Signalling Network Construction for Modelling Plant Defence Response

Plant defence signalling response against various pathogens, including viruses, is a complex phenomenon. In resistant interaction a plant cell perceives the pathogen signal, transduces it within the cell and performs a reprogramming of the cell metabolism leading to the pathogen replication arrest. This work focuses on signalling pathways crucial for the plant defence response, i.e., the salicylic acid, jasmonic acid and ethylene signal transduction pathways, in the Arabidopsis thaliana model plant. The initial signalling network topology was constructed manually by defining the representation formalism, encoding the information from public databases and literature, and composing a pathway diagram. The manually constructed network structure consists of 175 components and 387 reactions. In order to complement the network topology with possibly missing relations, a new approach to automated information extraction from biological literature was developed. This approach, named Bio3graph, allows for automated extraction of biological relations from the literature, resulting in a set of (component1, reaction, component2) triplets and composing a graph structure which can be visualised, compared to the manually constructed topology and examined by the experts. Using a plant defence response vocabulary of components and reaction types, Bio3graph was applied to a set of 9,586 relevant full text articles, resulting in 137 newly detected reactions between the components. Finally, the manually constructed topology and the new reactions were merged to form a network structure consisting of 175 components and 524 reactions. The resulting pathway diagram of plant defence signalling represents a valuable source for further computational modelling and interpretation of omics data. The developed Bio3graph approach, implemented as an executable language processing and graph visualisation workflow, is publically available at http://ropot.ijs.si/bio3graph/and can be utilised for modelling other biological systems, given that an adequate vocabulary is provided.     

植物过氧化物酶体在活性氧信号网络中的作用

过氧化物酶体是高度动态、代谢活跃的细胞器,主要参与脂肪酸等脂质的代谢及产生和清除不同的活性氧(reactive oxygen species, ROS)。ROS是细胞有氧代谢的副产物。当胁迫长期作用于植物,过量的ROS会引起氧胁迫,损害细胞结构和功能的完整性,导致细胞代谢减缓,活性降低,甚至死亡;但低浓度的ROS则作为分子信号,感应细胞ROS/氧化还原变化,从而触发由环境因素导致的过氧化物酶体动力学以及依赖ROS信号网络改变而产生快速、特异性的应答。ROS也可以通过直接或间接调节细胞生长来控制植物的发育,是植物发育的重要调节剂。此外,过氧化物酶体的动态平衡由ROS、过氧化物酶体蛋白酶及自噬过程调节,对于维持细胞的氧化还原平衡至关重要。本文就过氧化物酶体中ROS的产生和抗氧化剂的调控机制进行综述,以期为过氧化物酶体如何感知环境变化,以及在细胞应答中,ROS作为重要信号分子的研究提供参考。     

Anatomical Network Analysis Shows Decoupling of Modular Lability and Complexity in the Evolution of the Primate Skull

Modularity and complexity go hand in hand in the evolution of the skull of primates. Because analyses of these two parameters often use different approaches, we do not know yet how modularity evolves within, or as a consequence of, an also-evolving complex organization. Here we use a novel network theory-based approach (Anatomical Network Analysis) to assess how the organization of skull bones constrains the co-evolution of modularity and complexity among primates. We used the pattern of bone contacts modeled as networks to identify connectivity modules and quantify morphological complexity. We analyzed whether modularity and complexity evolved coordinately in the skull of primates. Specifically, we tested Herbert Simon’s general theory of near-decomposability, which states that modularity promotes the evolution of complexity. We found that the skulls of extant primates divide into one conserved cranial module and up to three labile facial modules, whose composition varies among primates. Despite changes in modularity, statistical analyses reject a positive feedback between modularity and complexity. Our results suggest a decoupling of complexity and modularity that translates to varying levels of constraint on the morphological evolvability of the primate skull. This study has methodological and conceptual implications for grasping the constraints that underlie the developmental and functional integration of the skull of humans and other primates.     

Preserved Modular Network Organization in the Sedated Rat Brain

Translation of resting-state functional connectivity (FC) magnetic resonance imaging (rs-fMRI) applications from human to rodents has experienced growing interest, and bears a great potential in pre-clinical imaging as it enables assessing non-invasively the topological organization of complex FC networks (FCNs) in rodent models under normal and various pathophysiological conditions. However, to date, little is known about the organizational architecture of FCNs in rodents in a mentally healthy state, although an understanding of the same is of paramount importance before investigating networks under compromised states. In this study, we characterized the properties of resting-state FCN in an extensive number of Sprague-Dawley rats (n = 40) under medetomidine sedation by evaluating its modular organization and centrality of brain regions and tested for reproducibility. Fully-connected large-scale complex networks of positively and negatively weighted connections were constructed based on Pearson partial correlation analysis between the time courses of 36 brain regions encompassing almost the entire brain. Applying recently proposed complex network analysis measures, we show that the rat FCN exhibits a modular architecture, comprising six modules with a high between subject reproducibility. In addition, we identified network hubs with strong connections to diverse brain regions. Overall our results obtained under a straight medetomidine protocol show for the first time that the community structure of the rat brain is preserved under pharmacologically induced sedation with a network modularity contrasting from the one reported for deep anesthesia but closely resembles the organization described for the rat in conscious state.     

Systems Analysis of Auxin Transport in the Arabidopsis Root Apex

Auxin is a key regulator of plant growth and development. Within the root tip, auxin distribution plays a crucial role specifying developmental zones and coordinating tropic responses. Determining how the organ-scale auxin pattern is regulated at the cellular scale is essential to understanding how these processes are controlled. In this study, we developed an auxin transport model based on actual root cell geometries and carrier subcellular localizations. We tested model predictions using the DII-VENUS auxin sensor in conjunction with state-of-the-art segmentation tools. Our study revealed that auxin efflux carriers alone cannot create the pattern of auxin distribution at the root tip and that AUX1/LAX influx carriers are also required. We observed that AUX1 in lateral root cap (LRC) and elongating epidermal cells greatly enhance auxin’s shootward flux, with this flux being predominantly through the LRC, entering the epidermal cells only as they enter the elongation zone. We conclude that the nonpolar AUX1/LAX influx carriers control which tissues have high auxin levels, whereas the polar PIN carriers control the direction of auxin transport within these tissues.     

A Role for Auxin and Auxin Transport Inhibitors on the Ca Content of Artificially Induced Parthenocarpic Fruits

Artificially induced parthenocarpic fruits of apples, pears and tomatoes, as well as seeded fruits treated with 2,3,5-triiodobenzoic acid, frequently show symptoms of Ca deficiency and a low Ca content. It was concluded that auxins, probably produced by the seeds, play a significant role in Ca translocation into fruits. Exogenous indoleacetic acid but not 4-chlorophenoxyacetic acid applications could replace the effect of seeds in this respect. Auxin transport, rather than auxin accumulation, seems to be necessary for Ca transport, as can be concluded from the effect of auxin transport inhibitors.     

Auxin Antagonistic Effects of Auxin Precursors of the Substituted Amide Type

Cucumber seeds were germinated in Petri-dishes for 6 days withdifferent doses of a number of N-monosubstituted amide derivativesof some chlorophenoxy-alkane-carboxylic acids. Doses of theamides studied were roughly equivalent to 0.1, 1, 10, 100, and1,000 p.p.m. in water. The gross morphological effects of theamide treatments were studied, both with and without the additionof 1 and 10 p.p.m., respectively, of the corresponding carboxylicacid. The amides studied were the N-methyl-, N-ethyl-, N-propyl-,N-iso-propyl-, N-butyl-, and N-benzyl-amides of 2,4-dichlorophenoxyaceticacid (2,4-D), -(2,4-dichlorophenoxy)-propionic acid (2,4-DP),2,4,5-trichlorophenoxyacetic acid (2,4,5-T), and -(2,4,5-trichlorophenoxy)-propionicacid (2,4,s-TP). Thirteen of the twenty-one amide derivatives studied antagonizedthe auxintype plant-growth-regulating effects of their parentcarboxylic acid. The antagonisms observed involved not onlya decrease in the stimulatory effects of the externally appliedauxin acids (counteractions of the abnormal swellings of differentplant parts), but also reduced significantly their inhibitoryeffects, i.e. the inhibitions of growth in length of the hypocotyland of the roots. Since some auxin-type stimulatory effectswere observed with all of the amides studied, it is suggestedthat the thirteen amide derivatives play a double role as plantgrowth regulators in cucumber tissues: (1) to a certain extentthey are transformed by plant enzymes to the corresponding carboxylicacid, i.e. to auxin; and (2) the amides themselves exert anti-auxineffects.     

Auxin: A major regulator of organogenesis

Plant development is characterized by the continuous initiation of tissues and organs. The meristems, which are small stem cell populations, are involved in this process. The shoot apical meristem produces lateral organs at its flanks and generates the growing stem. These lateral organs are arranged in a stereotyped pattern called phyllotaxis. Organ initiation in the peripheral zone of the meristem involves accumulation of the plant hormone auxin. Auxin is transported in a polar way by influx and efflux carriers located at cell membranes. Polar localization of the PIN1 efflux carrier in meristematic cells generates auxin concentration gradients and PIN1 localization depends, in turn, on auxin gradients: this feedback loop generates a dynamic auxin distribution which controls phyllotaxis. Furthermore, PIN-dependent local auxin gradients represent a common module for organ initiation, in the shoot and in the root.     

Auxin Content and Auxin Catabolism in Relation to the Growth Polarity

The auxin level in the root fragments of carrot cultivated in vitro is inversely related to the auxin-oxidase activity. In the morphological basal region, auxin catabolism is low and, in consequence, auxin content is high. This accumulation of the endogenous auxin leads to the induction of callus. In such new tissues, IAA-oxidase activity is also very low and, similarly, the auxin content is high: thus, cells can growth rapidly. Consequently the growth polarity is directly related to the auxin catabolism.     

Signalling through the grapevine

The 5th Barossa Meeting on 'Cell Signalling and Molecular Medicine' was held in November 2011 in the Barossa Valley, South Australia. The combination of an inspirational environment and outstanding science led to a superb meeting that highlighted the versatility of cellular signalling systems and how they can be targeted by novel therapeutic approaches.     

A Role for Auxin in Flower Development

Auxin has long been implicated in many aspects of plant growth and development including flower development. However, the exact roles of auxin in flower development have not been well defined until the recent identification of auxin biosynthesis mutants. Auxin is necessary for the inltiation of floral primordia, and the disruption of auxin biosynthesis, polar auxin transport or auxin signaling leads to the failure of flower formation. Auxin also plays an essential role in specifying the number and Identity of floral organs. Further analysis of the relationship between the auxin pathways and the known flower development genes will provide critical information regarding mechanisms of organogenesis and pattern formation in plants.