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1.
Ji Guo Su Xiao Ming Han Xiao Zhang Yan Xue Hou Jian Zhuo Zhu Yi Dong Wu 《Journal of biomolecular structure & dynamics》2016,34(3):560-571
Protein collective motions play a critical role in many biochemical processes. How to predict the functional motions and the related key residue interactions in proteins is important for our understanding in the mechanism of the biochemical processes. Normal mode analysis (NMA) of the elastic network model (ENM) is one of the effective approaches to investigate the structure-encoded motions in proteins. However, the motion modes revealed by the conventional NMA approach do not necessarily correspond to a specific function of protein. In the present work, a new analysis method was proposed to identify the motion modes responsible for a specific function of proteins and then predict the key residue interactions involved in the functional motions by using a perturbation approach. In our method, an internal coordinate that accounts for the specific function was introduced, and the Cartesian coordinate space was transformed into the internal/Cartesian space by using linear approximation, where the introduced internal coordinate serves as one of the axes of the coordinate space. NMA of ENM in this internal/Cartesian space was performed and the function-relevant motion modes were identified according to their contributions to the specific function of proteins. Then the key residue interactions important for the functional motions of the protein were predicted as the interactions whose perturbation largely influences the fluctuation along the internal coordinate. Using our proposed methods, the maltose transporter (MalFGK2) from E. Coli was studied. The functional motions and the key residue interactions that are related to the channel-gating function of this protein were successfully identified. 相似文献
2.
Although a number of recent studies have demonstrated biotic homogenization, these have mainly focused on larger spatial scales. Homogenizing effects are equally important at finer resolutions, e.g. through increasing similarity between habitats, which may result in a simplification of ecosystem structure and function. One major cause of homogenization is the expanding ranges of alien species, although it is not clear whether they are inherently homogenizing at smaller scales. We therefore assessed whether the alien flora is less complex across habitats than the resident native flora of Mediterranean Islands. From a regional data base, we examined floristic lists for between‐habitat taxonomic and functional similarity, and within‐habitat functional diversity, using resampled data sets to control for sample size biases. Aliens and natives showed equivalent complexity in most respects. At the taxonomic level, between‐island and between‐habitat similarities were almost identical, and when ecosystem function was measured by a functional group classification system, this was also true of between‐habitat similarities and within‐habitat diversities. When ecosystem function was measured using Grime's CSR classification, aliens were found to be more functionally homogenous between‐habitats and less functionally diverse within habitats. However, since the CSR profiles of aliens and natives differed, simplification is not inevitable due to ecological segregation of the two floras (aliens tend to be recruited to disturbed habitats rather than displacing natives). One deficiency is a lack of large scale species abundance data. A simple simulation exercise indicated that this is likely to lead to substantial overestimation of true levels of similarity, although would only influence the comparison between aliens and natives if they have different abundance distribution curves. The results indicate that alien floras are not intrinsically more simple than natives, but a higher proportion of competitive strategists among aliens may still cause small‐scale homogenization as these include many strong competitors that are likely to dominate communities. 相似文献
3.
We studied vegetation responses to disturbances originated by ants and voles in subalpine grasslands in the Eastern Pyrenees.
We compared the effects of these small-scale disturbances with those of a large-scale disturbance caused by ploughing. We
wanted to know if these soil disturbances promoted species richness through the existence of a specific guild of plants colonizing
these areas, and if this guild was the same for all soil disturbances, independently of their extent. In general, grassland
vegetation seemed to recover relatively quickly from soil-displacement disturbances, and the effects could be scaled up in
time and space in terms of species richness and composition. Vole mound composition was similar to that in the surrounding
grassland, suggesting that mounds were rapidly colonized by the neighbouring vegetation. Vegetation composition differed between
the grassland and the ant mounds. Grasses and erect dicots coped well with repeated disturbance, while rosette-forming species
and sedges were very sensitive to it. Landscape processes could be important to understanding recolonization. Species from
xeric grasslands were found in mesic grasslands when disturbed by ploughing and on the tops of active ant mounds. Furrows
in mesic grasslands recovered well, but decades after disturbance showed long persistence of some xeric species and increased
species richness compared to terraces, while xeric grasslands showed decreased richness. This suggests that, because of those
disturbances, within-habitat diversity was increased, although landscape diversity was not. However, specific disturbances
showed idiosyncratic effects, which could enhance the species richness globally. In ant-affected areas, the grassland itself
showed the highest plant species richness, partially associated to the presence of some species with elaiosomes not, or only
rarely, found in adjacent grasslands without ant mounds. Therefore, soil disturbances occurring at different spatial scales
contributed to complexity in vegetation patterns in addition to abiotic factors and grazing.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
Nomenclature of the species follows Tutin et al. (1964–1980) and Bolòs et al. (1993). 相似文献
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6.
T. Miedaner F. J. Fromme H. H. Geiger 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1995,91(6-7):862-868
The amount of genetic variation for resistance to foot rot caused by Pseudocercosporella herpotrichoides, Fusarium spp., and Microdochium nivale and for resistance to head blight caused by Fusarium culmorum are important parameters when estimating selection gain from recurrent selection in winter rye. One-hundred and eighty-six full-sib families of the selfincompatible population variety Halo, representing the Petkus gene pool, were tested for foot-rot resistance at five German location-year combinations (environments) and for head-blight resistance in three environments with artificial inoculation in all but one environment. Foot-rot rating was based on 25 stems per plot scored individually on a 1–9 scale. Head-blight resistance was plotwise scored on a 1–9 scale and, additionally, grain-weight per spike was measured relative to the non-inoculated control plots. Significant estimates of genotypic variance and medium-sized heritabilities (h
2=0.51–0.69) were observed in the combined analyses for all resistance traits. In four out of five environments, the amount of genetic variance was substantially smaller for foot-rot than for head-blight rating. Considerable environmental effects and significant genotype-environment interactions were found for both foot-rot and head-blight resistance. Coefficients of error-corrected correlation among environments were considerably closer than phenotypic correlations. No significant association was found between the resistances to both diseases (r=-0.20 to 0.17). In conclusion, intra-population improvement by recurrent selection should lead to substantial higher foot-rot and head-blight resistances due to significant quantitative genetic variation within Halo. Selection should be carried out in several environments. Lack of correlation between foot-rot and head-blight resistance requires separate infection tests for improving both resistances. 相似文献
7.
Field-measured grazing rates (ml/animal/d) of cladocerans (mostly daphniids) and diaptomids were assembled from various published
studies and plotted as a function of corresponding phytoplankton concentration (μg l−1 f.w.). Filtering rates of both zooplankton groups initially increased with seston concentration until maximal grazing rates
were observed at approximately 4 × 102 and 1 × 102 μg l−1 for cladocerans and copepods, respectively; at higher algal concentrations, filtering rates of both declined as a function
of food concentration. The shape of these curves are most consistent with Holling's (1966) Type 3 functional response.
We found little support for the Type 3 functional response in published laboratory studies of Daphnia; most investigators report either a Type 1 or Type 2 response. The one study in which the Type 3 response was observed involved
experiments where animals were acclimated at low food concentrations for 24 h, whereas those studies associated with response
Types 1 or 2 had acclimation periods of only 1 to 3 h. We therefore assembled relevant data from the literature to examine
the effect of acclimation period on the feeding rates of Daphnia at low food concentrations. In the absence of any acclimation, animals filtered at extremely low rates. After 2 h of acclimation,
however, filtering rates increased 4 to 5-fold but declined again with longer durations; after > 70 h of pre-conditioning,
filtering rates were almost as low as they had been with no acclimation.
We also found little support for the Type 3 functional response in published studies of copepods. The only study associated
with a Type 3 response involved a marine copepod that had been subjected to a starvation period of 48 h; however, an analysis
of the effects of acclimation period did not yield conclusive evidence that filtering rates of freshwater copepods (Diaptomus and Eudiaptomus) decrease significantly with acclimation duration.
The low filtering rates associated with long acclimation periods in laboratory experiments appears to be a direct result of
animals becoming emaciated from prolonged exposure to low food concentrations, a situation which renders them incapable of
high filtering rates. This may explain the Type 3 functional response for field cladocerans, since zooplankton in food-limiting
situations are constantly exposed to low food concentrations, and would therefore have low body carbon and consequently less
energy to filter-feed. We cannot, however, use this to explain the Type 3 response for field diaptomids, since copepods in
the laboratory did not appear to lose body carbon even after 72 h of feeding at very low food levels, and there was inconclusive
evidence that either Diaptomus or Eudiaptomus decrease their filtering rates with acclimation period.
Although Incipient Limiting Concentrations (ILC) for Daphnia ranged from 1 to 8.5 × 103 μg 1−1, more than half of these fell between 1 and 3 × 103 μg l−1, bracketing the value of 2.7 × 102 μg l−1 for field cladocerans. There was, however, a great deal of variation in reported maximum ingestion rates (MIR), maximum filtering
rates (MFR) and ILC values for Daphnia magna. ILC values from the few laboratory studies of freshwater copepods ranged between 0.5 to 2.8 × 103 μg 1−1, and was higher than the ILC value of approximately 0.2 × 103 μg l−1 calculated for field populations of D. minutus. Generally, there was considerable agreement among laboratory studies regarding the shape of grazing-rate and ingestion-rate
curves when data were converted to similar units and presented on standardized scales. 相似文献
8.
9.
K. Yoshikawa 《Journal of biological physics》2002,28(4):701-712
The mechanism of the self-regulation of gene expression in living cells is generally explained by considering complicated networks of key-lock relationships, and in fact there is a large body of evidence on a hugenumber of key-lock relationships. However, in the present article we stress that with the network hypothesis alone it is impossible to fully explain the mechanism of self-regulation in life. Recently, it has been established that individual giant DNA molecules, larger than several tens of kilo base pairs, undergo a large discrete transition in their higher-order structure. It has become clear that nonspecific weak interactions with various chemicals, suchas polyamines, small salts, ATP and RNA, cause on/off switching in the higher-order structure of DNA. Thus, the field parameters of the cellular environment should play important roles in the mechanism of self-regulation, in addition to networks of key and locks. This conformational transition induced by field parameters may be related to rigid on/off regulation, whereas key-lock relationships may be involved in a more flexible control of gene expression. 相似文献
10.
CLUE-S模型在南京市土地利用变化研究中的应用 总被引:8,自引:3,他引:5
土地利用/覆盖变化模型是研究区域景观动态并解释其驱动机制的重要技术手段.应用CLUE-S模型,在Landsat TM影像等相关数据支持下,对南京地区1998-2006年土地利用的时空动态变化进行了研究.结果表明:各土地利用类型变化受地形因素影响最大,人均GDP与城镇用地和农业用地的分布呈显著相关,城乡主干道对土地利用变化的贡献显著大于省级及以上道路;海拔较高区域林地的发生比率较高,而地形低平区域农田、城建用地的发生比率较高.经检验,在300 m空间分辨率水平,对南京地区2003年、2006年土地利用状况模拟的精度分别达到了85.7%和84.1%;而通过将研究区分成若干子区,分别修正模型参数并重新模拟,准确率提高到89.7%和88.3%,分区赋值法有效地提高了模拟精度.研究表明,CLUE-S模型对城市发展的空间结构也有较强的预测能力,对指导城市规划、分析景观动态的驱动机制有重要参考价值. 相似文献