Genome-wide investigation of light and carbon signaling interactions in Arabidopsis

BACKGROUND: Light and carbon are two essential signals influencing plant growth and development. Little is known about how carbon and light signaling pathways intersect or influence one another to affect gene expression. RESULTS: Microarrays are used to investigate carbon and light signaling interactions at a genome-wide level in Arabidopsis thaliana. A classification system, 'InterAct Class', is used to classify genes on the basis of their expression profiles. InterAct classes and the genes within them are placed into theoretical models describing interactions between carbon and light signaling. Within InterAct classes there are genes regulated by carbon (201 genes), light (77 genes) or through carbon and light interactions (1,247 genes). We determined whether genes involved in specific biological processes are over-represented in the population of genes regulated by carbon and/or light signaling. Of 29 primary functional categories identified by the Munich Information Center for Protein Sequences, five show over-representation of genes regulated by carbon and/or light. Metabolism has the highest representation of genes regulated by carbon and light interactions and includes the secondary functional categories of carbon-containing-compound/carbohydrate metabolism, amino-acid metabolism, lipid metabolism, fatty-acid metabolism and isoprenoid metabolism. Genes that share a similar InterAct class expression profile and are involved in the same biological process are used to identify putative cis elements possibly involved in responses to both carbon and light signals. CONCLUSIONS: The work presented here represents a method to organize and classify microarray datasets, enabling one to investigate signaling interactions and to identify putative cis elements in silico through the analysis of genes that share a similar expression profile and biological function

An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis

<p>Abstract</p> <p>Background</p> <p>Light and carbon are two important interacting signals affecting plant growth and development. The mechanism(s) and/or genes involved in sensing and/or mediating the signaling pathways involving these interactions are unknown. This study integrates genetic, genomic and systems approaches to identify a genetically perturbed gene network that is regulated by the interaction of carbon and light signaling in Arabidopsis.</p> <p>Results</p> <p>Carbon and light insensitive (<it>cli</it>) mutants were isolated. Microarray data from <it>cli186 </it>is analyzed to identify the genes, biological processes and gene networks affected by the integration of light and carbon pathways. Analysis of this data reveals 966 genes regulated by light and/or carbon signaling in wild-type. In <it>cli186</it>, 216 of these light/carbon regulated genes are misregulated in response to light and/or carbon treatments where 78% are misregulated in response to light and carbon interactions. Analysis of the gene lists show that genes in the biological processes "energy" and "metabolism" are over-represented among the 966 genes regulated by carbon and/or light in wild-type, and the 216 misregulated genes in <it>cli186</it>. To understand connections among carbon and/or light regulated genes in wild-type and the misregulated genes in <it>cli186</it>, the microarray data is interpreted in the context of metabolic and regulatory networks. The network created from the 966 light/carbon regulated genes in wild-type, reveals that <it>cli186 </it>is affected in the light and/or carbon regulation of a network of 60 connected genes, including six transcription factors. One transcription factor, HAT22 appears to be a regulatory "hub" in the <it>cli186 </it>network as it shows regulatory connections linking a metabolic network of genes involved in "amino acid metabolism", "C-compound/carbohydrate metabolism" and "glycolysis/gluconeogenesis".</p> <p>Conclusion</p> <p>The global misregulation of gene networks controlled by light and carbon signaling in <it>cli186 </it>indicates that it represents one of the first Arabidopsis mutants isolated that is specifically disrupted in the integration of both carbon and light signals to control the regulation of metabolic, developmental and regulatory genes. The network analysis of misregulated genes suggests that <it>CLI186 </it>acts to integrate light and carbon signaling interactions and is a master regulator connecting the regulation of a host of downstream metabolic and regulatory processes.</p

A multi-wavelength polarimetric study of the blazar CTA 102 during a Gamma-ray flare in 2012

We perform a multi-wavelength polarimetric study of the quasar CTA 102 during an extraordinarily bright $\gamma$-ray outburst detected by the {\it Fermi} Large Area Telescope in September-October 2012 when the source reached a flux of F$_{>100~\mathrm{MeV}} =5.2\pm0.4\times10^{-6}$ photons cm$^{-2}$ s$^{-1}$. At the same time the source displayed an unprecedented optical and NIR outburst. We study the evolution of the parsec scale jet with ultra-high angular resolution through a sequence of 80 total and polarized intensity Very Long Baseline Array images at 43 GHz, covering the observing period from June 2007 to June 2014. We find that the $\gamma$-ray outburst is coincident with flares at all the other frequencies and is related to the passage of a new superluminal knot through the radio core. The powerful $\gamma$-ray emission is associated with a change in direction of the jet, which became oriented more closely to our line of sight ($\theta\sim$1.2$^{\circ}$) during the ejection of the knot and the $\gamma$-ray outburst. During the flare, the optical polarized emission displays intra-day variability and a clear clockwise rotation of EVPAs, which we associate with the path followed by the knot as it moves along helical magnetic field lines, although a random walk of the EVPA caused by a turbulent magnetic field cannot be ruled out. We locate the $\gamma$-ray outburst a short distance downstream of the radio core, parsecs from the black hole. This suggests that synchrotron self-Compton scattering of near-infrared to ultraviolet photons is the probable mechanism for the $\gamma$-ray production.Comment: Accepted for publication in The Astrophysical Journa

Cryptochrome 1, Cryptochrome 2, and Phytochrome A Co-Activate the Chloroplast psbD Blue Light–Responsive Promoter

The reaction center core of photosystem II is composed of two chlorophyll binding proteins, D1 and D2, that are encoded by the chloroplast genes psbA and psbD. These chlorophyll binding proteins are damaged during photochemistry, especially under high irradiance. Photosystem II function is maintained under these conditions through turnover and resynthesis of D1 and D2. Blue light–activated transcription of psbD from a special light-responsive promoter is part of the repair system. In this study, light-activated chloroplast and psbD transcription were studied after dark adaptation of 21-day-old light-grown Arabidopsis plants. Illumination of dark-adapted plants with red light increased chloroplast transcription activity and transcription from the psbD light-responsive promoter. Blue light further increased chloroplast transcription activity and stimulated differential transcription from the psbD light-responsive promoter. Photoreceptor mutants showed that blue light–specific activation of chloroplast transcription and the psbD light-responsive promoter involve cryptochrome 1 (cry1) or cryptochrome 2 (cry2) and phytochrome A (phyA). Blue light–induced activation of the psbD light-responsive promoter was normal in det2-1 and hy5-1 but attenuated in det3-1. Therefore, cry1/cry2/phyA–mediated blue light activation of the psbD light-responsive promoter in 21-day-old Arabidopsis plants does not involve hy5, a transcription factor that mediates other phyA and blue light–induced responses

Light- and Carbon-Signaling Pathways. Modeling Circuits of Interactions

Here, we report the systematic exploration and modeling of interactions between light and sugar signaling. The data set analyzed explores the interactions of sugar (sucrose) with distinct light qualities (white, blue, red, and far-red) used at different fluence rates (low or high) in etiolated seedlings and mature green plants. Boolean logic was used to model the effect of these carbon/light interactions on three target genes involved in nitrogen assimilation: asparagine synthetase (ASN1 and ASN2) and glutamine synthetase (GLN2). This analysis enabled us to assess the effects of carbon on light-induced genes (GLN2/ASN2) versus light-repressed genes (ASN1) in this pathway. New interactions between carbon and blue-light signaling were discovered, and further connections between red/far-red light and carbon were modeled. Overall, light was able to override carbon as a major regulator of ASN1 and GLN2 in etiolated seedlings. By contrast, carbon overrides light as the major regulator of GLN2 and ASN2 in light-grown plants. Specific examples include the following: Carbon attenuated the blue-light induction of GLN2 in etiolated seedlings and also attenuated the white-, blue-, and red-light induction of GLN2 and ASN2 in light-grown plants. By contrast, carbon potentiated far-red-light induction of GLN2 and ASN2 in light-grown plants. Depending on the fluence rate of far-red light, carbon either attenuated or potentiated light repression of ASN1 in light-grown plants. These studies indicate the interaction of carbon with blue, red, and far-red-light signaling and set the stage for further investigation into modeling this complex web of interacting pathways using systems biology approaches

Function and fate of myofibroblasts after myocardial infarction.

The importance of cardiac fibroblasts in the regulation of myocardial remodelling following myocardial infarction (MI) is becoming increasingly recognised. Studies over the last few decades have reinforced the concept that cardiac fibroblasts are much more than simple homeostatic regulators of extracellular matrix turnover, but are integrally involved in all aspects of the repair and remodelling of the heart that occurs following MI. The plasticity of fibroblasts is due in part to their ability to undergo differentiation into myofibroblasts. Myofibroblasts are specialised cells that possess a more contractile and synthetic phenotype than fibroblasts, enabling them to effectively repair and remodel the cardiac interstitium to manage the local devastation caused by MI. However, in addition to their key role in cardiac restoration and healing, persistence of myofibroblast activation can drive pathological fibrosis, resulting in arrhythmias, myocardial stiffness and progression to heart failure. The aim of this review is to give an appreciation of both the beneficial and detrimental roles of the myofibroblast in the remodelling heart, to describe some of the major regulatory mechanisms controlling myofibroblast differentiation including recent advances in the microRNA field, and to consider how this cell type could be exploited therapeutically

A Tight Connection between Gamma-Ray Outbursts and Parsec-scale Jet Activity in the Quasar 3C 454.3

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