Adaptive combinatorial design to explore large experimental spaces: approach and validation.

Systems biology requires mathematical tools not only to analyse large genomic datasets, but also to explore large experimental spaces in a systematic yet economical way. We demonstrate that two-factor combinatorial design (CD), shown to be useful in software testing, can be used to design a small set of experiments that would allow biologists to explore larger experimental spaces. Further, the results of an initial set of experiments can be used to seed further 'Adaptive' CD experimental designs. As a proof of principle, we demonstrate the usefulness of this Adaptive CD approach by analysing data from the effects of six binary inputs on the regulation of genes in the N-assimilation pathway of Arabidopsis. This CD approach identified the more important regulatory signals previously discovered by traditional experiments using far fewer experiments, and also identified examples of input interactions previously unknown. Tests using simulated data show that Adaptive CD suffers from fewer false positives than traditional experimental designs in determining decisive inputs, and succeeds far more often than traditional or random experimental designs in determining when genes are regulated by input interactions. We conclude that Adaptive CD offers an economical framework for discovering dominant inputs and interactions that affect different aspects of genomic outputs and organismal responses.

Molecular and functional regulation of two NO3- uptake systems by N- and C-status of Arabidopsis plants.

Root NO3- uptake and expression of two root NO3- transporter genes (Nrt2;1 and Nrt1) were investigated in response to changes in the N- or C-status of hydroponically grown Arabidopsis thaliana plants. Expression of Nrt2;1 is up-regulated by NO3 - starvation in wild-type plants and by N-limitation in a nitrate reductase (NR) deficient mutant transferred to NO3- as sole N source. These observations show that expression of Nrt2;1 is under feedback repression by N-metabolites resulting from NO3- reduction. Expression of Nrt1 is not subject to such a repression. However, Nrt1 is over-expressed in the NR mutant even under N-sufficient conditions (growth on NH4NO3 medium), suggesting that expression of this gene is affected by the presence of active NR, but not by N-status of the plant. Root 15NO3- influx is markedly increased in the NR mutant as compared to the wild-type. Nevertheless, both genotypes have similar net 15NO3- uptake rates due to a much larger 14NO3- efflux in the mutant than in the wild-type. Expressions of Nrt2;1 and Nrt1 are diurnally regulated in photosynthetically active A. thaliana plants. Both increase during the light period and decrease in the first hours of the dark period. Sucrose supply prevents the inhibition of Nrt2;1 and Nrt1 expressions in the dark. In all conditions investigated, Nrt2;1 expression is strongly correlated with root 15NO3- influx at 0.2 mM external concentration. In contrast, changes in the Nrt1 mRNA level are not always associated with similar changes in the activities of high- or low-affinity NO3- transport systems.

Three functional transporters for constitutive, diurnally regulated, and starvation-induced uptake of ammonium into Arabidopsis roots.

Ammonium and nitrate are the prevalent nitrogen sources for growth and development of higher plants. 15N-uptake studies demonstrated that ammonium is preferred up to 20-fold over nitrate by Arabidopsis plants. To study the regulation and complex kinetics of ammonium uptake, we isolated two new ammonium transporter (AMT) genes and showed that they functionally complemented an ammonium uptake-deficient yeast mutant. Uptake studies with 14C-methylammonium and inhibition by ammonium yielded distinct substrate affinities between

Abolition of Posttranscriptional Regulation of Nitrate Reductase Partially Prevents the Decrease in Leaf NO3- Reduction when Photosynthesis Is Inhibited by CO2 Deprivation, but Not in Darkness.

The activity of nitrate reductase (NR) in leaves is regulated by light and photosynthesis at transcriptional and posttranscriptional levels. To understand the physiological role of these controls, we have investigated the effects of light and CO2 on in vivo NO3- reduction in transgenic plants of Nicotiana plumbaginifolia lacking either transcriptional regulation alone or transcriptional and posttranscriptional regulation of NR. The abolition of both levels of NR regulation did not modify the light/dark changes in exogenous 15NO3- reduction in either intact plants or detached leaves. The same result was obtained for 15N incorporation into free amino acids in leaves after 15NO3- was supplied to the roots, and for reduction of endogenous NO3- after transfer of the plants to an N-deprived solution. In the light, however, deregulation of NR at the posttranscriptional level partially prevented the inhibition of leaf 15NO3- reduction resulting from the removal of CO2 from the atmosphere We concluded from these observations that in our conditions deregulation of NR in the transformants investigated had little impact on the adverse effect of darkness on leaf NO3- reduction, and that posttranscriptional regulation of NR is one of the mechanisms responsible for the short-term coupling between photosynthesis and leaf NO3- reduction in the light.