Capacity planning tool for multiservice IP networks

This paper describes a network planning tool that has been developed in order to provide support for network planners who need to dimension next generation IP networks to meet quality of service (QoS) objectives. Specifically, the proposed network planning tool takes account of the new technologies that enable QoS in IP-based networks (i.e., DiffServ/MPLS) and allows for multiple QoS constraints so that guaranteed performance can be achieved for each of the traffic classes. The primary-decisions for the planning tool include determining class-based bandwidth allocations on the links, total link capacities and how traffic of each class is to be routed through the network. Furthermore, the planning tool incorporates traffic characterisation and dimensioning procedures that allow the known burstiness of IP traffic to be effectively modelled. After discussing some of the specific features and algorithms that have been incorporated into the planning methodology, the planning tool is briefly described and the solution to a simple network problem is demonstrated. The simulation results demonstrate the capability of the tool in achieving the required performance levels for the traffic classes

Increased Abundance of Proteins Involved in Phytosiderophore Production in Boron-Tolerant Barley1[C][W]

Boron (B) phytotoxicity affects cereal-growing regions worldwide. Although B-tolerant barley (Hordeum vulgare) germplasm is available, molecules responsible for this tolerance mechanism have not been defined. We describe and use a new comparative proteomic technique, iTRAQ peptide tagging (iTRAQ), to compare the abundances of proteins from B-tolerant and -intolerant barley plants from a ‘Clipper’ × ‘Sahara’ doubled-haploid population selected on the basis of a presence or absence of two B-tolerance quantitative trait loci. iTRAQ was used to identify three enzymes involved in siderophore production (Iron Deficiency Sensitive2 [IDS2], IDS3, and a methylthio-ribose kinase) as being elevated in abundance in the B-tolerant plants. Following from this result, we report a potential link between iron, B, and the siderophore hydroxymugineic acid. We believe that this study highlights the potency of the iTRAQ approach to better understand mechanisms of abiotic stress tolerance in cereals, particularly when applied in conjunction with bulked segregant analysis

Analysis of the oryza sativa plasma membrane proteome using combined protein and peptide fractionation approaches in conjunction with mass spectrometry

To identify integral and peripheral plasma membrane (PM) proteins from Oryza sativa (rice), highly enriched PM fractions from rice suspension cultured cells were analyzed using two complementary approaches. The PM was enriched using aqueous two-phase partitioning and high pH carbonate washing to remove soluble, contaminating proteins and characterized using enzymatic and immunological analyses. Proteins from the carbonate-washed PM (WPM) were analyzed by either one-dimensional gel electrophoresis (1D-SDS-PAGE) followed by tryptic proteolysis or proteolysis followed by strong cation exchange liquid chromatography (LC) with subsequent analysis of the tryptic peptides by LC-MS/MS (termed Gel-LC-MS/MS and 2D-LC-MS/MS, respectively). Combining the results of these two approaches, 438 proteins were identified on the basis of two or more matching peptides, and a further 367 proteins were identified on the basis of single peptide matches after data analysis with two independent search algorithms. Of these 805 proteins, 350 were predicted to be PM or PM-associated proteins. Four hundred and twenty-five proteins (53%) were predicted to be integrally associated with a membrane, via either one or many (up to 16) transmembrane domains, a GPI-anchor, or membrane-spanning β-barrels. Approximately 80% of the 805 identified proteins were assigned a predicted function, based on similarity to proteins of known function or the presence of functional domains. Proteins involved in PM-related activities such as signaling (21% of the 805 proteins), transporters and ATPases (14%), and cellular trafficking (8%), such as via vesicles involved in endo- and exocytosis, were identified. Proteins that are involved in cell wall biosynthesis were also identified (5%) and included three cellulose synthase (CESA) proteins, a cellulose synthase-like D (CSLD) protein, cellulases, and several callose synthases. Approximately 20% of the proteins identified in this study remained functionally unclassified despite being predicted to be membrane proteins.Siria H. A. Natera, Kristina L. Ford, Andrew M. Cassin, John H. Patterson, Edward J. Newbigin and Antony Baci

Genomes and Transcriptomes of Partners in Plant-Fungal- Interactions between Canola (Brassica napus) and Two Leptosphaeria Species

Leptosphaeria maculans ‘brassicae’ is a damaging fungal pathogen of canola (Brassica napus), causing lesions on cotyledons and leaves, and cankers on the lower stem. A related species, L. biglobosa ‘canadensis’, colonises cotyledons but causes few stem cankers. We describe the complement of genes encoding carbohydrate-active enzymes (CAZys) and peptidases of these fungi, as well as of four related plant pathogens. We also report dual-organism RNA-seq transcriptomes of these two Leptosphaeria species and B. napus during disease. During the first seven days of infection L. biglobosa ‘canadensis’, a necrotroph, expressed more cell wall degrading genes than L. maculans ‘brassicae’, a hemi-biotroph. L. maculans ‘brassicae’ expressed many genes in the Carbohydrate Binding Module class of CAZy, particularly CBM50 genes, with potential roles in the evasion of basal innate immunity in the host plant. At this time, three avirulence genes were amongst the top 20 most highly upregulated L. maculans ‘brassicae’ genes in planta. The two fungi had a similar number of peptidase genes, and trypsin was transcribed at high levels by both fungi early in infection. L. biglobosa ‘canadensis’ infection activated the jasmonic acid and salicylic acid defence pathways in B. napus, consistent with defence against necrotrophs. L. maculans‘brassicae’ triggered a high level of expression of isochorismate synthase 1, a reporter for salicylic acid signalling. L. biglobosa ‘canadensis’ infection triggered coordinated shutdown of photosynthesis genes, and a concomitant increase in transcription of cell wall remodelling genes of the host plant. Expression of particular classes of CAZy genes and the triggering of host defence and particular metabolic pathways are consistent with the necrotrophic lifestyle of L. biglobosa ‘canadensis’, and the hemibiotrophic life style of L. maculans ‘brassicae’

Arabinogalactan proteins have deep roots in eukaryotes:identification of genes and epitopes in brown algae and their role in <i>Fucus serratus</i> embryo development

International audienceArabinogalactan proteins (AGPs) are highly glycosylated, hydroxyproline-rich proteins found at the cell surface of plants, where they play key roles in developmental processes. Brown algae are marine, multicellular, photosynthetic eukaryotes. They belong to the phylum Stramenopiles, which is unrelated to land plants and green algae (Chloroplastida). Brown algae share common evolutionary features with other multicellular organisms, including a carbohydrate-rich cell wall. They differ markedly from plants in their cell wall composition, and AGPs have not been reported in brown algae. Here we investigated the presence of chimeric AGP-like core proteins in this lineage. We report that the genome sequence of the brown algal model Ectocarpus siliculosus encodes AGP protein backbone motifs, in a gene context that differs considerably from what is known in land plants. We showed the occurrence of AGP glycan epitopes in a range of brown algal cell wall extracts. We demonstrated that these chimeric AGP-like core proteins are developmentally regulated in embryos of the order Fucales and showed that AGP loss of function seriously impairs the course of early embryogenesis. Our findings shine a new light on the role of AGPs in cell wall sensing and raise questions about the origin and evolution of AGPs in eukaryotes

<i>Asparagus</i> Spears as a Model to Study Heteroxylan Biosynthesis during Secondary Wall Development

<div><p>Garden asparagus (<i>Asparagus officinalis</i> L.) is a commercially important crop species utilized for its excellent source of vitamins, minerals and dietary fiber. However, after harvest the tissue hardens and its quality rapidly deteriorates because spear cell walls become rigidified due to lignification and substantial increases in heteroxylan content. This latter observation prompted us to investigate the <i>in vitro</i> xylan xylosyltransferase (XylT) activity in asparagus. The current model system for studying heteroxylan biosynthesis, <i>Arabidopsis</i>, whilst a powerful genetic system, displays relatively low xylan XylT activity in <i>in vitro</i> microsomal preparations compared with garden asparagus therefore hampering our ability to study the molecular mechanism(s) of heteroxylan assembly. Here, we analyzed physiological and biochemical changes of garden asparagus spears stored at 4 °C after harvest and detected a high level of xylan XylT activity that accounts for this increased heteroxylan. The xylan XylT catalytic activity is at least thirteen-fold higher than that reported for previously published species, including <i>Arabidopsis</i> and grasses. A biochemical assay was optimized and up to seven successive Xyl residues were incorporated to extend the xylotetraose (Xyl₄) acceptor backbone. To further elucidate the xylan biosynthesis mechanism, we used RNA-seq to generate an <i>Asparagus</i> reference transcriptome and identified five putative xylan biosynthetic genes (<i>AoIRX9</i>, <i>AoIRX9-L</i>, <i>AoIRX10</i>, <i>AoIRX14_A</i>, <i>AoIRX14_B</i>) with <i>AoIRX9</i> having an expression profile that is distinct from the other genes. We propose that <i>Asparagus</i> provides an ideal biochemical system to investigate the biochemical aspects of heteroxylan biosynthesis and also offers the additional benefit of being able to study the lignification process during plant stem maturation.</p></div

Endosymbiosis undone by stepwise elimination of the plastid in a parasitic dinoflagellate.

Organelle gain through endosymbiosis has been integral to the origin and diversification of eukaryotes, and, once gained, plastids and mitochondria seem seldom lost. Indeed, discovery of nonphotosynthetic plastids in many eukaryotes--notably, the apicoplast in apicomplexan parasites such as the malaria pathogen Plasmodium--highlights the essential metabolic functions performed by plastids beyond photosynthesis. Once a cell becomes reliant on these ancillary functions, organelle dependence is apparently difficult to overcome. Previous examples of endosymbiotic organelle loss (either mitochondria or plastids), which have been invoked to explain the origin of eukaryotic diversity, have subsequently been recognized as organelle reduction to cryptic forms, such as mitosomes and apicoplasts. Integration of these ancient symbionts with their hosts has been too well developed to reverse. Here, we provide evidence that the dinoflagellate Hematodinium sp., a marine parasite of crustaceans, represents a rare case of endosymbiotic organelle loss by the elimination of the plastid. Extensive RNA and genomic sequencing data provide no evidence for a plastid organelle, but, rather, reveal a metabolic decoupling from known plastid functions that typically impede organelle loss. This independence has been achieved through retention of ancestral anabolic pathways, enzyme relocation from the plastid to the cytosol, and metabolic scavenging from the parasite's host. Hematodinium sp. thus represents a further dimension of endosymbiosis--life after the organelle.We thank Nick Katris for assistance with Toxoplasma transformation and Ellen Nisbet for critically reading this report. This work was supported by Australian Research Council (ARC) Grants DP130100572 and DP1093395; a King Abdullah University of Science and Technology Faculty Baseline Research Fund; and Victorian Life Sciences Computation Initiative Grant VR0254. S.G.G. was supported by Science Foundation Ireland Grant 13/SIRG/2125; F. was supported by an Australia Award; A.M.C. and A.B. were supported by ARC Centre of Excellence in Plant Cell Walls Grant CE110001007; and M.J.M. was supported by the National Health and Medical Research Council as a Principal Research Fellow.This is the accepted manuscript of a paper published in the Proceedings of the National Academy of Sciences (Gornik et al., PNAS 2015, 112, 18, 5767-5772, doi:10.1073/pnas.1423400112). The final version is available at http://dx.doi.org/10.1073/pnas.142340011

Endosymbiosis undone by stepwise elimination of the plastid in a parasitic dinoflagellate

Organelle gain through endosymbiosis has been integral to the origin and diversification of eukaryotes, and, once gained, plastids and mitochondria seem seldom lost. Indeed, discovery of nonphotosynthetic plastids in many eukaryotes-notably, the apicoplast in apicomplexan parasites such as the malaria pathogen Plasmodiumhighlights the essential metabolic functions performed by plastids beyond photosynthesis. Once a cell becomes reliant on these ancillary functions, organelle dependence is apparently difficult to overcome. Previous examples of endosymbiotic organelle loss (either mitochondria or plastids), which have been invoked to explain the origin of eukaryotic diversity, have subsequently been recognized as organelle reduction to cryptic forms, such as mitosomes and apicoplasts. Integration of these ancient symbionts with their hosts has been too well developed to reverse. Here, we provide evidence that the dinoflagellate Hematodinium sp., a marine parasite of crustaceans, represents a rare case of endosymbiotic organelle loss by the elimination of the plastid. Extensive RNA and genomic sequencing data provide no evidence for a plastid organelle, but, rather, reveal a metabolic decoupling from known plastid functions that typically impede organelle loss. This independence has been achieved through retention of ancestral anabolic pathways, enzyme relocation from the plastid to the cytosol, and metabolic scavenging from the parasite\u27s host. Hematodinium sp. thus represents a further dimension of endosymbiosis-life after the organelle