MUCKE aims to mine a large volume of images, to structure them conceptually and to use this conceptual structuring in order to improve large-scale image retrieval. The last decade witnessed important progress concerning low-level image representations. However, there are a number problems which need to be solved in order to unleash the full potential of image mining in applications. The central problem with low-level representations is the mismatch between them and the human interpretation of image content. This problem can be instantiated, for instance, by the incapability of existing descriptors to capture spatial relationships between the concepts represented or by their incapability to convey an explanation of why two images are similar in a content-based image retrieval framework. We start by assessing existing local descriptors for image classification and by proposing to use co-occurrence matrices to better capture spatial relationships in images. The main focus in MUCKE is on cleaning large scale Web image corpora and on proposing image representations which are closer to the human interpretation of images. Consequently, we introduce methods which tackle these two problems and compare results to state of the art methods. Note: some aspects of this deliverable are withheld at this time as they are pending review. Please contact the authors for a preview.

http://ieeexplore.ieee.org/iel2/4524/12820/00592460.pdf

Image Processing

In recent years salicylic acid (SA) has been the focus of intensive research due to its function as an endogenous signal mediating local and systemic plant defence responses against pathogens. It has also been found that SA plays a role during the plant response to abiotic stresses such as drought, chilling, heavy metal toxicity, heat, and osmotic stress. In this sense, SA appears to be, just like in mammals, an 'effective therapeutic agent' for plants. Besides this function during biotic and abiotic stress, SA plays a crucial role in the regulation of physiological and biochemical processes during the entire lifespan of the plant. The discovery of its targets and the understanding of its molecular modes of action in physiological processes could help in the dissection of the complex SA signalling network, confirming its important role in both plant health and disease. Here, the evidence that supports the role of SA during plant growth and development is reviewed by comparing experiments performed by exogenous application of SA with analysis of genotypes affected by SA levels and/or perception.

/pdf/salicylic-acid-beyond-defence-its-role-in-plant-growth-and-52s29ljscg.pdf

Salicylic acid beyond defence: its role in plant growth and development.

Eukaryotic mitogen-activated protein kinase (MAPK) cascades have evolved to transduce environmental and developmental signals into adaptive and programmed responses MAPK cascades relay and amplify signals via three types of reversibly phosphorylated kinases leading to the phosphorylation of substrate proteins, whose altered activities mediate a wide array of responses, including changes in gene expression Cascades may share kinase components, but their signaling specificity is maintained by spaciotemporal constraints and dynamic protein-protein interactions and by mechanisms that include crossinhibition, feedback control, and scaffolding Plant MAPK cascades regulate numerous processes, including stress and hormonal responses, innate immunity, and developmental programs Genetic analyses have uncovered several predominant MAPK components shared by several of these processes including the Arabidopsis thaliana MAPKs MPK3, 4, and 6 and MAP2Ks MKK1, 2, 4, and 5 Future work needs to focus on identifying substrates of MAPKs, and on understanding how specificity is achieved among MAPK signaling pathways

Mitogen-Activated Protein Kinase Signaling in Plants

https://www.cell.com/molecular-plant/pdf/S1674-2052(15)00087-8.pdf

Signaling Mechanisms in Pattern-Triggered Immunity (PTI)

Many changes in environmental conditions and hormones are mediated by MAPK (mitogen-activated protein kinase) cascades in all eukaryotes, including plants. Studies of MAPK pathways in genetic model organisms are especially informative in revealing the molecular mechanisms by means of which MAPK cascades are controlled and modulate cellular processes. The present review highlights recent insights into MAPK-based signalling in Arabidopsis thaliana (thale cress), revealing the complexity and future challenges to understanding signal-transduction networks on a global scale.

Arabidopsis MAPKs: a complex signalling network involved in multiple biological processes.

Loss-of-function, dominant-negative, and change-of-function genetic approaches were used to investigate the role played by the Arabidopsis mitogen-activated protein (MAP) kinase MPK6 throughout development. Plants homozygous for T-DNA null alleles of MPK6 displayed reduced male fertility and abnormal anther development. In addition, a portion of the seed produced by mpk6 plants was found to contain embryos that had burst out of their seed coats. To address potential functional redundancy, a dominant-negative version of MPK6 was constructed by changing the TEY activation loop motif to the amino acid sequence AEF. Plants expressing MPK6AEF via the MPK6 native promoter were found to produce excessive stomata, consistent with the recently described role of MPK6 in stomatal patterning. A novel floral phenotype characterized by abnormal sepal development was also observed in MPK6AEF lines. The gene expression pattern of the MPK6 native promoter was determined using a YFP-MPK6 fusion construct, and expression was observed throughout most plant tissues, consistent with a role for MPK6 in multiple developmental processes. The YFP-MPK6 construct was found to rescue the fertility phenotype of mpk6 null alleles, indicating that the fusion protein retains its biological activity. It was also observed, however, that plants expressing YFP-MPK6 displayed reduced apical dominance and a shortening of inflorescence internodes. These results suggest that the YFP tag modifies the activity of MPK6 in a manner that affects inflorescence development but not anther development. Taken together, the present results indicate that MPK6 is involved in the regulation of multiple aspects of plant development.

Mutational evidence that the Arabidopsis MAP kinase MPK6 is involved in anther, inflorescence, and embryo development

Leaf shape is mutable, changing in ways modulated by both development and environment within genotypes. A complete model of leaf phenotype would incorporate the changes in leaf shape during juvenile-to-adult phase transitions and the ontogeny of each leaf. Here, we provide a morphometric description of >33,000 leaflets from a set of tomato (Solanum spp) introgression lines grown under controlled environment conditions. We first compare the shape of these leaves, arising during vegetative development, with >11,000 previously published leaflets from a field setting and >11,000 leaflets from wild tomato relatives. We then quantify the changes in shape, across ontogeny, for successive leaves in the heteroblastic series. Using principal component analysis, we then separate genetic effects modulating (1) the overall shape of all leaves versus (2) the shape of specific leaves in the series, finding the former more heritable than the latter and comparing quantitative trait loci regulating each. Our results demonstrate that phenotype is highly contextual and that unbiased assessments of phenotype, for quantitative genetic or other purposes, would ideally sample the many developmental and environmental factors that modulate it.

Resolving Distinct Genetic Regulators of Tomato Leaf Shape within a Heteroblastic and Ontogenetic Context

An Arabidopsis thaliana mitogen-activated protein (MAP) kinase cascade composed of MEKK1, MKK1/MKK2, and MPK4 was previously described as a negative regulator of defense response. MEKK1 encodes a MAP kinase kinase kinase and is a member of a tandemly duplicated gene family with MEKK2 and MEKK3. Using T-DNA insertion lines, we isolated a novel deletion mutant disrupting this gene family and found it to be phenotypically wild-type, in contrast with the mekk1 dwarf phenotype. Follow-up genetic analyses indicated that MEKK2 is required for the mekk1, mkk1 mkk2, and mpk4 autoimmune phenotypes. We next analyzed a T-DNA insertion in the MEKK2 promoter region and found that although it does not reduce the basal expression of MEKK2, it does prevent the upregulation of MEKK2 that is observed in mpk4 plants. This mekk2 allele can rescue the mpk4 autoimmune phenotype in a dosage-dependent manner. We also found that expression of constitutively active MPK4 restored MEKK2 abundance to wild-type levels in mekk1 mutant plants. Finally, using mass spectrometry, we showed that MEKK2 protein levels mirror MEKK2 mRNA levels. Taken together, our results indicate that activated MPK4 is responsible for regulating MEKK2 RNA abundance. In turn, the abundance of MEKK2 appears to be under cellular surveillance such that a modest increase can trigger defense response activation.

Deletion of a Tandem Gene Family in Arabidopsis: Increased MEKK2 Abundance Triggers Autoimmunity when the MEKK1-MKK1/2-MPK4 Signaling Cascade Is Disrupted

TILLING (for Targeting Induced Local Lesions IN Genomes) is a well-established method for identifying plants carrying point mutations in genes of interest. A traditional TILLING project requires a significant investment of time and resources to establish the mutant population and screening infrastructure. Here, we describe a modified TILLING procedure that substantially reduces the investment needed to perform mutation screening. Our motivation for developing iTILLING was to make it practical for individual laboratories to rapidly perform mutation screens using specialized genetic backgrounds. With iTILLING, M2 seeds are collected in bulk from the mutagenized population of plants, greatly reducing the labor needed to manage the mutant lines. Growth of the M2 seedlings for mutation screening, tissue collection, and DNA extraction are all performed in 96-well format. Mutations are then identified using high-resolution melt-curve analysis of gene-specific polymerase chain reaction products. Individual plants carrying mutations of interest are transferred from the 96-well growth plates to soil. One scientist can complete an iTILLING screen in less than 4 months. As a proof-of-principle test, we applied iTILLING to Arabidopsis (Arabidopsis thaliana) plants that were homozygous for the mekk1-1 (for MAPK/ERK kinase kinase 1) mutation and also carried a MEKK1 rescue construct. The goal of our screen was to identify mutations in the closely linked MEKK2 and MEKK3 loci. We obtained five mutations in MEKK2 and seven mutations in MEKK3, all located within 20 kb of the mekk1-1 T-DNA insertion. Using repeated iterations of the iTILLING process, mutations in three or more tandemly duplicated genes could be generated.

iTILLING: A Personalized Approach to the Identification of Induced Mutations in Arabidopsis

Plants have a remarkable ability to alter their development in response to myriad environmental cues or stress. This phenotypic plasticity allows them to continually adapt to their local environment, a necessity for plants as sessile organisms. A host of environmental cues can be interpreted by plants, including light, temperature and nutrients, and these inputs are integrated and translated into a range of developmental outputs from shoot elongation, regulation of root gravitropism, altered flowering time, growth cessation of leaves, and timing of germination. This plasticity enables growth optimisation for the local environment, allows range expansion into hetergeneous habitats, and may provide an advantage as the changing climate affects growth conditions around the globe. Using model organisms such as Arabidopsis, molecular mechanisms for plastic growth responses are becoming more defined. Studies of growth and plasticity in less-characterized species could expand our knowledge of the range of plasticity present in nature.



Key Concepts: 



Multiple environmental signals are integrated to regulate plant development.




Plasticity gives plants the ability to optimise growth in varied environments.




Developmental plasticity comes from the meristem, which continuously produces organs throughout the plant life cycle.




Environmental cues can lead to changes in mRNA and protein abundance or activity, or they can be stored as epigenetic changes.




Roots and shoots respond to different environmental conditions but employ similar cellular processes.




Plants’ ability to optimise growth for a local environment may provide an advantage as habitats are altered by the changing climate.






Keywords:

phenotypic plasticity;
developmental plasticity;
plant development;
climate change;
flowering time;
germination;
plant morphology

Susan M. Bush

Papers

Mutational evidence that the Arabidopsis MAP kinase MPK6 is involved in anther, inflorescence, and embryo development

Resolving Distinct Genetic Regulators of Tomato Leaf Shape within a Heteroblastic and Ontogenetic Context

Deletion of a Tandem Gene Family in Arabidopsis: Increased MEKK2 Abundance Triggers Autoimmunity when the MEKK1-MKK1/2-MPK4 Signaling Cascade Is Disrupted

iTILLING: A Personalized Approach to the Identification of Induced Mutations in Arabidopsis

Phenotypic and Developmental Plasticity in Plants