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At least 271 records · Page 15Linked to original sources
PubMed2006

Isolation and characterization of a GCN5-interacting protein from Arabidopsis thaliana.

An Arabidopsis protein, AtEML, was isolated based on its interaction with the histone acetyltransferase AtGCN5 in a yeast two-hybrid screen. RNA blot and RT-PCR analysis showed that AtEML is expressed in flowers, leaves, stems and siliques. The promoter region of AtEML has several cis-acting elements associated with response to biotic and abiotic stress conditions, and the accumulation of the AtEML transcript was found to be regulated by cold and salt treatments. In vitro and in vivo protein-protein interaction assays indicated that AtEML interacts with AtGCN5 through the N-terminal region. Furthermore, AtEML was shown to activate expression of the lacZ reporter gene in yeast through recruitment of AtGCN5. Such recruitment was accompanied by an increase in histone H3 acetylation at the promoter driving lacZ expression, as determined by chromatin immunoprecipitation. A higher level of AtEML gene expression was detected in the Arabidopsis gcn5 knockout mutant as compared to wild type Arabidopsis, indicating that AtEML expression is regulated by AtGCN5. These results suggest that AtEML may be a transcription factor that co-ordinates the expression of target stress regulated genes through involvement in recruiting AtGCN5 to their promoters.

Amino Acid Sequence↗
PubMed2004

Plant immunization.

Plant immunization is the process of activating natural defense system present in plant induced by biotic or abiotic factors. Plants are pre-treated with inducing agents stimulate plant defense responses that form chemical or physical barriers that are used against the pathogen invasion. Inducers used usually give the signals to rouse the plant defense genes ultimately resulting into induced systemic resistance. In many plant-pathogen interactions, R-Avr gene interactions results in localized acquired resistance or hypersensitive response and at distal ends of plant, a broad spectrum resistance is induced known as systemic acquired resistance (SAR). Various biotic or abiotic factors induce systemic resistance in plants that is phenotypically similar to pathogen-induced systemic acquired resistance (SAR). Some of the biotic or abiotic determinants induce systemic resistance in plants through salicylic acid (SA) dependent SAR pathway, others require jasmonic acid (JA) or ethylene. Host plant remains in induced condition for a period of time, and upon challenge inoculation, resistance responses are accelerated and enhanced. Induced systemic resistance (ISR) is effective under field conditions and offers a natural mechanism for biological control of plant disease.

Gene Expression Regulation, Plant↗
PubMed2001

The molecular roots of compositional inheritance.

Non-covalent compositional assemblies, made of monomeric mutually catalytic molecules, constitute an alternative to alphabet-based informational biopolymers as a mechanism of primordial inheritance. Such assemblies appear implicitly in many "Metabolism First" origin of life scenarios, and more explicitly in the Graded Autocatalysis Replication Domain (GARD) model [Segréet al. (2000). Proc. Natl Acad. Sci. U.S.A.97, 4112-4117]. In the present work, we provide a detailed analysis of the quantitative molecular roots of such behavior. It is demonstrated that the fidelity of reproduction provided by a newly defined heritability measure eta(*)(s), strongly depends on the values of molecular recognition parameters and on assembly size. We find that if the catalytic rate acceleration coefficients are distributed normally, transfer of compositional information becomes impossible, due to frequent "compositional error catastrophes". In contrast, if the catalytic acceleration rates obey a lognormal distribution, as actually predicted by a statistical formalism for molecular repertoires, high reproduction fidelity is obtained. There is also a clear dependence on assembly size N, whereby maximal eta is seen in a narrow range around N approximately 3.5 N(G)/lambda, where N(G)is the size of the primordial molecular repertoire and lambda is a molecular interaction statistical parameter. Such relationships help define the physicochemical conditions that could underlie the early steps in pre-biotic evolution.

Animals↗
PubMed2004

High-throughput techniques for analyzing complex bacterial communities.

A more complete understanding of microbial diversity and the environmental processes they control will require much more than a biotic inventory. It will require a deeper understanding of the basic features of systems organization and inter-population interactions. Communities, not total biomass, control net process rates driving the biogeochemical cycles sustaining the biosphere. Although the general patterns of macroorganismal diversity are relatively well known, spatial and temporal patterns of microorganismal diversity are essentially unknown. Having tools capable of resolving these patterns is a prerequisite to developing an understanding of the relationship between community structure and function. This talk discusses conceptual and technical developments that now provide the framework for systematically resolving temporal and spatial patterns of microorganisms and relating those patterns to processes at local and system levels. Of particular emphasis will be ongoing studies using highly parallel analyses with DNA microarrays for intensive monitoring of microbial populations in environmental systems. Although microarray technology is reasonably well established for studies of model organisms in well-defined laboratory settings, the application of this technology to environmental systems of uncharacterized diversity imposes additional demands on implementation; in particular, the requirement for optimized discrimination between target and non-target nucleic acids in complex, and undefined, mixtures. To increase the resolving power (information content) of our DNA microarray format, we are investigating the use of thermal dissociation of hybrids immobilized on individual array elements to resolve target and non-target sequences that differ by a single nucleotide. These studies, combined with specialized algorithms for optimizing the readout of the microarray should serve for informed environmental application. Initial studies have validated the general approach for analyses of sediment systems.

Bacteria↗
PubMed2000

Ozone/biotic disease interactions: molecular biomarkers as a new experimental tool.

Current climate change scenarios predict a further increase of tropospheric ozone which is well known to inhibit plant photosynthesis and growth processes. Ozone can also predispose plants to enhanced biotic attack, as proposed in particular for necrotrophic fungi, root-rot fungi and bark beetles. However, at present it does not seem possible to predict whether increased ambient ozone will lead to a higher or lower disease likelihood in particular plant-pathogen systems. It has been stated repeatedly in the literature that periods of high ambient ozone are essentially non-coincident with infection periods of most fungal pathogens. This implies minimal interactive risks. However, it now appears that the various ozone-induced metabolic changes can persist in plants over days or months. Visible ozone symptoms also may be greatly delayed. Certain stress transcripts, proteins and metabolites have been developed as ozone biomarkers in controlled exposure experiments, but these biomarkers remain to be examined on field sites. A simple epidemiological scenario based on 'memory' time spans of ozone effects is proposed as a tool to make ozone-plant disease interactions more predictable.

Journal Article↗
PubMed2002

Interference competition and species coexistence.

Interference competition is ubiquitous in nature. Yet its effects on resource exploitation remain largely unexplored for species that compete for dynamic resources. Here, I present a model of exploitative and interference competition with explicit resource dynamics. The model incorporates both biotic and abiotic resources. It considers interference competition both in the classical sense (i.e. each species suffers a net reduction in per capita growth rate via interference from, and interference on, the other species) and in the broad sense (i.e. each species suffers a net reduction in per capita growth rate via interference from, but can experience an increase in growth rate via interference on, the other species). Coexistence cannot occur under classical interference competition even when the species inferior at resource exploitation is superior at interference. Such a trade-off can, however, change the mechanism of competitive exclusion from dominance by the superior resource exploiter to a priority effect. Now the inferior resource exploiter can exclude the superior resource exploiter provided it has a higher initial abundance. By contrast, when interference is beneficial to the interacting species, coexistence is possible via a trade-off between exploitation and interference. These results hold regardless of whether the resource is biotic or abiotic, indicating that the outcome of exploitative and interference competition does not depend on the exact nature of resource dynamics. The model makes two key predictions. First, species that engage in costly interference mechanisms (e.g. territoriality, overgrowth or undercutting, allelopathy and other forms of chemical competition) should not be able to coexist unless they also engage in beneficial interference mechanisms (e.g. predation or parasitism). Second, exotic invasive species that displace native biota should be superior resource exploiters that have strong interference effects on native species with little or negative cost. The first prediction provides a potential explanation for patterns observed in several natural systems, including plants, aquatic invertebrates and insects. The second prediction is supported by data on invasive plants and vertebrates.

Animals↗
PubMed1995

Epiphyte size and taxonomy as biological indicators of ecological and toxicological factors in Lake Saint-François (Québec).

To assess the potential of the epiphyton community for monitoring spatial and temporal variations in the environmental quality of freshwater ecosystems, this paper describes the response of epiphytons to ecological and toxicological factors in Lake Saint-François, a fluvial lake of the St. Lawrence River (Québec). First, community descriptions and biotic indices based on size structure and on taxonomic composition were compared to test if size could usefully describe epiphyton response to environmental factors. Secondly, the relative contribution of ecological and toxicological variables in explaining the variation observed in epiphyton was quantified. A size-based approach classified the sites similarly to taxonomic analysis, but a larger portion of variance in size could be explained indicating a stronger relationship with environmental factors. Among both taxonomy and size-based biotic indices, the slope of the normalized size spectra performed best in terms of total explained variance. There were strong interactions between toxicological and ecological variables. These interactions should be considered in the planning and interpretation of biomonitoring studies. In such surveys, samples should be collected at sites with similar ecological characteristics: for example, the same macrophyte type and sediment texture. Interpretation of the data should consider the possible covariance of toxicological and ecological variables.

Journal Article↗
PubMed1998

Higher-order predators and the regulation of insect herbivore populations.

Empirical research has not supported the prediction that populations of terrestrial herbivorous arthropods are regulated solely by their natural enemies. Instead, both natural enemies (top-down effects) and resources (bottom-up effects) may play important regulatory roles. This review evaluates the hypothesis that higher-order predators may constrain the top-down control of herbivore populations. Natural enemies of herbivorous arthropods generally are not top predators within terrestrial food webs. Insect pathogens and entomopathogenic nematodes inhabiting the soil may be attacked by diverse micro- and mesofauna. Predatory and parasitic insects are attacked by their own suite of predators, parasitoids, and pathogens. The view of natural enemy ecology that has emerged from laboratory studies, where natural enemies are often isolated from all elements of the biotic community except for their hosts or prey, may be an unreliable guide to field dynamics. Experimental work suggests that interactions of biological control agents with their own natural enemies can disrupt the effective control of herbivore populations. Disruption has been observed experimentally in interactions of bacteria with bacteriophages, nematodes with nematophagous fungi, parasitoids with predators, parasitoids with hyperparasitoids, and predators with other predators. Higher-order predators have been little studied; manipulative field experiments will be especially valuable in furthering our understanding of their roles in arthropod communities.

Animals↗
PubMed2000

Aquatic humus from an unpolluted Brazilian dark-brown stream: general characterization and size fractionation of bound heavy metals.

The main pool of dissolved organic carbon in tropical aquatic environments, notably in dark-coloured streams, is concentrated in humic substances (HS). Aquatic HS are large organic molecules formed by micro-biotic degradation of biopolymers and polymerization of smaller organic molecules. From an environmental point of view, the study of metal humic interactions is often aimed at predicting the effect of aquatic HS on the bioavailability of heavy metal ions in the environment. In the present work the aquatic humic substances (HS) isolated from a dark-brown stream (located in an environmental protection area near Cubatão city in São Paulo-State, Brazil) by means of the collector XAD-8 were investigated. FTIR studies showed that the carboxylic carbons are probably the most important binding sites for Hg(II) ions within humic molecules. 13C-NMR and 1H-NMR studies of aquatic HS showed the presence of constituents with a high degree of aromaticity (40% of carbons) and small substitution. A special five-stage tangential-flow ultrafiltration device (UF) was used for size fractionation of the aquatic HS under study and for their metal species in the molecular size range 1-100 kDa (six fractions). The fractionation patterns showed that metal traces remaining in aquatic HS after their XAD-8 isolation have different distributions. Generally, the major percentage of traces of Mn, Cd and Ni (determined by ICP-AES) was preferably complexed by molecules with relatively high molecular size. Cu was bound by fractions with low molecular size and Co showed no preferential binding site in the various humic fractions. Moreover, the species formed between aquatic HS and Hg(II), prepared by spiking (determined by CVAAS), appeared to be concentrated in the relatively high molecular size fraction F1 (> 100 kDa).

Environmental Monitoring↗
PubMed2006

Molecular modeling of pathogenesis-related proteins of family 5.

The family of pathogenesis-related (PR) 5 proteins have diverse functions, and some of them are classified as thaumatins, osmotins, and inhibitors of alpha-amylase or trypsin. Although the specific function of many PR5 in plants is unknown, they are involved in the acquired systemic resistance and response to biotic stress, causing the inhibition of hyphal growth and reduction of spore germination, probably by a membrane permeabilization mechanism or by interaction with pathogen receptors. We have constructed three-dimensional models of four proteins belonging to the Rosaceae and Fagaceae botanical families by using the technique of comparative molecular modelling by homology. There are four main structural differences between all the PR5, corresponding to regions with replacements of amino acids. Folding and the secondary structures are very similar for all of them. However, the isoelectric point and charge distributions differ for each protein.

Amino Acid Sequence↗
PubMed2005

Root border-like cells of Arabidopsis. Microscopical characterization and role in the interaction with rhizobacteria.

Plant roots of many species produce thousands of cells that are released daily into the rhizosphere. These cells are commonly termed border cells because of their major role in constituting a biotic boundary layer between the root surface and the soil. In this study, we investigated the occurrence and ultrastructure of such cells in Arabidopsis (Arabidopsis thaliana) using light and electron microscopy coupled to high-pressure freezing. The secretion of cell wall molecules including pectic polysaccharides and arabinogalactan-proteins (AGPs) was examined also using immunofluorescence microscopy and a set of anticarbohydrate antibodies. We show that root tips of Arabidopsis seedlings released cell layers in an organized pattern that differs from the rather randomly dispersed release observed in other plant species studied to date. Therefore, we termed such cells border-like cells (BLC). Electron microscopical results revealed that BLC are rich in mitochondria, Golgi stacks, and Golgi-derived vesicles, suggesting that these cells are actively engaged in secretion of materials to their cell walls. Immunocytochemical data demonstrated that pectins as well as AGPs are among secreted material as revealed by the high level of expression of AGP-epitopes. In particular, the JIM13-AGP epitope was found exclusively associated with BLC and peripheral cells in the root cap region. In addition, we investigated the function of BLC and root cap cell AGPs in the interaction with rhizobacteria using AGP-disrupting agents and a strain of Rhizobium sp. expressing a green fluorescent protein. Our findings demonstrate that alteration of AGPs significantly inhibits the attachment of the bacteria to the surface of BLC and root tip.

Arabidopsis↗
PubMedDate not supplied

Density-dependent insect-mold interactions: effects on fungal growth and spore production.

Larvae of saprophagous insects often have been suspected of being competitors of filamentous fungi on decaying organic matter, which negatively influence mold development. Of interest, the role of insects in determining fungal growth and the onset of sporulation largely has been ignored. I used Aspergillus niger and the vinegar fly Drosophila melanogaster as an ecological model system to analyze the influence of insect larvae on daily fungal growth and the start of conidiospore production. I used an artificial substrate to test whether the effect of larval density (one, five and 10 larvae) and inoculation date of the mold (2 and 3 d ahead of the addition of larvae) significantly altered fungal growth. Fungal growth (area covered by hyphal tissue of the artificial patch) was affected negatively by the number of larvae and by the time that elapsed between inoculation with fungal spores and transfer of larvae to the patches. Whereas one larva had only a minor effect on fungal growth, five or 10 larvae strongly hampered mold development. As time between inoculation with spores and introduction of fly larvae increased, mold increased, indicating a priority effect for the fungus. When 10 larvae were transferred at the same time as the patches were inoculated with spores, almost no mold was visible within the period of observation (after 12 d). In comparison with control treatment (no insect larvae), an increase in larval density caused an increasing delay of several days in the start of spore production. Thus only minor changes in the density of insect larvae and the time that larvae entered the patches after inoculation with spores had an enormous effect on fungal growth and spore production. Therefore insects co-occurring with mold on ephemeral resources might constitute an important biotic factor driving local fungal population dynamics. The mechanisms leading to the suppression of fungal growth and the evolutionary implications of insect-mold interactions are discussed.

Animals↗
PubMed2006

Ubiquitination-mediated protein degradation and modification: an emerging theme in plant-microbe interactions.

Post-translational modification is central to protein stability and to the modulation of protein activity. Various types of protein modification, such as phosphorylation, methylation, acetylation, myristoylation, glycosylation, and ubiquitination, have been reported. Among them, ubiquitination distinguishes itself from others in that most of the ubiquitinated proteins are targeted to the 26S proteasome for degradation. The ubiquitin/26S proteasome system constitutes the major protein degradation pathway in the cell. In recent years, the importance of the ubiquitination machinery in the control of numerous eukaryotic cellular functions has been increasingly appreciated. Increasing number of E3 ubiquitin ligases and their substrates, including a variety of essential cellular regulators have been identified. Studies in the past several years have revealed that the ubiquitination system is important for a broad range of plant developmental processes and responses to abiotic and biotic stresses. This review discusses recent advances in the functional analysis of ubiquitination-associated proteins from plants and pathogens that play important roles in plant-microbe interactions.

Models, Biological↗
PubMed2004

Antagonistic interaction between abscisic acid and jasmonate-ethylene signaling pathways modulates defense gene expression and disease resistance in Arabidopsis.

The plant hormones abscisic acid (ABA), jasmonic acid (JA), and ethylene are involved in diverse plant processes, including the regulation of gene expression during adaptive responses to abiotic and biotic stresses. Previously, ABA has been implicated in enhancing disease susceptibility in various plant species, but currently very little is known about the molecular mechanisms underlying this phenomenon. In this study, we obtained evidence that a complex interplay between ABA and JA-ethylene signaling pathways regulate plant defense gene expression and disease resistance. First, we showed that exogenous ABA suppressed both basal and JA-ethylene-activated transcription from defense genes. By contrast, ABA deficiency as conditioned by the mutations in the ABA1 and ABA2 genes, which encode enzymes involved in ABA biosynthesis, resulted in upregulation of basal and induced transcription from JA-ethylene responsive defense genes. Second, we found that disruption of AtMYC2 (allelic to JASMONATE INSENSITIVE1 [JIN1]), encoding a basic helix-loop-helix Leu zipper transcription factor, which is a positive regulator of ABA signaling, results in elevated levels of basal and activated transcription from JA-ethylene responsive defense genes. Furthermore, the jin1/myc2 and aba2-1 mutants showed increased resistance to the necrotrophic fungal pathogen Fusarium oxysporum. Finally, using ethylene and ABA signaling mutants, we showed that interaction between ABA and ethylene signaling is mutually antagonistic in vegetative tissues. Collectively, our results indicate that the antagonistic interactions between multiple components of ABA and the JA-ethylene signaling pathways modulate defense and stress responsive gene expression in response to biotic and abiotic stresses.

Abscisic Acid↗
PubMed2002

The tundra-taiga interface and its dynamics: concepts and applications.

The tundra-taiga interface is a dominant vegetation boundary that is related to climate and has an importance at a global level for its contribution to land atmosphere interactions, biodiversity and land use. However, our understanding of the precise location, dynamics and characteristics of the boundary, and its environmental and biotic drivers at a circumpolar level is poor. Our understanding has been constrained for various reasons, perhaps including a quest by researchers to denote 2- or even 3-dimensional tree distribution limits to a single line on a map. Current rapid sociological and environmental changes in the north necessitate better definitions to be made of characteristics associated with the tundra-taiga interface so that changes can be monitored and identified, and implications of these changes can be assessed. This concept paper introduces some of the complexities of adequately defining the boundary and suggests characteristics and processes that could focus future research at a collaborative, circumpolar level to create baseline data and to monitor and predict changes in the boundary zone.

Animals↗
PubMedDate not supplied

Biological characteristics of the Calliphora vomitoria agglutinin.

The galactose specific agglutinin from Calliphora vomitoria was found to be expressed in the haemolymph of all the larval instars, but could not be detected at any other time during the life cycle. The haemagglutinating activity was insensitive to wounding of the tegument or injection of saline; however, a significant increase in haemagglutinating titre could be induced upon inoculation of the haemocoel with biotic or abiotic particulate material. The agglutinin also actively agglutinated several bacterial species and appeared capable of playing a role in particle--haemocyte interaction. The presence of the purified agglutinin significantly increased the attachment of fetuin-derivatized beads to haemocytes in vitro, and this activity could be specifically reduced by the addition of galactose, suggesting that the agglutinin may act as an opsonin.

Animals↗
PubMed2004

A unified statistical model for functional mapping of environment-dependent genetic expression and genotype x environment interactions for ontogenetic development.

The effects of quantitative trait loci (QTL) on phenotypic development may depend on the environment (QTL x environment interaction), other QTL (genetic epistasis), or both. In this article, we present a new statistical model for characterizing specific QTL that display environment-dependent genetic expressions and genotype x environment interactions for developmental trajectories. Our model was derived within the maximum-likelihood-based mixture model framework, incorporated by biologically meaningful growth equations and environment-dependent genetic effects of QTL, and implemented with the EM algorithm. With this model, we can characterize the dynamic patterns of genetic effects of QTL governing growth curves and estimate the global effect of the underlying QTL during the course of growth and development. In a real example with rice, our model has successfully detected several QTL that produce differences in their genetic expression between two contrasting environments. These detected QTL cause significant genotype x environment interactions for some fundamental aspects of growth trajectories. The model provides the basis for deciphering the genetic architecture of trait expression adjusted to different biotic and abiotic environments and genetic relationships for growth rates and the timing of life-history events for any organism.

Chromosome Mapping↗