Introduction to ion trap mass spectrometry: Application to the structural characterization of plant oligosaccharides

This review will focus on ion trap mass spectrometry (ITMS) and the application of this technique to the structural analysis of carbohydrates. The basic principles of operation of the electrostatic ion traps are briefly described and the applicability of the technique to the structural characterization of carbohydrates is illustrated with the analysis of arabinoxylan oligosaccharides by ion trap mass spectrometry.     

His164 regulates accessibility to the active site in fungal 17beta-hydroxysteroid dehydrogenase

17beta-Hydroxysteroid dehydrogenase from the fungus Cochliobolus lunatus (17beta-HSDcl) is an NADPH-dependent member of the short-chain dehydrogenase/ reductase superfamily. To study the catalytic properties of this enzyme, we prepared several specific mutations of 17beta-HSDcl (Tyr167Phe, His164Trp/Gly, Tyr212Ala). Wild-type 17beta-HSDcl and the 17beta-HSDcl mutants were evaluated by chromatographic, kinetic and thermodynamic means. The Tyr167Phe mutation resulted in a complete loss of enzyme activity, while substitution of His164 with Trp and Gly both resulted in higher specificity number (V/K) for the steroid substrates, which are mainly a consequence of easier accessibility of steroid substrates to the active-site hollow under optimized conditions. The Tyr212Ala mutant showed increased activity in the oxidative direction, which appears to be a consequence of increased NADPH dissociation. The kinetic characterizations and thermodynamic analyses also suggest that His164 and Tyr212 in 17beta-HSDcl have a role in the opening and closing of the active site of this enzyme and in the discrimination between oxidized and reduced coenzyme.     

链霉菌ZG0429的分类鉴定与链霉亲和素的分离纯化研究

从土壤中筛选得到1株高产链霉亲和素的放线菌ZG0429,根据形态观察、培养特征、生理生化鉴定以及16S rRNA序列分析,初步判定该菌株为链霉菌属中的淡紫灰链霉菌(Streptomyces lavendulae)。经发酵,ZG0429的链霉亲和素产量可达201.0mg/L。进一步采用硫铵沉淀和凝胶过滤层析纯化,链霉亲和素的回收率为76.87%,纯度可以达到97.03%。该方法简单易行,成本低廉,可得到高产量、高纯度、高活性的目的蛋白,为链霉亲和素发酵产品的大规模纯化提供了依据。     

Synthesis, characterization and luminescence property of heterobimetallic trinuclear Mo(W)-Ag-S clusters containing 1,2-bis(diphenylphosphino)-1,2-dicarba-closo-dodecaborane

Reactions of (NH₄)₂MS₄ or (NH₄)₂MOS₃ (M = Mo, W) with AgSCN and closo carborane diphosphine ligand 1,2-(PPh₂)₂-1,2-C₂B₁₀H₁₀ (L) in CH₂Cl₂ yielded four heterobimetallic trinuclear Mo(W)-Ag-S clusters: [Ag₂MoS₄L₂] (1), [Ag₂WS₄L₂] (2), [Ag₂MoOS₃L₂] (3) and [Ag₂WS₄L₂] (4), respectively. All the new clusters have been characterized by elemental analysis, FT-IR, UV-Vis, ¹H and ¹³C NMR spectroscopy and their molecular structures (except for 3) were further confirmed by single-crystal X-ray diffraction. X-ray crystal structure analysis showed that the closo carborane diphosphine ligand was coordinated bidentately to Ag(I) atom through its two phosphorus atoms, resulting in a stable five-member chelating ring between the diphosphine ligand and the metal. The coordination sphere of the central M atom, as well as all the Ag atoms, was tetrahedron. The skeletons of these clusters could be classified into two types: with (NH₄)₂MS₄, the three metal atoms (two Ag atoms and one M atom) are in a linear conformation, while with (NH₄)₂MOS₃, the conformation of the heterobimetallic trinuclear cluster is butterfly shaped. The luminescence properties of the clusters were investigated in CH₂Cl₂ solution at room temperature and for the first time the butterfly-shaped Ag-W-S cluster containing the Ag₂WS₄ core has been proved to show luminescence property.     

Robustness of an odds-ratio test in a stratified group sequential trial with a binary outcome measure

Many clinical trials compare two or more treatment groups by using a binary outcome measure. For example, the goal could be to determine whether the frequency of pain episodes is significantly reduced in the treatment group (arm A) as compared to the control group (arm B). However, for ethical or regulatory reasons, group sequential designs are commonly employed. Then, based on a binomial distribution, the stopping boundaries for the interim analyses are constructed for assessing the difference in the response probabilities between the two groups. This is easily accomplished by using any of the standard procedures, e.g., those discussed by Jennison and Turnbull (2000), and using one of the most commonly used software packages, East (2000). Several factors are known to often affect the primary outcome of interest, but their true distributions are not known in advance. In addition, these factors may cause heterogeneous treatment responses among individuals in a group, and their exact effect size may be unknown. To limit the effect of such factors on the comparison of the two arms, stratified randomization is used in the actual conduct of the trial. Then, a stratified analysis based on the odds ratio proposed in Jennison and Turnbull (2000, pages 251-252) and consistent with the stratified design is undertaken. However, the stopping rules used for the interim analyses are those obtained for determining the differences in response rates in a design that was not stratified. The purpose of this paper is to assess the robustness of such an approach on the performance of the odds ratio test when the underlying distribution and effect size of the factors that influence the outcome may vary. The simulation studies indicate that, in general, the stratified approach offers consistently better results than does the unstratified approach, as long as the difference in the weighted average of the response probabilities across strata between the two groups remains closer to the hypothesized values, irrespective of the differences in the (allocation) distributions and heterogeneous response rate. However, if the response probabilities deviate significantly from the hypothesized values so that the difference in the weighted average is less than the hypothesized value, then the proposed study could be significantly underpowered.     

Genetic relationship of discrete-time survival with fertility and production in dairy cattle using bivariate models

Bivariate analyses of functional longevity in dairy cattle measured as survival to next lactation (SURV) with milk yield and fertility traits were carried out. A sequential threshold-linear censored model was implemented for the analyses of SURV. Records on 96 642 lactations from 41 170 cows were used to estimate genetic parameters, using animal models, for longevity, 305 d-standardized milk production (MY305), days open (DO) and number of inseminations to conception (INS) in the Spanish Holstein population; 31% and 30% of lactations were censored for DO and INS, respectively. Heritability estimates for SURV and MY305 were 0.11 and 0.27 respectively; while heritability estimates for fertility traits were lower (0.07 for DO and 0.03 for INS). Antagonist genetic correlations were estimated between SURV and fertility (-0.78 and -0.54 for DO and INS, respectively) or production (-0.53 for MY305), suggesting reduced functional longevity with impaired fertility and increased milk production. Longer days open seems to affect survival more than increased INS. Also, high productive cows were more problematic, less functional and more liable to being culled. The results suggest that the sequential threshold model is a method that might be considered at evaluating genetic relationship between discrete-time survival and other traits, due to its flexibility.     

恒河猴皮肤干细胞的体外培养纯化与鉴定

探索恒河猴皮肤干细胞的体外培养及纯化条件,为进一步的研究奠定基础. 通过组织块培养法和消化培养法 在体外培养恒河猴表皮细胞,然后用Ⅳ型胶原吸附法吸附20 min,获得快吸附细胞. 对快吸附细胞进行克隆培养,并进行免疫细胞化学双标染色、RT PCR鉴定 β1 整合素和角蛋白15的表达,用流式细胞仪鉴定纯化前后的细胞中 β1 整合素和角蛋白15的阳性细胞比例,并通过透射电镜观察细胞的超微结构. 组织块培养法和消化培养法均可获得表皮细胞,Ⅳ型胶原纯化后的细胞胞体较小,饱满,核/浆比例大,细胞镶嵌状排列. 细胞克隆分析显示,细胞全克隆生长率高. 细胞免疫荧光显示,分选后的细胞显示 β1 整合素和角蛋白15阳性. RT PCR检查呈现 β1 整合素和角蛋白15的特异性片段. 流式细胞仪检查显示,纯化前的细胞中角蛋白15阳性细胞占总细胞中的比例为8％, β1 整合素阳性细胞的比例为10.7％;纯化后,角蛋白15阳性细胞的比例为89.4％, β1 整合素阳性细胞的比例为88.5％. 通过组织块培养法和消化培养法均可培养获得活性良好的表皮细胞,Ⅳ型胶原吸附法是一种简便、有效的皮肤干细胞分离方法,可以为进一步的眼表上皮替代重建眼表提供足量的高纯度的干细胞建立可靠的物质基础.     

Contemplating Risk Assessment: A Critique of NRC (1983, 1996)

Assessing risks involves developing predictive mathematical models, using interpretations of data that are based on scientific assumptions or theories and knowledge of how the data were created. The predictions are used for developing strategies that affect many people in society. Often, it is sufficient that the models that are used are justifiable by a well-accepted set of assumptions or theories, reflecting the state-of-the art science at the time. However, this does not ensure that the “best” decision would be made, nor does it ensure that the decision processes would be fair by ensuring that concerned and affected individuals would be able to participate, effectively presenting arguments on their own behalf. Because of these concerns, procedures of risk analysis, including the management of the process, have been written about, for example, in a National Research Council (NRC 1996 NRC. 1996. Understanding Risk, Informing Decisions in a Democratic Society, Washington, DC, , USA: National Academy Press.  [Google Scholar]) publication, with the intention of getting stakeholders (interested participants) more involved in the risk analysis process. This publication suggests that Risk Characterization be expanded to include an active participation of stakeholders. Such an expansion would affect the risk assessor's approach toward science compared to the present approach, as implied in the seminal NRC (1983) NRC (National Research Council). 1983. Risk Assessment in the Federal Government: Managing the Process, Washington, DC, , USA: National Academy Press.  [Google Scholar] publication. Both of these NRC publications have had great influence on the development of risk analysis management and policy in the United States and elsewhere. Subsequent risk assessment guidance documents have generally relied heavily on these publications, but have focused mainly on managerial attitudes (or policy) toward the uncertainty that is inherent in risk assessment and in communicating to the public the risk assessment conclusions and decisions made from them. Subsequent documents have not, unlike NRC (1996) NRC. 1996. Understanding Risk, Informing Decisions in a Democratic Society, Washington, DC, , USA: National Academy Press.  [Google Scholar], focused on the risk assessors' attitude toward science inference that would better help ensure that risk assessments contain the type of information that could be used to empower stakeholders. Thus, in this Perspective article I focus on the two NRC “foundation documents,” identifying and contrasting two types of approaches toward science, one narrow and the other expansive. The latter approach is designed to increase stakeholders' involvement more than the former. The features of the expansive approach include a contemplative method toward science, where the risk assessor does not express opinions or take a stand regarding the scientific material, but rather considers many possibilities, presents discussions that include direct challenges to assumptions, and uses falsification principles for excluding theories.     

Failure of sequential therapy to eradicate Helicobacter pylori in previously treated subjects

BACKGROUND: Recently, studies in adults and subsequently in children have demonstrated a very high success rate for sequential therapy as a primary therapy when compared to traditional therapy regimens. METHODs: We report our experience with a sequential therapy regimen for the eradication of Helicobacter pylori in five infected children and a young adult, whose conventional therapy regimens had been unsuccessful. RESULTS: Five patients failed the sequential therapy. All of them experienced between two and four failures of traditional therapy prior to the sequential treatment protocol. The only patient who succeeded on the sequential therapy had just one previous failure. All of our patients who had failed sequential therapy achieved eradication of the bacteria with quadruple therapy. CONCLUSIONS: In view of our disappointing results, sequential therapy is unsuccessful as a therapy for children and young adults who have failed previous treatment regimens. At the present time, quadruple therapy is indicated for this group. Well-designed placebo-controlled trials are indicated to further characterize this group of patients.     

A longitudinal study to assess the persistence of vancomycin-resistant Enterococcus faecium (VREF) on an intensive broiler farm in the United Kingdom

Seven years after the ban of avoparcin, VREF could still be isolated within sectors of the UK broiler industry. The aim of this study was to assess whether there is a carryover of VREF between consecutive flocks of birds, to conduct a preliminary investigation of possible routes of entry of VREF into broiler houses and to follow the dynamics of VREF shed by growing birds. A series of nine visits were made to two of six houses on a conventional broiler farm. A total of 343 vanA VREF were recovered from environmental (95/843) and faecal (248/416) samples. Significant differences were observed in the carryover of VREF between pre- and postcohort postcleaning and disinfection visits (RR 0.57, P=0.006). Ninety-nine percent of the VREF isolates were resistant to more than five antimicrobials, with 42 isolates (n=49) positive for erm(B) and 32 (n=40) for vat(E). Pulsed field gel electrophoresis (PFGE) typing identified 50 PFGE types within 15 different PFGE clusters of 90% similarity, demonstrating a high level of genetic diversity within VREF populations from epidemiologically related broiler flocks and broiler houses. Further characterization of Tn1546 from different clones showed a low diversity of Tn-types, suggesting horizontal transfer of resistance determinants between different genetic clones. Thus, this study does not only show the persistence of VREF but also of multi-drug resistant lineages of VREF.