583 research outputs found
Progress toward the production of transgenic grapevines by Agrobacterium-mediated transformation
Grape possesses the basic prerequisites for Agrobacterium-mediated transformation it is a host for Agrobacterium and plant regeneration can be induced from cultured grape explants. Leaf explants were cocultivated with disarmed Agrobacterium vectors carrying kanamycin resistance and GUS genes and cultured on shoot-inducing medium containing kanamycin. After 21 d, intense and sharply-defined blue regions were observed, including some blue organized meristematic structures, consistent with plant-driven GUS gene expression. No GUS activity was detected in control explants. Among single leaf tips excised from over 200 regenerated shoots, one was GUS positive. The recovery of transgenic shoots might be improved by increasing the frequency or modifying the site of transformation and/or regeneration
Identification and analysis of seven effector protein families with different adaptive and evolutionary histories in plant-associated members of the Xanthomonadaceae.
The Xanthomonadaceae family consists of species of non-pathogenic and pathogenic γ-proteobacteria that infect different hosts, including humans and plants. In this study, we performed a comparative analysis using 69 fully sequenced genomes belonging to this family, with a focus on identifying proteins enriched in phytopathogens that could explain the lifestyle and the ability to infect plants. Using a computational approach, we identified seven phytopathogen-enriched protein families putatively secreted by type II secretory system: PheA (CM-sec), LipA/LesA, VirK, and four families involved in N-glycan degradation, NixE, NixF, NixL, and FucA1. In silico and phylogenetic analyses of these protein families revealed they all have orthologs in other phytopathogenic or symbiotic bacteria, and are involved in the modulation and evasion of the immune system. As a proof of concept, we performed a biochemical characterization of LipA from Xac306 and verified that the mutant strain lost most of its lipase and esterase activities and displayed reduced virulence in citrus. Since this study includes closely related organisms with distinct lifestyles and highlights proteins directly related to adaptation inside plant tissues, novel approaches might use these proteins as biotechnological targets for disease control, and contribute to our understanding of the coevolution of plant-associated bacteria
Global organization of metabolic fluxes in the bacterium, Escherichia coli
Cellular metabolism, the integrated interconversion of thousands of metabolic
substrates through enzyme-catalyzed biochemical reactions, is the most
investigated complex intercellular web of molecular interactions. While the
topological organization of individual reactions into metabolic networks is
increasingly well understood, the principles governing their global functional
utilization under different growth conditions pose many open questions. We
implement a flux balance analysis of the E. coli MG1655 metabolism, finding
that the network utilization is highly uneven: while most metabolic reactions
have small fluxes, the metabolism's activity is dominated by several reactions
with very high fluxes. E. coli responds to changes in growth conditions by
reorganizing the rates of selected fluxes predominantly within this high flux
backbone. The identified behavior likely represents a universal feature of
metabolic activity in all cells, with potential implications to metabolic
engineering.Comment: 15 pages 4 figure
Functional characterization of a melon alcohol acyl-transferase gene family involved in the biosynthesis of ester volatiles. Identification of the crucial role of a threonine residue for enzyme activity
Volatile esters, a major class of compounds contributing to the aroma of many fruit, are synthesized by
alcohol acyl-transferases (AAT). We demonstrate here that, in Charentais melon (Cucumis melo var.
cantalupensis), AAT are encoded by a gene family of at least four members with amino acid identity ranging
from 84% (Cm-AAT1/Cm-AAT2) and 58% (Cm-AAT1/Cm-AAT3) to only 22% (Cm-AAT1/Cm-AAT4).
All encoded proteins, except Cm-AAT2, were enzymatically active upon expression in yeast and show
differential substrate preferences. Cm-AAT1 protein produces a wide range of short and long-chain acyl
esters but has strong preference for the formation of E-2-hexenyl acetate and hexyl hexanoate. Cm-AAT3
also accepts a wide range of substrates but with very strong preference for producing benzyl acetate.
Cm-AAT4 is almost exclusively devoted to the formation of acetates, with strong preference for cinnamoyl
acetate. Site directed mutagenesis demonstrated that the failure of Cm-AAT2 to produce volatile esters is
related to the presence of a 268-alanine residue instead of threonine as in all active AAT proteins. Mutating
268-A into 268-T of Cm-AAT2 restored enzyme activity, while mutating 268-T into 268-A abolished
activity of Cm-AAT1. Activities of all three proteins measured with the prefered substrates sharply increase
during fruit ripening. The expression of all Cm-AAT genes is up-regulated during ripening and inhibited in
antisense ACC oxidase melons and in fruit treated with the ethylene antagonist 1-methylcyclopropene
(1-MCP), indicating a positive regulation by ethylene. The data presented in this work suggest that the
multiplicity of AAT genes accounts for the great diversity of esters formed in melon
Opinion dynamics: models, extensions and external effects
Recently, social phenomena have received a lot of attention not only from
social scientists, but also from physicists, mathematicians and computer
scientists, in the emerging interdisciplinary field of complex system science.
Opinion dynamics is one of the processes studied, since opinions are the
drivers of human behaviour, and play a crucial role in many global challenges
that our complex world and societies are facing: global financial crises,
global pandemics, growth of cities, urbanisation and migration patterns, and
last but not least important, climate change and environmental sustainability
and protection. Opinion formation is a complex process affected by the
interplay of different elements, including the individual predisposition, the
influence of positive and negative peer interaction (social networks playing a
crucial role in this respect), the information each individual is exposed to,
and many others. Several models inspired from those in use in physics have been
developed to encompass many of these elements, and to allow for the
identification of the mechanisms involved in the opinion formation process and
the understanding of their role, with the practical aim of simulating opinion
formation and spreading under various conditions. These modelling schemes range
from binary simple models such as the voter model, to multi-dimensional
continuous approaches. Here, we provide a review of recent methods, focusing on
models employing both peer interaction and external information, and
emphasising the role that less studied mechanisms, such as disagreement, has in
driving the opinion dynamics. [...]Comment: 42 pages, 6 figure
Functional diversity of chemokines and chemokine receptors in response to viral infection of the central nervous system.
Encounters with neurotropic viruses result in varied outcomes ranging from encephalitis, paralytic poliomyelitis or other serious consequences to relatively benign infection. One of the principal factors that control the outcome of infection is the localized tissue response and subsequent immune response directed against the invading toxic agent. It is the role of the immune system to contain and control the spread of virus infection in the central nervous system (CNS), and paradoxically, this response may also be pathologic. Chemokines are potent proinflammatory molecules whose expression within virally infected tissues is often associated with protection and/or pathology which correlates with migration and accumulation of immune cells. Indeed, studies with a neurotropic murine coronavirus, mouse hepatitis virus (MHV), have provided important insight into the functional roles of chemokines and chemokine receptors in participating in various aspects of host defense as well as disease development within the CNS. This chapter will highlight recent discoveries that have provided insight into the diverse biologic roles of chemokines and their receptors in coordinating immune responses following viral infection of the CNS
A Bayesian Approach to the Evolution of Metabolic Networks on a Phylogeny
The availability of genomes of many closely related bacteria with diverse metabolic capabilities offers the possibility of tracing metabolic evolution on a phylogeny relating the genomes to understand the evolutionary processes and constraints that affect the evolution of metabolic networks. Using simple (independent loss/gain of reactions) or complex (incorporating dependencies among reactions) stochastic models of metabolic evolution, it is possible to study how metabolic networks evolve over time. Here, we describe a model that takes the reaction neighborhood into account when modeling metabolic evolution. The model also allows estimation of the strength of the neighborhood effect during the course of evolution. We present Gibbs samplers for sampling networks at the internal node of a phylogeny and for estimating the parameters of evolution over a phylogeny without exploring the whole search space by iteratively sampling from the conditional distributions of the internal networks and parameters. The samplers are used to estimate the parameters of evolution of metabolic networks of bacteria in the genus Pseudomonas and to infer the metabolic networks of the ancestral pseudomonads. The results suggest that pathway maps that are conserved across the Pseudomonas phylogeny have a stronger neighborhood structure than those which have a variable distribution of reactions across the phylogeny, and that some Pseudomonas lineages are going through genome reduction resulting in the loss of a number of reactions from their metabolic networks
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