Using linkage models to explore skull kinematic diversity and functional convergence in arthrodire placoderms

Biomechanical models offer a powerful set of tools for quantifying the diversity of function across fossil taxa. A computer‐based four‐bar linkage model previously developed to describe the potential feeding kinematics of Dunkleosteus terrelli is applied here to several other arthrodire placoderm taxa from different lineages. Arthrodire placoderms are a group of basal gnathostomes showing one of the earliest diversifications of jaw structures. The linkage model allows biomechanical variation to be compared across taxa, identify trends in skull morphology among arthrodires that potentially influence function and explore the role of linkage systems in the early evolution of jaw structures. The linkage model calculates various kinematic metrics including gape angle, effective mechanical advantage, and kinematic transmission coefficients. Results indicate that the arthrodire feeding system may be more diverse and complex than previously thought. A range of potential kinematic profiles among arthrodire taxa illustrate a diversity of feeding function comparable with modern teleost fishes. Previous estimates of bite force in Dunkleosteus are revised based on new morphological data. High levels of kinematic transmission among arthrodires suggest the potential for rapid gape expansion and possible suction feeding. Morphological comparisons indicate that there were several morphological solutions for obtaining these fast kinematics, which allowed different taxa to achieve similar kinematic profiles while varying other aspects of the feeding apparatus. Mapping of key morphological components of the linkage system on a general placoderm phylogeny illustrates the potential importance of four‐bar systems to the early evolution of jaw structures. J. Morphol. 271:990–1005, 2010. © 2010 Wiley‐Liss, Inc.     

Prediction of the pilot-scale recovery of a recombinant yeast enzyme using integrated models

This article describes the rapid prediction of recovery process performance for a new recombinant enzyme product on the basis of a broad portfolio of computer models and highly targeted experimentation. A process model for the recombinant system was generated by linking unit operation models in an integrated fashion, with required parameter estimation and physical property determination accomplished using data from scale-down studies. This enabled the generic modeling framework established for processing of a natural enzyme from bakers' yeast to be applied. An experimental study of the same operations at the pilot scale showed that the process model gave a conservative prediction of recombinant enzyme recovery. The model successfully captured interactions leading to a low overall product yield and indicated the need for further study of precipitate breakage in the feed zone of a disc stack centrifuge in order to improve performance. The utility of scale-down units as an aid to fast model generation and the advantage of integrating computer modeling and scale-down studies to accelerate bioprocess development are highlighted.     

How Microbes Can Achieve Balanced Growth in a Fluctuating Environment

A microbial colony needs several essential nutrients in order to grow. Moreover, the colony requires these nutrients in fixed combinations, which are dictated by the chemical composition of its biomass. Unfortunately, ambient availabilities of the various nutrients vary all the time. This poses the question of how microbes can achieve balanced growth.The present solution to this problem is novel in that the allocation of molecular building blocks among assimilatory machineries within the cell is regarded as dynamic. This paper shows that allocation can be adapted so as to achieve balanced growth, nearly regardless of environmental conditions. Moreover, it is shown that a feedback mechanism, which monitors internal stores, is able to achieve this allocation.     

Incorporating rhizosphere processes into field-scale (agro)ecosystem models

Three different strategies for incorporating rhizosphere processes within field-scale models are compared, taking triple-cropped irrigated rice production as a common system and CH₄ emission as a common focus of interest. The strategies may be characterised as homogeneous (model I; root C deposition is added to the bulk soil compartment), areal (model II; roots contribute via aerenchymatous exchange to an increased soil–atmosphere interfacial surface area), and volumetric (model III; roots create around themselves a specific rhizosphere compartment). Model I is simpler than model II, which is simpler than model III. With identical parameters all models lead to similar seasonally integrated CH₄ emissions, but when the pattern of emission and the simulated CH₄ concentration in the soil is brought into the reckoning, the following order of precedence (greater is better) becomes clear: model IIImodel II>model I. Current field-scale models of soil organic matter (SOM) transformation, especially in rice soils, could be improved by taking explicit account of the rhizosphere and the processes which occur within it.     

Modelling the growth of a methanotrophic biofilm: Estimation of parameters and variability

This article discusses the growth of methanotrophic biofilms. Several independent biofilm growths scenarios involving different inocula were examined. Biofilm growth, substrate removal and product formation were monitored throughout the experiments. Based on the oxygen consumption it was concluded that heterotrophs and nitrifiers co-existed with methanotrophs in the biofilm. Heterotrophic biomass grew on soluble polymers formed by the hydrolysis of dead biomass entrapped in the biofilm. Nitrifier populations developed because of the presence of ammonia in the mineral medium. Based on these experimental results, the computer program AQUASIM was used to develop a biological model involving methanotrophs, heterotrophs and nitrifiers. The modelling of six independent growth experiments showed that stoichiometric and kinetic parameters were within the same order of magnitude. Parameter estimation yielded an average maximum growth rate for methanotrophs, μ_m, of 1.5 ± 0.5 d⁻¹, at 20 °C, a decay rate, b_m, of 0.24 ± 0.1 d⁻¹, a half saturation constant, , of 0.06 ± 0.05 mg CH₄/L, and a yield coefficient, , of 0.57 ±: 0.04 g X/g CH₄. In addition, a sensitivity analysis was performed on this model. It indicated that the most influential parameters were those related to the biofilm (i.e. density; solid-volume fraction; thickness). This suggests that in order to improve the model, further research regarding the biofilm structure and composition is needed.     

The effects of amino acid replacements of glycine 20 on conformational stability and catalysis of staphylococcal nuclease

Staphylococcal nuclease (SNase) is a well-established model for protein folding studies. Its three-dimensional structure has been determined. The enzyme, Ca2+, and DNA or RNA substrate form a ternary complex. Glycine 20 is the second position of the first beta-turn of SNase, which may serve as the folding initiation site for the SNase polypeptide. To study the role of Gly20 in the conformational stability and catalysis of SNase, three mutants, in which Gly20 was replaced by alanine, valine, or isoleucine, were constructed and studied by using circular dichroism spectra, intrinsic and ANS-binding fluorescence spectra, stability and activity assays. The mutations have little effect on the conformational integrity of the mutants. However, the catalytic activity is reduced drastically by the mutations, and the stability of the protein is progressively decreased in the order G20A相似文献   

Modelling Plant Responses to Elevated CO2: How Important is Leaf Area Index?

BACKGROUND AND AIMS: The problem of increasing CO(2) concentration [CO(2)] and associated climate change has generated much interest in modelling effects of [CO(2)] on plants. While variation in growth and productivity is closely related to the amount of intercepted radiation, largely determined by leaf area index (LAI), effects of elevated [CO(2)] on growth are primarily via stimulation of leaf photosynthesis. Variability in LAI depends on climatic and growing conditions including [CO(2)] concentration and can be high, as is known for agricultural crops which are specifically emphasized in this report. However, modelling photosynthesis has received much attention and photosynthesis is often represented inadequately detailed in plant productivity models. Less emphasis has been placed on the modelling of leaf area dynamics, and relationships between plant growth, elevated [CO(2)] and LAI are not well understood. This Botanical Briefing aims at clarifying the relative importance of LAI for canopy assimilation and growth in biomass under conditions of rising [CO(2)] and discusses related implications for process-based modelling. MODEL: A simulation exercise performed for a wheat crop demonstrates recent experimental findings about canopy assimilation as affected by LAI and elevation of [CO(2)]. While canopy assimilation largely increases with LAI below canopy light saturation, effects on canopy assimilation of [CO(2)] elevation are less pronounced and tend to decline as LAI increases. Results from selected model-testing studies indicate that simulation of LAI is often critical and forms an important source of uncertainty in plant productivity models, particularly under conditions of limited resource supply. CONCLUSIONS: Progress in estimating plant growth and productivity under rising [CO(2)] is unlikely to be achieved without improving the modelling of LAI. This will depend on better understanding of the processes of substrate allocation, leaf area development and senescence, and the role of LAI in controlling plant adaptation to environmental changes.