Microsecond simulations of mdm2 and its complex with p53 yield insight into force field accuracy and conformational dynamics

The p53‐MDM2 complex is both a major target for cancer drug development and a valuable model system for computational predictions of protein‐ligand binding. To investigate the accuracy of molecular simulations of MDM2 and its complex with p53, we performed a number of long (200 ns to 1 µs) explicit‐solvent simulations using a range of force fields. We systematically compared nine popular force fields (AMBER ff03, ff12sb, ff14sb, ff99sb, ff99sb‐ildn, ff99sb‐ildn‐nmr, ff99sb‐ildn‐phi, CHARMM22*, and CHARMM36) against experimental chemical shift data, and found similarly accurate results, with microsecond simulations achieving better agreement compared to 200‐ns trajectories. Although the experimentally determined apo structure has a closed binding cleft, simulations in all force fields suggest the apo state of MDM2 is highly flexible, and able to sample holo‐like conformations, consistent with a conformational selection model. Initial structuring of the MDM2 lid region, known to competitively bind the binding cleft, is also observed in long simulations. Taken together, these results show molecular simulations can accurately sample conformations relevant for ligand binding. We expect this study to inform future computational work on folding and binding of MDM2 ligands. Proteins 2015; 83:1665–1676. © 2015 Wiley Periodicals, Inc.     

Effects of pine wilt disease invasion on soil properties and Masson pine forest communities in the Three Gorges reservoir region,China

Pine wilt disease (PWD) has caused significant Masson pine mortality in the Three Gorges reservoir region in central China. In this study, five uniform Masson pine stand types infected by PWD were selected and surveyed on slopes and aspects with similar environmental conditions. In sites that had been infected, soil bulk density was reduced, and the difference among the groups was statistically significant (P < 0.05) at the 0–10 cm and 10–20 cm soil layers, but not at 20–40 cm. Other soil water‐related physical properties, excluding noncapillary porosity, significantly differed among the groups in all soil layers. Additionally, the values of available phosphorus, sodium, potassium, calcium, and magnesium were higher in the invaded stands, but the total nitrogen and organic matter contents were lower. Masson pine does not become reestablished following PWD‐induced mortality but is instead replaced by broad‐leaved tree species. Among the 19 examined environmental variables, five were found to be significantly related with the ordination of plant community structure: Masson pine stumps (MPS), K⁺, capillary water holding capacity (CWHC), capillary porosity (CP), and soil water content (SWC). Among these factors, the plant community structure was principally related to MPS and K⁺. The findings of this study show that the outbreak of PWD has impacted Masson pine forest soil properties and altered forest community composition. The disease is negatively related with the presence of Masson pine and positively associated with that of broad‐leaved tree species.     

Multiple forms and specificity of coniferyl alcohol dehydrogenase from cambial regions of higher plants

Alcohol dehydrogenases of 89 species of plants, from the Bryophyta, Pteridophyta, Gymnosperms and Angiosperms were examined by starch gel electrophoresis for their substrate and coenzyme specificities. High activities and multiple bands were observed with EtOH and NAD in most species. The same, but weaker banding patterns were also observed with benzyl alcohol and salicin. When coniferyl alcohol was used as substrate, activity was found only with NADP as coenzyme and the resulting bands were distinct from those obtained with the other substrates. Most plants tested had only one or occasionally a second coniferyl alcohol dehydrogenase band. Salix species were an exception, with multiple bands found in each of the species tested.     

Enrichment of a common wheat genetic map and QTL mapping for fatty acid content in grain

DArT and SSR markers were used to saturate and improve a previous genetic map of RILs derived from the cross Chuan35050 × Shannong483. The new map comprised 719 loci, 561 of which were located on specific chromosomes, giving a total map length of 4008.4 cM; the rest 158 loci were mapped to the most likely intervals. The average chromosome length was 190.9 cM and the marker density was 7.15 cM per marker interval. Among the 719 loci, the majority of marker loci were DArTs (361); the rest included 170 SSRs, 100 EST-SSRs, and 88 other molecular and biochemical loci. QTL mapping for fatty acid content in wheat grain was conducted in this study. Forty QTLs were detected in different environments, with single QTL explaining 3.6-58.1% of the phenotypic variations. These QTLs were distributed on 16 chromosomes. Twenty-two QTLs showed positive additive effects, with Chuan35050 increasing the QTL effects, whereas 18 QTLs were negative with increasing effects from Shannong483. Six sets of co-located QTLs for different traits occurred on chromosomes 1B, 1D, 2D, 5D, and 6B.     

雌先熟植物茄参（茄科）的繁育系统

对分布于云南西北部的茄参（Mandragoraca caulescens）的繁育系统进行了研究。茄参的花期为5月底到6月初,单花持续时间为（9．9±2．8）d,其性表达方式为雌性先熟。有三种昆虫拜访茄参的花,白背熊蜂蜂王是最有效的传粉昆虫,但其访花频率很低;苍蝇和蚂蚁的访花频率较高,但苍蝇传粉效率十分有限;蚂蚁是窃蜜者。授粉实验证明茄参具有部分自交亲和能力,但由于雌性先熟,不具备主动自交能力。人工添加异交花粉显著提高了结实率和结籽数,证明茄参存在花粉限制。茄科的大部分植物是严格自交不亲和的,但茄参族的茄参是自交部分亲和,这和茄科天仙子族的部分成员类似。我们认为这两个独立起源于新世界向欧亚大陆扩散事件的族,各自从自交不亲和向自交亲和转变可能与高山地区恶劣的自然条件有关,这种繁育系统的进化模式是否具有普遍性值得进一步研究。     

中国油橄榄适生区研究

油橄榄在中国引种已50多年,引种初期对其特殊的生态习性了解不够深入,出现了许多问题。作者从近40年的栽培实践中,认真分析了我国亚热带地区与地中海亚热带地区气候的差异,认为中国发展油橄榄生产的最佳适生区是西部干旱河谷地区,其中以甘南自龙江河谷和滇西北及川西南金沙江河谷发展的潜力最大。     

Filter materials for phosphorus removal from wastewater in treatment wetlands—A review

This paper aims to collect and analyse existing information on different filter media used for phosphorus (P) removal from wastewater in constructed wetlands. The most commonly used materials are categorized as natural materials (considered in 39 papers), industrial byproducts (25 papers) and man-made products (10 papers). A majority of studies on sorbents have been carried out in lab-scale systems as batch experiments, and only very few studies have highlighted results on full-scale systems. Among the great variety of filter media studied, most of materials had a pH level >7 and high Ca (CaO) content. The highest P-removal capacities were reported for various industrial byproducts (up to 420 g P kg⁻¹ for some furnace slags), followed by natural materials (maximum 40 g P kg⁻¹ for heated opoka) and man-made filter media (maximum 12 g P kg⁻¹ for Filtralite). We found a significant positive Spearman Rank Order Correlation between the P retention and CaO and Ca content of filter materials (R² = 0.51 and 0.43, respectively), whereas the relation of P retention to pH level was weak (R² = 0.22) but significant. There is probably an optimal level of hydraulic loading rate at which the P removal is the highest. Additional important factors determining the applicability of filter materials in treatment wetlands such as saturation time, availability at a local level, content of heavy metals, and the recyclability of saturated filter media as fertilizer should be taken into consideration.     

直突摇蚊亚科部分属28S rDNA D1序列的分子系统发育关系(双翅目,摇蚊科)

利用28S rDNA D1部分基因序列对直突摇蚊亚科代表性属级阶元进行了分子系统学研究。测定了12个内群属和2种外群的28SrDNAD1片段,并结合GenBank中3个同亚科种类该基因的同源序列进行了分析。采用2种建树方法(距离邻近法NJ和最大俭约法MP)分析了直突摇蚊亚科内属级分类单元的分子系统发育关系。结果表明,滨海摇蚊属Clunio位于系统发育树的基部,与该属营海洋生活的特殊性一致。心突摇蚊属和真开氏摇蚊属互为姐妹群,流环足摇蚊属和刀突摇蚊属互为姐妹群,此结果与基于形态学的系统发育研究相结果一致。其它属间的系统发育关系因尚无前人研究而有待做进一步研究。本研究同时证明28S rDNA D1基因片段在分析摇蚊科昆虫属级及属内阶元关系上具有一定的指导意义。     

猪细小病毒VP2蛋白N端甘氨酸富集区的缺失对病毒样颗粒形成及免疫原性的影响

猪细小病毒(PPV)VP2蛋白N端连续9个甘氨酸富集的编码区是VP3蛋白的切割位点,常规PCR扩增容易导致该区段的缺失,为研究该缺失对PPV病毒样颗粒(VLPs)的影响,探索VP2病毒样颗粒上适合外源基因插入的位点,构建了该区段缺失的VP2的真核表达载体pCI-△VP2,并以完整VP2作为对照,采用脂质体介导法转染Vero细胞,通过生物信息学技术、SDS-PAGE、Western blotting、间接免疫荧光以及正染和免疫电镜对表达产物进行分析观察;进一步将重组质粒以核酸疫苗的方式直接肌注免疫小鼠,采用间接ELISA试验、淋巴细胞增殖试验和T细胞亚群流式细胞技术,分析免疫小鼠的体液和细胞免疫应答.结果显示,缺失△VP2和完整VP2在Vero细胞中均能自我装配成VLPs,并具有与完整病毒粒子类似血凝性,pCI-△VP2和pCI-VP2均可诱导小鼠产生较强的特异性体液免疫应答和良好的细胞免疫应答.结果表明,甘氨酸富集区的缺失不影响VP2病毒样颗粒的装配和免疫原性,△VP2同样可进行PPV VLPs疫苗和抗原转运载体的研制,为VLPs载体改造和修饰位点的探索提供了新方向,为VP2基因结构与蛋白质功能的关系提供了新的理论依据.