The ubiquitin system and jasmonate signaling

The ubiquitin (Ub) system is involved in most, if not all, biological processes in eukaryotes. The major specificity determinants of this system are the E3 ligases, which bind and ubiquitinate specific sets of proteins and are thereby responsible for target recruitment to the proteasome or other cellular processing machineries. The Ub system contributes to the regulation of the production, perception and signal transduction of plant hormones. Jasmonic acid (JA) and its derivatives, known as jasmonates (JAs), act as signaling compounds regulating plant development and plant responses to various biotic and abiotic stress conditions. We provide here an overview of the current understanding of the Ub system involved in JA signaling

Metabolite profiling of Triterpene Saponins in medicago truncatula hairy roots by liquid chromatography fourier transform Ion Cyclotron resonance mass spectrometry

Triterpenes are one of the largest classes of plant natural products, with an enormous variety in structure and bioactivities. Here, triterpene saponins from hairy roots of the model legume Medicago truncatula were profiled with reversed-phase liquid chromatography coupled to negative-ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (LC ESI FT-ICR MS). Owing to the accuracy of the FT-ICR MS, reliable molecular formulas of the detected compounds could be predicted, which, together with the generated MS" spectra, allowed the tentative identification of 79 different saponins, of which 61 had not been detected previously in M. truncatula. Upon collision-induced dissociation of saponins that contain a uronic acid residue in the sugar chain, fragment ions resulting from cross-ring cleavages of the uronic acid residues were observed. The identified saponins are glycosides of 10 different sapogenins, of which three were not detected before in M. truncatula. Zanhic acid glycosides, which are prevalent in the aerial parts of M. truncatula, were absent in the hairy root extract's. This metabolite compendium will facilitate future functional genomic studies of triterpene saponin biosynthesis in M. truncptula

The JAZ proteins: a crucial interface in the jasmonate signaling cascade

Jasmonates are phytohormones that regulate many aspects of plant growth, development, and defense. Within the signaling cascades that are triggered by jasmonates, the JASMONATE-ZIM DOMAIN (JAZ) repressor proteins play a central role. The endogenous bioactive JA-Ile conjugate mediates the binding of JAZ proteins to the F-box protein CORONATINE INSENSITIVE1 (COI1), part of the Skp1/Cullin/F-box SCF(COI1) ubiquitin E3 ligase complex. Upon the subsequent destruction of the JAZ proteins by the 26S proteasome, multiple transcription factors are relieved from JAZ-mediated repression, allowing them to activate their respective downstream responses. However, many questions remain regarding the targets, specificity, function, and regulation of the different JAZ proteins. Here, we review recent studies on the model plant Arabidopsis thaliana that provided essential and novel insights. JAZ proteins have been demonstrated to interact with a broad array of transcription factors that each control specific downstream processes. Recruitment of the corepressor TOPLESS unveiled a mechanism for JAZ-mediated gene repression. Finally, the presence of JAZ proteins was also found to be regulated by alternative splicing and interactions with proteins from other hormonal signaling pathways. Overall, these contemporary findings underscore the value of protein-protein interaction studies to acquire fundamental insight into molecular signaling pathways

The use of high resolution digital surface models for change detection and viewshed analysis in the area around the pyramids of Giza, Egypt

One of the biggest threats to cultural heritage is related to their rapidly changing and developing surroundings. The Giza pyramid plateau is a prime example of this phenomenon, as it is threatened by the enormous urban expansion of Cairo over the last decades. Documenting, monitoring and modelling such a pressure requires accurate and detailed geographic data, which can be derived from recent up-to-date, high resolution satellite images. Remote sensing techniques have proven to be very useful to visualize and analyze urban sprawl and land use changes in two dimensions. The impact assessment of urban sprawl near specific heritage sites, however; needs to be complemented with accurate 2.5D-information. In an attempt to do so, digital surface models (DSMs) from Ikonos-2 (2005) and GeoEye-1 stereoscopic images (2009 and 2011) have been computed in order to analyze recent urban changes. Change detection methods are mainly developed for large scale high resolution aerial images; however this paper focuses on the one hand DSM creation and its challenges resulting in an improvement of 2.5D change detection method for small scale satellite imagery in mainly informal areas. On the other hand a view shed evolution is presented. The combination of the enhanced digital terrain extraction (eATE) module of Erdas Imagine® and ground control points collected in the field provides accurate and high resolution DSMs. The impact of shadow and different urban morphologies however influence the pixel-wise comparison of the two DSMs, which results in different approaches for different city districts. The resulting 2.5D change model clarifies not only the urban sprawl, but also the increase in building levels, directly related to pressure on the famous pyramids. This pressure is furthermore analyzed by creating different view sheds through time from the plateau towards the city and vice versa. An integration of population statistics complements the model, hence allowing it to become a useful policy instrument

Airborne photogrammetry and LIDAR for DSM extraction and 3D change detection over an urban area : a comparative study

A digital surface model (DSM) extracted from stereoscopic aerial images, acquired in March 2000, is compared with a DSM derived from airborne light detection and ranging (lidar) data collected in July 2009. Three densely built-up study areas in the city centre of Ghent, Belgium, are selected, each covering approximately 0.4 km(2). The surface models, generated from the two different 3D acquisition methods, are compared qualitatively and quantitatively as to what extent they are suitable in modelling an urban environment, in particular for the 3D reconstruction of buildings. Then the data sets, which are acquired at two different epochs t(1) and t(2), are investigated as to what extent 3D (building) changes can be detected and modelled over the time interval. A difference model, generated by pixel-wise subtracting of both DSMs, indicates changes in elevation. Filters are proposed to differentiate 'real' building changes from false alarms provoked by model noise, outliers, vegetation, etc. A final 3D building change model maps all destructed and newly constructed buildings within the time interval t(2) - t(1). Based on the change model, the surface and volume of the building changes can be quantified

Applied surveying education : documenting cultural heritage in 3D in the city of Ghent (Belgium) using laser scanning and photo modelling

For several years the city of Ghent (Belgium) and the Ghent University, Department of Geography have been working together to document and measure important cultural heritage sites in 3D. The partnership enables master students in Geomatics and Surveying at the Ghent University to take part in a project driven measuring campaign. During the project, students use and compare several 3D data acquisition methods. This allows the students to implement their theoretical knowledge in the field. The used methods are analysed and critically compared by the students. Through this hands-on-training, students are encouraged to think “outside the box”. When problems occur, they are stimulated to think how these problems could have happened and most importantly how they can solve them. The documentation of these historic monuments in Ghent will be used during future renovation works and archaeological research. This paper will discuss the measurements in the Ghent City Museum (Stadsmuseum or STAM). The following methods are applied during the extensive field work: engineering surveying using total station and GNSS, photo modelling and laser scanning. The deliverables are created in a CAD or GIS environment. After successful completion of the course, students have gained a significant expertise concerning the processing of topographic data, 3D point clouds and imagery in an integrated way. This knowledge can be used after their studies to assess which equipment is most suitable for any given survey project. The final products of the photo modelling and the laser scanning process is a 3D model. Furthermore, digital elevation models and orthorectified images of the historic monument can be created. The orthorectified images are visualised and processed into high resolution orthophoto plans, in a CAD or GIS environment

Photogrammetric restitution of a presumed ancient Asclepius temple in Titani, Peloponnesos, Greece

Close range photogrammetry is a useful tool for the documentation and registration of archaeological sites. In this case, photogrammetric restitution is applied to a presumed Esclepion Classical temple site in Titani, Peloponnesos, Greece. The archaeological remains that are recorded and processed in this stage are small fragments of walls, made out of irregular shaped stones. The fragmentary remains and the need to record both the facades of the stones as well as the upper surfaces, complicate the photogrammetric recording and processing workflow. The use of 3D documentation is important for the documentation, conservation and possible further excavation of the site. Stereographic pictures in combination with terrestrial topographic measurements are processed in the photogrammetric software VirtuoZoTM. The stereo photographs were taken by a non-metric high resolution digital single lens reflex camera with a minimum overlap of 65 percent. Targets placed on the remains of the walls were measured by total station to obtain ground control points for the orientation of each 3D stereo model in an absolute coordinate system (HGRS87). The photogrammetric processing of the stereo models results in very accurate digital elevation models and orthophotos of the walls. Further combining of these final products and merging these products in a CAD software leads to a 3D presentation of the archaeological excavation, which can be further used to evolve this archaeological site