Occurrence of dead core in catalytic particles containing immobilized enzymes: analysis for the Michaelis–Menten kinetics and assessment of numerical methods

In this article, the occurrence of dead core in catalytic particles containing immobilized enzymes is analyzed for the Michaelis–Menten kinetics. An assessment of numerical methods is performed to solve the boundary value problem generated by the mathematical modeling of diffusion and reaction processes under steady state and isothermal conditions. Two classes of numerical methods were employed: shooting and collocation. The shooting method used the ode function from Scilab software. The collocation methods included: that implemented by the bvode function of Scilab, the orthogonal collocation, and the orthogonal collocation on finite elements. The methods were validated for simplified forms of the Michaelis–Menten equation (zero-order and first-order kinetics), for which analytical solutions are available. Among the methods covered in this article, the orthogonal collocation on finite elements proved to be the most robust and efficient method to solve the boundary value problem concerning Michaelis–Menten kinetics. For this enzyme kinetics, it was found that the dead core can occur when verified certain conditions of diffusion–reaction within the catalytic particle. The application of the concepts and methods presented in this study will allow for a more generalized analysis and more accurate designs of heterogeneous enzymatic reactors.     

A generalized finite difference method for modeling cardiac electrical activation on arbitrary, irregular computational meshes

A generalized finite difference (GFD) method is presented that can be used to solve the bi-domain equations modeling cardiac electrical activity. Classical finite difference methods have been applied by many researchers to the bi-domain equations. However, these methods suffer from the limitation of requiring computational meshes that are structured and orthogonal. Finite element or finite volume methods enable the bi-domain equations to be solved on unstructured meshes, although implementations of such methods do not always cater for meshes with varying element topology. The GFD method solves the bi-domain equations on arbitrary and irregular computational meshes without any need to specify element basis functions. The method is useful as it can be easily applied to activation problems using existing meshes that have originally been created for use by finite element or finite difference methods. In addition, the GFD method employs an innovative approach to enforcing nodal and non-nodal boundary conditions. The GFD method performs effectively for a range of two and three-dimensional test problems and when computing bi-domain electrical activation moving through a fully anisotropic three-dimensional model of canine ventricles.     

广义岭回归在家禽育种值估计中的应用

讨论了岭回归方法应用于混合线性模型方程组中估计家禽育种值的方法,其实质是将传统的混合线性模型方程组理解为一种广义岭回归估计,为确定遗传参数的估计提供了一种途径;同时,以番鸭为例,考虑了一个性状和两个固定效应,采用广义岭回归法对公番鸭育种值进行了估计,并与最佳线性无偏预测法(BLUP 法)进行了比较,结果表明,广义岭回归方法和BLUP 法估计的育种值及其排序非常接近,其相关系数和秩相关系数分别达到了0.998~(**)和0.986~(**),且采用广义岭回归法预测的误差率低(在±10%以内);表明在混合线性模型方程组中使用广义岭回归估计动物育种值的方法具有可行性,并可省去估计遗传参数的过程,使BLUP 法在动物选育中的应用更具实用性.     

Derivation of general equations describing tracer diffusion in any two-compartment tissue with application to ionic diffusion in cylindrical muscle bundles

A set of generalized diffusion equations have been derived which describe radioactive tracer movement in any tissue that can be modeled as a distributed two-compartment system. These equations have been applied to ionic tracer movement in cylindrical muscle bundles, and the boundary conditions used correspond to experimental conditions during various ionic tracer diffusion experiments on cardiac papillary muscles. Specifically, solutions were obtained for extra- and intracellular tracer washout as well as for the extra- and intracellular steady-state tracer diffusion experiments of Weidmann (1966). These solutions are presented in series form as well as in graphical form and are compared with the corresponding experimental data. A comparison of these solutions with those obtained using simple exponential kinetics is presented, and it is shown that there is a marked discrepancy between these two methods of analysis for bundles of any appreciable diameter.     

Boundary conditions at the cartilage-synovial fluid interface for joint lubrication and theoretical verifications

The objective of this study is to establish and verify the set of boundary conditions at the interface between a biphasic mixture (articular cartilage) and a Newtonian or non-Newtonian fluid (synovial fluid) such that a set of well-posed mathematical problems may be formulated to investigate joint lubrication problems. A "pseudo-no-slip" kinematic boundary condition is proposed based upon the principle that the conditions at the interface between mixtures or mixtures and fluids must reduce to those boundary conditions in single phase continuum mechanics. From this proposed kinematic boundary condition, and balances of mass, momentum and energy, the boundary conditions at the interface between a biphasic mixture and a Newtonian or non-Newtonian fluid are mathematically derived. Based upon these general results, the appropriate boundary conditions needed in modeling the cartilage-synovial fluid-cartilage lubrication problem are deduced. For two simple cases where a Newtonian viscous fluid is forced to flow (with imposed Couette or Poiseuille flow conditions) over a porous-permeable biphasic material of relatively low permeability, the well known empirical Taylor slip condition may be derived using matched asymptotic analysis of the boundary layer at the interface.     

Conditions under Which the Mean Fertility Is Maximized When a Population Is at a Stable Equilibrium

It is assumed that there is a population with two alleles at one locus, random mating of adults and selection only involving differential fertilities. By making use of the Kuhn-Tucker theory of optimization under constraints, conditions are derived under which stable equilibrium frequencies x, y and z of the three genotypes are the same as those that maximize the mean fertility of the population. We derive all sets of frequencies of this type for the Hadeler-Liberman symmetric fertility model and all such sets for which at least one genotype is missing for the general model. If the population has frequencies that are initially near those at which there is both a stable equilibrium and maximization of the mean fertility, then the mean fertility (t) at time t is nondecreasing with t as t -> &. It is found that it is possible for the stable equilibrium maximum points (x, y, z) to be one or two points on a ridge on which the mean fertility is maximized or the entire set of points on the ridge. Furthermore, may be smaller on this ridge than at another stable equilibrium point at which is not even locally maximized.     

Continuous-Flow Capillary Assay for Measuring Bacterial Chemotaxis

Bacterial chemotaxis may have a significant impact on the structure and function of bacterial communities. Quantification of chemotactic motion is necessary to identify chemoeffectors and to determine the bacterial transport parameters used in predictive models of chemotaxis. When the chemotactic bacteria consume the chemoeffector, the chemoeffector gradient to which the bacteria respond may be significantly perturbed by the consumption. Therefore, consumption of the chemoeffector can confound chemotaxis measurements if it is not accounted for. Current methods of quantifying chemotaxis use bacterial concentrations that are too high to preclude chemoeffector consumption or involve ill-defined conditions that make quantifying chemotaxis difficult. We developed a method of quantifying bacterial chemotaxis at low cell concentrations (~10⁵ CFU/ml), so metabolism of the chemoeffector is minimized. The method facilitates quantification of bacterial-transport parameters by providing well-defined boundary conditions and can be used with volatile and semivolatile chemoeffectors.     

Glucose oxidase overproducing and negative mutants ofAspergillus niger

Summary A colony staining method was used to isolate mutants inAspergillus niger which showed altered glucose oxidase induction. The mutants were isolated under weakly or non-inducing conditions. A stable glucose-oxidase-negative mutant and a series of overproducing mutants were found. Among the overproducing mutants, different phenotypes were found with respect to glucose oxidase induction. The mutants were tested for glucose oxidase production in surface and submerged cultures, indicating a fair correspondence between those methods. From the characteristics of the mutants it can be concuded that oxygen- and carbonsource-dependent induction are mediated by different factors.     

Direction change of plant root growth by the impenetrable boundary

Spatial boundary conditions must be considered when utilizing mathematical modeling of plant root growth in the container or along with the imbedding solid obstacle. Using basic root growth principles and the geometry of the boundary surface, a mathematical model can be designed to keep all root elements inside the container or outside the obstacle without passing through the boundary after the minimum deflection of growth direction, and it is based on the minimum friction between root tips and soil and energy saving principles. Such a mathematical method is used to simulate the spatial distribution of root growth and the morphological architecture of the root system near the boundary. The validity of this model is supported by experimental observations that confirm some typical characteristics predicted by the simulations. This model can be widely used in resolving boundary condition complications where water and nutrients are consumed by plants in a spatially limited or heterogeneous resource field.     

Accommodating linkage disequilibrium in genetic-association analyses via ridge regression

Large-scale genetic-association studies that take advantage of an extremely dense set of genetic markers have begun to produce very compelling statistical associations between multiple makers exhibiting strong linkage disequilibrium (LD) in a single genomic region and a phenotype of interest. However, the ultimate biological or "functional" significance of these multiple associations has been difficult to discern. In fact, the LD relationships between not only the markers found to be associated with the phenotype but also potential functionally or causally relevant genetic variations that reside near those markers have been exploited in such studies. Unfortunately, LD, especially strong LD, between variations at neighboring loci can make it difficult to distinguish the functionally relevant variations from nonfunctional variations. Although there are (rare) situations in which it is impossible to determine the independent phenotypic effects of variations in LD, there are strategies for accommodating LD between variations at different loci, and they can be used to tease out their independent effects on a phenotype. These strategies make it possible to differentiate potentially causative from noncausative variations. We describe one such approach involving ridge regression. We showcase the method by using both simulated and real data. Our results suggest that ridge regression and related techniques have the potential to distinguish causative from noncausative variations in association studies.     

A system boundary identification method for life cycle assessment

Purpose

Life cycle assessment (LCA) is a useful tool for quantifying the overall environmental impacts of a product, process, or service. The scientific scope and boundary definition are important to ensure the accuracy of LCA results. Defining the boundary in LCA is difficult and there are no commonly accepted scientific methods yet. The objective of this research is to present a comprehensive discussion of system boundaries in LCA and to develop an appropriate boundary delimitation method.

Methods

A product system is partitioned into the primary system and interrelated subsystems. The hierarchical relationship of flow and process is clarified by introducing flow- and process-related interventions. A system boundary curve model of the LCA is developed and the threshold rules for judging whether the system boundary satisfies the research requirement are proposed. Quantitative criteria from environmental, technical, geographical and temporal dimensions are presented to limit the boundaries of LCA. An algorithm is developed to identify an appropriate boundary by searching the process tree and evaluating the environmental impact contribution of each process while it is added into the studied system.

Results and discussion

The difference between a limited system and a theoretically complete system is presented. A case study is conducted on a color TV set to demonstrate and validate the method of boundary identification. The results showed that the overall environmental impact indicator exhibits a slow growth after a certain number of processes considered, and the gradient of the fitting curve trends to zero gradually. According to the threshold rules, a relatively accurate system boundary could be obtained.

Conclusions

It is found from this research that the system boundary curve describes the growth of life cycle impact assessment (LCIA) results as processes are added. The two threshold rules and identification methods presented can be used to identify system boundary of LCA. The case study demonstrated that the methodology presented in this paper is an effective tool for the boundary identification.     

Inclusion of Residual Tissue in Biobanks: Opt-In or Opt-Out?

Residual samples are an important source of tissue for biobanks. They refer to leftover tissue that is obtained in the course of clinical care. Residual samples can be included through an opt-in method-that is, a person explicitly expresses consent to include residual tissue-or an opt-out method-that is, the tissue is stored unless a person explicitly refuses. At the moment there is a renewed interest in the appropriate method for the inclusion of residual samples in biobanks. The expansion of biobanks and rapid developments in biomedical research underscore the need to evaluate the proper procedure. In this article we revisit the arguments in favor and against opt-in and opt-out methods for residual tissue research. We conclude firstly that an opt-out method is only justifiable when certain conditions are met: (1) awareness has to be raised, (2) sufficient information has to be provided, and (3) a genuine possibility to object has to be offered. An opt-out procedure that fulfills these conditions can be called a "thick" opt-out method. As a consequence, the dichotomy between opt-in and opt-out is less stark than usually suggested, as both methods require a certain amount of effort. Secondly, we conclude that because of the diversity of tissue and research, not every situation can be treated alike. There are at least four situations that require opt-in procedures: (1) research with higher risks or increased burdens, (2) the use of controversial or high-impact techniques, (3) research on sensitive tissue types, and (4) research involving vulnerable patients. We suggest that further interdisciplinary debate should answer the question when to opt-in or when to opt-out.     

Initial limb budding is independent of apical ectodermal ridge activity; evidence from a limbless mutant

Outgrowth of normal chick limb bud mesoderm is dependent on the presence of a specialized epithelium called the apical ectodermal ridge. This ectodermal ridge is induced by the mesoderm at about the time of limb bud formation. The limbless mutation in the chick affects apical ectodermal ridge formation in the limb buds of homozygotes. The initial formation of the limb bud appears to be unaffected by the mutation but no ridge develops and further outgrowth, which is normally dependent on the ridge, does not take place. As a result, limbless chicks develop without limbs. In the present study, which utilized a pre-limb-bud recombinant technique, limbless mesoderm induced an apical ectodermal ridge in grafted normal flank ectoderm. However, at stages when normal flank ectoderm is capable of responding to ridge induction, limbless flank ectoderm did not form a ridge or promote outgrowth of a limb in response to normal presumptive wing bud mesoderm. We conclude from this that the limbless mutation affects the ability of the ectoderm to form a ridge. In addition, because the limbless ectoderm has no morphological ridge and no apparent ridge activity (i.e. it does not stabilize limb elements in stage-18 limb bud mesoderm), the limbless mutant demonstrates that the initial formation of the limb bud is independent of apical ectodermal ridge activity.     

Several novel methods for immobilization of enzymes, microbial cells and organelles

Two novel methods--"photo-crosslinkable resin prepolymer method" and "urethane prepolymer method"--have been developed in our laboratory. These methods have the following advantages : 1) Prepolymers of desired properties, such as optional chain length, hydrophilicity or hydrophobicity, and ionic character etc., can be used for entrapment of biocatalysts : (2) preparation of gel-entrapped biocatalysts can be easily achieved under very mild conditions. Photo-crosslinked gels are conveniently obtained by several minutes illumination with near-UV light, of a mixture of liquid prepolymers having photo-sensitive functional groups, an appropriate sensitizer and the solution or suspension of biocatalyst. Formation of polyurethane gels is completed by only mixing water-miscible urethane prepolymers with the aqueous solution or suspension of biocatalyst. The biocatalysts entrapped by these methods are useful for a variety of purposes.     

A Theoretical Foundation for Life-Cycle Assessment

The presence of value judgments in life-cycle impact assessment (LCIA) has been a constant source of controversy. According to a common interpretation, the international standard on LCIA requires that the assessment methods used in published comparisons be "value free." Epistemologists argue that even natural science rests on "constitutive" and "contextual" value judgments. The example of the equivalency potential for climate change, the global warming potential (GWP), demonstrates that any impact assessment method inevitably contains not only constitutive and contextual values, but also preference values. Hence, neither life-cycle assessment (LCA) as a whole nor any of its steps can be "value free." As a result, we suggest a more comprehensive definition of objectivity in LCA that allows arguments about values and their relationship to facts. We distinguish three types of truth claims: factual claims, which are based on natural science; normative claims, which refer to preference values; and relational claims, which address the proper relation between factual knowledge and values. Every assessment method, even the GWP, requires each type of claim. Rational arguments can be made about each type of claim. Factual truth claims can be assessed using the scientific method. Normative claims can be based on ethical arguments. The values of individuals or groups can be elicited using various social science methods. Relational claims must follow the rules of logic. Relational claims are most important for the development of impact assessment methods. Because LCAs are conducted to satisfy the need of decision makers to consider environmental impacts, relational claims about impact assessment methods should refer to this goal. This article introduces conditions that affect environmental decision making and discusses how LCA—values and all—can be defended as a rational response to the challenge of moving uncertain scientific information into the policy arena.     

A monitoring method for Atg4 activation in living cells using peptide-conjugated polymeric nanoparticles

To date, several principal methods are presently used to monitor the autophagic process, but they have some potential experimental pitfalls or limitations that make them not applicable to living cells. In order to improve on the currently developed detection methods for autophagy, we report here fluorescent peptide-conjugated polymeric nanoparticles loaded with a lysosome staining dye in their core. The fluorescent peptide is designed to be specifically cleaved by the Atg4 cysteine protease, which plays a crucial role in autophagy activation. In this study, we demonstrate that peptide-conjugated polymeric nanoparticles can be used to visualize Atg4 activity in both cell-free and cell culture systems. The fluorescence imaging of cells incubated with nanoparticles demonstrates that Atg4 activity is activated in the autophagy-induced conditions, but suppressed in the autophagy-inhibited conditions. These results indicate that Atg4 activity is correlated with autophagic flux through its own regulatory pathway. Therefore, our strategy provides an alternative detection method that can clearly distinguish between an "autophagy active" and "autophagy inactive" state in cultured cells. As our nanoparticles are highly cell-permeable and biocompatible, this detection system has general applicability to living cells and can be extended to cell-based screening to evaluate newly developed compounds.     

A continuous cable method for determining the transient potential in passive dendritic trees of known geometry

Models using cable equations are increasingly employed in neurophysiological analyses, but the amount of computer time and memory required for their implementation are prohibitively large for many purposes and many laboratories. A mathematical procedure for determining the transient voltage response to injected current or synaptic input in a passive dendritic tree of known geometry is presented that is simple to implement since it is based on one equation. It proved to be highly accurate when results were compared to those obtained analytically for dendritic trees satisfying equivalent cylinder constraints. In this method the passive cable equation is used to express the potential for each interbranch segment of the dendritic tree. After applying boundary conditions at branch points and terminations, a system of equations for the Laplace transform of the potential at the ends of the segments can be readily obtained by inspection of the dendritic tree. Except for the starting equation, all of the equations have a simple format that varies only with the number of branches meeting at a branch point. The system of equations is solved in the Laplace domain, and the result is numerically inverted back to the time domain for each specified time point (the method is independent of any time increment t). The potential at any selected location in the dendritic tree can be obtained using this method. Since only one equation is required for each interbranch segment, this procedure uses far fewer equations than comparable compartmental approaches. By using significantly less computer memory and time than other methods to attain similar accuracy, this method permits extensive analyses to be performed rapidly on small computers. One hopes that this will involve more investigators in modeling studies and will facilitate their motivation to undertake realistically complex dendritic models.     

Review and perspective on the use of mixed-function oxygenase enzymes in biological monitoring

It is often suggested that changes in simple biochemical/physiological responses may be useful for predicting the impacts of pollutants at population and community levels of biological organization. There are serious conceptual constraints to such a thesis and its seems likely that such simple responses can go no further than serving as early warning systems for delineating potential areas of pollutant impact--areas which (if shown to be significant in size) can then be subjected to more detailed population and community type studies. Environmental testing is a prerequisite for any response suggested to have value as a biological monitoring index and the induction of mixed-function oxygenase (MFO) enzymes has now been validated in a large number of field studies worldwide. Investigations have progressed from documenting induction near localized sources of hydrocarbon contamination to more diffuse sources of mixed organic pollution originating from industrial and domestic sources. Studies in the Great Lakes and Europe have demonstrated that the induction of MFO enzymes is a biological response of sufficient sensitivity to discriminate water quality differences over broad geographical areas. We suggest that as an early warning system, the induction of these enzymes can fulfill the requirement of "most sensitive biological response" for assessing a variety of organic pollution conditions. Given the high level of sensitivity of the MFO enzyme response, negative as well as positive field trials can be of value in addressing concerns about the toxicological significance of "high-profile" chemicals (and potent inducers) such as polycyclic aromatic hydrocarbons and organochlorines. MFO enzyme induction can also be an economical tool for environmental managers for reacting to real or perceived concerns about pollution such as effects on commercial fish stocks at sites of petroleum hydrocarbon development in the oceans.     

Estimating stomatal and biochemical limitations during photosynthetic induction

Understanding stomatal and biochemical components that limit photosynthesis under different conditions is important for both the targeted improvement of photosynthesis and the elucidation of how stomata and biochemistry affect plant performance in an ecological context. Limitation analyses have not yet been extensively applied to conditions of photosynthetic induction after an increase in irradiance. Moreover, few studies have systematically assessed how well various limitation analyses actually work. Here we build on two general ways of estimating limitations, one that sequentially removes the effect of a limitation (elimination) and one that uses a tangent plane approximation (differential), by including the ternary effect and boundary layer conductance so that they are consistent with gas exchange data. We apply them to the analysis of temporal and time‐integrated limitations during photosynthetic induction, calculating limitations either independent of the time course (one‐step) or make use of the entire time course (stepwise). We show that the stepwise differential method is the best method to use when time steps are small enough. We further show that the differential method predicts limitations near exact when the internal CO₂ concentration stays constant. This last insight has important implications for the general use of limitation analyses beyond photosynthetic induction.