Leap frog in slow motion: Divergent responses of tree species and life stages to climatic warming in Great Basin subalpine forests

In response to climate warming, subalpine treelines are expected to move up in elevation since treelines are generally controlled by growing season temperature. Where treeline is advancing, dispersal differences and early life stage environmental tolerances are likely to affect how species expand their ranges. Species with an establishment advantage will colonize newly available habitat first, potentially excluding species that have slower establishment rates. Using a network of plots across five mountain ranges, we described patterns of upslope elevational range shift for the two dominant Great Basin subalpine species, limber pine and Great Basin bristlecone pine. We found that the Great Basin treeline for these species is expanding upslope with a mean vertical elevation shift of 19.1 m since 1950, which is lower than what we might expect based on temperature increases alone. The largest advances were on limber pine‐dominated granitic soils, on west aspects, and at lower latitudes. Bristlecone pine juveniles establishing above treeline share some environmental associations with bristlecone adults. Limber pine above‐treeline juveniles, in contrast, are prevalent across environmental conditions and share few environmental associations with limber pine adults. Strikingly, limber pine is establishing above treeline throughout the region without regard to site characteristic such as soil type, slope, aspect, or soil texture. Although limber pine is often rare at treeline where it coexists with bristlecone pine, limber pine juveniles dominate above treeline even on calcareous soils that are core bristlecone pine habitat. Limber pine is successfully “leap‐frogging” over bristlecone pine, probably because of its strong dispersal advantage and broader tolerances for establishment. This early‐stage dominance indicates the potential for the species composition of treeline to change in response to climate change. More broadly, it shows how species differences in dispersal and establishment may result in future communities with very different specific composition.     

The flow of power law fluids in elastic networks and porous media

The flow of power law fluids, which include shear thinning and shear thickening as well as Newtonian as a special case, in networks of interconnected elastic tubes is investigated using a residual-based pore scale network modeling method with the employment of newly derived formulae. Two relations describing the mechanical interaction between the local pressure and local cross-sectional area in distensible tubes of elastic nature are considered in the derivation of these formulae. The model can be used to describe shear dependent flows of mainly viscous nature. The behavior of the proposed model is vindicated by several tests in a number of special and limiting cases where the results can be verified quantitatively or qualitatively. The model, which is the first of its kind, incorporates more than one major nonlinearity corresponding to the fluid rheology and conduit mechanical properties, that is non-Newtonian effects and tube distensibility. The formulation, implementation, and performance indicate that the model enjoys certain advantages over the existing models such as being exact within the restricting assumptions on which the model is based, easy implementation, low computational costs, reliability, and smooth convergence. The proposed model can, therefore, be used as an alternative to the existing Newtonian distensible models; moreover, it stretches the capabilities of the existing modeling approaches to reach non-Newtonian rheologies.     

Normal mode analysis of human lysozyme: study of the relative motion of the two domains and characterization of the harmonic motion

A normal mode analysis of human lysozyme has been carried out at room temperature. Human lysozyme is an enzyme constituted of two domains separated by an active site cleft, the motion of which is thought to be relevant for biological function. This motion has been described as a hinge bending motion. McCammon et al. have determined the characteristics of the hinge bending motion but they assumed a prior knowledge of the hinge axis. In this work we propose a method which is free from this assumption and determines the hinge axis and root mean square (rms) rotation angle which give the best agreement with the pattern of changes in all the distances between nonhydrogen atoms in the two domains, obtained by the normal mode analysis. The hinge axis we found is notably different from the one previously determined and goes, roughly, through the C alpha 55 and C alpha 76, i.e., it is located at the base of the beta-sheet of the second domain. The rms value for the rotation angle is also twice as large as the previous one: 3.37 degrees. It is shown that this hinge bending motion provides a fairly good approximation of the dynamics of human lysozyme and that the normal mode with the lowest frequency has a dominating contribution to this hinge bending motion. A study of the accessible surface area of the residues within the cleft reveals that the motion does not result in a better exposure to the solvent of these residues. A characterization of the thermally excited state (under the hypothesis of the harmonicity of the potential energy surface) has been done using the concept of topology of atom packing. Under this hypothesis the thermal fluctuations result only in a small change of the topology of atom packing, leading therefore to nearly elastic deformations of the protein.     

The Role of the Contractile Vacuole in the Osmoregulation of Tetrahymena pyriformis*

The relationship of cell size and contractile vacuole efflux to osmotic stress was studied in Tetrahymena pyriformis strain W, after transfer into fresh solutions iso- or hypoosmotic to the growth medium. Microscopic measurements of the cell and contractile vacuole dimensions, made with an image-sharing ocular at 27 C, allowed the calculation of the cell size and shape and the vacuolar efflux rate which provide a measure of osmoregulation. The contractile vacuole cycles have no homeostatic oscillations. In 0.03–0.10 osmolar solutions, the cell size and shape are constant while the vacuolar efflux rate has an inverse linear dependence upon extracellular osmolarity. Regression analyses indicate that for cells with systole faster than 0.1 sec (the major part of the population), it is only the final diastolic volume of the contractile vacuole that is related to osmotic stress while the frequency of systole is independent of osmotic stress and has a constant period of 7.7 ± 0.2 sec. Therefore, osmotic stress upon Tetrahymena is regulated by a corresponding change in the filling rate of its contractile vacuole to allow an unaltered cell size and shape. Kinetic measurements of vacuoles during diastole fit the model (dV/dt = K_1-K₂A), where (dV/dt) is the vacuolar filling rate and (A) is the vacuolar surface area. This dependence of vacuolar volume upon its surface area may be ascribed either to elastic components of the vacuolar membrane or to an increasing leakiness of this membrane during diastole. Mitochondrial inhibitors were used to observe the energy requirements of vacuolar operation and of intracellular secretion of water.     

Indentation as a technique to assess the mechanical properties of fallback foods

A number of living primates feed part-year on seemingly hard food objects as a fallback. We ask here how hardness can be quantified and how this can help understand primate feeding ecology. We report a simple indentation methodology for quantifying hardness, elastic modulus, and toughness in the sense that materials scientists would define them. Suggested categories of fallback foods—nuts, seeds, and root vegetables—were tested, with accuracy checked on standard materials with known properties by the same means. Results were generally consistent, but the moduli of root vegetables were overestimated here. All these properties are important components of what fieldworkers mean by hardness and help understand how food properties influence primate behavior. Hardness sensu stricto determines whether foods leave permanent marks on tooth tissues when they are bitten on. The force at which a food plastically deforms can be estimated from hardness and modulus. When fallback foods are bilayered, consisting of a nutritious core protected by a hard outer coat, it is possible to predict their failure force from the toughness and modulus of the outer coat, and the modulus of the enclosed core. These forces can be high and bite forces may be maximized in fallback food consumption. Expanding the context, the same equation for the failure force for a bilayered solid can be applied to teeth. This analysis predicts that blunt cusps and thick enamel will indeed help to sustain the integrity of teeth against contacts with these foods up to high loads. Am J Phys Anthropol 140:643–652, 2009. © 2009 Wiley-Liss, Inc.     

Computation of elastic constants of solids using molecular simulation: comparison of constant volume and constant pressure ensemble methods

We compute the elastic stiffness tensor of fcc argon at 60 K and 1 bar using molecular simulation tools. Three different methods are investigated: explicit deformations of the simulation box, strain fluctuations at constant pressure and stress fluctuations at constant volume. Statistical ensemble sampling is done using molecular dynamics and Monte Carlo simulations. We observe a good agreement between the different methods and sampling algorithms excepted with molecular dynamics simulations in the (NpT) ensemble. There, we notice a strong dependence of the computed elastic constants with the barostat parameter, whereas molecular dynamics simulations in the (NVT) ensemble are not affected by the thermostat parameter.     

弹性橡胶管芯技术用于困难气道行双腔气管导管插管的可行性研究

目的:研究弹性橡胶管芯技术应用于困难气道行双腔气管导管插管的可行性。方法:选择择期胸科手术并行双腔气管导管插管患者40例,并将其随机分为Mc Coy喉镜组(M组)和弹性橡胶管芯组(B组)。M组患者使用Mc Coy喉镜行双腔气管插管,B组患者以弹性橡胶管芯行双腔气管插管。观察和比较插管前后两组患者生命体征的变化、插管次数、所用时间以及由插管造成的损伤发生率。结果:1插管后即刻以及插管后1 min、5min,患者平均动脉压(MAP)、心率(HR)均呈不同程度升高,B组升高程度明显小于M组(P<0.01)。2B组插管时遇到的阻力明显小于M组(P<0.05),插管尝试次数以及完成插管所用的时间均少于或短于M组(P<0.05)。3术后3小时以及24小时,B组由插管导致的声嘶与咽痛的发生率明显低于M组(P<0.05)。4术后48小时,B组患者气道粘膜损伤的发生率明显低于M组(P<0.05)。结论:弹性橡胶管芯技术应用于困难气道行双腔气管导管插管安全有效。     

Predicting drug resistance of the HIV-1 protease using molecular interaction energy components

Drug resistance significantly impairs the efficacy of AIDS therapy. Therefore, precise prediction of resistant viral mutants is particularly useful for developing effective drugs and designing therapeutic regimen. In this study, we applied a structure-based computational approach to predict mutants of the HIV-1 protease resistant to the seven FDA approved drugs. We analyzed the energetic pattern of the protease-drug interaction by calculating the molecular interaction energy components (MIECs) between the drug and the protease residues. Support vector machines (SVMs) were trained on MIECs to classify protease mutants into resistant and nonresistant categories. The high prediction accuracies for the test sets of cross-validations suggested that the MIECs successfully characterized the interaction interface between drugs and the HIV-1 protease. We conducted a proof-of-concept study on a newly approved drug, darunavir (TMC114), on which no drug resistance data were available in the public domain. Compared with amprenavir, our analysis suggested that darunavir might be more potent to combat drug resistance. To quantitatively estimate binding affinities of drugs and study the contributions of protease residues to causing resistance, linear regression models were trained on MIECs using partial least squares (PLS). The MIEC-PLS models also achieved satisfactory prediction accuracy. Analysis of the fitting coefficients of MIECs in the regression model revealed the important resistance mutations and shed light into understanding the mechanisms of these mutations to cause resistance. Our study demonstrated the advantages of characterizing the protease-drug interaction using MIECs. We believe that MIEC-SVM and MIEC-PLS can help design new agents or combination of therapeutic regimens to counter HIV-1 protease resistant strains.     

Predicting order of conformational changes during protein conformational transitions using an interpolated elastic network model

The decryption of sequence of structural events during protein conformational transitions is essential to a detailed understanding of molecular functions ofvarious biological nanomachines. Coarse‐grained models have proven useful by allowing highly efficient simulations of protein conformational dynamics. By combining two coarse‐grained elastic network models constructed based on the beginning and end conformations of a transition, we have developed an interpolated elastic network model to generate a transition pathway between the two protein conformations. For validation, we have predicted the order of local and global conformational changes during key ATP‐driven transitions in three important biological nanomachines (myosin, F₁ ATPase and chaperonin GroEL). We have found that the local conformational change associated with the closing of active site precedes the global conformational change leading to mechanical motions. Our finding is in good agreement with the distribution of intermediate experimental structures, and it supports the importance of local motions at active site to drive or gate various conformational transitions underlying the workings of a diverse range of biological nanomachines. Proteins 2010. © 2010 Wiley‐Liss, Inc.