . 综述了糖组学的分离和结构鉴定技术及其最新进展 .     

磷蛋白组的研究技术及其进展

真核细胞中蛋白质磷酸化是一个重要事件。真核细胞利用可逆的蛋白磷酸化来控制许多细胞过程包括信号转换、基因表达、细胞周期等。磷蛋白组的研究涉及磷蛋白的分离和鉴定 ,磷酸化残基定位和定量分析。由于蛋白质磷酸化是一个动态过程 ,在细胞中磷蛋白含量低 ,磷酸化位点可变 ,且磷酸肽的质谱信号常常会受到抑制 ,所以磷蛋白的分析存在更多的困难。本文介绍了国内外在磷酸蛋白的分离鉴定及定量分析方面的研究技术以及进展情况。目前 ,质谱仍然是核心的鉴定技术 ,寻找更好富集方法是最大的挑战。定量蛋白组学是对蛋白质的差异表达进行精确的定量分析。目前还不存在一种独立的方法可以完成磷蛋白的分离、鉴定 ,以及磷酸位点的定位和定量分析。随着样品分离技术和相关仪器的发展 ,磷酸蛋白快速、准确、全面分析鉴定将能够实现。     

Exponential and diphasic ventilatory response to hypoxia in conscious lambs

This study was undertaken to test the hypothesis that in the neonate the hypoxic chemoreflex drive adapts to steady-state hypoxia but not to progressive hypoxia. First we have compared the ventilatory (VE) response of 2-day-old conscious lambs to steady-state hypoxia with their response to progressive hypoxia. Second, we have quantified the chemoreceptor excitatory function operating at the end of each period of hypoxia by studying the immediate VE response to the withdrawal of the hypoxic stimulus. Lambs responded to steady-state hypoxia [fractional concentration of inspired O2 (FIO2) = 0.08] by a diphasic VE response but responded to progressive hypoxia (FIO2 0.21-0.08) by an exponential VE increase. Hyperventilation in steady-state hypoxia was transient; VE increased immediately from 532 to a mean peak response of 712 ml X kg-1 X min-1 and decreased to 595 ml X kg-1. min-1 within 10 min. With progressive hypoxia, VE increased within 13 min from 514 to 705 ml X kg-1 X min-1. At the end of steady-state and progressive hypoxia the abrupt withdrawal of the hypoxic drive caused an instantaneous VE decrease to 390 and 399 ml X kg-1 X min-1, respectively; the VE decrease was respectively 306 and 205 ml X kg-1 X min-1 (P less than 0.05). This demonstrates that during steady-state hypoxia the lambs had suffered a loss of one third of the chemoreceptor excitatory function.(ABSTRACT TRUNCATED AT 250 WORDS)     

Metabolic Flux Analysis during the Exponential Growth Phase of Saccharomyces cerevisiae in Wine Fermentations

As a consequence of the increase in global average temperature, grapes with the adequate phenolic and aromatic maturity tend to be overripe by the time of harvest, resulting in increased sugar concentrations and imbalanced C/N ratios in fermenting musts. This fact sets obvious additional hurdles in the challenge of obtaining wines with reduced alcohols levels, a new trend in consumer demands. It would therefore be interesting to understand Saccharomyces cerevisiae physiology during the fermentation of must with these altered characteristics. The present study aims to determine the distribution of metabolic fluxes during the yeast exponential growth phase, when both carbon and nitrogen sources are in excess, using continuous cultures. Two different sugar concentrations were studied under two different winemaking temperature conditions. Although consumption and production rates for key metabolites were severely affected by the different experimental conditions studied, the general distribution of fluxes in central carbon metabolism was basically conserved in all cases. It was also observed that temperature and sugar concentration exerted a higher effect on the pentose phosphate pathway and glycerol formation than on glycolysis and ethanol production. Additionally, nitrogen uptake, both quantitatively and qualitatively, was strongly influenced by environmental conditions. This work provides the most complete stoichiometric model used for Metabolic Flux Analysis of S. cerevisiae in wine fermentations employed so far, including the synthesis and release of relevant aroma compounds and could be used in the design of optimal nitrogen supplementation of wine fermentations.     

Rank Difference Analysis of Microarrays (RDAM), a novel approach to statistical analysis of microarray expression profiling data

Background  

A key step in the analysis of microarray expression profiling data is the identification of genes that display statistically significant changes in expression signals between two biological conditions.