Low genetic diversity and population connectivity fuel vulnerability to climate change for the Tertiary relict pine Pinus bungeana

Endemic species are important components of regional biodiversity and hold the key to understanding local adaptation and evolutionary processes that shape species distributions. This study investigated the biogeographic history of a relict conifer Pinus bungeana Zucc. ex Endl. confined to central China. We examined genetic diversity in P. bungeana using genotyping-by-sequencing and chloroplast and mitochondrial DNA markers. We performed spatial and temporal inference of recent genetic and demographic changes, and dissected the impacts of geography and environmental gradients on population differentiation. We then projected P. bungeana's risk of decline under future climates. We found extremely low nucleotide diversity (average π 0.0014), and strong population structure (global F_ST 0.234) even at regional scales, reflecting long-term isolation in small populations. The species experienced severe bottlenecks in the early Pliocene and continued to decline in the Pleistocene in the western distribution, whereas the east expanded recently. Local adaptation played a small (8%) but significant role in population diversity. Low genetic diversity in fragmented populations makes the species highly vulnerable to climate change, particularly in marginal and relict populations. We suggest that conservation efforts should focus on enhancing gene pool and population growth through assisted migration within each genetic cluster to reduce the risk of further genetic drift and extinction.     

STABILIZATION MECHANISM IN SWIMMING ODONTOCETE CETACEANS BY PHASED MOVEMENTS

Propulsive movements of the caudal oscillating flukes produce large forces that could induce equally large recoil forces at the cranial end of the animal, and, thus, affect stability. To examine these vertical oscillations, video analysis was used to measure the motions of the rostrum, pectoral flipper, caudal peduncle, and fluke tip for seven odontocete cetaceans: Delphinapterus leucas, Globicephala melaena, Lagenorhynchus obliquidens, Orcinus orca, Pseudorca crassidens, Stenella plagiodon , and Tursiops truncatus. Animals swam over a range of speeds of 1.4–7.30 m/sec. For each species, oscillatory frequency of the fluke tip increased linearly with swimming speed. Peak-to-peak amplitude at each body position remained constant with respect to swimming speed for all species. Mean peak-to-peak amplitude ranged from 0.02 to 0.06 body length at the rostrum and from 0.17 to 0.25 body length at the fluke tip. The phase relationships between the various body components remain constant with respect to swimming speed. Oscillations of the rostrum were nearly in phase with the fluke tip with phase differences out of—9.4°-33.0° of a cycle period of 360°. Pectoral flipper oscillations trailed fluke oscillations by 60.9°-123.4°. The lower range in amplitude at the rostrum compared to the fluke tip reflects increased resistance to vertical oscillation at the cranial end, which enhances the animal's stability. This resistance is likely due to both active and passive increased body stiffness, resistance on the flippers, phased movements of body components, and use of a lift-based propulsion. Collectively, these mechanisms stabilize the body of cetaceans during active swimming, which can reduce locomotor energy expenditure and reduce excessive motions of the head affecting sensory capabilities.     

Relationship between grass species richness and ecosystem stability in Kruger National Park, South Africa

The relationship between grass species richness and ecosystem stability was investigated in the Kruger National Park. A total of 135 489 individual grasses were identified from 189 sites spread across 19 485 km² of savanna biome, making this one of the largest studies of its kind. At each site, grass percentage abundance and standing crop were measured at one year intervals to provide an index of ecosystem function. A severe drought that affected the region between 1991 and 1993 provided a convenient perturbation. At the height of the drought, mean species richness declined by 12.7% while standing crop declined by 38.1%, from 3199 to 1979 kg ha^?1. Percentage grass abundance declined to 87.5% of its pre‐drought value. After the drought had passed species richness, standing crop and percentage abundance recovered to 92.1%, 113.8% and 92.8% of their pre‐perturbation values, respectively. Statistical analysis of these responses revealed that grass assemblages of low species richness were more resistant to drought than assemblages of high species richness. Species‐poor sites also showed better recovery from perturbation after the drought had passed. These findings suggest that ecosystem stability may be negatively related to grass species richness in South African savanna grasslands.     

Insights into the local residual entropy of proteins provided by NMR relaxation.

A simple model is used to illustrate the relationship between the dynamics measured by NMR relaxation methods and the local residual entropy of proteins. The expected local dynamic behavior of well-packed extended amino acid side chains are described by employing a one-dimensional vibrator that encapsulates both the spatial and temporal character of the motion. This model is then related to entropy and to the generalized order parameter of the popular "model-free" treatment often used in the analysis of NMR relaxation data. Simulations indicate that order parameters observed for the methyl symmetry axes in, for example, human ubiquitin correspond to significant local entropies. These observations have obvious significance for the issue of the physical basis of protein structure, dynamics, and stability.     

Characterization of a buried neutral histidine residue in Bacillus circulans xylanase: NMR assignments, pH titration, and hydrogen exchange.

Bacillus circulans xylanase contains two histidines, one of which (His 156) is solvent exposed, whereas the other (His 149) is buried within its hydrophobic core. His 149 is involved in a network of hydrogen bonds with an internal water and Ser 130, as well as a potential weak aromatic-aromatic interaction with Tyr 105. These three residues, and their network of interactions with the bound water, are conserved in four homologous xylanases. To probe the structural role played by His 149, NMR spectroscopy was used to characterize the histidines in BCX. Complete assignments of the 1H, 13C, and 15N resonances and tautomeric forms of the imidazole rings were obtained from two-dimensional heteronuclear correlation experiments. An unusual spectroscopic feature of BCX is a peak near 12 ppm arising from the nitrogen bonded 1H epsilon 2 of His 149. Due to its solvent inaccessibility and hydrogen bonding to an internal water molecule, the exchange rate of this proton (4.0 x 10(-5) s-1 at pH*7.04 and 30 degrees C) is retarded by > 10(6)-fold relative to an exposed histidine. The pKa of His 156 is unperturbed at approximately 6.5, as measured from the pH dependence of the 15N- and 1H-NMR spectra of BCX. In contrast, His 149 has a pKa < 2.3, existing in the neutral N epsilon 2H tautomeric state under all conditions examined. BCX unfolds at low pH and 30 degrees C, and thus His 149 is never protonated significantly in the context of the native enzyme. The structural importance of this buried histidine is confirmed by the destablizing effect of substituting a phenylalanine or glutamine at position 149 in BCX.     

Perturbations of the denatured state ensemble: modeling their effects on protein stability and folding kinetics.

By considering the denatured state of a protein as an ensemble of conformations with varying numbers of sequence-specific interactions, the effects on stability, folding kinetics, and aggregation of perturbing these interactions can be predicted from changes in the molecular partition function. From general considerations, the following conclusions are drawn: (1) A perturbation that enhances a native interaction in denatured state conformations always increases the stability of the native state. (2) A perturbation that promotes a non-native interaction in the denatured state always decreases the stability of the native state. (3) A change in the denatured state ensemble can alter the kinetics of aggregation and folding. (4) The loss (or increase) in stability accompanying two mutations, each of which lowers (or raises) the free energy of the denatured state, will be less than the sum of the effects of the single mutations, except in cases where both mutations affect the same set of partially folded conformations. By modeling the denatured state as the ensemble of all non-native conformations of hydrophobic-polar (HP) chains configured on a square lattice, it can be shown that the stabilization obtained from enhancement of native interactions derives in large measure from the avoidance of non-native interactions in the D state. In addition, the kinetic effects of fixing single native contacts in the denatured state or imposing linear gradients in the HH contact probabilities are found, for some sequences, to significantly enhance the efficiency of folding by a simple hydrophobic zippering algorithm. Again, the dominant mechanism appears to be avoidance of non-native interactions. These results suggest stabilization of native interactions and imposition of gradients in the stability of local structure are two plausible mechanisms involving the denatured state that could play a role in the evolution of protein folding and stability.     

静电作用与修饰铜锌超氧化物歧化酶的稳定性

铜锌超氧化物歧化酶(Cu, Zn-SOD)表面的赖氨酸经化学修饰后, 酶的稳定性显著提高. 赖氨酸被修饰后, 酶的电荷结构遂发生变化, 从而影响到酶分子电场. 使用FDPB方法(有限差分法求解Poission-Boltzman方程)计算了酶修饰前后的静电场变化, 以及对维持酶的结构稳定起重要作用的Cu, Zn配位结构的影响.结果表明, Cu, Zn配位体的两级离解常数在酶修饰后分别约下降10³, 10⁶.     

一类竞争扩散方程组在Neumann边条件下解的渐近行为

本文主要采用比较方法讨论了一类竞争扩散方程组在Neumann边条件下解的渐近行为,得到了解的稳定性区域．     

捕食者有无限时滞效应的两种群系统的全局渐近稳定性

本文用Liapunov泛函方法研究捕食者有无限时滞效应的捕食-被捕食系统的平衡状态的稳定性．文章提供了判定系统的平衡状态全局渐近稳定的简单条件,不要求积分核指数衰减.