Because the product of a single gene can influence many aspects of plant growth and development, it is necessary to understand how gene products act in concert and upon each other to effect adaptive changes to stressful conditions. We conducted experiments to improve our understanding of the responses of loblolly pine (Pinus taeda) to drought stress. Water was withheld from rooted plantlets of to a measured water potential of Ϫ1 MPa for mild stress and Ϫ1.5 MPa for severe stress. Net photosynthesis was measured for each level of stress. RNA was isolated from needles and used in hybridizations against a microarray consisting of 2,173 cDNA clones from five pine expressed sequence tag libraries. Gene expression was estimated using a two-stage mixed linear model. Subsequently, data mining via inductive logic programming identified rules (relationships) among gene expression, treatments, and functional categories. Changes in RNA transcript profiles of loblolly pine due to drought stress were correlated with physiological data reflecting photosynthetic acclimation to mild stress or photosynthetic failure during severe stress. Analysis of transcript profiles indicated that there are distinct patterns of expression related to the two levels of stress. Genes encoding heat shock proteins, late embryogenic-abundant proteins, enzymes from the aromatic acid and flavonoid biosynthetic pathways, and from carbon metabolism showed distinctive responses associated with acclimation. Five genes shown to have different transcript levels in response to either mild or severe stress were chosen for further analysis using real-time polymerase chain reaction. The real-time polymerase chain reaction results were in good agreement with those obtained on microarrays.

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Free Air [CO(2)] Enrichment (FACE) allows for plant growth under fully open-air conditions of elevated [CO(2)] at concentrations expected to be reached by mid-century. We used Arabidopsis thaliana ecotypes Col-0, Cvi-0, and WS to analyze changes in gene expression and metabolite profiles of plants grown in "SoyFACE" (http://www.soyface.uiuc.edu/), a system of open-air rings within which [CO(2)] is elevated to approximately 550 ppm. Data from multiple rings, comparing plants in ambient air and elevated [CO(2)], were analyzed by mixed model ANOVA, linear discriminant analysis (LDA) and data-mining tools. In elevated [CO(2)], decreases in the expression of genes related to chloroplast functions characterized all lines but individual members of distinct multi-gene families were regulated differently between lines. Also, different strategies distinguished the lines with respect to the regulation of genes related to carbohydrate biosynthesis and partitioning, N-allocation and amino acid metabolism, cell wall biosynthesis, and hormone responses, irrespective of the plants' developmental status. Metabolite results paralleled reactions seen at the level of transcript expression. Evolutionary adaptation of species to their habitat and intrinsic genetic plasticity seem to determine the nature of responses to elevated [CO(2)]. Irrespective of their underlying genetic diversity, and evolutionary adaptation to different habitats, a small number of common, predominantly stress-responsive, signature transcripts appear to characterize responses of the Arabidopsis ecotypes in FACE.

Phospholipase D (PLD) has been implicated in a variety of stresses including osmotic stress and wounding. PLDalpha1-derived phosphatidic acid interacts with ABI1 phosphatase 2C and promotes abscisic acid signalling. It has also been shown to regulate proline biosynthesis negatively. Plants with abrogated PLDalpha show insensitivity to abscisic acid (ABA) and impaired stomatal conductance. The goal in the present study was to identify early PLDalpha-mediated events in response to progressive drought stress in Arabidopsis. Water was withheld from 7-week-old Arabidopsis thaliana (Col-0) and antisense-PLDalpha1 (anti-PLDalpha) in a controlled environment chamber. Diurnal leaf water potential (LWP) and photosynthesis measurements were recorded five and three times a day, respectively. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and microarray analyses were conducted using RNA from shoots collected at the fourth LWP time point on the ninth day after stress imposition. Anti-PLDalpha experienced severe water stress (-1.28 MPa) at the same time period that Col-0 experienced less water stress (-0.31 MPa). Diurnal LWP measurements showed that anti-PLDalpha had a lower LWP than Col-0 in both control and drought-stress conditions. Photosynthesis was also more affected in anti-PLDalpha than in Col-0. Anti-PLDalpha plants recovered fully following rehydration after 10 d of stress. qRT-PCR revealed up to 18-fold lower values for PLDalpha transcripts in stressed anti-PLDalpha plants when compared with stressed Col-0. Microarray expression profiles revealed distinct gene expression patterns in Col-0 and anti-PLDalpha. No differences in gene expression were detected between the two genotypes in the absence of drought stress. ROP8, PLDdelta, and lipid transfer proteins were among the differentially expressed genes between the two genotypes.

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A multimodal network (MMN) is a novel graph-theoretic formalism designed to capture the structure of biological networks and to represent relationships derived from multiple biological databases. MMNs generalize the standard notions of graphs and hypergraphs, which are the bases of current diagrammatic representations of biological phenomena and incorporate the concept of mode. Each vertex of an MMN is a biological entity, a biot, while each modal hyperedge is a typed relationship, where the type is given by the mode of the hyperedge. The current paper defines MMNs and concentrates on the structural aspects of MMNs. A companion paper develops MMNs as a representation of the semantics of biological networks and discusses applications of the MMNs in managing complex biological data. The MMN model has been implemented in a database system containing multiple kinds of biological networks.