Enhanced AFLP genome scans detect local adaptation in high-altitude populations of a small rodent (Microtus arvalis)

Adaptation to adverse environmental conditions such as high altitude requires physiological and/or morphological changes. Genome scans provide a means to identify the genetic basis of such adaptations without previous knowledge about the particular genetic variants or traits under selection. In this study, we scanned 3027 amplified fragment length polymorphisms (AFLP) in four populations of the common vole Microtus arvalis for loci associated with local adaptation and high altitude. We investigated voles from two populations at high elevation (~2000 m a.s.l.) representing the upper limit of the altitudinal distribution of the species and two geographically close low-altitude populations (<600 m a.s.l.). Statistical analysis incorporated a new Bayesian F(ST) outlier approach specifically developed for AFLP markers, which considers the intensity of AFLP bands instead of mere presence/absence and allows to derive population-based estimates of allele frequencies and F(IS) values. Computer simulations showed that this approach increases the statistical power of the detection of AFLP markers under selection almost to the power of single nucleotide polymorphism (SNP) data without compromising specificity. Our enhanced genome scan resulted in 20 prime candidate markers for positive selection, which show mostly extremely high allele frequency differences between the low- and high-altitude populations. The comparison of global- and pairwise-enhanced genome scans demonstrated further that very strong selective signatures may also be associated with single populations suggesting the importance of local adaptation in alpine populations of common voles.     

Bioavailability to Fish of Sediment PAH as an Indicator of the Success of In Situ Remediation Treatments at an Experimental Oil Spill

A weathered medium crude oil was applied to experimental plots of Scirpus pungens (Three-square Bulrush) in a freshwater wetland to determine the efficacy of strategies for shoreline oil spill bioremediation based on nutrient enrichment (bioremediation) and plant growth (phytoremediation). Plots were unoiled, oiled with no added nutrients, or oiled with repeated applications of phosphate and nitrate fertilizers. Following initial treatments, the experimental plots were raked to simulate the activity of wave action on oil penetration, and plants in one fertilized plot were cut repeatedly. The sediments were sampled at regular intervals for 15 months after oiling, and the loss of oil was assessed by 4-day laboratory tests of polynuclear aromatic hydrocarbon (PAH) bioaccumulation by trout, as demonstrated by increases in activity of liver cytochrome P450 (CYP1A) enzymes. Oil alone, oil mixed with sediments in the lab, and oiled sediments from treated plots all induced CYP1A activity relative to untreated controls, indicating the presence and bioavailability of PAH. Induction did not vary with nutrient treatments, but declined by 80% within 15 months of oiling, and chemical analyses indicated equivalent losses of hydrocarbons in sediment. These results demonstrate that bioavailable PAHs persisted in measurable quantities for at least 1.25 years following oiling, and that stimulation of plant growth did not affect the rate of oil disappearance. The controlling factors were likely weathering and sediment movement.     

A continuum theoretical model and finite elements simulation of bacterial flagellar filament phase transition

The Bacterial flagellar filament can undergo a polymorphic phase transition in response to both mechanical and chemical variations in vitro and in vivo environments. Under mechanical stimuli, such as viscous flow or forces induced by motor rotation, the filament changes its phase from left-handed normal (N) to right-handed semi-coiled (SC) via phase nucleation and growth. Our detailed mechanical analysis of existing experiments shows that both torque and bending moment contribute to the filament phase transition. In this paper, we establish a non-convex and non-local continuum model based on the Ginzburg-Landau theory to describe main characteristics of the filament phase transition such as new-phase nucleation, growth, propagation and the merging of neighboring interfaces. The finite element method (FEM) is adopted to simulate the phase transition under a displacement-controlled loading condition (rotation angle and bending deflection). We show that new-phase nucleation corresponds to the maximum torque and bending moment at the stuck end of the filament. The hysteresis loop in the loading and unloading curves indicates energy dissipation. When the new phase grows and propagates, torque and bending moment remain static. We also find that there is a drop in load when the two interfaces merge, indicating a concomitant reduction in the interfacial energy. Finally, the interface thickness is governed by the coefficients of the gradient of order parameters in the non-local interface energy. Our continuum theory and the finite element method provide a method to study the mechanical behavior of such biomaterials.     

沼液的定价方法及其应用效果研究

为了探索沼液的商品化,采用养分含量定价和应用效果定价2种方法确定了沼液的价格,并分析了沼液施用后对土壤基本理化性状的影响作用。结果发现:采用养分含量定价法得到的沼液价格为78.12元/m³,采用沼液应用效果定价法得到的沼液的价格为111.4元/ m³;沼液的实际应用价值要明显高于其养分含量的市场价;沼液施用后可降低土壤容重,增加土壤孔隙度,增加土壤有机质、土壤全氮、土壤有效磷及有效钾含量,有利于土壤肥力的保持。     

Modelling the fracture-healing process as a moving-interface problem using an interface-capturing approach

We present a novel numerical model of the fracture-healing process using interface-capturing techniques, a well-known approach from fields like fluid dynamics, to describe tissue growth. One advantage of this method is its direct connection to experimentally observable parameters, including tissue-growth velocities. In our model, osteogenesis, chondrogenesis and revascularisation are triggered by mechanical stimuli via mechano-transduction based on previously established hypothesis of Claes and Heigele. After experimentally verifying the convergence of the numerical method, we compare the predictions of our model with those of the already established Ulm bone-healing model, which serves as a benchmark, and corroborate our results with existing animal experiments. We demonstrate that the new model can predict the history of the interfragmentary movement and forecast a tissue evolution that appears similar to the experimental results. Furthermore, we compare the relative tissue concentration in the healing domain with outcomes of animal experiments. Finally, we discuss the possible application of the model to new fields, where numerical simulations could also prove beneficial.     

Calculations of apparent ruminal synthesis and intestinal absorption of biotin in dairy cows as influenced by the extraction method

Abstract

Biotin is present in nature either free or as biocytin, which is only degraded under the action of a specific enzyme: biotinidase. This enzyme is not included in analytical assays generally used. A method for sample preparation using biotinidase was developed in our laboratory before analysis by ELISA. Three cows equipped with duodenal and ileal cannulae were used to compare the effects of methods of sample preparation on calculations of apparent ruminal synthesis and intestinal absorption of biotin. There was no apparent ruminal synthesis of biotin, no matter whether free or total biotin was measured (p = 0.84). Results also suggested that rumen microbes cannot utilize nor degrade biocytin present in the feed. Estimates of apparent intestinal absorption were influenced by the sample preparation method (p = 0.002). Analysis of free biotin caused an artefact, suggesting intestinal synthesis of this vitamin; whereas determination of total biotin concentrations showed that absorption was taking place in the small intestine.     

南京地区12种常绿阔叶树种冬季抗寒性动态变化

选取南京地区露地引种的12种常绿阔叶树种,借助电导法对其抗寒性进行研究,结果表明:12种常绿树种在2003年与2005年冬季期间,抗寒能力高低排序具有很好的一致性与重复性.12种常绿树种在2005年10月至2006年3月期间随冬季低温诱导进行其抗寒能力呈逐渐增强趋势,其中在1月中旬树种抗寒能力均达到最强,而通常在10月份或3月份期间树种抗寒能力最弱.比较而言,12种常绿阔叶树种对冬季低温条件响应的快慢程度各有差异,其中樟科的香樟(Cinnamomum camphora)、浙江樟(Cinnamomum japonicum)属于低温快速响应型,而冬青科的冬青(Ilex purpurea)、大叶冬青(Ilex latifolia)属于低温滞缓响应型,其余树种为正常响应型.12种常绿阔叶树种试验所得抗寒能力结果与引种地冬季观察结果具有很好的对应性.研究结果可为常绿阔叶树种进一步向较高纬度地区的引种与栽培管理工作提供重要的参考.     

Role of a reaction coordinate in free energy calculations

Abstract

The free energy calculation method emerges as a viable technique for ‘in-silico’ calorimetry. Efficient sampling techniques and the good choice of a reaction path connecting the reactant and the product state enable accurate computations of the free energy differences. We argue that in many cases the thermodynamic integration technique has the lowest variance when the transformation between the reactant and the product state proceeds along the natural path of the studied chemical reaction. We provide examples of free energy calculations for the fragmentation of the charged clusters and the swapping reaction of oligomer formation in proteins that follow a tentative reaction mechanism.     

鼎突多刺蚁脑部组织切片方法初探及其脑部结构

膜翅目昆虫蚂蚁具有明显的多态现象,社会性生活中的分工亦非常明确。而作为蚁科中的鼎突多刺蚁还有着较高的药用保健价值。因此对其神经系统的研究有着重要的生物学意义。但蚂蚁脑部坚硬的外骨骼使得对其的组织学切片有一定难度。本试验即对鼎突多刺蚁的脑部组织切片方法进行了摸索和研究。