Genetic Basis of Carnivorous Leaf Development

Plant carnivory is often manifested as dramatic changes in the structure and morphology of the leaf. These changes appear to begin early in leaf development. For example, the development of the Sarracenia purpurea leaf primordium is associated with the formation of an adaxial ridge, whose growth along with that of the leaf margin resulted in a hollow structure that later developed into a pitcher. In Nepenthes khasiana, pitcher formation occurs during the initial stages of leaf development, although this has not been shown at the primordial stage. The formation of the Utricularia gibba trap resulted from the growth of the dome-shaped primordium in both the longitudinal and transverse directions. Recent research has begun to unfold the genetic basis of the development of the carnivorous leaf. We review these findings and discuss them in relation to the flat-shaped leaves of the model plant Arabidopsis.

Statistical estimates of multiple transcription factors binding in the model plant genomes based on ChIP-seq data

The development of high-throughput genomic sequencing coupled with chromatin immunoprecipitation technologies allows studying the binding sites of the protein transcription factors (TF) in the genome scale. The growth of data volume on the experimentally determined binding sites raises qualitatively new problems for the analysis of gene expression regulation, prediction of transcription factors target genes, and regulatory gene networks reconstruction. Genome regulation remains an insufficiently studied though plants have complex molecular regulatory mechanisms of gene expression and response to environmental stresses. It is important to develop new software tools for the analysis of the TF binding sites location and their clustering in the plant genomes, visualization, and the following statistical estimates. This study presents application of the analysis of multiple TF binding profiles in three evolutionarily distant model plant organisms. The construction and analysis of non-random ChIP-seq binding clusters of the different TFs in mammalian embryonic stem cells were discussed earlier using similar bioinformatics approaches. Such clusters of TF binding sites may indicate the gene regulatory regions, enhancers and gene transcription regulatory hubs. It can be used for analysis of the gene promoters as well as a background for transcription networks reconstruction. We discuss the statistical estimates of the TF binding sites clusters in the model plant genomes. The distributions of the number of different TFs per binding cluster follow same power law distribution for all the genomes studied. The binding clusters in Arabidopsis thaliana genome were discussed here in detail.

Populus trichocarpa (Black Cottonwood) As a Model for Plant Genomic Studies: A Review

Numerous plants have been the subject of recent research in the pharmacological, cosmetic, and agro-alimentary domains due to their chemical composition and multiple therapeutic capabilities. Populus trichocarpa is one of the most common trees found in deciduous forests (Salicaceae family). The current study examines Populus trichocarpa as a model plant for plant genomics research, as well as the most recent findings on phytochemical composition and medicinal potential. More than 45,000 potential protein-coding genes were discovered. In the Populus genome, a whole-genome duplication event was discovered, with approximately 8,000 pairs of duplicated genes surviving. Furthermore, the reproductive biology of Populus provides new opportunities and challenges in the study and analysis of natural genetic and phenotypic variation. In the present review, we endeavour to describe and compile the available knowledge on Populus trichocarpa as a model plant for genomic investigations and to bring that material up to date of Populus trichocarpa's phytochemical and medicinal properties.

Mineral Materials as a Neutralizing Agent Used on Soil Contaminated with Copper

The aim of the investigation was to evaluate the response of plants, using black mustard (Brassica nigra L. Koch) as a model plant, to soil contamination with copper (0, 200, 400, 600 mg Cu kg−1 of soil), and to determine the effectiveness of the Cu immobilization with mineral neutralizing materials, such as lime, clay and zeolite. The plant yield depended on soil contamination and mineral amendments. In the series without neutralizing materials, the level of 600 mg Cu kg−1 reduced the yield and increased leaf greenness. Lime alleviated the toxicity of Cu in objects with 200 mg Cu kg−1. Zeolite slightly mitigated the harmful effects of Cu at the level of 400 and 600 mg kg−1. Zeolite lowered the SPAD index. In the chemical composition of plants, the content of Cu, K, Mg, Na and Ca in plants increased to 400 mg Cu kg−1, while the content of P decreased to 600 mg Cu kg−1. Among the materials, lime reduced the Cu accumulation in plants the most, followed by clay. Cu narrowed the majority of ratios and widened the Ca:P and K:Ca ratios in plants. The applied mineral materials, except lime, did not significantly affect the formation of these indicators.

Ploidy Mosaics - Does Endopolyploidy in Explants Affects the Cytogenetic Stability of Orchids Regenerated From PLBs?

The induction and regeneration of protocorm-like bodies (PLBs) is a morphogenetic pathway widely used for orchid micropropagation. As endopolyploidy, i.e., the coexistence of cells with different ploidy levels, is a common feature in orchid tissues, a natural question arises when using somatic tissues as explants for orchid micropropagation: does endopolyploidy in explants affect the cytogenetic stability of regenerated plantlets? To answer this question, Epidendrum fulgens was used as a model plant, and flow cytometry (FC) was used to analyze endopolyploidy in pollinia, petals, labella, leaf bases, leaf tips, root tips, protocorms bases and protocorms apexes, which were subsequently used as explants for PLB induction and plant regeneration. The ploidy screening showed contrasting ploidy patterns in the samples. Endopolyploidy was detected in all tissues, with C-values ranging from 1C to 16C. Protocorm bases and root tips presented the highest proportion of endopolyploidy, while petals and protocorm apexes showed the lowest proportion. Flower parts presented high oxidation for PLB induction and pollinia failed to produce PLB or callus. The highest induction rate was observed at 10 µM TDZ, with 92%, 22%, and 0.92% for protocorm bases, leaves, and root tips, respectively. Plantlets were more easily regenerated from PLBs induced from protocorm bases than from leaves and roots. Doubled ploidy levels were registered in a proportion of 11% and 33% for PLB-regenerated plantlets obtained from protocorm bases and leaf bases, respectively, which was not directly associated with the proportion of endopolyploid cells or cycle value of explants.

Detection and Location of Model-Plant Mismatch in Multiple Input Multiple Output Systems under Model Predictive Controller Using Granger Causality Method

In closed-loop control systems, the model accuracy exerts large influences on the controllability, stability and quality of the whole process. Among all the faults that could affect the system performance, Model Plant Mismatch (MPM) is the one that not only directly threatens the system stability but also deteriorates the controller performance. Meanwhile, MPM has a major influence on the qualities of outputs about industrial products. In this work, a new detection method based on Granger Causality is proposed to detect and locate the MPM in multiple input multiple output systems. Causality can reflect the relations between the mismatch fault and its negative effects on model predictive control(MPC) systems. With the assistance of disturbance transfer function models, the causality method can further be used to locate the mismatch positions and get the correct channels of each kind of mismatches. The proposed method was examined and validated in the Wood-Berry process in contrast to the decussation location method under model predictive controller.

A Taphrina strain infecting the model plant Arabidopsis thaliana.

Yeasts are important plant-associated organisms that can modulate host immunity to either promote or prevent disease. Mechanisms of plant-yeast interactions, specifically of yeast perception by the plant innate immune system, remain unknown. Progress has been hindered by the scarcity of yeast species associated with the model plant Arabidopsis thaliana (Arabidopsis). We have previously isolated Taphrina strain M11 from wild Arabidopsis in the field. Taphrina are poorly studied dimorphic yeast-like fungi that are plant pathogens, often producing plant hormones and causing tumour-like leaf deformation symptoms on their hosts. Here we characterize the interaction of M11 with Arabidopsis. Infection of Arabidopsis with the birch pathogen T. betulina, used as a non-host control, shows early HR, enhanced ROS accumulation, and limitation of growth, demonstrating that Arabidopsis has immunity against non-adapted yeasts. M11 triggered limited cell death, an attenuated ROS response, and grew in planta, as well as subtle but clear leaf deformation symptoms, demonstrating it is pathogenic. Hormone responsive promoter-reporter analysis demonstrated activation of cytokinin signalling during infection. Mutant infection assays indicate jasmonate and ethylene were required for immunity against M11. Analysis of the Taphrina M11 genome was used to mine evidence for yeast specific PAMPs which may underlie host immune responses against yeast-like fungi.