Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “biotic interactions”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 199 records · Page 11Linked to original sources
PubMed2001

Does nonneutral evolution shape observed patterns of DNA variation in animal mitochondrial genomes?

Early studies of animal mitochondrial DNA (mtDNA) assumed that nucleotide sequence variation was neutral. Recent analyses of sequences from a variety of taxa have brought the validity of this assumption into question. Here we review analytical methods used to test for neutrality and evidence for nonneutral evolution of animal mtDNA. Evaluations of mitochondrial haplotypes in different nuclear backgrounds identified differences in performance, typically favoring coevolved mitochondrial and nuclear genomes. Experimental manipulations also indicated that certain haplotypes have an advantage over others; however, biotic and historical effects and cyto-nuclear interactions make it difficult to assess the relative importance of nonneutral factors. Statistical analyses of sequences have been used to argue for nonneutrality of mtDNA; however, rejection of neutral patterns in the published literature is common but not predominant. Patterns of replacement and synonymous substitutions within and between species identified a trend toward an excess of replacement mutations within species. This pattern has been viewed as support for the existence of mildly deleterious mutations within species; however, other alternative explanations that can produce similar patterns cannot be eliminated.

Animals↗
PubMed1989

Malaria as anthropo-ecosystem. Part III: Diversity of MAES.

Diversity being one of the main characteristics of Malaria Anthropo-Ecosystem (MAES) is reflected in time and space. Temporal diversity of MAES generally may be divided into two types--long time periods usually on a global scale, and various local fluctuations expressed as malaria periodicity. Geographical confinement of MAES is determined by interactions of various elements of the latter with biotic and abiotic components of the environment. The diversity of the MAES within climatic zones of South and South-East Asia is shown to be of many types of sub-systems depending, apart from climatic conditions, on types of human activity in those ecosystems.

Animals↗
PubMed2006

Asymmetric coexistence: bidirectional abiotic and biotic effects between goose barnacles and mussels.

1. Species coexistence depends on the net effect of interacting species, representing the sum of multiple interaction components that may act simultaneously and vary independently depending on ambient environmental conditions. Consequently, for a comprehensive understanding of the compound nature of species interactions and coexistence, a mechanistic approach that allows a separate evaluation of each interaction component is required. 2. Two sessile filter-feeders, the goose barnacle Capitulum mitella and the mussel Septifer virgatus, coexist on moderately wave-exposed rocky shores in south-western Japan. In the upper intertidal, Capitulum positively influenced Septifer survivorship and growth through amelioration of thermal stress and of physical disturbance. On the other hand, these species are potential competitors as they have similar body sizes and modes of resource utilization. These opposite processes, facilitation and competition, are based on abiotic characteristics and biotic functions of the two species, respectively. 3. In order to quantify the bidirectional abiotic, biotic and net effects, a series of experimental manipulations was conducted involving the use of living neighbours with both abiotic and biotic effects, and artificial mimics to simulate abiotic effects without biotic effects. 4. Capitulum had strong positive abiotic effects on the mussel survivorship in most experimental periods, while the biotic effect was negligible or weakly negative, suggesting that the net effect of Capitulum on mussel survival was largely attributable to the abiotic effect. In contrast, a significantly negative biotic effect on the mussel growth rate was always present, though this was cancelled out by the larger, positive abiotic effect. In the case of Septifer, its abiotic and biotic effects on the survivorship of goose barnacles were negligible, while those on the growth rate showed temporal variation. 5. With respect to the relationship between species interaction and environmental conditions, the strength of abiotic facilitative effect of Capitulum on mussel survival increased with increasing abiotic stress, while the strength of biotic effect was negligible or weakly negative. As regards the effects of mussels on goose barnacles, our study indicated no obvious relationship. These results point to the importance of decomposing interaction for an accurate, mechanistic understanding of species relations and coexistence.

Animals↗
PubMed2006

Plasma membrane surface potential (psiPM) as a determinant of ion bioavailability: A critical analysis of new and published toxicological studies and a simplified method for the computation of plant psiPM.

Plasma membranes (PMs) are negatively charged, and this creates a negative PM surface electrical potential (psiPM) that is also controlled by the ionic composition of the bathing medium. The psiPM controls the distribution of ions between the PM surface and the medium so that negative potentials increase the surface activity of cations and decrease the surface activity of anions. All cations reduce the negativity of psiPM, and these common ions are effective in the following order: Al3+ > H+ > Cu2+ > Ca2+ = Mg2+ > Na+ = K+. These ions, especially H+, Ca2+, and Mg2+, are known to reduce the uptake and biotic effectiveness of cations and to have the opposite effects on anions. Toxicologists commonly interpret the interactions between toxic cations (commonly metals) and ameliorative cations (commonly H+, Ca2+, and Mg2+) as competitions for binding sites at a PM surface ligand. The psiPM is rarely considered in this biotic ligand model, which incorporates the free ion activity model. The thesis of this article is that psiPM effects are likely to be more important to bioavailability than site-specific competition. Furthermore, psiPM effects could give the false appearance of competition even when it does not occur. The electrostatic approach can account for the bioavailability of anions, whereas the biotic ligand model cannot, and it can account for interactions among cations when competition does not occur. Finally, a simplified procedure is presented for the computation of psiPM for plants, and the possible use of psiPM in a general assessment of the bioavailability of ions is considered.

Acids↗
PubMed2005

Nitric oxide signaling in plants.

Plants have four nitric oxide synthase (NOS) enzymes. NOS1 appears mitochondrial, and inducible nitric oxide synthase (iNOS) chloroplastic. Distinct peroxisomal and apoplastic NOS enzymes are predicted. Nitrite-dependent NO synthesis is catalyzed by cytoplasmic nitrate reductase or a root plasma membrane enzyme, or occurs nonenzymatically. Nitric oxide undergoes both catalyzed and uncatalyzed oxidation. However, there is no evidence of reaction with superoxide, and S-nitrosylation reactions are unlikely except during hypoxia. The only proven direct targets of NO in plants are metalloenzymes and one metal complex. Nitric oxide inhibits apoplastic catalases/ascorbate peroxidases in some species but may stimulate these enzymes in others. Plants also have the NO response pathway involving cGMP, cADPR, and release of calcium from internal stores. Other known targets include chloroplast and mitochondrial electron transport. Nitric oxide suppresses Fenton chemistry by interacting with ferryl ion, preventing generation of hydroxyl radicals. Functions of NO in plant development, response to biotic and abiotic stressors, iron homeostasis, and regulation of respiration and photosynthesis may all be ascribed to interaction with one of these targets. Nitric oxide function in drought/abscisic acid (ABA)-induction of stomatal closure requires nitrate reductase and NOS1. Nitric oxide synthasel likely functions to produce sufficient NO to inhibit photosynthetic electron transport, allowing nitrite accumulation. Nitric oxide is produced during the hypersensitive response outside cells undergoing programmed cell death immediately prior to loss of plasma membrane integrity. A plasma membrane lipid-derived signal likely activates apoplastic NOS. Nitric oxide diffuses within the apoplast and signals neighboring cells via hydrogen peroxide (H2O2)-dependent induction of salicylic acid biosynthesis. Response to wounding appears to involve the same NOS and direct targets.

Nitric Oxide↗
PubMed2006

Evolutionary responses of natives to introduced species: what do introductions tell us about natural communities?

Biological invasions dramatically affect the distribution, abundance and reproduction of many native species. Because of these ecological effects, exotic species can also influence the evolution of natives exposed to novel interactions with invaders. Evolutionary changes in natives in response to selection from exotics are usually overlooked, yet common responses include altered anti-predator defenses, changes in the spectrum of resources and habitats used, and other adaptations that allow native populations to persist in invaded areas. Whether a native population is capable of responding evolutionarily to selection from invaders will depend on the demographic impact of the invader, the genetic architecture and genetic variability of the native population and potentially the history of previous invasions. In some cases, natives will fail to evolve or otherwise adapt, and local or global extinction will result. In other cases, adaptive change in natives may diminish impacts of invaders and potentially promote coexistence between invaders and natives. Here, we review the evidence for evolutionary responses of native species to novel community members. We also discuss how the effects of introduced species may differ from those caused by natural range expansions of native species. Notably, introduced species may come from remote biotas with no previous evolutionary history with the native community. In addition, the rate of addition of introduced species into communities is much greater than all but the most extreme cases of historical biotic exchange. Understanding the evolutionary component of exotic/native species interactions is critical to recognizing the long-term impacts of biological invasions, and to understanding the role of evolutionary processes in the assembly and dynamics of natural communities.

Animals↗
PubMed1999

Photochemical oxidants: state of the science.

Atmospheric photochemical processes resulting in the production of tropospheric ozone (O(3)) and other oxidants are described. The spatial and temporal variabilities in the occurrence of surface level oxidants and their relationships to air pollution meteorology are discussed. Models of photooxidant formation are reviewed in the context of control strategies and comparisons are provided of the air concentrations of O(3) at select geographic locations around the world. This overall oxidant (O(3)) climatology is coupled to human health and ecological effects. The discussion of the effects includes both acute and chronic responses, mechanisms of action, human epidemiological and plant population studies and briefly, efforts to establish cause-effect relationships through numerical modeling. A short synopsis is provided of the interactive effects of O(3) with other abiotic and biotic factors. The overall emphasis of the paper is on identifying the current uncertainties and gaps in our understanding of the state of the science and some suggestions as to how they may be addressed.

Journal Article↗
PubMed1999

Source-sink regulation by sugar and stress.

The regulation of carbon partitioning between source and sink tissues in higher plants is not only important for plant growth and development, but insight into the underlying regulatory mechanism is also a prerequisite to modulating assimilate partitioning in transgenic plants. Hexoses, as well as sucrose, have been recognised as important signal molecules in source-sink regulation. Components of the underlying signal transduction pathways have been identified and parallels, as well as distinct differences, to known pathways in yeast and animals have become apparent. There is accumulating evidence for crosstalk, modulation and integration between signalling pathways responding to phytohormones, phosphate, light, sugars, and biotic and abiotic stress-related stimuli. These complex interactions at the signal transduction levels and co-ordinated regulation of gene expression seem to play a central role in source-sink regulation.

Carbohydrate Metabolism↗
PubMed2001

Adaptations to biotic and abiotic stress: Macaranga-ant plants optimize investment in biotic defence.

Obligate ant plants (myrmecophytes) in the genus Macaranga produce energy- and nutrient-rich food bodies (FBs) to nourish mutualistic ants which live inside the plants. These defend their host against biotic stress caused by herbivores and pathogens. Facultative, 'myrmecophilic' interactions are based on the provision of FBs and/or extrafloral nectar (EFN) to defending insects that are attracted from the vicinity. FB production by the myrmecophyte, M. triloba, was limited by soil nutrient content under field conditions and was regulated according to the presence or absence of an ant colony. However, increased FB production promoted growth of the ant colonies living in the plants. Ant colony size is an important defensive trait and is negatively correlated to a plant's leaf damage. Similar regulatory patterns occurred in the EFN production of the myrmecophilic M. tanarius. Nectar accumulation resulting from the absence of consumers strongly decreased nectar flow, which increased again when consumers had access to the plant. EFN flow could be induced via the octadecanoid pathway. Leaf damage increased levels of endogenous jasmonic acid (JA), and both leaf damage and exogenous JA application increased EFN flow. Higher numbers of nectary visiting insects and lower numbers of herbivores were present on JA-treated plants. In the long run, this decreased leaf damage significantly. Ant food production is controlled by different regulatory mechanisms which ensure that costs are only incurred when counterbalanced by defensive effects of mutualistic insects.

Adaptation, Physiological↗
PubMed1988

In vitro interactions between Blastomyces dermatitidis and other zoopathogenic fungi.

The results of in vitro interactions between colonies of Blastomyces dermatitidis and six other zoopathogenic fungi are reported. The interactions were found to range from neutral with Histoplasma capsulatum and Candida albicans to strongly antagonistic with Microsporum gypseum, Pseudallescheria boydii, and Sporothrix schenckii, and including lysis by Cryptococcus neoformans. These observations suggest that interactions between zoopathogenic fungi may be one of the biotic factors likely to influence the occurrence of B. dermatitidis in natural systems.

Blastomyces↗
PubMed2004

Biochemical indicators of stress and metabolism: applications for marine ecological studies.

Studies investigating the effects of temperature, food availability, or other physical factors on the physiology of marine animals have led to the development of biochemical indicators of growth rate, metabolic condition, and physiological stress. Measurements of metabolic enzyme activity and RNA/DNA have been especially valuable as indicators of condition in studies of marine invertebrates and fishes, groups for which accurate determination of field metabolic rates is difficult. Properly calibrated and applied, biochemical indicators have been successfully used in studies of rocky intertidal ecology, where two decades of experimentation have generated rigorous, testable models for determining the relative influences of biotic and abiotic factors on species distribution, abundance, and interaction. Biochemical indicators of condition and metabolic activity (metabolic enzymes, RNA/DNA) have been used to test nutrient-productivity models by demonstrating tight linkages between nearshore oceanographic processes (such as upwelling) and benthic rocky intertidal ecosystems. Indices of condition and heat stress (heat shock proteins, or Hsps) have begun to be used to test environmental stress models by comparing condition, activity, and Hsp expression of key rocky intertidal predator and prey species. Using biochemical indicators of condition and stress in natural systems holds great promise for understanding mechanisms by which organisms respond to rapid environmental change.

Animals↗
PubMed2006

Plant-mediated interactions between pathogenic microorganisms and herbivorous arthropods.

Plant-mediated interactions between pathogenic microorganisms and arthropod herbivores occur when arthropod infestation or pathogen infection changes the shared host plant in ways that affect a subsequent attacker of the opposite type. Interest in such "tripartite" interactions has increased as the ecological and plant physiological framework for understanding and contextualizing them has developed. The outcomes of plant-mediated interactions are variable, and only a few provisional patterns can be identified at present. However, these interactions can have important consequences not only for individual pathogens and herbivores, but also for the population dynamics of both types of organisms in managed and natural ecosystems. Research has focused on the role of two plant response pathways in mediating tripartite interactions, one involving jasmonic acid and the other salicylic acid. Further studies of plant-mediated interactions will facilitate an understanding of how plants coordinate and integrate their defenses against multiple biotic threats.

Animals↗
PubMed1993

Multiple coding and the evolutionary properties of RNA secondary structure.

This article evaluates evolutionary properties of the transition from RNA primary sequence to RNA secondary structure. It focuses on the restrictions that the conservation of a protein code in an RNA sequence puts on its potential to evolve towards a specific secondary structure. Restricting the mutations to those that do not affect the coding for a protein restricts both the accessibility and the connectivity of the sequence space. The accessibility is restricted because only certain point mutations are allowed. The connectivity is restricted because no insertions and deletions are allowed. Simulating an evolutionary search process for a specific secondary structure shows that (i) the reduction of allowable point mutations allows for adaptation to some large-scale topology, but strongly reduces the possibility of small-scale adaptations, (ii) the abolition of insertions and deletions has very little effect on the results of the search process. During the evolutionary search process for a secondary structure with a specific topology and a high frequency of base-pairing the quasispecies moves into a subspace in which the similarity between secondary structures of neighboring sequences is relatively high. Increased similarity between second structures of neighboring sequences is also found in the Rev responsive element (RRE) in the lentiviruses Caprine arthritis-encephalitis virus and Visna virus. In these viruses a biased nucleotide frequency in the RRE region suggests that selection for the RRE RNA secondary structure affects the amino acid sequence of the env gene. Our results show a variation in the ruggedness of fitness landscapes which are based on a high degree of epistatic interactions. Fitness landscapes play an essential role, not only in biotic evolution, but also in all kinds of optimization processes (Hill Climbing, Simulated Annealing, Genetic Algorithms, etc). Variation in their ruggedness should therefore be taken into account in the analysis of these processes.

Amino Acid Sequence↗
PubMed2005

System, trends and perspectives of proteomics in dicot plants. Part III: Unraveling the proteomes influenced by the environment, and at the levels of function and genetic relationships.

This review is devoted to the proteomics studies in dicotyledoneous (dicot) plants, such as Arabidopsis, Medicago, potato, soybean, and tomato, under the influence of the environment and at the functional and genetic relationship levels, where the two core technologies, two-dimensional gel electrophoresis (2-DGE) and mass spectrometry (MS) have been instrumental in unraveling the proteomes affected therein. Abiotic and biotic stress responses, including the affect of allergens, the symbiotic interaction between the members of the Leguminoseae family and genera of nitrogen fixing bacteria, phosphoproteomics, and proteomics in revealing the genetic relationships between species and genera have been the subject of many proteomics studies, and these are discussed in this review. In all, these studies have complemented and extended the studies of developmental proteomics [G.K. Agrawal, M. Yonekura, Y. Iwahashi, H. Iwahashi, R. Rakwal, J. Chromatogr. B (2004)].

Cold Temperature↗
PubMed2001

Activation of tomato PR and wound-related genes by a mutagenized tomato MAP kinase kinase through divergent pathways.

A mitogen-activated protein kinase kinase (MAPKK) gene, tMEK2, was isolated from tomato cv. Bonny Best. By mutagenesis, a permanently active variant, tMEK2MUT, was created. Both wild-type tMEK2 and mutant tMEK2MUT were driven by a newly described strong plant constitutive promoter, tCUP, in a tomato protoplast transient gene expression system. Pathogenesis-related genes, PRlb1, PR3 and Twi1, and a wound-inducible gene, ER5, were activated by tMEK2MUT. Specific inhibitors of p38 class MAPK inhibited tMEK2MUT-induced activation of PR3 and ER5 genes but not that of the PRlb1 or Twi1 gene. Arabidopsis dual-specificity protein tyrosine phosphatase 1 (DsPTP1) and maize protein phosphatase 1 (PP1) inhibited tMEK2MUT-induced activation of the ER5 gene and the Twi1 gene, respectively, whereas PRlb1 and PR3 were not affected by either AtDsPTP1, or maize PP1, or Arabidopsis protein phosphatase 2A (PP2A). We have demonstrated for the first time that a single MAPKK activates an array of PR and wound-related genes. Our observation indicates that the activation of the genes downstream of tMEK2 occurs through divergent pathways and that tMEK2 may play an important role in the interaction of signal transduction pathways that mediate responses to both biotic (e.g. disease) and abiotic stresses (e.g. wound responsiveness).

Amino Acid Sequence↗
PubMed2000

[Factors affecting colonization of introduced microorganisms on plant roots].

Microorganisms such as biological control agents (BCA), plant growth-promoting rhizobacteria (PGPR) and yield increasing bacteria (YIB) were introduced along growing roots. The colonization process of introduced bacteria was proved that they attached root tipfirst, then distributed along roots, multiplicated there, and survived as certain population size. The colonization location was closely related with root exudates, which was usually at the junction between cortex cells or at the base of lateral roots or root hairs. The variation of colonization by introduced microorganisms in the rhizosphere was caused by biotic and abiotic factors. Biotic factors included the physiological characters of introduced microorganisms and interactions between introduced microorganisms and native microbes. The more important factors were plant genotypes which associated with introduced beneficial microbes and regulated the population and community of those microbes affecting the colonization of introduced microorganisms. Abiotic factors here referred to soil environmental conditions, e.g., soil texture, water content, soil temperature and pH value.

Ecosystem↗
PubMed2005

The origins of life -- the 'protein interaction world' hypothesis: protein interactions were the first form of self-reproducing life and nucleic acids evolved later as memory molecules.

The 'protein interaction world' (PIW) hypothesis of the origins of life assumes that life emerged as a self-reproducing and expanding system of protein interactions. In mainstream molecular biology, 'replication' refers to the material copying of molecules such as nucleic acids. However, PIW is conceptualized as an abstract communication system constituted by the interactions between proteins, in which 'replication' happens at the level of self-reproduction of these interactions between proteins. Densely concentrated peptide interaction systems may have reproduced and expanded as 'protocell' vesicles surrounded by lipid bi-layer membranes. Protocells led to the emergence of proto-RNA molecules of greater chemical stability which served as chemically differentiated 'memories' of peptide interaction states, thereby facilitating the reproduction and expansion of protocells. Simplification-driven expansion led to the selection of biotic amino acids and the reduction of the typical RNA alphabet to the four usual bases (A, C, G and U). Dense interactions between RNA molecules led to the emergence of the RNA interaction subsystem of the cell, and to the emergence of 'memories' of RNA interactions in the form of DNA molecules with greater chemical stability. The expansion of DNA molecule interactions led to the dense clustering and encapsulation of DNA molecules within the cell nucleus. RNA molecules therefore serve as memories of protein interactions and DNA molecules are memories of RNA interactions. We believe that the PIW hypothesis is more evolutionarily plausible than the mainstream RNA world hypothesis, and has greater explanatory power.

Evolution, Molecular↗
PubMed2005

Connecting plant-microbial interactions above and belowground: a fungal endophyte affects decomposition.

Mutualisms can strongly affect the structure of communities, but their influence on ecosystem processes is not well resolved. Here we show that a plant-microbial mutualism affects the rate of leaf litter decomposition using the widespread interaction between tall fescue grass (Lolium arundinaceum) and the fungal endophyte Neotyphodium coenophialum. In grasses, fungal endophytes live symbiotically in the aboveground tissues, where the fungi gain protection and nutrients from their host and often protect host plants from biotic and abiotic stress. In a field experiment, decomposition rate depended on a complex interaction between the litter source (collected from endophyte-infected or endophyte-free plots), the decomposition microenvironment (endophyte-infected or endophyte-free plots), and the presence of mesoinvertebrates (manipulated by the mesh size of litter bags). Over all treatments, decomposition was slower for endophyte-infected fescue litter than for endophyte-free litter. When mesoinvertebrates were excluded using fine mesh and litter was placed in a microenvironment with the endophyte, the difference between endophyte-infected and endophyte-free litter was strongest. In the presence of mesoinvertebrates, endophyte-infected litter decomposed faster in microenvironments with the endophyte than in microenvironments lacking the endophyte, suggesting that plots differ in the detritivore assemblage. Indeed, the presence of the endophyte in plots shifted the composition of Collembola, with more Hypogastruridae in the presence of the endophyte and more Isotomidae in endophyte-free plots. In a separate outdoor pot experiment, we did not find strong effects of the litter source or the soil microbial/microinvertebrate community on decomposition, which may reflect differences between pot and field conditions or other differences in methodology. Our work is among the first to demonstrate an effect of plant-endophyte mutualisms on ecosystem processes under field conditions.

Animals↗