Neutral space analysis for a Boolean network model of the fission yeast cell cycle network

BackgroundInteractions between genes and their products give rise to complex circuits known as gene regulatory networks (GRN) that enable cells to process information and respond to external stimuli. Several important processes for life, depend of an accurate and context-specific regulation of gene expression, such as the cell cycle, which can be analyzed through its GRN, where deregulation can lead to cancer in animals or a directed regulation could be applied for biotechnological processes using yeast. An approach to study the robustness of GRN is through the neutral space. In this paper, we explore the neutral space of a Schizosaccharomyces pombe (fission yeast) cell cycle network through an evolution strategy to generate a neutral graph, composed of Boolean regulatory networks that share the same state sequences of the fission yeast cell cycle.ResultsThrough simulations it was found that in the generated neutral graph, the functional networks that are not in the wildtype connected component have in general a Hamming distance more than 3 with the wildtype, and more than 10 between the other disconnected functional networks. Significant differences were found between the functional networks in the connected component of the wildtype network and the rest of the network, not only at a topological level, but also at the state space level, where significant differences in the distribution of the basin of attraction for the G1 fixed point was found for deterministic updating schemes.ConclusionsIn general, functional networks in the wildtype network connected component, can mutate up to no more than 3 times, then they reach a point of no return where the networks leave the connected component of the wildtype. The proposed method to construct a neutral graph is general and can be used to explore the neutral space of other biologically interesting networks, and also formulate new biological hypotheses studying the functional networks in the wildtype network connected component

A neurophenomenological approach to non-ordinary states of consciousness: hypnosis, meditation, and psychedelics

No contemporary unifying framework has been provided for the study of non-ordinary states of consciousness (NSCs) despite increased interest in hypnosis, meditation, and psychedelics. NSCs induce shifts in experiential contents (what appears to the experiencer) and/or structure (how it appears). This can allow the investigation of the plastic and dynamic nature of experience from a multiscale perspective that includes mind, brain, body, and context. We propose a neurophenomenological (NP) approach to the study of NSCs which highlights their role as catalysts of transformation in clinical practice by refining our understanding of the relationships between experiential (subjective) and neural dynamics. We outline the ethical implications of the NP approach for standard conceptions of health and pathology as well as the crucial role of experience-based know-how in NSC-related research and application. Keywords: agency; altered states of consciousness; hypnosis; meditation; psychedelics; sel

VOLATILE -MEDIATED EFFECTS PREDOMINATE IN PARABURKHOLDERIA PHYTOFIRMANS GROWTH PROMOTION AND SALT STRESS TOLERANCE OF ARABIDOPSIS THALIANA

Abiotic stress has a growing impact on plant growth and agricultural activity worldwide. Specific plant growth promoting rhizobacteria have been reported to stimulate growth and tolerance to abiotic stress in plants, and molecular mechanisms like phytohormone synthesis and 1-aminocyclopropane-1-carboxylate deamination are usual candidates proposed to mediate these bacterial effects. Paraburkholderia phytofirmans PsJN is able to promote growth of several plant hosts, and improve their tolerance to chilling, drought and salinity. This work investigated bacterial determinants involved in PsJN stimulation of growth and salinity tolerance in Arabidopsis thaliana, showing bacteria enable plants to survive long-term salinity treatment, accumulating less sodium within leaf tissues relative to non-inoculated controls. Inactivation of specific bacterial genes encoding ACC deaminase, auxin catabolism, N-acyl-homoserine-lactone production, and flagellin synthesis showed these functions have little influence on bacterial induction of salinity tolerance. Volatile organic compound emission from strain PsJN was shown to reproduce the effects of direct bacterial inoculation of roots, increasing plant growth rate and tolerance to salinity evaluated both in vitro and in soil. Furthermore, early exposure to VOCs from P. phytofirmans was sufficient to stimulate long-term effects observed in Arabidopsis growth in the presence and absence of salinity. Organic compounds were analyzed in the headspace of PsJN cultures, showing production of 2-undecanone, 7-hexanol, 3-methylbutanol and dimethyldisulfide. Exposure of A. thaliana to different quantities of these molecules showed that they are able to influence growth in a wide range of added amounts. Exposure to a blend of the first three compounds was found to mimic the effects of PsJN on both general growth promotion and salinity tolerance. To our knowledge, this is the first report on volatile compound-mediated induction of plant abiotic stress tolerance by a Paraburkholderia species

Geographic variation in thermal physiological performance of the intertidal crab Petrolisthes violaceus along a latitudinal gradient

© 2014. Published by The Company of Biologists Ltd. Environmental temperature has profound effects on the biological performance and biogeographical distribution of ectothermic species. Variation of this abiotic factor across geographic gradients is expected to produce physiological differentiation and local adaptation of natural populations depending on their thermal tolerances and physiological sensitivities. Here, we studied geographic variation in whole-organism thermal physiology of seven populations of the porcelain crab Petrolisthes violaceus across a latitudinal gradient of 3000 km, characterized by a cline of thermal conditions. Our study found that populations of P. violaceus show no differences in the limits of their thermal performance curves and demonstrate a negative correlation of their optimal temperatures with latitude. Additionally, our findings show that high-latitude populations of P. violaceus exhibit broader thermal tolerances, which is consistent with the climatic variability hypothesis. Interestingly, under a future scenario of warming oceans, the thermal safety margins of P. violaceus indicate that lower latitude populations can physiologically tolerate the ocean-warming scenarios projected by the IPCC for the end of the twenty-first century.Link_to_subscribed_fulltex

Gene networks underlying the early regulation of Paraburkholderia phytofirmans PsJN induced systemic resistance in Arabidopsis.

Plant defense responses to biotic stresses are complex biological processes, all governed by sophisticated molecular regulations. Induced systemic resistance (ISR) is one of these defense mechanisms where beneficial bacteria or fungi prime plants to resist pathogens or pest attacks. In ISR, the defense arsenal in plants remains dormant and it is only triggered by an infection, allowing a better allocation of plant resources. Our group recently described that the well-known beneficial bacterium Paraburkholderia phytofirmans PsJN is able to induce Arabidopsis thaliana resistance to Pseudomonas syringae pv. tomato (Pst) DC3000 through ISR, and that ethylene, jasmonate and salicylic acid are involved in this protection. Nevertheless, the molecular networks governing this beneficial interaction remain unknown. To tackle this issue, we analyzed the temporal changes in the transcriptome of PsJN-inoculated plants before and after being infected with Pst DC3000. These data were used to perform a gene network analysis to identify highly connected transcription factors. Before the pathogen challenge, the strain PsJN regulated 405 genes (corresponding to 1.8% of the analyzed genome). PsJN-inoculated plants presented a faster and stronger transcriptional response at 1-hour post infection (hpi) compared with the non-inoculated plants, which presented the highest transcriptional changes at 24 hpi. A principal component analysis showed that PsJN-induced plant responses to the pathogen could be differentiated from those induced by the pathogen itself. Forty-eight transcription factors were regulated by PsJN at 1 hpi, and a system biology analysis revealed a network with four clusters. Within these clusters LHY, WRKY28, MYB31 and RRTF1 are highly connected transcription factors, which could act as hub regulators in this interaction. Concordantly with our previous results, these clusters are related to jasmonate, ethylene, salicylic, acid and ROS pathways. These results indicate that a rapid and specific response of PsJN-inoculated plants to the virulent DC3000 strain could be the pivotal element in the protection mechanism

Overexpression of GlyI and GlyII genes in transgenic tomato (Solanum lycopersicum Mill.) plants confers salt tolerance by decreasing oxidative stress

The glyoxalase system plays an important role in various physiological processes in plants, including salt stress tolerance. We report the effects of overexpressing glyoxalase I and glyoxalase II genes in transgenic tomato (Solanum lycopersicum Mill.) cv. Ailsa Craig. Stable expression of both transgenes was detected in the transformed tomato plants under salt stress. The transgenic lines overexpressing GlyI and GlyII under a high NaCl concentration (800 mM) showed reduced lipid peroxidation and the production of H2O2 in leaf tissues. A greater decrease in the chlorophyll a+b content in wild-type (WT) compared with transgenic lines was also observed. These results suggest that the over expression of two genes, GlyI and GlyII, may enhance salt stress tolerance by decreasing oxidative stress in transformed tomato plants. This work will help our understanding of the putative role of the glyoxalase system in the tolerance to abiotic stress in tomato plants

Effects of the Plant Growth-Promoting Bacterium <i>Burkholderia</i><i> phytofirmans</i> PsJN throughout the Life Cycle of <i>Arabidopsis thaliana</i>

<div><p>Plant growth-promoting rhizobacteria (PGPR) induce positive effects in plants, such as increased growth or reduced stress susceptibility. The mechanisms behind PGPR/plant interaction are poorly understood, as most studies have described short-term responses on plants and only a few studies have analyzed plant molecular responses under PGPR colonization. Here, we studied the effects of the PGPR bacterial model <i>Burkholderia</i><i>phytofirmans</i> PsJN on the whole life cycle of <i>Arabidopsis thaliana</i> plants. We reported that at different plant developmental points, strain PsJN can be found in the rhizosphere and also colonizing their internal tissues. In early ontogeny, strain PsJN increased several growth parameters and accelerated growth rate of the plants. Also, an Arabidopsis transcriptome analysis revealed that 408 genes showed differential expression in PsJN-inoculated plants; some of these genes are involved in stress response and hormone pathways. Specifically, genes implicated in auxin and gibberellin pathways were induced. Quantitative transcriptional analyses of selected genes in different developmental stages revealed that the beginning of these changes could be evidenced early in development, especially among the down-regulated genes. The inoculation with heat-killed bacteria provoked a more severe transcriptional response in plants, but was not able to induce plant growth-promotion. Later in ontogeny, the growth rates of inoculated plants decreased with respect to the non-inoculated group and, interestingly, the inoculation accelerated the flowering time and the appearance of senescence signs in plants; these modifications correlate with the early up-regulation of flowering control genes. Then, we show that a single inoculation with a PGPR could affect the whole life cycle of a plant, accelerating its growth rate and shortening its vegetative period, both effects relevant for most crops. Thus, these findings provide novel and interesting aspects of these relevant biological interactions.</p> </div

Effects of <i>Burkholderia</i><i>phytofirmans</i> PsJN on <i>Arabidopsis</i><i>thaliana</i> roots.

<p>A) <i>In vitro</i> growth of primary roots under different treatments. Media and SE are the result of at least 30 plants per treatment and results are representative of three independent experiments. Same letters indicate non-significant differences among treatments (One way ANOVA, p<0.05). B) Representative photographs of root hairs formed at the primary root tip region of 8 DAS Arabidopsis seedlings grown in indicated treatments. K-PsJN represents the killed bacteria treatment. C) Representative photograph of epifluorescence images of root colonization of <i>A. thaliana</i> plants by strain PsJN::GFP; bacterial cells are observed as colonies attached to the surface of the root (arrow), bar represents 200 μm. D) Confocal microscope image of a root colonization by strain PsJN::GFP at the root tip, bar represents 10 µm. E) Confocal microscope of a root colonized endophytically by PsJN :: GFP (roots were washed with ethanol and sterile water before being observed under microscope); cells are observed as colony attached to lateral root emergence and in an intercellular position, between the epidermal layer, bar represents 30 µm.</p

Effects of <i>Burkholderia phytofirmans</i> PsJN on aerial zone during long-term growth of <i>Arabidopsis thaliana</i> plants.

<p>A) Representative photographs of <i>A. thaliana</i> rosettes of plants exposed to the different treatments (K-PsJN represents the killed bacteria treatment) at 18 DAS, bars correspond to 0.5 cm. B–D) Graphic representation of rosette media areas (B) average rosette leaf number per plant (C) and average rosette leaf areas (D) of plants subjected to the different treatments. Media and SE were calculated with at least 12 plants per treatment, and results are representative of three independent experiments. Asterisks indicate significant differences among PsJN treatment and the two other treatments in each time (One or two-way ANOVA, p<0.05). E) Representative photographs of the adaxial surface of third rosette leaves from 40 DAS plants. Bars represent 100 µm.</p

Effects of <i>Burkholderia</i><i>phytofirmans</i> PsJN on flowering and senescence of <i>Arabidopsis thaliana</i> plants.

<p>A) Percentage of plants presenting floral primordia in the different treatments. B) Number of senescent leaves in plants of the different treatments at different days after sowing. Asterisks represent significant differences (One way ANOVA, p<0.05). Media and SE represent measurements of at least 12 plants per treatments and results are representative of three independent experiments.</p