Plant-soil feedback in the ‘real world’: how does fire fit into all of this?

Aims: Plant–soil feedback (PSF) is an important mechanism controlling plant growth, vegetation dynamics, and longer-term and larger-scale patterns of plant community diversity. We know that feedback between plants and soil biota depends on several external factors, such as nutrient and water availability, and interactions with neighbouring plants. We argue that in the ‘real world’, PSF are not working in isolation but instead proceed within a complex context of multiple interacting factors. Fire is one of those complex external factors which could greatly alter PSF by re-setting or re-directing plant-soil biota interactions. Methods: We reviewed key literature on the effects of fire on soil biota and soil physicochemical properties with soil depth, to generate predictions on the complex effects of fire on PSF. Results: We highlight that fire has strong potential to directly and indirectly affect the strength of PSF. To what extent this influences longer-term plant community trajectories depends on the interactions between fire characteristics and ecosystem type. Here, we conceptualized these effects of fire on soil properties and biota, and then discuss the main pathways through which fire should alter PSF. Conclusions: We think that PSF processes should be nullified under and after fire. Average neutral PSF responses are expected to be more common in the short-term or within the timeframe required for major soil microbial players to regain their pre-fire abundances and diversity. We conclude by providing directions for future research and possible methods to study fire effects on PSF both in the field and under controlled conditions.EEA San LuisFil: Kardol, P. Swedish University of Agricultural Sciences. Department of Forest Ecology and Management; SueciaFil: Yang, T. Agriculture and Agri-Food Canada. Swift Current Research & Development Centre; CanadáFil: Arroyo, Daniel Nicolas. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Luis; ArgentinaFil: Teste, Francois Philippe. Agriculture and Agri-Food Canada. Swift Current Research & Development Centre; CanadáFil: Teste, Francois Philippe. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis; ArgentinaFil: Teste, Francois Philippe. Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis; Argentin

Experimental study of the reduction of field emission by gas injection in vacuum for accelerator applications

LGEP 2014 ID = 1590International audienceField emission current from surfaces under vacuum and at high field strengths can be reduced by the injection of gas into the evacuated volume. In this paper, the effects of H 2 , He, N 2 , and Ar on this "dark" current emitted from a tungsten carbide point cathode for 2 cm gap distance is studied. Exposure to any of these gases at pressures on the order of 10 −3 –10 −2 Pa was found to reduce the emission current by up to 90% with a time constant on the order of ∼1 minute as compared to the current at 10 −6 Pa. The effect was strongly dependent on the gas nature, with Ar and N 2 having larger effects at lower pressures than He and H 2 . The reduction was reversible, with the current increasing to near its original value with a time constant on the order of ∼1–10 minutes after pumping down. The effect of the gas remained in the absence of electric field, whatever the gas pressure. Mechanisms for these and related phenomena are discussed

Patterns of plant naturalization show that facultative mycorrhizal plants are more likely to succeed outside their native Eurasian ranges

The naturalization of an introduced species is a key stage during the invasion process. Therefore, identifying the traits that favor the naturalization of non-native species can help understand why some species are more successful when introduced to new regions. The ability and the requirement of a plant species to form a mutualism with mycorrhizal fungi, together with the types of associations formed may play a central role in the naturalization success of different plant species. To test the relationship between plant naturalization success and their mycorrhizal associations we analysed a database composed of mycorrhizal status and type for 1981 species, covering 155 families and 822 genera of plants from Europe and Asia, and matched it with the most comprehensive database of naturalized alien species across the world (GloNAF). In mainland regions, we found that the number of naturalized regions was highest for facultative mycorrhizal, followed by obligate mycorrhizal and lowest for non-mycorrhizal plants, suggesting that the ability of forming mycorrhizas is an advantage for introduced plants. We considered the following mycorrhizal types: arbuscular, ectomycorrhizal, ericoid and orchid mycorrhizal plants. Further, dual mycorrhizal species were those that included observations of arbuscular mycorrhizas as well as observations of ectomycorrhizas. Naturalization success (based on the number of naturalized regions) was highest for arbuscular mycorrhizal and dual mycorrhizal plants, which may be related to the low host specificity of arbuscular mycorrhizal fungi and the consequent high availability of arbuscular mycorrhizal fungal partners. However, these patterns of naturalization success were erased in islands, suggesting that the ability to form mycorrhizas may not be an advantage for establishing self-sustaining populations in isolated regions. Taken together our results show that mycorrhizal status and type play a central role in the naturalization process of introduced plants in many regions, but that their effect is modulated by other factorsFil: Moyano, Jaime. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; ArgentinaFil: Dickie, Ian. University of Canterbury; Nueva ZelandaFil: Rodriguez Cabal, Mariano Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; ArgentinaFil: Nuñez, Martin Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; Argentin

Drosophila TET acts with PRC1 to activate gene expression independently of its catalytic activity

Enzymes of the ten-eleven translocation (TET) family play a key role in the regulation of gene expression by oxidizing 5-methylcytosine (5mC), a prominent epigenetic mark in many species. Yet, TET proteins also have less characterized noncanonical modes of action, notably in Drosophila, whose genome is devoid of 5mC. Here, we show that Drosophila TET activates the expression of genes required for larval central nervous system (CNS) development mainly in a catalytic-independent manner. Genome-wide profiling shows that TET is recruited to enhancer and promoter regions bound by Polycomb group complex (PcG) proteins. We found that TET interacts and colocalizes on chromatin preferentially with Polycomb repressor complex 1 (PRC1) rather than PRC2. Furthermore, PRC1 but not PRC2 is required for the activation of TET target genes. Last, our results suggest that TET and PRC1 binding to activated genes is interdependent. These data highlight the importance of TET noncatalytic function and the role of PRC1 for gene activation in the Drosophila larval CNS

WNP: A Novel Algorithm for Gene Products Annotation from Weighted Functional Networks

Predicting the biological function of all the genes of an organism is one of the fundamental goals of computational system biology. In the last decade, high-throughput experimental methods for studying the functional interactions between gene products (GPs) have been combined with computational approaches based on Bayesian networks for data integration. The result of these computational approaches is an interaction network with weighted links representing connectivity likelihood between two functionally related GPs. The weighted network generated by these computational approaches can be used to predict annotations for functionally uncharacterized GPs. Here we introduce Weighted Network Predictor (WNP), a novel algorithm for function prediction of biologically uncharacterized GPs. Tests conducted on simulated data show that WNP outperforms other 5 state-of-the-art methods in terms of both specificity and sensitivity and that it is able to better exploit and propagate the functional and topological information of the network. We apply our method to Saccharomyces cerevisiae yeast and Arabidopsis thaliana networks and we predict Gene Ontology function for about 500 and 10000 uncharacterized GPs respectively

Functional Expression of Human Adenine Nucleotide Translocase 4 in Saccharomyces Cerevisiae

The adenine nucleotide translocase (ANT) mediates the exchange of ADP and ATP across the inner mitochondrial membrane. The human genome encodes multiple ANT isoforms that are expressed in a tissue-specific manner. Recently a novel germ cell-specific member of the ANT family, ANT4 (SLC25A31) was identified. Although it is known that targeted depletion of ANT4 in mice resulted in male infertility, the functional biochemical differences between ANT4 and other somatic ANT isoforms remain undetermined. To gain insight into ANT4, we expressed human ANT4 (hANT4) in yeast mitochondria. Unlike the somatic ANT proteins, expression of hANT4 failed to complement an AAC-deficient yeast strain for growth on media requiring mitochondrial respiration. Moreover, overexpression of hANT4 from a multi-copy plasmid interfered with optimal yeast growth. However, mutation of specific amino acids of hANT4 improved yeast mitochondrial expression and supported growth of the AAC-deficient yeast on non-fermentable carbon sources. The mutations affected amino acids predicted to interact with phospholipids, suggesting the importance of lipid interactions for function of this protein. Each mutant hANT4 and the somatic hANTs exhibited similar ADP/ATP exchange kinetics. These data define common and distinct biochemical characteristics of ANT4 in comparison to ANT1, 2 and 3 providing a basis for study of its unique adaptation to germ cells

Glycogen metabolic genes are involved in trehalose-6-phosphate synthase-mediated regulation of pathogenicity by the rice blast fungus Magnaporthe oryzae.

© 2013 Badaruddin et al.Editor - Peter N. Dodds, Commonwealth Scientific and Industrial Research Organisation (CSIRO), AustraliaThis work was funded by the Biotechnology and Biological Sciences Research Council and a European Research Council Advanced Investigator Award to NJT. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.The filamentous fungus Magnaporthe oryzae is the causal agent of rice blast disease. Here we show that glycogen metabolic genes play an important role in plant infection by M. oryzae. Targeted deletion of AGL1 and GPH1, which encode amyloglucosidase and glycogen phosphorylase, respectively, prevented mobilisation of glycogen stores during appressorium development and caused a significant reduction in the ability of M. oryzae to cause rice blast disease. By contrast, targeted mutation of GSN1, which encodes glycogen synthase, significantly reduced the synthesis of intracellular glycogen, but had no effect on fungal pathogenicity. We found that loss of AGL1 and GPH1 led to a reduction in expression of TPS1 and TPS3, which encode components of the trehalose-6-phosphate synthase complex, that acts as a genetic switch in M. oryzae. Tps1 responds to glucose-6-phosphate levels and the balance of NADP/NADPH to regulate virulence-associated gene expression, in association with Nmr transcriptional inhibitors. We show that deletion of the NMR3 transcriptional inhibitor gene partially restores virulence to a Δagl1Δgph1 mutant, suggesting that glycogen metabolic genes are necessary for operation of the NADPH-dependent genetic switch in M. oryzae.Biotechnology and Biological Sciences Research Council (BBSRC)European Research Council (ERC

Reference genes for gene expression studies in wheat flag leaves grown under different farming conditions

<p>Abstract</p> <p>Background</p> <p>Internal control genes with highly uniform expression throughout the experimental conditions are required for accurate gene expression analysis as no universal reference genes exists. In this study, the expression stability of 24 candidate genes from <it>Triticum aestivum </it>cv. Cubus flag leaves grown under organic and conventional farming systems was evaluated in two locations in order to select suitable genes that can be used for normalization of real-time quantitative reverse-transcription PCR (RT-qPCR) reactions. The genes were selected among the most common used reference genes as well as genes encoding proteins involved in several metabolic pathways.</p> <p>Findings</p> <p>Individual genes displayed different expression rates across all samples assayed. Applying geNorm, a set of three potential reference genes were suitable for normalization of RT-qPCR reactions in winter wheat flag leaves cv. Cubus: <it>TaFNRII </it>(ferredoxin-NADP(H) oxidoreductase; AJ457980.1), <it>ACT2 </it>(actin 2; TC234027), and <it>rrn26 </it>(a putative homologue to RNA 26S gene; AL827977.1). In addition of these three genes that were also top-ranked by NormFinder, two extra genes: <it>CYP18-2 </it>(Cyclophilin A, AY456122.1) and <it>TaWIN1 </it>(14-3-3 like protein, AB042193) were most consistently stably expressed.</p> <p>Furthermore, we showed that <it>TaFNRII, ACT2</it>, and <it>CYP18-2 </it>are suitable for gene expression normalization in other two winter wheat varieties (Tommi and Centenaire) grown under three treatments (organic, conventional and no nitrogen) and a different environment than the one tested with cv. Cubus.</p> <p>Conclusions</p> <p>This study provides a new set of reference genes which should improve the accuracy of gene expression analyses when using wheat flag leaves as those related to the improvement of nitrogen use efficiency for cereal production.</p