Some indications for inverse DNA duplication

The Continuum Model postulates that preparations for the initiation of DNA synthesis takes place continuously, and in all phases of the cell cycle. There are no G1-specific events involved in the initiation of DNA synthesis. The statistical predictions of the Continuum Model are now presented with four basic variables: (1) the rate of initiator synthesis, (2) the time for passage through the replication-segregation sequence, (3) the amount of initiator required for initiation of DNA synthesis in a particular cell, and (4) the variation in equipartition of cells at division. Computer simulations reveal that the Continuum Model is consistent with both α-and β-curves, as well as the quartile test for β-curves. It also explains sister-sister correlations, and the correlations between cell mass at various times in the division cycle and cell interdivision times. With one additional parameter, the Continuum Model can also explain mother-daughter correlation. The Continuum Model accounts for the statistical data which has previously been used to support the Transition-Probability Model. It has a simple biochemical basis, and can explain the observed biochemical and biological observations of cell growth and division.     

Protocol for MM/PBSA molecular dynamics simulations of proteins

Continuum solvent models have been employed in past years for understanding processes such as protein folding or biomolecular association. In the last decade, several attempts have been made to merge atomic detail molecular dynamics simulations with solvent continuum models. Among continuum models, the Poisson-Boltzmann solvent accessible surface area model is one of the oldest and most fundamental. Notwithstanding its wide usage for simulation of biomolecular electrostatic potential, the Poisson-Boltzmann equation has been very seldom used to obtain solvation forces for molecular dynamics simulation. We propose here a fast and reliable methodology to implement continuum forces in standard molecular mechanics and dynamics algorithms. Results for a totally unrestrained 1 ns molecular dynamics simulation of a small protein are quantitatively similar to results obtained by explicit solvent molecular dynamics simulations.     

Native Religions and Cultures of North America: Anthropology of the Sacred

Native Religions and Cultures of North America: Anthropology of the Sacred. Lawrence E. Sullivan. ed. New York: Continuum, 2000. 249 pp.     

Feeding tests with caddis larvae (Insecta: Trichoptera) and amphipods (Crustacea: Amphipoda) on Platanus orientalis (Platanaceae) and other leaf litter

In the southern parts of the Mediterranean region, as in the island of Crete, there are few species of riparian trees and shrubs among the dominant Platanus orientalis. Feeding tests have shown that leaves of Platanus are not eaten by aquatic shredders of continental and Cretean origin. The large quantities of organic matter are therefore not used as a source of food and energy by the stream communities. In addition, the high winter flow shortly after leaf fall, and the short courses of rivers result in loss of most of the leaf litter to the sea. The River Continuum Concept does therefore not apply to this region. Field observations have shown that amphipods and limnephilid larvae are shifting from shredding to scraping habits if no leaf litter except Platanus was available.     

A novel approach to estimate trabecular bone anisotropy using a database approach

Continuum finite element (FE) models of bones have become a standard pre-clinical tool to estimate bone strength. These models are usually based on clinical CT scans and material properties assigned are chosen as isotropic based only on the density distribution. It has been shown, however, that trabecular bone elastic behavior is best described as orthotropic. Unfortunately, the use of orthotropic models in FE analysis derived from CT scans is hampered by the fact that the measurement of a trabecular orientation (fabric) is not possible from clinical CT images due to the low resolution of such images. In this study, we explore the concept of using a database (DB) of high-resolution bone models to derive the fabric information that is missing in clinical images. The goal of this study was to investigate if models with fabric derived from a relatively small database can already produce more accurate results than isotropic models.     

A continuum method for determining membrane protein insertion energies and the problem of charged residues

Continuum electrostatic approaches have been extremely successful at describing the charged nature of soluble proteins and how they interact with binding partners. However, it is unclear whether continuum methods can be used to quantitatively understand the energetics of membrane protein insertion and stability. Recent translation experiments suggest that the energy required to insert charged peptides into membranes is much smaller than predicted by present continuum theories. Atomistic simulations have pointed to bilayer inhomogeneity and membrane deformation around buried charged groups as two critical features that are neglected in simpler models. Here, we develop a fully continuum method that circumvents both of these shortcomings by using elasticity theory to determine the shape of the deformed membrane and then subsequently uses this shape to carry out continuum electrostatics calculations. Our method does an excellent job of quantitatively matching results from detailed molecular dynamics simulations at a tiny fraction of the computational cost. We expect that this method will be ideal for studying large membrane protein complexes.     

Limnological imbalances: an antipodean viewpoint

SUMMARY. 1. It is argued that modern limnology is excessively concerned with the study of fresh waters in the northern temperate region. Limnology has been and is unbalanced in its interests and emphases and, as a result, many widely held limnological concepts need revision. 2. The genesis of the argument is outlined. It involved the initial assumption that Australia was limnologically distinctive. Later, it was realized that since most of the world is arid, semi-arid, tropical or semi-tropical, Australia was much less distinctive than originally thought. 3. Other limnological assumptions considered in the paper concern saline lakes and salinization, the importance and nature of temporary bodies of standing fresh water, biological diversity in tropical fresh waters, the evolutionary importance of permanent freshwater lakes, and the global applicability of the River Continuum Concept. Consideration suggests that some widely-held views on these matters are erroneous. 4. Thus, saline lakes are more important (scientifically, commercially), widespread and numerous environments than is generally thought. Salinization is a significant environmental hazard for many rivers in semiarid regions. Temporary bodies of standing fresh water are geographically widespread and abundant aquatic environments with high species diversity, and in which many species have restricted distributions and low dispersal abilities. Biological diversity appears to be low in tropical fresh waters. Permanent freshwater lakes are perhaps less important loci for the evolution of the freshwater biota than generally thought, temporary fresh waters more so. Finally, the River Continuum does not seem to be applicable to many running waters outside the north temperate region. 5. A number of suggestions are made of how a better balance in limnology may be arrived at: how a more globally comprehensive intellectual framework may be built. Suggestions include: an increased awareness of the frequently different natures of waters within and beyond the northern temperate region; recognition of the potential benefits to be gained from the study of waters outside the northern temperate region;     

土壤干旱胁迫下非水力根信号调控夏玉米气体交换对大气环境的响应

对不同程度土壤干旱胁迫下夏玉米非水力根信号的产生以及气体交换过程对大气环境的响应进行了试验研究。充足底墒播种后采用3个土壤水分处理等级(0~200cm土壤相对湿度为>80%、60%~70%、40%~50%,代号为W T1、W T2和W T3)。生育期内遮去自然降水。试验结果表明,在拔节期轻度和中度土壤干旱胁迫的情况下,玉米根系合成大量ABA传输到地上部分,参与控制气孔开度和气体交换过程对大气环境变化的响应并调节水分消耗。在日变化过程中,当光强和水汽压亏缺较高时,由于蒸腾速率较高,非水力根信号物质向冠层的传输速率也较高,ABA在叶片中的累积影响了气孔开张对光强响应的敏感度,气孔开度受到抑制,并且随着ABA累积和浓度的增加,气孔抑制作用越强;在水汽压亏缺较低的情况下,非水力根信号物质向冠层的传输速率较低,ABA的代谢过程以及再分配过程能够保证这种信号物质保持在低水平,从而保证一定程度的气孔开度和光合、蒸腾速率。这种策略能够使夏玉米在轻、中等干旱条件下保证最大的光合作用,同时在可能的胁迫情况下降低蒸腾作用以提高水分利用效率。     

不同肥力水平农田生态系统SPAC水分状态及能量特征

通过对农田生态系统土壤 -植物 -大气连续体系 (SPAC)水分、温度等昼夜观测 ,确定温度是影响 SPAC水分能量的重要因素 ,土壤水势呈现温度正效应 ,植物、大气水势呈现温度负效应。温度与土壤 -植物间水势差 (ψS- P)和植物 -大气间水势差 (ψP- A)呈正相关。农田生态系统 SPAC水分热力学函数研究得出 ,不论高、低肥区 ,冬小麦在不同生长发育时期 ,水分的相对偏摩尔自由能 (ΔG)均为土壤 >植物 >大气 ;水分相对偏摩尔熵 (ΔS)、焓 (ΔH)均为大气 >植物 >土壤 ;冬小麦在拔节期和扬花期 ,土壤水 ΔG皆为高肥区 <低肥区 ;植物水分 ΔG拔节期为高肥区 >低肥区 ,扬花期相反为高肥区 <低肥区 ;两个生育期大气水分 ΔG均为高肥区 >低肥区。在拔节期土壤 -植物间水分的 ΔG差值 (ΔGS- P=ΔGS-ΔGP)、植物 -大气间水分ΔG差值 (ΔGP- A=ΔGP-ΔGA)均为高肥区 <低肥区 ,扬花期ΔGS- P为高肥区 >低肥区 ,而ΔGP- A为高肥区 <低肥区。     

A non-linearly elastic, finite deformation analysis applicable to the static mechanics of excised lungs

Continuum mechanical analyses of lung behavior require a constitutive relationship for the parenchyma. For a homogeneous, isotropic, elastic material this relationship is dependent upon the strain invariants. Furthermore, the sparse data available indicate that the relationship should be exponential in form. A suitable equation has previously appeared in the literature. In this paper it is developed for application to whole lung experiments.     

Anthropologies of Violence and Resistance

Encounters with Violence in Latin America: Urban Poor Perceptions from Colombia and Guatemala. Caroline O. N. Moser and Cathy McIlwaine. New York: Routledge, 2004. 272 pp.
Violence: Theory and Ethnography. Pamela J. Stewart and Andrew Strathern. New York: Continuum, 2002. 196 pp.
Shadows of War: Violence, Power, and International Profiteering in the Twenty-First Century. Carolyn Nordstrom. Berkeley: University of California Press, 2004. 293 pp.     

Finite element model of stresses in the anterior lens capsule of the eye

Continuum biomechanics continues to aid in the design of clinical procedures and biomedical devices. Such design requires detailed information on the biomechanical properties of the tissues of interest as well as appropriate methods of analysis. In this paper, we use a fully nonlinear, virtual work based finite element method to study the normal stress field in the anterior lens capsule of the porcine eye. The analysis shows that recently measured regional variations in material symmetry may combine with regional variations in membrane thickness to yield a nearly uniform and equibiaxial stress field in normalcy. These findings are discussed in terms of potential implications to the underlying mechanobiology and in particular, in terms of perturbations in stress that result from cataract surgery, the most commonly performed surgical procedure in North America.     

Can prey exhibit threat-sensitive generalization of predator recognition? Extending the Predator Recognition Continuum Hypothesis

Despite the importance of predator recognition in mediating predator-prey interactions, we know little about the specific characteristics that prey use to distinguish predators from non-predators. Recent experiments indicate that some prey who do not innately recognize specific predators as threats have the ability to display antipredator responses upon their first encounter with those predators if they are similar to predators that the prey has recently learned to recognize. The purpose of our present experiment is to test whether this generalization of predator recognition is dependent on the level of risk associated with the known predator. We conditioned fathead minnows to chemically recognize brown trout either as a high or low threat and then tested the minnows for their responses to brown trout, rainbow trout (closely related predator) or yellow perch (distantly related predator). When the brown trout represents a high-risk predator, minnows show an antipredator response to the odour of brown trout and rainbow trout but not to yellow perch. However, when the brown trout represents a low-risk predator, minnows display antipredator responses to brown trout, but not to the rainbow trout or yellow perch. We discuss these results in the context of the Predator Recognition Continuum Hypothesis.     

Finite element model of stresses in the anterior lens capsule of the eye

Continuum biomechanics continues to aid in the design of clinical procedures and biomedical devices. Such design requires detailed information on the biomechanical properties of the tissues of interest as well as appropriate methods of analysis. In this paper, we use a fully nonlinear, virtual work based finite element method to study the normal stress field in the anterior lens capsule of the porcine eye. The analysis shows that recently measured regional variations in material symmetry may combine with regional variations in membrane thickness to yield a nearly uniform and equibiaxial stress field in normalcy. These findings are discussed in terms of potential implications to the underlying mechanobiology and in particular, in terms of perturbations in stress that result from cataract surgery, the most commonly performed surgical procedure in North America.     

Discrimination of native loop conformations in membrane proteins: decoy library design and evaluation of effective energy scoring functions

The recent determination of crystal structures for several important membrane proteins opens the way for comparative modeling of their membrane-spanning regions. However, the ability to predict correctly the structures of loop regions, which may be critical, for example, in ligand binding, remains a considerable challenge. To meet this challenge, accurate scoring methods have to discriminate between candidate conformations of an unknown loop structure. Some success in loop prediction has been reported for globular proteins; however, the proximity of membrane protein loops to the lipid bilayer casts doubt on the applicability of the same scoring methods to this problem. In this work, we develop "decoy libraries" of non-native folds generated, using the structures of two membrane proteins, with molecular dynamics and Monte Carlo techniques over a range of temperatures. We introduce a new approach for decoy library generation by constructing a flat distribution of conformations covering a wide range of Calpha-root-mean-square deviation (RMSD) from the native structure; this removes possible bias in subsequent scoring stages. We then score these decoy conformations with effective energy functions, using increasingly more cpu-intensive implicit solvent models, including (1) simple Coulombic electrostatics with constant or distance-dependent dielectrics; (2) atomic solvation parameters; (3) the effective energy function (EEF1) of Lazaridis and Karplus; (4) generalized Born/Analytical Continuum Solvent; and (5) finite-difference Poisson-Boltzmann energy functions. We show that distinction of native-like membrane protein loops may be achieved using effective energies with the assumption of a homogenous environment; thus, the absence of the adjacent lipid bilayer does not affect the scoring ability. In particular, the Analytical Continuum Solvent and finite-difference Poisson-Boltzmann energy functions are seen to be the most powerful scoring functions. Interestingly, the use of the uncharged states of ionizable sidechains is shown to aid prediction, particularly for the simplest energy functions.     

SER-HIS-ASP catalytic triad in model non-aqueous solvent environment: a computational study

Emerging new properties and applications of enzymes in organic solvents and ionic liquids are unabating. By applying a combined Quantum Mechanics/Continuum Mechanics computation on a prototypical catalytic triad serine-histidine-aspartate (SER-HIS-ASP) interacting with ethanol or acetonitrile molecules, the major difference between protic and aprotic solvents in effecting transition-state stabilization has been analyzed. Moderately polar aprotic solvent acetonitrile is predicted to be unable to stabilize the transition state in replacing the role of the oxyanion-hole environment, whereas protic ethanol solvent molecules of similar polarity to acetonitrile are adequate in re-gaining the enzymatic activities.     

A 3D model of muscle reveals the causes of nonuniform strains in the biceps brachii

Biomechanical models generally assume that muscle fascicles shorten uniformly. However, dynamic magnetic resonance (MR) images of the biceps brachii have recently shown nonuniform shortening along some muscle fascicles during low-load elbow flexion (J. Appl. Physiol. 92 (2002) 2381). The purpose of this study was to uncover the features of the biceps brachii architecture and material properties that could lead to nonuniform shortening. We created a three-dimensional finite-element model of the biceps brachii and compared the tissue strains predicted by the model with experimentally measured tissue strains. The finite-element model predicted strains that were within one standard deviation of the experimentally measured strains. Analysis of the model revealed that the variation in fascicle lengths within the muscle and the curvature of the fascicles were the primary factors contributing to nonuniform strains. Continuum representations of muscle, combined with in vivo image data, are needed to deepen our understanding of how complex geometric arrangements of muscle fibers affect muscle contraction mechanics.     

Backbone conformational dependence of peptide acidity

Electrostatic interactions at the protein surface yield over a billion-fold range of amide hydrogen exchange rates. This range is equivalent to the maximal degree of attenuation in exchange rates that have been shown to occur for amides buried within the protein interior. Continuum dielectric analysis of Ala-Ala, Ala-Gly, Gly-Ala and trans-Pro-Ala peptide conformer acidities predicts that the relative orientation of the two neighboring peptide groups can account for a million-fold variation in hydroxide-catalyzed hydrogen exchange rates. As in previous protein studies, an internal dielectric value of 3 was found to be applicable to simple model peptides, presumably reflecting the short lifetime of the peptide anion intermediate. Despite the million-fold range in conformer acidities, the small differences in the experimental exchange rates for these peptides are accurately predicted. Ala-Ala conformers with an extended N-terminal residue and the C-terminal residue in the α conformation are predicted to account for over 60% of the overall hydrogen exchange reaction, despite constituting only 12% of the protein coil population.     

Comparison between Generalized-Born and Poisson–Boltzmann methods in physics-based scoring functions for protein structure prediction

Continuum solvent models such as Generalized-Born and Poisson–Boltzmann methods hold the promise to treat solvation effect efficiently and to enable rapid scoring of protein structures when they are combined with physics-based energy functions. Yet, direct comparison of these two approaches on large protein data set is lacking. Building on our previous work with a scoring function based on a Generalized-Born (GB) solvation model, and short molecular-dynamics simulations, we further extended the scoring function to compare with the MM-PBSA method to treat the solvent effect. We benchmarked this scoring function against seven publicly available decoy sets. We found that, somewhat surprisingly, the results of MM-PBSA approach are comparable to the previous GB-based scoring function. We also discussed the effect to the scoring function accuracy due to presence of large ligands and ions in some native structures of the decoy sets.