Understanding the large reaction networks found in biological systems is a daunting task. One approach is to divide a network into more manageable smaller modules, thus simplifying the problem. This is a common strategy used in engineering. However, the process of identifying biological modules is still in its infancy and very little is understood about the range and capabilities of motif structures found in biological modules. In order to delineate these modules, a library of functional motifs has been generated via in silico evolution techniques. On the basis of their functional forms, networks were evolved from four broad areas: oscillators, bistable switches, homeostatic systems and frequency filters. Some of these motifs were constructed from simple mass action kinetics, others were based on Michaelis-Menten kinetics as found in protein/protein networks and the remainder were based on Hill equations as found in gene/protein interaction networks. The purpose of the study is to explore the capabilities of different network architectures and the rich variety of functional forms that can be generated. Ultimately, the library may be used to delineate functional motifs in real biological networks.

Cell death is a vital process for multicellular organisms. Programmed cell death (PCD) functions in a variety of processes including growth, development, and immune responses for homeostasis maintenance. In particular, plants and animals utilize PCD to control pathogen invasion and infected cell populations. Despite some similarity, there are a number of key differences between how these organisms initiate and regulate cell death. In contrast to animals, plants are sessile, lack a circulatory system, and have additional cellular structures, including cell walls and chloroplasts. Plant cells have the autonomous ability to induce localized cell death using conserved eukaryotic pathways as well as unique plant-specific pathways. Thus, in order to successfully infect host cells, pathogens must subvert immune responses and avoid detection to prevent PCD and allow infection. Here we discuss the roles of cell death in plant immune responses and the tactics pathogens utilize to avert cell death.

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Eukaryotic GCN2 (general control nonderepressible 2) is a serine/threonine protein kinase that plays an essential role in modulating amino acid metabolism in response to nutrient deprivation. A wide spectrum of GCN2 functions in yeast and mammals has been characterized that spans from responses to amino acid deficiency, development, differentiation and proper functions of mammalian organs to organism's life span, tumor cell survival and immune responses. Here we demonstrate that Arabidopsis thaliana GCN2 (AtGCN2) plays crucial roles in plant growth and development. We present evidence that AtGCN2 negatively regulates seed germination under diverse environmental conditions. Our genetic data supported the notion that AtGCN2 is required for leaf morphology and normal cellular physiology by controlling chlorophyll contents. Our gene expression analyses revealed that AtGCN2 negatively regulates several transcription factor genes that play important roles in plant gibberellic acid-related crosstalk. We concluded that AtGCN2 plays pivotal roles in various cellular processes essential for normal growth and development, hence expanding the functions of this general regulator beyond being merely a stress player.