Autumn Leaves: Curing the Window Plague in IDEs

Navigating large software systems is difficult as the various artifacts are distributed in a huge space, while the relationships between different artifacts often remain hidden and obscure. As a consequence, developers using a modern interactive development environment (IDE) are forced to open views on numerous source artifacts to reveal these hidden relationships, leading to a crowded workspace with many opened windows or tabs. Developers often lose the overview in such a cluttered workspace as IDEs provide little support to get rid of unused windows. AutumnLeaves automatically selects windows unlikely for future use to be closed or grayed out while important ones are displayed more prominently. This reduces the number of windows opened at a time and adds structure to the developer's workspace. We validate AutumnLeaves with a benchmark evaluation using recorded navigation data of various developers to determine the prediction quality of the employed algorithms.

Senescence-related gene expression profiles of rosette leaves of Arabidopsis thaliana: Leaf age versus plant age

Senescence is a form of programmed cell death (PCD) which leads to the death of whole organs, e.g., leaves or flowers, and eventually to the death of entire plants. Like all forms of PCD, senescence is a highly regulated and energy consuming process. Senescence parameters, like protein content, chlorophyll content, expression of photosynthesis-associated genes or senescence-associated genes (SAGs), reveal that senescence occurs in old leaves derived from young plants (6 week old) as well as in young leaves derived from older plants (8 week old), indicating that it is governed by the actual age of the leaves. in order to analyse the differential gene expression profiles during leaf senescence, hybridizations of high-density genome arrays were performed with: i) individual leaves within the rosette of a 6-week-old plant and ii) leaves of the same position within the rosette but harvested from plants of different ages, ranging from 5 to 8 weeks. Cluster and genetree analyses, according to the expression pattern revealed that genes which are up-regulated with respect to the age of the entire plant, showed completely different expression profiles with respect to the age of the individual leaves within one rosette. This was observed even though the actual difference in leaf age was approximately the same. This indicates that gene expression appears to be governed by different parameters: i) the age of the individual leaf and ii) the age and developmental stage of the entire plant.

Sulfate and Nitrate Assimilation in Leaves of Quercus ilex and Quercus pubescens Grown Near Natural CO2 Springs in Central Italy

The effect of long-term exposure to elevated pCO2 concentrations on sulfate and nitrate assimilation was studied under field conditions using leaves from Quercus ilex and Quercus pubescens trees growing with ambient or elevated CO2 concentrations in the vicinity of three natural CO2 springs, Bossoleto, Laiatico and Sulfatara, in Tuscany, Italy. The activity of the key enzymes of sulfate assimilation, adenosine 5′-phosphosulfate reductase (APR) and nitrate assimilation, nitrate reductase (NR), were measured together with the levels of acid soluble thiols, and soluble non-proteinogenic nitrogen compounds. Whereas NR activity remained unaffected in Q. ilex or increased Q. pubescence, APR activity decreased in the area of CO2 springs. The latter changes were often accompanied by increased GSH concentrations, apparently synthesized from H2S and SO2 present in the gas mixture emitted from the CO2 springs. Thus, the diminished APR activity in leaves of Q. ilex and Q. pubescence from spring areas can best be explained by the exposure to gaseous sulfur compounds. Although the concentrations of H2S and SO2 in the gas mixture emitted from the vents at the CO2 springs were low at the Bossoleto and Laiatico spring, these sulfur gases pose physiological effects, which may override consequences of elevated pCO2.

Wounding of Arabidopsis halleri leaves enhances cadmium accumulation that acts as a defense against herbivory

Approximately 0.2 % of all angiosperms are classified as metal hyperaccumulators based on their extraordinarily high leaf metal contents, for example >1 % zinc, >0.1 % nickel or >0.01 % cadmium (Cd) in dry biomass. So far, metal hyperaccumulation has been considered to be a taxon-wide, constitutively expressed trait, the extent of which depends solely on available metal concentrations in the soil. Here we show that in the facultative metallophyte Arabidopsis halleri, both insect herbivory and mechanical wounding of leaves trigger an increase specifically in leaf Cd accumulation. Moreover, the Cd concentrations accumulated in leaves can serve as an elemental defense against herbivory by larvae of the Brassicaceae specialist small white (Pieris rapae), thus allowing the plant to take advantage of this non-essential trace element and toxin. Metal homeostasis genes are overrepresented in the systemic transcriptional response of roots to the wounding of leaves in A. halleri, supporting that leaf Cd accumulation is preceded by systemic signaling events. A similar, but quantitatively less pronounced transcriptional response was observed in A. thaliana, suggesting that the systemically regulated modulation of metal homeostasis in response to leaf wounding also occurs in non-hyperaccumulator plants. This is the first report of an environmental stimulus influencing metal hyperaccumulation.

Metabolomics reveals herbivore-induced metabolites of resistance and susceptibility in maize leaves and roots

Plants respond to herbivory by reprogramming their metabolism. Most research in this context has focused on locally induced compounds that function as toxins or feeding deterrents. We developed an ultra-high-pressure liquid chromatography time-of-flight mass spectrometry (UHPLC-TOF-MS)-based metabolomics approach to evaluate local and systemic herbivore-induced changes in maize leaves, sap, roots and root exudates without any prior assumptions about their function. Thirty-two differentially regulated compounds were identified from Spodoptera littoralis-infested maize seedlings and isolated for structure assignment by microflow nuclear magnetic resonance (CapNMR). Nine compounds were quantified by a high throughput direct nano-infusion tandem mass spectrometry/mass spectrometry (MS/MS) method. Leaf infestation led to a marked local increase of 1,3-benzoxazin-4-ones, phospholipids, N-hydroxycinnamoyltyramines, azealic acid and tryptophan. Only few changes were found in the root metabolome, but 1,3-benzoxazin-4-ones increased in the vascular sap and root exudates. The role of N-hydroxycinnamoyltyramines in plant–herbivore interactions is unknown, and we therefore tested the effect of the dominating p-coumaroyltyramine on S. littoralis. Unexpectedly, p-coumaroyltyramine was metabolized by the larvae and increased larval growth, possibly by providing additional nitrogen to the insect. Taken together, this study illustrates that herbivore attack leads to the induction of metabolites that can have contrasting effects on herbivore resistance in the leaves and roots.