Quantifying soil organic carbon in complex landscapes: an example of grassland undergoing encroachment of woody plants

The invasion of woody plants into grass‐dominated ecosystems has occurred worldwide during the past century with potentially significant impacts on soil organic carbon (SOC) storage, ecosystem carbon sequestration and global climate warming. To date, most studies of tree and shrub encroachment impacts on SOC have been conducted at small scales and results are equivocal. To quantify the effects of woody plant proliferation on SOC at broad spatial scales and to potentially resolve inconsistencies reported from studies conducted at fine spatial scales, information regarding spatial variability and uncertainty of SOC is essential. We used sequential indicator simulation (SIS) to quantify spatial uncertainty of SOC in a grassland undergoing shrub encroachment in the Southern Great Plains, USA. Results showed that both SOC pool size and its spatial uncertainty increased with the development of woody communities in grasslands. Higher uncertainty of SOC in new shrub‐dominated communities may be the result of their relatively recent development, their more complex above‐ and belowground architecture, stronger within‐community gradients, and a greater degree of faunal disturbance. Simulations of alternative sampling designs demonstrated the effects of spatial uncertainty on the accuracy of SOC estimates and enabled us to evaluate the efficiency of sampling strategies aimed at quantifying landscape‐scale SOC pools. An approach combining stratified random sampling with unequal point densities and transect sampling of landscape elements exhibiting strong internal gradients yielded the best estimates. Complete random sampling was less effective and required much higher sampling densities. Results provide novel insights into spatial uncertainty of SOC and its effects on estimates of carbon sequestration in terrestrial ecosystem and suggest effective protocol for the estimating of soil attributes in landscapes with complex vegetation patterns.     

Molecular dynamics simulation of dark-adapted rhodopsin in an explicit membrane bilayer: coupling between local retinal and larger scale conformational change

The light-driven photocycle of rhodopsin begins the photoreceptor cascade that underlies visual response. In a sequence of events, the retinal covalently attached to the rhodopsin protein undergoes a conformational change that communicates local changes to a global conformational change throughout the whole protein. In turn, the large-scale protein change then activates G-proteins and signal amplification throughout the cell. The nature of this change, involving a coupling between a local process and larger changes throughout the protein, may be important for many membrane proteins. In addition, functional work has shown that this coupling occurs with different efficiency in different lipid settings. To begin to understand the nature of the efficiency of this coupling in different lipid settings, we present a molecular dynamics study of rhodopsin in an explicit dioleoyl-phosphatidylcholine bilayer. Our system was simulated for 40 ns and provides insights into the very early events of the visual cascade, before the full transition and activation have occurred. In particular, we see an event near 10 ns that begins with a change in hydrogen bonding near the retinal and that leads through a series of coupled changes to a shift in helical tilt. This type of event, though rare on the molecular dynamics time-scale, could be an important clue to the types of coupling that occur between local and large-scale conformational change in many membrane proteins.     

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.     

短杆菌肽通道内离子K~＋，Na~＋，Li~＋与水的相关性

基于右手螺旋短杆菌肽Ａ离子通道模型,利用分子动力学计算机模拟方法研究了通道内离子Ｋ＋,Ｎａ＋,Ｌｉ＋与水分子的相关性．     

Setting up and running molecular dynamics simulations of membrane proteins

Molecular dynamics simulations have become a popular and powerful technique to study lipids and membrane proteins. We present some general questions and issues that should be considered prior to embarking on molecular dynamics simulation studies of membrane proteins and review common simulation methods. We suggest a practical approach to setting up and running simulations of membrane proteins, and introduce two new (related) methods to embed a protein in a lipid bilayer. Both methods rely on placing lipids and the protein(s) on a widely spaced grid and then 'shrinking' the grid until the bilayer with the protein has the desired density, with lipids neatly packed around the protein. When starting from a grid based on a single lipid structure, or several potentially different lipid structures (method 1), the bilayer will start well-packed but requires more equilibration. When starting from a pre-equilibrated bilayer, either pure or mixed, most of the structure of the bilayer stays intact, reducing equilibration time (method 2). The main advantages of these methods are that they minimize equilibration time and can be almost completely automated, nearly eliminating one time consuming step in MD simulations of membrane proteins.     

喀斯特高原山地石漠化区叶蝉群落结构及其多样性动态变化

为了探讨喀斯特石漠化治理区叶蝉群落对生态功能变动的动态响应,在中国贵州毕节撒拉溪朝营小流域按不同等级石漠化程度设置样地,并设置响应对照组,在2013-2014年5-10月每月对样地进行野外调查,系统采集叶蝉标本和在室内开展生物多样性研究,以期分析高原山地不同等级石漠化程度下叶蝉群落的时空格局,特别是对石漠化治理效果的生态学响应。结果表明,共采得叶蝉3049头,隶属11亚科53属,其中优势类群为小叶蝉亚科、角顶叶蝉亚科、大叶蝉亚科,分别占总数的44.70%、21.78%、14.66%。与对照组相比,治理区内样地叶蝉的属数、个体数都有增加,并表现出明显的季节变动,在7月、8月物种丰富度指数最高;随着石漠化治理的深入,叶蝉种数、个体数呈增加趋势。总体上,石漠化等级与叶蝉群落结构特征指数呈现显著的负相关,石漠化等级越低,叶蝉的Shannon-Wiener多样性指数和Margale丰富度指数越大。各等级石漠化样地的Pieluo均匀度指数与优势度指数呈现反向耦合。     

Computational fluid dynamics endpoints for assessment of adenotonsillectomy outcome in obese children with obstructive sleep apnea syndrome

Background

Improvements in obstructive sleep apnea syndrome (OSAS) severity may be associated with improved pharyngeal fluid mechanics following adenotonsillectomy (AT). The study objective is to use image-based computational fluid dynamics (CFD) to model changes in pharyngeal pressures after AT, in obese children with OSAS and adenotonsillar hypertrophy.

Methods

Three-dimensional models of the upper airway from nares to trachea, before and after AT, were derived from magnetic resonance images obtained during wakefulness, in a cohort of 10 obese children with OSAS. Velocity, pressure, and turbulence fields during peak tidal inspiratory flow were computed using commercial software. CFD endpoints were correlated with polysomnography endpoints before and after AT using Spearman?s rank correlation (r_s).

Results

Apnea hypopnea index (AHI) decreases after AT was strongly correlated with reduction in maximum pressure drop (dP_TAmax) in the region where tonsils and adenoid constrict the pharynx (r_s=0.78, P=0.011), and with decrease of the ratio of dP_TAmax to flow rate (r_s=0.82, P=0.006). Correlations of AHI decrease to anatomy, negative pressure in the overlap region (including nasal flow resistance), or pressure drop through the entire pharynx, were not significant. In a subgroup of subjects with more than 10% improvement in AHI, correlations between flow variables and AHI decrease were stronger than in all subjects.

Conclusions

The correlation between change in dP_TAmax and improved AHI suggests that dP_TAmax may be a useful index for internal airway loading due to anatomical narrowing, and may be better correlated with AHI than direct airway anatomic measurements.     

Human erythrocyte flickering: temperature,ATP concentration,water transport,and cell aging,plus a computer simulation

Images of human erythrocytes from a healthy donor were recorded under differential interference contrast (DIC) microscopy; they were acquired rapidly (~336 Hz) and the intensity of the centermost pixel of each cell was recorded for ~60 s (20,000 values). Various techniques were used to analyze the data, including detrended fluctuation analysis (DFA) and multiscale entropy (MSE); however, power spectrum analysis was deemed the most appropriate for metrifying and comparing results. This analysis was used to compare cells from young and old populations, and after perturbing normal conditions, with changes in temperature, adenosine triphosphate (ATP) concentration (using NaF, an inhibitor of glycolysis, and α-toxin, a pore-forming molecule used to permeabilize red cells to ATP), and water transport rates [using glycerol, and p-chloromercuriphenylsulfonic acid (pCMBS) to inhibit aquaporins, AQPs]. There were measurable differences in the membrane fluctuation characteristics in populations of young and old cells, but there was no significant change in the flickering time series on changing the temperature of an individual cell, by depleting it of ATP, or by competing with the minor water exchange pathway via AQP3 using glycerol. However, pCMBS, which inhibits AQP1, the major water exchange pathway, inhibited flickering in all cells, and yet it was restored by the membrane intercalating species dibutyl phthalate (DBP). We developed a computer model to simulate acquired displacement spectral time courses and to evaluate various methods of data analysis, and showed how the flexibility of the membrane, as defined in the model, affects the flickering time course.