Estimating binding free energy of a putative growth factors EGF–VEGF complex – a computational bioanalytical study

Epidermal growth factor (EGF) and homodimeric vascular endothelial growth factor (VEGF) bind to cell surface receptors. They are responsible for cell growth and angiogenesis, respectively. Docking of the individual proteins as monomeric units using ZDOCK 2.3.2 reveals a partial blocking of the receptor binding site of VEGF by EGF. The receptor binding site of EGF is not affected by VEGF. The calculated binding energy is found to be intermediate between the binding energies calculated for Alzheimer’s Aß42 and the barnase/barstar complex.     

Growth Respiration of a Flood-Tolerant and a Flood-Intolerant Senecio Species: Correlation between Calculated and Experimental Values

Root growth respiration of Senecio aquaticus Hill (flood-tolerant) and Senecio jacobaea L. (flood-sensitive) was calculated, assuming different P: O ratios. The growth respiration values were calculated on the basis of the chemical composition of root and shoot dry matter, in combination with published data on the energy costs of biosynthetic and transport processes. The comparison between calculated and experimental values suggests a relatively low efficiency of ATP utilization in the roots of the flood-tolerant species. Root growth respiration of S. congestus (R.Br.)DC., which is also flood-tolerant, and Plantago lanceolata L. were also determined. The data showed that not all the flood-tolerant species investigated had high root growth respiration values. An “overflow model’ is proposed to explain observed differences in root growth respiration between species.     

Macromolecule synthesis of Escherichia coli BB at a lower or transient growth state.

Macromolecule synthesis in Escherichia coli BB at lower growth rates was investigated. The results indicate that a deviation in ribonucleic acid (RNA) content per cell at a lower growth rate from the exponential relationship to a specific growth rate is entirely attributable to the presence of nonviable cells, in which the RNA content is lower than in viable cells. Based on this fact, a mathematical expression of macromolecule contents versus specific growth rate was devised. Moreover, continuous changes in macromolecule content during unbalanced growth from late-logarithmic phase to stationary phase were measured. Although growth rates changed continuously, the data on deoxyribonucleic acid (DNA) or RNA content versus the specific growth rate calculated from the increments in cell number satisfactorily fitted the exponential lines obtained under balanced growth at a higher growth rate. However, no such relationship was observed in the plot of DNA or RNA content versus the specific growth rate calculated from the increments in optical density.     

Macromolecule synthesis of Escherichia coli BB at a lower or transient growth state.

Macromolecule synthesis in Escherichia coli BB at lower growth rates was investigated. The results indicate that a deviation in ribonucleic acid (RNA) content per cell at a lower growth rate from the exponential relationship to a specific growth rate is entirely attributable to the presence of nonviable cells, in which the RNA content is lower than in viable cells. Based on this fact, a mathematical expression of macromolecule contents versus specific growth rate was devised. Moreover, continuous changes in macromolecule content during unbalanced growth from late-logarithmic phase to stationary phase were measured. Although growth rates changed continuously, the data on deoxyribonucleic acid (DNA) or RNA content versus the specific growth rate calculated from the increments in cell number satisfactorily fitted the exponential lines obtained under balanced growth at a higher growth rate. However, no such relationship was observed in the plot of DNA or RNA content versus the specific growth rate calculated from the increments in optical density.     

Growth kinetics of individual Bacillus subtilis cells and correlation with nucleoid extension

The growth rate of individual cells of Bacillus subtilis (doubling time, 120 min) has been calculated by using a modification of the Collins-Richmond principle which allows the growth rate of mononucleate, binucleate, and septate cells to be calculated separately. The standard Collins-Richmond equation represents a weighted average of the growth rate calculated from these three major classes. Both approaches strongly suggest that the rate of length extension is exponential. By preparing critical-point-dried cells, in which major features of the cell such as nucleoids and cross-walls can be seen, it has also been possible to examine whether nucleoid extension is coupled to length extension. Growth rates for nucleoid movement are parallel to those of total length extension, except possibly in the case of septate cells. Furthermore, by calculating the growth rate of various portions of the cell surface, it appears likely that the limits of the site of cylindrical envelope assembly lie between the distal tips of the nucleoid; the old poles show zero growth rate. Coupling of nucleoid extension with increase of cell length is envisaged as occurring through an exponentially increasing number of DNA-surface attachment sites occupying most of the available surface.     

Speed of fetal growth: a new methodological approach

We suggest a new method to calculate fetal growth velocity. Fetal growth curves are divided in small linear units, and corresponding slopes calculated as growth rates. An example is detailed to set out statistical contingencies for methodological reliability. Specific interest of the method is discussed.     

微量量热法研究酸奶菌种的适宜生长温度及最佳生长温度

测定酸奶菌种保加利亚孔杆菌、嗜热链球菌及二者混合菌在乳中生长的热谱图曲线,确定了各菌种及混合菌的适宜生长温度范围,计算出了各菌种在不同温度下的生长速率常数。用计算机拟合k-T方程,求出各菌种的最佳生长温度。     

Ligation of the uterine artery and early postnatal food restriction - animal models for growth retardation

Intrauterine growth restriction (IUGR) is one of the major causes of short stature in child- and adulthood. The cause of IUGR is unknown, however, an impaired uteroplacental function during the second half of human pregnancy might be an important factor, by affecting the programming of somatotropic axis and leading to postnatal growth failure into adulthood. Two rat models with perinatally induced growth retardation were used to examine the long-term effects of perinatal insults on growth. IUGR rats were prepared from pregnant dams, with a bilateral uterine artery ligation at day 17 of their pregnancy. Since the rat is relatively immature at birth, an early postnatal food restriction model was included as another model to broaden the time window of sensitive period of organogenesis. An individual growth curve was calculated of each animal (n = 813). From these individual growth curves the predicted growth curve for each experimental group was calculated by multilevel analysis. The proposed mathematical model allows us to estimate the growth potentials of these rat models with precision and could provide basic information to investigate the relationships among a number of other variables in future studies. Furthermore, we concluded that both pre- and early postnatal malnutrition leads to irreversible slowing down of postnatal growth.     

The Ontogeny of Encephalization: Tradeoffs Between Brain Growth,Somatic Growth,and Life History in Hominoids and Platyrrhines

This study examines variation in brain growth relative somatic growth in four hominoids and three platyrrhines to determine whether there is a trade-off during ontogeny. I predicted that somatic growth would be reduced during periods of extensive brain growth, and species with larger degrees of encephalization would reach a smaller body size at brain growth completion because more energy is directed towards the brain. I measured cranial capacity and skeletal size in over 500 skeletal specimens from wild populations. I calculated nonlinear growth curves and velocity curves to determine brain/body growth allometry during ontogeny. In addition, I calculated linear regressions to describe the brain/body allometry during the postnatal period prior to brain size reaching an asymptote. The results showed that somatic growth is not substantially reduced in species with extensive brain growth, and body size at brain growth completion was larger in species with greater degrees of encephalization. Furthermore, large body size at brain growth completion was not correlated with interbirth interval, but was significantly correlated with prolonged juvenile periods and late age at maturity when data were corrected for phylogeny. These results indicate that neither reduction in body growth nor reproductive rate are compensatory mechanisms for the energetic costs of brain growth. Other avenues for meeting energetic costs must be in effect. In addition, the results show that somatic growth in encephalized species is particularly slow during the juvenile period after brain growth at or near completion, suggesting that these growth patterns are explained by reasons other than energetic costs.     

On second order sensitivity for stage-based population projection matrix models

In this paper we present a simple method for identifying life-history perturbations in population projection matrices that yield an accelerating population growth rate. Accelerating growth means that the dependence of the growth rate on the perturbation is convex. Convexity, when the second sensitivity of the growth rate is positive, is calculated using a new formula derived from the transfer function of the perturbed system. This formula is used to explore the relationship between stasis and growth probabilities from stage-structured population projection matrices.     

Modelling the influence of assimilate availability on root growth and architecture

A model has been designed to simulate rubber seedling root development as related to assimilate availability. Each root of the system is defined both as an element of a network of axes, characterized by its order, position and connections and as an individual sink competing for assimilates. At each time step, the growth of each root is calculated as a function of its own growth potential and of assimilate availability calculated within the whole plant. The potential elongation rate of a root is estimated by its apical diameter, which reflects the size of the meristem. When a root is initiated, the apical diameter depends on root type, but it varies thereafter according to assimilate availability. Thus, the latter controls both current and potential elongation. The model was able to simulate periodicity in root development as related to shoot growth and to reproduce differences in sensitivity to assimilate availability related to root type. It thereby validated the hypothesis that root growth but also root system architecture depend on assimilate allocation and that apical diameter is a good indicator of root growth potential. Provided that specific calibration is done, this model may be used for other species.     

The determination of the parameter of Bertalanffy's growth differential equations by means of nonlinear internal regression

A short survey is given on various parameterized versions of the logistic law of growth and of Bertalanffy's growth differential equations. To examine the validity of these various growth expressions internal nonlinear regressions were performed, and the results of the calculations are presented. The body length growth of man within the embryonic development serves as examples of a growth process. The parameters in the differential equations will be adjusted to the course of the divided central differences calculated from means of measured values of this growth process.     

A novel image-analysis technique for kinematic study of growth and curvature

Kinematic analysis has provided important insights into the biology of growth by revealing the distribution of expansion within growing organs. Modern methods of kinematic analysis have made use of new image-tracking algorithms and computer-assisted evaluation, but these methods have yet to be adapted for examination of growth in a variety of plant species or for analysis of graviresponse. Therefore, a new image-analysis program, KineRoot, was developed to study spatio-temporal patterns of growth and curvature of roots. Graphite particles sprinkled on the roots create random patterns that can be followed by image analysis. KineRoot tracks the displacement of patterns created by the graphite particles over space and time using three search algorithms. Following pattern tracking, the edges of the roots are identified automatically by an edge detection algorithm that provides root diameter and root midline. Local growth rate of the root is measured by projecting the tracked points on the midline. From the shape of the root midline, root curvature is calculated. By combining curvature measurement with root diameter, the differential growth ratio between the greater and lesser curvature edges of a bending root is calculated. KineRoot is capable of analyzing a large number of images to generate local root growth and root curvature data over several hours, permitting kinematic analysis of growth and gravitropic responses for a variety of root types.     

Numerical modelling of shape regulation and growth stresses in trees

The main objective of this paper is to present the results of a study of the interactions between the growth and design of a tree with regards to biomechanical factors at the plant level. A numerical incremental model dedicated to the calculation of tree mechanical behaviour has been integrated in the plant architecture simulation software AMAPpara. At any stage of tree growth, a new equilibrium was calculated considering the weight increment applied on the structure, i.e. the mass of new wood layers and vegetative elements, as well as the biomechanical reaction caused by cell maturation strains in both normal and reaction wood. The resulting incremental displacements allowed the tree shape to be modified. The field of growth stresses was calculated within the stem, using a cumulative process taking into consideration the past history of each growth ring. The simulation results of trunk and branch shape, as well as internal stresses, were examined after consideration of different growth strategies. A block of trees was also simulated in order to show the influence of spatial competition on stem curvature and the variability in growth stress.     

Relationship of tree growth and climatic factors at treeline of Picea likiangensis var. balfouriana forest in Basu County,Xizang

 与传统方法相比, 利用树木年轮学方法研究树线过渡区树木生长温度敏感性高低的问题更注重比较树木个体间的生长情况, 从各个树轮序列间的生长一致性程度和树轮序列对气候因素(气温、降水)的响应一致性程度可探讨树线过渡区树木生长的温度敏感性。为了认识高山树线过渡区内树木生长的温度敏感性问题, 选择西藏昌都地区八宿县的一条川西云杉树线过渡区为研究对象, 比较了过渡区内树木个体间的生长一致性, 分析了树木生长与气候因素的相关性及其在个体间的异同。结果显示: 树线过渡区内树轮生长在个体间的一致性较低, 树轮生长与气温的关系在树木个体间的一致性也较低, 而树轮生长与当年4-9月降水的关系相对较强。西藏八宿树线过渡区属于干旱区, 相对于气温而言, 降水对树木生长的影响更大。此外, 小生境的异质性及干扰事件的发生也有可能降低树木对温度的敏感性。在全球变暖及极端气候事件增加的背景下, 树木生长的温度敏感性被高估可能会导致对树线过渡区位置及树线过渡区内群落生产力等的预测产生偏差, 这一问题应该在区域生态模拟研究和相关林业经营与管理上得到重视。     

Are growth rates of Escherichia coli in batch cultures limited by respiration?

Batch cultures of Escherichia coli were grown in minimal media supplemented with various carbon sources which supported growth at specific growth rates from 0.2 to 1.3/h. The respiration rates of the cultures were measured continuously. With few exceptions, the specific rate of oxygen consumption was about 20 mmol of O2/h per g (dry weight), suggesting that the respiratory capacity was limited at this value. The adenosine triphosphate (ATP) required for the production of cell material from the different carbon sources was calculated on the basis of known ATP requirements in the biochemical pathways and routes of macromolecular synthesis. The calculated ATP requirements, together with the measured growth rates and growth yields on the different carbon sources, were used to calculate the rate of ATP synthesis by oxidative phosphorylation. This rate was closely related to the respiration rate. We suggest that aerobic growth of E. coli in batch cultures is limited by the rate of respiration and the concomitant rate of ATP generation through oxidative phosphorylation.     

Comparison of definitions of the lag phase and the exponential phase in bacterial growth.

Different definitions for the lag time and of the duration of the exponential phase can be used to calculate these quantities from growth models. The conventional definitions were compared with newly proposed definitions. It appeared to be possible to derive values for the lag time and the duration of the exponential phase from the growth models and differences between the various definitions could be quantified. All the different values can be calculated from the growth parameters microm, lambda and alpha. Therefore, it appeared to be unnecessary to use complicated mathematical equations; simple equations were adequate. For the Gompertz model the conventional definition of the lag time did not differ appreciably from the newly proposed definition. The end-point of the exponential phase and thus the duration of the exponential phase differed considerably for the two definitions. For the logistic model the two definitions lead to considerable differences for all quantities. It is recommended that the conventional definition is used for calculating the lag time. For the duration of the exponential phase it is recommended that the new definition is used. The value can be calculated, however, directly from the conventional growth parameters.     

Studies on the Polymorphism of l-Glutamic Acid

The β-crystal formation of l-glutamic acid in the seeded solution was investigated; and it was found that the growth rate of the seed crystals in a-axis direction was nearly as large as that of the α-crystal, but the growth rate in b- and c-axes was little recognized. The activation energy of the crystallization process of the β-crystal in a-axis direction was calculated from the growth rate constants determined at various temperatures, and 6~7 kcal/mol was obtained. On the assumption that the crystallization of β-crystal growth was controlled by the diffusional operation, the thickness of the laminar film was calculated from the growth rate constant and the estimated value of the diffusional constant. The calculated value of the thickness was much greater than the value reported by Nernst; therefore, the crystallization process should be controlled by the surface reaction. The co-existence of a small quantity of amino acids caused a great reduction in the growth rate of the β-crystal.     

Forecasting the growth of multicell tumour spheroids: implications for the dynamic growth of solid tumours

The growth dynamics of multicell tumour spheroids (MTS) were analysed by means of mathematical techniques derived from signal processing theory. Volume vs. time trajectories of individual spheroids were fitted with the Gompertz growth equation and the residuals (i.e. experimental volume determinations minus calculated values by fitting) were analysed by fast fourier transform and power spectrum. Residuals were not randomly distributed around calculated growth trajectories demonstrating that the Gompertz model partially approximates the growth kinetics of three-dimensional tumour cell aggregates. Power spectra decreased with increasing frequency following a 1/f(delta) power-law. Our findings suggest the existence of a source of 'internal' variability driving the time-evolution of MTS growth. Based on these observations, a new stochastic Gompertzian-like mathematical model was developed which allowed us to forecast the growth of MTS. In this model, white noise is additively superimposed to the trend described by the Gompertz growth equation and integrated to mimic the observed intrinsic variability of MTS growth. A correlation was found between the intensity of the added noise and the particular upper limit of volume size reached by each spheroid within two MTS populations obtained with two different cell lines. The dynamic forces generating the growth variability of three-dimensional tumour cell aggregates also determine the fate of spheroid growth with a strong predictive significance. These findings suggest a new approach to measure tumour growth potential.     

A new combined differential-discrete cellular automaton approach for biofilm modeling: application for growth in gel beads

The theoretical basis and quantitative evaluation of a new approach for modeling biofilm growth are presented here. Soluble components (e.g., substrates) are represented in a continuous field, whereas discrete mapping is used for solid components (e.g., biomass). The spatial distribution of substrate is calculated by applying relaxation methods to the reaction-diffusion mass balance. A biomass density map is determined from direct integration in each grid cell of a substrate-limited growth equation. Spreading and distribution of biomass is modeled by a discrete cellular automaton algorithm. The ability of this model to represent diffusion-reaction-microbial growth systems was tested for a well-characterized system: immobilized cells growing in spherical gel beads. Good quantitative agreement with data for global oxygen consumption rate was found. The calculated concentration profiles of substrate and biomass in gel beads corresponded to those measured. Moreover, it was possible, using the discrete spreading algorithm, to predict the spatial two- and three-dimensional distribution of microorganisms in relation to, for example, substrate flux and inoculation density. The new technique looks promising for modeling diffusion-reaction-microbial growth processes in heterogeneous systems as they occur in biofilms.