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Search Results: 1 - 10 of 299086 matches for " J. Allan Downie "
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Identification of protein secretion systems and novel secreted proteins in Rhizobium leguminosarum bv. viciae
Martin Krehenbrink, J Allan Downie
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-55
Abstract: Similarity searches using defined protein secretion systems from other Gram-negative bacteria as query sequences revealed that R. l. bv. viciae 3841 has ten putative protein secretion systems. These are the general export pathway (GEP), a twin-arginine translocase (TAT) secretion system, four separate Type I systems, one putative Type IV system and three Type V autotransporters. Mutations in genes encoding each of these (except the GEP) were generated, but only mutations affecting the PrsDE (Type I) and TAT systems were observed to affect the growth phenotype and the profile of proteins in the culture supernatant. Bioinformatic analysis and mass fingerprinting of tryptic fragments of culture supernatant proteins identified 14 putative Type I substrates, 12 of which are secreted via the PrsDE, secretion system. The TAT mutant was defective for the symbiosis, forming nodules incapable of nitrogen fixation.None of the R. l. bv. viciae 3841 protein secretion systems putatively involved in the secretion of proteins to the extracellular space (Type I, Type IV, Type V) is required for establishing the symbiosis with legumes. The PrsDE (Type I) system was shown to be the major route of protein secretion in non-symbiotic cells and to secrete proteins of widely varied size and predicted function. This is in contrast to many Type I systems from other bacteria, which typically secrete specific substrates encoded by genes often localised in close proximity to the genes encoding the secretion system itself.Rhizobium leguminosarum bv. viciae is a Gram-negative soil bacterium which forms a mutualistic symbiosis with legumes, resulting in nitrogen-fixing root nodules. This symbiotic relationship is initiated by an exchange of signals between the two partners. While the general features of this signal exchange are common to all rhizobia-plant symbioses, differences in the signalling molecules allow only certain bacterium-plant combinations to lead to a successful symbiosis. Plant-mad
Protein domains and architectural innovation in plant-associated Proteobacteria
David J Studholme, J Allan Downie, Gail M Preston
BMC Genomics , 2005, DOI: 10.1186/1471-2164-6-17
Abstract: We took a census of all protein domains and domain combinations (architectures) encoded in the completely-sequenced proteobacterial genomes. Nine protein domain families were identified that are found in phylogenetically disparate plant-associated bacteria but are absent from non-plant-associated bacteria. Most of these are known to play a role in the plant-associated lifestyle, but they also included domain of unknown function DUF1427, which is found in plant symbionts and pathogens of the alpha-, beta- and gamma-Proteobacteria, but not known in any other organism. Further, several domains were identified as being restricted to phytobacteria and Eukaryotes. One example is the RolB/RolC glucosidase family, which is found only in Agrobacterium species and in plants. We identified the 0.5% of Pfam protein domain families that were most significantly over-represented in the plant-associated Proteobacteria with respect to the background frequencies in the whole set of available proteobacterial proteomes. These included guanylate cyclase, domains implicated in aromatic catabolism, cellulase and several domains of unknown function.We identified 459 unique domain architectures found in phylogenetically diverse plant pathogens and symbionts that were absent from non-pathogenic and non-symbiotic relatives. The vast majority of these were restricted to a single species or several closely related species and so their distributions could be better explained by phylogeny than by lifestyle. However, several architectures were found in two or more very distantly related phytobacteria but absent from non-plant-associated bacteria. Many of the proteins with these unique architectures are predicted to be secreted.In Pseudomonas syringae pathovar tomato, those genes encoding genes with novel domain architectures tended to have atypical GC contents and were adjacent to insertion sequence elements and phage-like sequences, suggesting acquisition by horizontal transfer.By identifying dom
Nonlinear Time Series Analysis of Nodulation Factor Induced Calcium Oscillations: Evidence for Deterministic Chaos?
Saul Hazledine, Jongho Sun, Derin Wysham, J. Allan Downie, Giles E. D. Oldroyd, Richard J. Morris
PLOS ONE , 2009, DOI: 10.1371/journal.pone.0006637
Abstract: Legume plants form beneficial symbiotic interactions with nitrogen fixing bacteria (called rhizobia), with the rhizobia being accommodated in unique structures on the roots of the host plant. The legume/rhizobial symbiosis is responsible for a significant proportion of the global biologically available nitrogen. The initiation of this symbiosis is governed by a characteristic calcium oscillation within the plant root hair cells and this signal is activated by the rhizobia. Recent analyses on calcium time series data have suggested that stochastic effects have a large role to play in defining the nature of the oscillations. The use of multiple nonlinear time series techniques, however, suggests an alternative interpretation, namely deterministic chaos. We provide an extensive, nonlinear time series analysis on the nature of this calcium oscillation response. We build up evidence through a series of techniques that test for determinism, quantify linear and nonlinear components, and measure the local divergence of the system. Chaos is common in nature and it seems plausible that properties of chaotic dynamics might be exploited by biological systems to control processes within the cell. Systems possessing chaotic control mechanisms are more robust in the sense that the enhanced flexibility allows more rapid response to environmental changes with less energetic costs. The desired behaviour could be most efficiently targeted in this manner, supporting some intriguing speculations about nonlinear mechanisms in biological signaling.
Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics
Vinoy K Ramachandran, Alison K East, Ramakrishnan Karunakaran, J Allan Downie, Philip S Poole
Genome Biology , 2011, DOI: 10.1186/gb-2011-12-10-r106
Abstract: Carbon metabolism was dominated by organic acids, with a strong bias towards aromatic amino acids, C1 and C2 compounds. This was confirmed by induction of the glyoxylate cycle required for C2 metabolism and gluconeogenesis in all rhizospheres. Gluconeogenesis is repressed in R. leguminosarum by sugars, suggesting that although numerous sugar and putative complex carbohydrate transport systems are induced in the rhizosphere, they are less important carbon sources than organic acids. A common core of rhizosphere-induced genes was identified, of which 66% are of unknown function. Many genes were induced in the rhizosphere of the legumes, but not sugar beet, and several were plant specific. The plasmid pRL8 can be considered pea rhizosphere specific, enabling adaptation of R. leguminosarum to its host. Mutation of many of the up-regulated genes reduced competitiveness for pea rhizosphere colonization, while two genes specifically up-regulated in the pea rhizosphere reduced colonization of the pea but not alfalfa rhizosphere.Comparative transcriptome analysis has enabled differentiation between factors conserved across plants for rhizosphere colonization as well as identification of exquisite specific adaptation to host plants.Interactions between micro-organisms and plant roots in the rhizosphere are a key determinant of plant productivity. There is a two-way dialogue in which plants manipulate the rhizosphere's microbial community, which, in turn, profoundly alters plant growth [1]. Plants exude up to 11% of fixed carbon via their roots, including both small organic compounds and those that act as signaling molecules [2]. Carbon export on this scale must have a significant impact on rhizosphere micro-organisms, leading to alterations in community structure and function. The rhizosphere is an environment in which there are co-evolved mutualistic relationships between plants and microbes [1]. The best characterized beneficial associations are mutualisms with Rhizobium an
Real and Virtual Compton Scattering: the nucleon polarisabilities
E. J. Downie,H. Fonvieille
Physics , 2011, DOI: 10.1140/epjst/e2011-01495-x
Abstract: We give an overview of low-energy Compton scattering (gamma^(*) p --> gamma p) with a real or virtual incoming photon. These processes allow the investigation of one of the fundamental properties of the nucleon, i.e. how its internal structure deforms under an applied static electromagnetic field. Our knowledge of nucleon polarisabilities and their generalization to non-zero four-momentum transfer will be reviewed, including the presently ongoing experiments and future perspectives.
A Common Genomic Framework for a Diverse Assembly of Plasmids in the Symbiotic Nitrogen Fixing Bacteria
Lisa C. Crossman, Santiago Castillo-Ramírez, Craig McAnnula, Luis Lozano, Georgios S. Vernikos, José L. Acosta, Zara F. Ghazoui, Ismael Hernández-González, Georgina Meakin, Alan W. Walker, Michael F. Hynes, J. Peter W. Young, J. Allan Downie, David Romero, Andrew W. B. Johnston, Guillermo Dávila, Julian Parkhill, Víctor González
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0002567
Abstract: This work centres on the genomic comparisons of two closely-related nitrogen-fixing symbiotic bacteria, Rhizobium leguminosarum biovar viciae 3841 and Rhizobium etli CFN42. These strains maintain a stable genomic core that is also common to other rhizobia species plus a very variable and significant accessory component. The chromosomes are highly syntenic, whereas plasmids are related by fewer syntenic blocks and have mosaic structures. The pairs of plasmids p42f-pRL12, p42e-pRL11 and p42b-pRL9 as well large parts of p42c with pRL10 are shown to be similar, whereas the symbiotic plasmids (p42d and pRL10) are structurally unrelated and seem to follow distinct evolutionary paths. Even though purifying selection is acting on the whole genome, the accessory component is evolving more rapidly. This component is constituted largely for proteins for transport of diverse metabolites and elements of external origin. The present analysis allows us to conclude that a heterogeneous and quickly diversifying group of plasmids co-exists in a common genomic framework.
Identification of Late Embryogenesis Abundant (LEA) Protein Putative Interactors Using Phage Display
Rekha Kushwaha,Taylor D. Lloyd,Kim R. Sch?fermeyer,Santosh Kumar,Allan Bruce Downie
International Journal of Molecular Sciences , 2012, DOI: 10.3390/ijms13066582
Abstract: Arabidopsis thaliana seeds without functional SEED MATURATION PROTEIN1 (SMP1), a boiling soluble protein predicted to be of intrinsic disorder, presumed to be a LATE EMBRYOGENESIS ABUNDANT (LEA) family protein based on sequence homology, do not enter secondary dormancy after 3 days at 40 °C. We hypothesized that SMP1 may protect a heat labile protein involved in the promotion of secondary dormancy. Recombinant SMP1 and GmPM28, its soybean ( Glycine max), LEA4 homologue, protected the labile GLUCOSE-6-PHOSPHATE DEHYROGENASE enzyme from heat stress, as did a known protectant, Bovine Serum Albumin, whether the LEA protein was in solution or attached to the bottom of microtiter plates. Maintenance of a biological function for both recombinant LEA proteins when immobilized encouraged a biopanning approach to screen for potential protein interactors. Phage display with two Arabidopsis seed, T7 phage, cDNA libraries, normalized for transcripts present in the mature, dehydrated, 12-, 24-, or 36-h imbibed seeds, were used in biopans against recombinant SMP1 and GmPM28. Phage titer increased considerably over four rounds of biopanning for both LEA proteins, but not for BSA, at both 25 and at 41 °C, regardless of the library used. The prevalence of multiple, independent clones encoding portions of specific proteins repeatedly retrieved from different libraries, temperatures and baits, provides evidence suggesting these LEA proteins are discriminating which proteins they protect, a novel finding. The identification of putative LEA-interacting proteins provides targets for reverse genetic approaches to further dissect the induction of secondary dormancy in seeds in response to heat stress.
From where did the 2009 'swine-origin' influenza A virus (H1N1) emerge?
Adrian J Gibbs, John S Armstrong, Jean C Downie
Virology Journal , 2009, DOI: 10.1186/1743-422x-6-207
Abstract: A novel H1N1 influenza virus, Swine-Origin Influenza Virus (S-OIV), was first isolated in mid-April 2009 and, by the end of the month, the first complete genomic sequences were published, and the virus shown to be of a novel re-assortant [1]. The virus spread fast in the human population, and the resulting pandemic has already proved to be a significant and very costly cause of mortality and morbidity in the human population. It has created intense interest worldwide. Several hundred research papers, reports, reviews and summaries [2,3] have been published about this virus in the last six months. Many discuss its genealogy deduced from its gene sequences, however it seems that we have no clearer evidence of its immediate origins than we have of the influenzas that caused past influenza pandemics. So the search for its source must be intensified while the clues are still fresh. The possibility that human activity may have had some role in its origins should not be dismissed without a dispassionate analysis of all available evidence. If we wish to avoid future pandemics, rather than just minimizing the damage they cause, we must better understand what conditions produce them.Several phylogenetic studies of the gene sequences of S-OIV and other influenzas have now been reported [4-10]. In these studies the sequences have been compared using various techniques (e.g. statistical inference (SI), neighbour-joining, maximum parsimony and principal components analyses), and have involved various selections of the very large number of influenza gene sequences that are now publicly available. Most phylogenetic studies compared nucleotide sequences, and at least one compared the encoded amino acid sequences.All studies have concluded that S-OIV emerged into the human population on a single occasion, probably around January 2009 [8,11]. They agree that six of its genes, those encoding the polymerase proteins (PB2, PB1 and PA), the haemagglutinin (HA), the nucleoprotein (NP) and
Urban Pro-Poor Registrations: Complex-Simple the Overstrand Project
L Downie
Potchefstroom Electronic Law Journal/Potchefstroomse Elektroniese Regsblad , 2011,
Abstract: Low-cost housing which has been disposed of by private owners is extremely difficult for conveyancers to register. The law as it stands is often incapable of giving effect to the business transactions of the poor, thereby creating insecurity of tenure nationwide. The Land Titles Adjustment Act 111 of 1993 is currently the only legislation capable of dealing with this impasse. The Overstrand Municipality has provided the staff and infrastructure to run a pilot project under the Act, for which it is awaiting confirmation from the Department of Rural Development and Land Reform. This article discusses the legal issues arising and the potential of such an initiative to provide consumer protection for the low-literate and other vulnerable holders of rights. KEYWORDS: Security of tenure; deeds registration; alienation of land; pro poor registrations; customary marriages; consumer protection; low cost housing
Urban Pro-Poor Registrations: Complex-Simple the Overstrand Project
L Downie
Potchefstroom Electronic Law Journal/Potchefstroomse Elektroniese Regsblad , 2011,
Abstract: Low-cost housing which has been disposed of by private owners is extremely difficult for conveyancers to register. The law as it stands is often incapable of giving effect to the business transactions of the poor, thereby creating insecurity of tenure nationwide. The Land Titles Adjustment Act 111 of 1993 is currently the only legislation capable of dealing with this impasse. The Overstrand Municipality has provided the staff and infrastructure to run a pilot project under the Act, for which it is awaiting confirmation from the Department of Rural Development and Land Reform. This article discusses the legal issues arising and the potential of such an initiative to provide consumer protection for the low-literate and other vulnerable holders of rights.
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