D. Hagenbeek

To enable discovery of factors controlling specific developmental processes, screens on developmental stages other than etiolated seedlings are needed. Smalle et al. (1997) showed that leaf emergence was enhanced by the ethylene precursor ACC. This was exploited as an assay for mutants in ethylene response.

ABSTRACT Plants perceive a plethora of external signals and continuously adapt to changes in their environment. This phenotypic plasticity is obtained by integration of external signals as light and temperature, with internal, mainly hormonal signals that regulate development (Vandenbussche and Van Der Straeten, 2004).

The nuclear receptor peroxisome proliferator-activated receptor gamma (PPARgamma) is a key regulator of adipocyte differentiation in vivo and ex vivo and has been shown to control the expression of several adipocyte-specific genes. In this study, we used chromatin immunoprecipitation combined with deep sequencing to generate genome-wide maps of PPARgamma and retinoid X receptor (RXR)-binding sites, and RNA polymerase II (RNAPII) occupancy at very high resolution throughout adipocyte differentiation of 3T3-L1 cells. We identify >5000 high-confidence shared PPARgamma:RXR-binding sites in adipocytes and show that during early stages of differentiation, many of these are preoccupied by non-PPARgamma RXR-heterodimers. Different temporal and compositional patterns of occupancy are observed. In addition, we detect co-occupancy with members of the C/EBP family. Analysis of RNAPII occupancy uncovers distinct clusters of similarly regulated genes of different biological processes. PPARgamma:RXR binding is associated with the majority of induced genes, and sites are particularly abundant in the vicinity of genes involved in lipid and glucose metabolism. Our analyses represent the first genome-wide map of PPARgamma:RXR target sites and changes in RNAPII occupancy throughout adipocyte differentiation and indicate that a hitherto unrecognized high number of adipocyte genes of distinctly regulated pathways are directly activated by PPARgamma:RXR.

The physiological status of plants can nowadays be promptly monitored with non-invasive methods. This opens the possibility to continuously follow-up plant performance and permits to detect stress-induced deviations presymptomatically. Upon stress, plants may synthesize specific compounds, depending on the causal agent. Such compounds may alter the absorption of the light impinging on plant leaves, hence the spectrum of reflected, re-emitted, and transmitted light changes. UV-excited fluorescence imaging specifically allows visualization of the accumulation of phenolic compounds, e.g. those associated with the hypersensitive response to pathogens. By using imaging at regular intervals (time-lapse series) of tobacco mosaic virus (TMV) infection in resistant tobacco we aimed at the description and quantification of the kinetics of blue-green fluorescence compared to the visual development of the disease. Presymptomatic responses to TMV infection were observed with a multicolor fluorescence and reflectance imaging setup. The onset of increases in blue-green and chlorophyll fluorescence were comparable in timing, although further symptom development was strikingly different. Compounds known to accumulate during the hypersensitive response and displaying blue-green fluorescence revealed different dynamics of fluorescence evolution in time. The multichannel imaging system permitted to discern the key components salicylic acid and scopoletin. In contrast, for the compatible interaction between TMV and non-resistant tobacco, no presymptomatic responses were detected on inoculated leaves. This work proves the potential of multispectral imaging to unveil stress-associated signatures, and the power of blue-green fluorescence imaging to monitor accumulation of secondary compounds.

Thermal and chlorophyll fluorescence imaging are powerful tools for the study of spatial and temporal heterogeneity of leaf transpiration and photosynthetic performance. The relative advantages and disadvantages of these techniques are discussed. When combined, they can highlight pre-symptomatic responses not yet apparent in visual spectrum images and provide specific signatures for diagnosis of distinct diseases and abiotic stresses. In addition, their use for diagnosis and for selection for stomatal or photosynthetic mutants, these techniques can be applied for stress tolerance screening. For example, rapid screening for stomatal responses can be achieved by thermal imaging, while, combined with fluorescence imaging to study photosynthesis, they can potentially be used to derive leaf water use efficiency as a screening parameter. A particular advantage of imaging is that it allows continuous automated monitoring of dynamic spatial variation. Examples of applications include the study of growth and development of plant lines differing in stress resistance, yield, circadian clock-controlled responses, and the possible interactions between these parameters. In the future, such dual-imaging systems could be extended with complementary techniques such as hyperspectral and blue-green fluorescence imaging. This would result in an increased number of quantified parameters which will increase the power of stress diagnosis and the potential for screening of stress-tolerant genotypes.

Prerequisites for optimal, high crop yield are disease‐free growth and an equilibrated supply of nutrients. Early signatures of stress‐altered physiology, before appearance of symptoms in the visible spectrum, allow timely treatment. Early detection of stress development was carried out on phaseolus vulgaris bean infected with the agriculturally important grey mould pathogen and under conditions of magnesium deficiency, limiting photosynthesis. During

... From these ChIP-seq analyses, we generated genome-wide high-resolution maps of PPARγ- and RXR-binding sites (FDR level <0.001). ... S3). The extent of this drop in occupancy at day 3 varies between different differentiations, but the observation is robust. ...