Pistil transcriptome analysis to disclose genes and gene products related to aposporous apomixis in Hypericum perforatum L.

Unlike sexual reproduction, apomixis encompasses a number of reproductive strategies,which permit maternal genome inheritance without genetic recombination and syngamy. The key biological features of apomixis are the circumvention of meiosis (i.e., apomeiosis),the differentiation of unreduced embryo sacs and egg cells, and their autonomous development in functional embryos through parthenogenesis, and the formation of viable endosperm either via fertilization-independent means or following fertilization with a sperm cell. Despite the importance of apomixis for breeding of crop plants and although much research has been conducted to study this process, the genetic control of apomixis is still not well understood. Hypericum perforatum is becoming an attractive model system for the study of aposporous apomixis. Here we report results from a global gene expression analysis of H. perforatum pistils collected from sexual and aposporous plant accessions for the purpose of identifying genes, biological processes and molecular functions associated with the aposporous apomixis pathway. Across two developmental stages corresponding to the expression of aposporous apomeiosis and parthenogenesis in ovules, a total of 224 and 973 unigenes were found to be significantly up- and down-regulated with a fold change >= 2 in at least one comparison, respectively.Differentially expressed genes were enriched for multiple gene ontology (GO) terms,including cell cycle, DNA metabolic process, and single-organism cellular process. For molecular functions, the highest scores were recorded for GO terms associated withDNA binding, DNA (cytosine-5-)-methyltransferase activity and heterocyclic compound binding. As deregulation of single components of the sexual developmental pathway is believed to be a trigger of the apomictic reproductive program, all genes involved in sporogenesis, gametogenesis and response to hormonal stimuli were analyzed in great detail. Overall, our data suggest that phenotypic expression of apospory is concomitant with the modulation of key genes involved in the sexual reproductive pathway. Furthermore, based on gene annotation and co-expression, we underline a putative role of hormones and key actors playing in the RNA-directed DNA methylation pathway in regulating the developmental changes occurring during aposporous apomixis in H. perforatum

Environmental Risk Assessment as a Case-Based Preference Elicitation Process

The traditional approaches to environmental risk analysis based on first principle methods don’t cover the assessment of systemic vulnerability, a meaningful component of the natural hazard. We argue that this complex task can be accomplished with a case-based approach through a process of pairwise preference elicitation. Up to now the main restriction of the case-base risk assessment was related to the scalability issue and the cognitive overload of the experts. In this paper we propose a methodology based on a mixed initiative strategy that combines the user preference elicitation and the machine rank approximation. The work includes both the case-based model and the related computational tools. We illustrate how a boosting algorithm can effectively estimate pairwise preferences and reduce the effort of the elicitation process. Experimental results, both on artificial data and a real world problem in the domain of civil defence, showed that a good trade-off can be achieved between the accuracy of the estimated preferences, and the elicitation effort of the end use

Case-Based Ranking for Decision Support Systems

Very often a planning problem can be formulated as a ranking problem: i.e. to find an order relation over a set of alternatives. The ranking of a finite set of alternatives can be designed as a preference elicitation problem. While the case-based preference elicitation approach is more effective with respect to the first principle methods, still the scaling problem remains an open issue because the elicitation effort has a quadratic relation with the number of alternative cases. In this paper we propose a solution based on the machine learning techniques. We illustrate how a boosting algorithm can effectively estimate pairwise preferences and reduce the effort of the elicitation process. Experimental results, both on artificial data and a real world problem in the domain of civil defence, showed that a good trade-off can be achieved between the accuracy of the estimated preferences, and the elicitation effort of the end use

Case-Based Ranking for Decision Suppor Systems

Very often a planning problem can be formulated as a ranking problem: i.e. to find an order relation over a set of alternatives. The ranking of a finite set of alternatives can be designed as a preference elicitation problem. While the case-based preference elicitation approach is more effective with respect to the first principle methods, still the scaling problem remains an open issue because the elicitation effort has a quadratic relation with the number of alternative cases. In this paper we propose a solution based on the machine learning techniques. We illustrate how a boosting algorithm can effectively estimate pairwise preferences and reduce the effort of the elicitation process. Experimental results, both on artificial data and a real world problem in the domain of civil defence, showed that a good trade-off can be achieved between the accuracy of the estimated preferences, and the elicitation effort of the end use

Untargeted and Targeted Metabolomics and Tryptophan Decarboxylase In Vivo Characterization Provide Novel Insight on the Development of Kiwifruits (<i>Actinidia deliciosa</i>)

Kiwifruit (Actinidia deliciosa cv. Hayward) is a commercially important crop with highly nutritional green fleshy fruits. The post-harvest maturation of the fruits is well characterized, but little is known about the metabolic changes that occur during fruit development. Here we used untargeted metabolomics to characterize the non-volatile metabolite profile of kiwifruits collected at different time points after anthesis, revealing profound metabolic changes before the onset of ripening including the depletion of many classes of phenolic compounds. In contrast, the phytohormone abscisic acid accumulated during development and ripening, along with two indolamines (serotonin and its precursor tryptamine), and these were monitored in greater detail by targeted metabolomics. The role of indolamines in kiwifruit development is completely unknown, so we also characterized the identity of genes encoding tryptophan decarboxylase in A. deliciosa and its close relative A. chinensis to provide insight into the corresponding biological processes. Our results indicate that abscisic acid and indolamines fulfill unrecognized functions in the development and ripening of kiwifruits

Connectivity by the Frontal Aslant Tract (FAT) explains local functional specialization of the superior and inferior frontal gyri in humans when choosing predictive over reactive strategies: a tractography-guided TMS study

Predictive and reactive behaviors represent two mutually exclusive strategies in a sensorimotor task. Predictive behavior consists in internally estimating timing and features of a target stimulus and relies on a cortical medial frontal system (superior frontal gyrus - SFG). Reactive behavior consists in waiting for actual perception of the target stimulus and relies on the lateral frontal cortex (inferior frontal gyrus - IFG). We investigated whether SFG-IFG connections by the frontal aslant tract (FAT) can mediate predictive/reactive interactions. In 19 healthy human volunteers, we applied online transcranial magnetic stimulation (TMS) to 6 spots along the medial and lateral terminations of the FAT, during the set period of a delayed reaction task. Such scenario can be solved using either predictive or reactive strategies. TMS increased the propensity towards reactive behavior if applied to a specific portion of the SFG and increased predictive behavior when applied to a specific IFG spot. The two active spots in the SFG and IFG were directly connected by a sub-bundle of FAT fibers as indicated by DWI-tractography. Since FAT connectivity identifies two distant cortical nodes with opposite functions, we propose that the FAT mediates mutually inhibitory interactions between SFG and IFG to implement a "winner takes all" decisional process. We hypothesize such role of the FAT to be domain-general, whenever competition occurs between internal predictive and external reactive behaviors. Finally, we also show that anatomical connectivity is a powerful factor to explain and predict the spatial distribution of brain stimulation effects.Significance StatementWe interact with sensory cues adopting two main mutually-exclusive strategies: a) trying to anticipate the occurrence of the cue or b) waiting for the GO-signal to be manifest and react to it. Here we showed, by using non-invasive brain stimulation (TMS), that two specific cortical regions in the superior frontal gyrus (SFG) and the inferior frontal gyrus (IFG) have opposite roles in facilitating a predictive or a reactive strategy. Importantly these two very distant regions but with highly interconnected functions are specifically connected by a small white matter bundle, which mediates the direct competition and exclusiveness between predictive and reactive strategies. More generally, implementing anatomical connectivity in TMS studies strongly reduces spatial noise

Modulating anosognosia for hemiplegia: The role of dangerous actions in emergent awareness

Anosognosia for hemiplegia is a lack of awareness of motor deficits following a right hemisphere lesion. Residual forms of awareness co-occur with an explicit denial of hemiplegia. The term emergent awareness refers to a condition in which awareness of motor deficits is reported verbally during the actual performance of an action involving the affected body part. In this study, two tasks were used to explore the potential effects of i) attempting actions which are impossible for sufferers of hemiplegia and ii) attempting actions which are potentially dangerous. Sixteen hemiplegic patients (8 anosognosic, and 8 non-anosognosic) were asked to perform both potentially dangerous and neutral actions. Our results confirm an increase in emergent awareness in anosognosic patients during the execution of both of these types of action. Moreover, actions that are potentially dangerous improved the degree of awareness. However, lesions in the fronto-temporal areas appear to be associated with a reduced effect of action execution (emergent awareness) while lesions in the basal ganglia and amygdale and the white matter underlying the insula and fronto-temporal areas are associated with a lesser degree of improvement resulting from attempting to perform dangerous actions

Volatile linalool activates grapevine resistance against downy mildew with changes in the leaf metabolome

Volatile organic compounds (VOCs) are produced by plants in response to biotic and abiotic stimuli. In grapevine, volatile terpenoids are triggered by downy mildew infection (caused by Plasmopara viticola), suggesting their involvement in plant defense responses. In particular, linalool was detected in leaves of downy mildew-resistant genotypes, but no information is available on its involvement in the defense mechanisms against P. viticola. The aim of this study was to investigate the defense mechanisms activated by linalool in grapevine leaves against P. viticola and to identify metabolic changes associated with linalool-induced resistance. Linalool treatment reduced downy mildew severity on leaf disks of susceptible grapevines (cultivar Pinot noir) and stimulated callose deposition at the sites of P. viticola infection. Moreover, the upregulation of defense-related genes was found in linalool-treated leaf disks, indicating the activation of grapevine defense mechanisms of salicylic acid and jasmonic acid pathways. Linalool treatment caused changes in the leaf metabolome of mock-inoculated and P. viticola-inoculated samples at one and six days post inoculation, as revealed by ultra-high pressure liquid chromatography-electrospray ionization-high-resolution quadrupole time of flight-mass spectrometry. Pathway analysis of annotated features with significant increases and decreases in abundance revealed the reprogramming of amino acid, phenylpropanoid, and terpenoid metabolisms in response to linalool treatment and P. viticola inoculation. In particular, features with significant increases in abundance in linalool-treated samples mainly belonged to putative phenylpropanoids, putative terpenoids, putative lipids, and lipid-like compounds, including molecules possibly associated with plant defense against pathogens, such as 2-phenylethanol, 2,4-heptadienal, α-terpineol, citral, and geraniol. These results demonstrated that linalool induces grapevine resistance against downy mildew, acting as a signaling molecule for plant resistance induction

Investigation of seasonal differences in strawberry metabolism from flowering through ripening

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