Transcriptional network dynamics in macrophage activation

Transcriptional regulatory networks govern cell differentiation and the cellular response to external stimuli. However, mammalian model systems have not yet been accessible for network analysis. Here, we present a genome-wide network analysis of the transcriptional regulation underlying the mouse macrophage response to bacterial lipopolysaccharide (LPS). Key to uncovering the network structure is our combination of time-series cap analysis of gene expression with in silico prediction of transcription factor binding sites. By integrating microarray and qPCR time-series expression data with a promoter analysis, we find dynamic subnetworks that describe how signaling pathways change dynamically during the progress of the macrophage LPS response, thus defining regulatory modules characteristic of the inflammatory response. In particular, our integrative analysis enabled us to suggest novel roles for the transcription factors ATF-3 and NRF-2 during the inflammatory response. We believe that our system approach presented here is applicable to understanding cellular differentiation in higher eukaryotes. (c) 2006 Elsevier Inc. All rights reserved.

A simulation model of cereal-legume intercropping systems for semi-arid regions I. Model development

Cereal-legume intercropping plays an important role in subsistence food production in developing countries, especially in situations of limited water resources. Crop simulation can be used to assess risk for intercrop productivity over time and space. In this study, a simple model for intercropping was developed for cereal and legume growth and yield, under semi-arid conditions. The model is based on radiation interception and use, and incorporates a water stress factor. Total dry matter and yield are functions of photosynthetically active radiation (PAR), the fraction of radiation intercepted and radiation use efficiency (RUE). One of two PAR sub-models was used to estimate PAR from solar radiation; either PAR is 50% of solar radiation or the ratio of PAR to solar radiation (PAR/SR) is a function of the clearness index (K-T). The fraction of radiation intercepted was calculated either based on Beer's Law with crop extinction coefficients (K) from field experiments or from previous reports. RUE was calculated as a function of available soil water to a depth of 900 mm (ASW). Either the soil water balance method or the decay curve approach was used to determine ASW. Thus, two alternatives for each of three factors, i.e., PAR/SR, K and ASW, were considered, giving eight possible models (2 methods x 3 factors). The model calibration and validation were carried out with maize-bean intercropping systems using data collected in a semi-arid region (Bloemfontein, Free State, South Africa) during seven growing seasons (1996/1997-2002/2003). The combination of PAR estimated from the clearness index, a crop extinction coefficient from the field experiment and the decay curve model gave the most reasonable and acceptable result. The intercrop model developed in this study is simple, so this modelling approach can be employed to develop other cereal-legume intercrop models for semi-arid regions. (c) 2004 Elsevier B.V. All rights reserved.

A simulation model of cereal-legume intercropping systems for semi-arid regions II. Model application

Smallholder farmers in Africa practice traditional cropping techniques such as intercropping. Intercropping is thought to offer higher productivity and resource milisation than sole cropping. In this study, risk associated with maize-bean intercropping was evaluated by quantifying long-term yield in both intercropping and sole cropping in a semi-arid region of South Africa (Bloemfontein, Free State) with reference to rainfall variability. The crop simulation model was run with different cultural practices (planting date and plant density) for 52 summer crop growing seasons (1950/1951-2001/2002). Eighty-one scenarios, consisted of three levels of initial soil water, planting date, maize population, and bean population, were simulated. From the simulation outputs, the total land equivalent ratio (LER) was greater than one. The intercrop (equivalent to sole maize) had greater energy value (EV) than sole beans, and the intercrop (equivalent to sole beans) had greater monetary value (MV) than sole maize. From these results, it can be concluded that maize-bean intercropping is advantageous for this semi-arid region. Soil water at planting was the most important factor of all scenario factors, followed by planting date. Irrigation application at planting, November/December planting and high plant density of maize for EV and beans for MV can be one of the most effective cultural practices in the study region. With regard to rainfall variability, seasonal (October-April) rainfall positively affected EV and MV, but not LER. There was more intercrop production in La Nina years than in El Nino years. Thus, better cultural practices may be selected to maximize maize-bean intercrop yields for specific seasons in the semi-arid region based on the global seasonal outlook. (c) 2004 Elsevier B.V. All rights reserved.

Functional-structural plant modelling using a combination of architectural analysis, L-systems and a canonical model of function

This paper presents a new method for producing a functional-structural plant model that simulates response to different growth conditions, yet does not require detailed knowledge of underlying physiology. The example used to present this method is the modelling of the mountain birch tree. This new functional-structural modelling approach is based on linking an L-system representation of the dynamic structure of the plant with a canonical mathematical model of plant function. Growth indicated by the canonical model is allocated to the structural model according to probabilistic growth rules, such as rules for the placement and length of new shoots, which were derived from an analysis of architectural data. The main advantage of the approach is that it is relatively simple compared to the prevalent process-based functional-structural plant models and does not require a detailed understanding of underlying physiological processes, yet it is able to capture important aspects of plant function and adaptability, unlike simple empirical models. This approach, combining canonical modelling, architectural analysis and L-systems, thus fills the important role of providing an intermediate level of abstraction between the two extremes of deeply mechanistic process-based modelling and purely empirical modelling. We also investigated the relative importance of various aspects of this integrated modelling approach by analysing the sensitivity of the standard birch model to a number of variations in its parameters, functions and algorithms. The results show that using light as the sole factor determining the structural location of new growth gives satisfactory results. Including the influence of additional regulating factors made little difference to global characteristics of the emergent architecture. Changing the form of the probability functions and using alternative methods for choosing the sites of new growth also had little effect. (c) 2004 Elsevier B.V. All rights reserved.

Spin exchange and superconductivity in a t-J(')-V model for two-dimensional quarter-filled systems

The effect of antiferromagnetic spin fluctuations on two-dimensional quarter-filled systems is studied theoretically. An effective t-J(')-V model on a square lattice which accounts for checkerboard charge fluctuations and next-nearest-neighbor antiferromagnetic spin fluctuations is considered. From calculations based on large-N theory on this model it is found that the exchange interaction J(') increases the attraction between electrons in the d(xy) channel only, so that both charge and spin fluctuations work cooperatively to produce d(xy) pairing.

Studies on the membrane interactions of the cyclotides kalata B1 and kalata B6 on model membrane systems by surface plasmon resonance

In this study we have demonstrated the interactions of kalata B1 and its naturally occurring analogue kalata B6 with five model lipid membranes and have analyzed the binding kinetics using surface plasmon resonance. Two kalata peptides showed a higher affinity for the phosphatidylethanolamine-containing membranes, indicating that the peptides would bind selectively to bacterial membranes. Also we have optimized the procedure for the immobilization of five liposome mixtures and have shown that the procedure provides reproducible levels of immobilized liposomes and could be used to screen the selective binding of putative antimicrobial peptides to model mammalian or microbial phospholipid membranes. (C) 2004 Elsevier Inc. All rights reserved.

Development of a quasi-chemical viscosity model for fully liquid slags in the Al2O3-CaO-'FeO'-MgO-SiO2 system. Part 1. Description of the model and its application to the MgO, MgO-SiO2, Al2O3-MgO and CaO-MgO sub-systems

A structurally-based quasi-chemical viscosity model for fully liquid slags in the Al2O3 CaO-'FeO'-MgO-SiO2 system has been developed. The model links the slag viscosities to the internal structures of the melts through the concentrations of various Si0.5O, Me2/nn+O and Me1/nn+Si0.25O viscous flow structural units. The concentrations of these structural units are derived from a quasi-chemical thermodynamic model of the system. The model described in this series of papers enables the viscosities of liquid slags to be predicted within experimental uncertainties over the whole range of temperatures and compositions in the Al2O3 CaOMgO-SiO2 system.

Development of a quasi-chemical viscosity model for fully liquid slags in the Al2O3-CaO-'FeO'-MgO-SiO2 system. Part 2. A review of the experimental data and the model predictions for the Al2O3-CaO-MgO, CaO-MgO-SiO2 and Al2O3-MgO-SiO2 systems

A structurally-based quasi-chemical viscosity model has been developed for the Al2O3 CaO-'FeO'-MgO-SiO2 system. The model links the slag viscosity to the internal structure of melts through the concentrations of various anion/cation Si0.5O, Me2/nn+O and Me1/nn+Si0.25O viscous flow structural units. The concentrations of structural units are derived from the quasi-chemical thermodynamic model. The focus of the work described in the present paper is the analysis of experimental data and the viscosity models for fully liquid slags in the Al2O3-CaO-MgO, Al2O3 MgO-SiO2 and CaO-MgO-SiO2 systems.

Development of a quasi-chemical viscosity model for fully liquid slags in the Al2O3-CaO-'FeO'-MgO-SiO2 system. Part 3. Summary of the model predictions for the Al2O3-CaO-MgO-SiO2 system and its sub-systems

A structurally-based quasi-chemical viscosity model for fully liquid slags in the Al2O3 CaO-'FeO'-MgOSiO2 system has been developed. The focus of the work described in the present paper is the analysis of the experimental data and viscosity models in the quaternary system Al2O3 CaO-MgO-SiO2 and its subsystems. A review of the experimental data, viscometry methods used and viscosity models available in the Al2O3 CaO-MgO-SiO2 and its sub-systems is reported. The quasi-chemical viscosity model is shown to provide good agreement between experimental data and predictions over the whole compositional range.