The Deuterator: software for the determination of backbone amide deuterium levels from H/D exchange MS data

Background  

The combination of mass spectrometry and solution phase amide hydrogen/deuterium exchange (H/D exchange) experiments is an effective method for characterizing protein dynamics, and protein-protein or protein-ligand interactions. Despite methodological advancements and improvements in instrumentation and automation, data analysis and display remains a tedious process. The factors that contribute to this bottleneck are the large number of data points produced in a typical experiment, each requiring manual curation and validation, and then calculation of the level of backbone amide exchange. Tools have become available that address some of these issues, but lack sufficient integration, functionality, and accessibility required to address the needs of the H/D exchange community. To date there is no software for the analysis of H/D exchange data that comprehensively addresses these issues.     

Prevalence of risk factors for cardiovascular disease in Canadians 55 to 74 years of age: results from the Canadian Heart Health Surveys, 1986-1992

BACKGROUND: By 2016, the proportion of Canadians older than 65 years of age will increase to 16%, and there will be an increase in the absolute number of cases of cardiovascular disease in older Canadians. The Canadian Heart Health Surveys database provides information about this population upon which health policy related to cardiovascular disease can be based. This paper presents for the first time population-based data on the risk factors for cardiovascular disease in older Canadians. METHODS: Canadians from all 10 provinces participated in surveys of cardiovascular risk factors; health insurance registries were used as sampling frames. In each province, probability samples of 2200 adults 18 to 74 years old not living in institutions, on reserves or in military camps were asked to participate in interviews and to undergo testing at clinics for major risk factors for cardiovascular disease. RESULTS: A total of 2739 men (response rate 70%) and 2617 women (response rate 66%) aged 55 to 74 years participated in the survey and also provided follow-up clinical measurements at the clinic. Overall, 52% of participants were hypertensive, 26% had isolated systolic hypertension, and 30% had a total blood cholesterol level of 6.2 mmol/L or greater. Rates of current smoking were lower in women than men (17% v. 22%). Overall, 87% of men and 78% of women who were current smokers smoked at least 10 cigarettes per day. Only slightly more than half of participants exercised at least once a week for at least 15 minutes, and almost half had a body mass index of 27 or greater. In only 4% was no major risk factor for cardiovascular disease detected. INTERPRETATION: Significant numbers of older Canadians have one or more major risk factors for cardiovascular disease. Many of these risk factors are amenable to modification.     

大鼠肠内容物细菌基因组DNA提取方法的比较

目的比较两种肠内容物前处理和两种提取方法对清洁级SD大鼠肠内容物细菌基因组DNA提取效率。方法分别选用PBS多次离心漂洗、液氮破细胞两种前处理方法和酚/氯仿抽提、试剂盒过柱法两种提取方法进行组合分析,对4份肠内容物和16份含金黄色葡萄球菌肠内容物进行随机提取。结果大鼠肠内容物细菌基因组DNA含量和纯度测定结果显示,与PBS反复离心相比,液氮研磨前处理能显著提高大鼠肠内容物基因组DNA。荧光定量PCR表明,液氮研磨前处理较PBS反复离心能更好地收集细菌基因组DNA,其Ct值最低。结论研究结果表明,采用液氮研磨试剂盒法在大鼠肠内容物DNA提取中是较为优良的方法,该方法为建立实验动物中微生物的定量PCR检测方法打下了基础。     

秦渭玫瑰精油研究

采用ISO9842和GB11538-89对在陕西渭南栽培的大马士革玫瑰“卡赞勒克”精油(工业化蒸馏法提取产品)进行了分析,结果表明,精油产品各项指标均符合ISO 9842和保加利亚БДС653标准要求。证明引种国际香型(纯甜型)玫瑰品种在陕西渭南栽培是成功的,所用精油提取工艺是合理的。     

草地贪夜蛾对不同品种玉米的适应性比较研究

为了解不同玉米品种对草地贪夜蛾生长发育的影响,本文通过比较草地贪夜蛾Spodoptera frugiperda取食2种糯质型玉米(明玉1203和苏玉糯5号)与3种普通玉米(苏玉29、苏玉30和郑单958)后的发育历期、死亡率、蛹重、成虫畸形率、繁殖力与幼虫取食选择率等生物学参数,分析了草地贪夜蛾对不同品种玉米的适应性差...     

高通量扩增子测序分析生防细菌对丹参根际和根表土壤真菌群落多样性的影响

利用高量测序方法探究生防细菌对丹参植株根际和根表土壤真菌群落多样性的影响。

向丹参植株根部施入生防细菌DS-R5,培养45 d后采集根际和根表土壤样品提取总DNA,扩增样品基因组DNA的V4―V5区后进行双端测序,利用生物信息学解析生防细菌对丹参植株根际和根表土壤真菌群落多样性的影响。

菌株DS-R5处理后增加了根际和根表土壤真菌群落的多样性和丰度;根际土壤共有物种种类大于根表土壤,说明菌株DS-R5处理后根际土壤处理与对照物种种类更接近,而对根表土壤中的微生物物种影响较大。真菌群落结构组成分析结果表明,不同土壤样品在门水平上共有优势真菌主要有子囊菌门、接合菌门、担子菌门和未分类;相比根表土壤对照样品,根表土壤处理样品中子囊菌门丰度下降了13.0%,接合菌门丰度升高了69.2%;根际土壤处理样品相比根际土壤对照样品,子囊菌门和接合菌门丰度分别升高了5.9%和8.9%,但二者差异无统计学意义。在属水平上,根表土壤样品经菌株DS-R5处理后提高了有益菌属的丰度,同时降低了有害菌属的丰度。

丹参植株施入生防细菌后,改变了根际土壤和根表土壤中微生物群落结构和多样性,本研究结果可以为利用生防细菌防控丹参根腐病提供理论参考。

     

Effects of Water Stress and Abscisic Acid on Transpiration Regulation in Wheat

The transpiration response to recurrent light periods was studied'n water-stressed wheat seedlings. Seedlings were stressed by three methods: addition of mannitol to the root medium, root cooling and drving of the roots in air. All three methods induced almost equal effects on transpiration regulation during alternating dark and light intervals. Exogenous abscisic acid supplied to the shoots of excised plants had qualitatively the same effect as water stress. Water stress and ABA increased the time lapse between light-on and the onset of transpiration increase and lowered the amplitude of transpiration increase in light. Weak light introduced before strong light shortened the delay times.     

两个苜蓿品种营养器官解剖结构特征比较

为了明确具有极强抗虫特性的‘草原4号紫花苜蓿’(Medicago sativa L.‘Caoyuan No.4’) 营养器官的解剖特征,该研究选择具有抗蓟马特性较强的‘草原2号杂花苜蓿’(Medicago varia Martin.‘Caoyuan No.2’)为对照,采用显微镜观察比较两品种的根、茎、叶解剖结构特征,为揭示‘草原4号紫花苜蓿’ 抗蓟马特性提供理论依据。结果显示：(1)‘草原4号紫花苜蓿’根部解剖结构的皮层薄壁细胞厚度、内皮层厚度、形成层厚度、木质部厚度和木射线宽度等5个指标均极显著高于(P＜0.01)‘草原2号杂花苜蓿’,其中木射线宽度(159.37 μm)是‘草原2号杂花苜蓿’的1.82倍。(2)‘草原4号紫花苜蓿’的茎部厚角组织厚度(21.4 μm)极显著高于‘草原2号杂花苜蓿’(P＜0.01),而韧皮部宽度、髓直径却均极显著低于‘草原2号杂花苜蓿’(P＜0.01)。(3)‘草原4号紫花苜蓿’叶片解剖构造的7个指标均极显著高于‘草原2号杂花苜蓿’(P＜0.01),其中栅栏组织层数(2～3层)极明显地高于‘草原2号杂花苜蓿’(1~2层)。研究表明,‘草原4号紫花苜蓿’的组织结构特征具有明显的抗虫特征,且其组织的抗虫特征比‘草原2号杂花苜蓿’更为突出。     

Palaeoenvironmental aspects of Late Ordovician Sericoidea shell concentrations in an impact crater,Tvären,Sweden

Frisk, Å.M. & Harper, D.A.T. 2010: Palaeoenvironmental aspects of Late Ordovician Sericoidea shell concentrations in an impact crater, Tvären, Sweden. Lethaia, Vol. 44, pp. 383–396. Numerous studies have reported the presence of the small, thin‐shelled cosmopolitan rhynchonelliformean Sericoidea as being environmentally controlled and, together with its close relatives, characteristic of deep‐water, distal, clastic Ordovician and Silurian settings. Assemblages of Sericoidea have been analysed from post‐impact strata in a newly formed Late Ordovician impact crater. In the crater succession, colonization of benthic faunas can be monitored through the post‐impact limestone, demonstrating a number of environmental preferences. Consequently, the crater, as a result of its restricted area, provides an experimental arena for faunal distributions to be correlated with specific environments. The continuous infilling of the crater following its formation reveals a transition from argillaceous mudstones to carbonates deposited in deeper‐water environments to shallower regimes. Rhynchonelliformean brachiopods inhabited the crater depression very late after the impact and are entirely represented by the genus Sericoidea, occurring abundantly in the upper third of the existing crater infill. The deep‐water regime that existed in the depression during the initial interval of crater formation had been substantially reduced. Clearly Sericoidea‐bearing associations associated with shaly substrates did not merely favour and occupy deep‐water environments as previously suggested. The unfavourable conditions triggered by the impact and the inhospitable aftermath allowed Sericoidea to exploit a less‐crowded ecospace. This reorganization, following the catastrophe, from a deep‐water related ecological niche to considerable shallower settings suggests that Sericoidea was a pioneer colonist displaying an opportunist r‐strategy. The shell beds analysed are related to shallower water and this may, moreover, help unravel the dilemma of the general absence of Sericoidea in the deeper‐water Foliomena fauna. □Dalby Limestone, impact crater, Late Ordovician, opportunists, Sericoidea, Tvären.