下辽河平原降雨中氮素的动态变化

为了了解降雨中氮对农田生态系统的影响,分析了2004-2006年下辽河平原连续3年定位收集的降雨观测资料与历史资料.结果表明:降雨中氮输入量季节变化显著,夏季最高,这主要与降雨量及空气中NH4 -N浓度变化有关;降雨中DON量与NO3--N含量相当,均接近24%,是雨水中氮的重要组分;与1985年相比,近3年降雨输入到该地区农田生态系统的年氮通量已有较大提高,降雨较多的2005年输入的无机氮量更是20年前的2倍以上;2004-2006年随降雨输入农田生态系统的氮平均占可利用肥料氮的28.3%,对农田生态系统有着重要影响.     

Hydrogen bond analysis of confined water in mesoporous silica using the reactive force field

ABSTRACT

The structural and dynamical properties of water confined in nanoporous silica with a pore diameter of 2.7?nm were investigated by performing large-scale molecular dynamics simulations using the reactive force field. The radial distribution function and diffusion coefficient of water were calculated, and the values at the centre of the pore agreed well with experimental values for real water. In addition, the pore was divided into thin coaxial layers, and the average number of hydrogen bonds, hydrogen bond lifetime and hydrogen bond strength were calculated as a function of the radial distance from the pore central axis. The analysis showed that hydrogen bonds involving silanol (Si–OH) have a longer lifetime, although the average number of hydrogen bonds per atom does not change from that at the pore centre. The longer lifetime, as well as smaller diffusion coefficient, of these hydrogen bonds is attributed to their greater strength.     

Insights on Na+ binding and conformational dynamics in multidrug and toxic compound extrusion transporter NorM

MATE (multidrug and toxic compound extrusion) transporter proteins mediate metabolite transport in plants and multidrug resistance in bacteria and mammals. MATE transporter NorM from Vibrio cholerae is an antiporter that is driven by Na+ gradient to extrude the substrates. To understand the molecular mechanism of Na+‐substrate exchange, molecular dynamics simulation was performed to study conformational changes of both wild‐type and mutant NorM with and without cation bindings. Our results show that NorM is able to bind two Na⁺ ions simultaneously, one to each of the carboxylic groups of E255 and D371 in the binding pocket. Furthermore, this di‐Na⁺ binding state is likely more efficient for conformational changes of NorM_VC toward the inward‐facing conformation than single‐Na⁺ binding state. The observation of two Na⁺ binding sites of NorM_VC is consistent with the previous study that two sites for ion binding (denoted as Na1/Na2 sites) are found in the transporter LeuT and BetP, another two secondary transporters. Taken together, our findings shed light on the structure rearrangements of NorM on Na⁺ binding and enrich our knowledge of the transport mechanism of secondary transporters. Proteins 2014; 82:240–249. © 2013 Wiley Periodicals, Inc.     

Effects of increased temperature on plant communities depend on landscape location and precipitation

Global climate change is affecting and will continue to affect ecosystems worldwide. Specifically, temperature and precipitation are both expected to shift globally, and their separate and interactive effects will likely affect ecosystems differentially depending on current temperature, precipitation regimes, and other biotic and environmental factors. It is not currently understood how the effects of increasing temperature on plant communities may depend on either precipitation or where communities lie on soil moisture gradients. Such knowledge would play a crucial role in increasing our predictive ability for future effects of climate change in different systems. To this end, we conducted a multi‐factor global change experiment at two locations, differing in temperature, moisture, aspect, and plant community composition, on the same slope in the northern Mongolian steppe. The natural differences in temperature and moisture between locations served as a point of comparison for the experimental manipulations of temperature and precipitation. We conducted two separate experiments, one examining the effect of climate manipulation via open‐top chambers (OTCs) across the two different slope locations, the other a factorial OTC by watering experiment at one of the two locations. By combining these experiments, we were able to assess how OTCs impact plant productivity and diversity across a natural and manipulated range of soil moisture. We found that warming effects were context dependent, with the greatest negative impacts of warming on diversity in the warmer, drier upper slope location and in the unwatered plots. Our study is an important step in understanding how global change will affect ecosystems across multiple scales and locations.     

C1188D mutation abolishes specific recognition between MLL1-CXXC domain and CpG site by inducing conformational switch of flexible N-terminal

Mixed lineage leukemia protein (MLL1 protein) recognizes the CpG site via its CXXC domain and is frequently associated with leukemia. The specific recognition is abolished by C1188D mutation, which also prevents MLL-related leukemia. In this paper, multiple molecular dynamic (MD) simulations were performed to investigate the mechanism of recognition and influences of C1188D mutation. Started from fully dissociated DNA and MLL1-CXXC domain, remarkably, the center of mass (COM) of MLL1-CXXC domain quickly concentrates on the vicinity of the CpG site in all 53 short MD simulations. Extended simulations of the wild type showed that the native complex formed in 500 ns among 4 of 53 simulations. In contrast, the C1188D mutant COM distributed broadly around the DNA and the native complex was not observed in any of the extended simulations. Simulations on the apo MLL1-CXXC domain further suggest that the wild type protein remained predominantly in an open form that closely resembles its structure in the native complex whereas C1188D mutant formed predominantly compact structures in which the N- terminal bends to D1188. This conformational switch hinders the formation of encounter complex, thus abolishes the recognition. Our study also provides clues to the study mechanism of recognition, by the CXXC domain from proteins like DNA methyltransferase and ten-eleven translocation enzymes.     

Structural dynamics of the mitochondrial ADP/ATP carrier revealed by molecular dynamics simulation studies

The mitochondrial adenosine diphosphate/adenosine triphosphate (ADP/ATP) carrier has been recently crystallized in complex with its specific inhibitor carboxyatractyloside (CATR). In the crystal structure, the six-transmembrane helix bundle that defines the nucleotide translocation pathway is closed on the matrix side due to sharp kinks in the odd-numbered helices. The closed conformation is further sealed by the loops protruding into the matrix that interact through an intricate network of charge-pairs. To gain insight into its structural dynamics we performed molecular dynamics (MD) simulation studies of the ADP/ATP carrier with and without its cocrystallized inhibitor. The two trajectories sampled a conformational space around two different configurations characterized by distinct salt-bridge networks with a significant shift from inter- to intrarepeat bonding on the matrix side in the absence of CATR. Analysis of the geometrical parameters defining the transmembrane helices showed that even-numbered helices can undergo a face rotation, whereas odd-numbered helices can undergo a change in the wobble angle with a conserved proline acting as molecular hinge. Our results provide new information on the dynamical properties of the ADP/ATP carrier and for the first time yield a detailed picture of a stable carrier conformation in absence of the inhibitor.     

Rain use efficiency as affected by climate warming and biofuel harvest: results from a 12‐year field experiment

The efficiency of a terrestrial ecosystem to use rainfall in production is critical in regulating the ecological functions of the earth system under global change. However, it remains unclear how rain use efficiency (RUE) will be altered by changes in climate and human activities such as biofuel harvest. In this study, we used RUE data from a long‐term experiment in a tallgrass prairie to analyze the effects of warming and biofuel harvest (clipping). From 2000 to 2011, experimental warming enhanced RUE in most years, with larger positive effects in normal and wet than dry hydrological years. Clipping decreased RUE in dry and normal hydrological years, but had no impact on RUE in wet years. The observed RUE responses resulted from treatment‐induced changes in both biologically ineffective (i.e., runoff and soil evaporation) and effective (i.e., transpiration) parts of precipitation. For example, litter cover was increased in warming plots, but reduced by clipping, leading to negative and positive effects on runoff and soil evaporation, respectively. The dominance of C₄ species, which usually have higher water use efficiency than C₃ species, was enhanced by warming, but reduced by clipping. Moreover, RUE was positively correlated with ratios of rainfall in the late growing season (June–August), when the growth of C₄ plants was most active, relative to that in the other seasons. Our results indicate that RUE is positively influenced by climate warming, but negatively affected by biofuel harvest in tallgrass prairie of the Great Plains. These findings highlight the important roles of plant community structure and temporal distribution of precipitation in regulating ecosystem RUE.