A study of seed storage protein accumulation by ectopic expression in Arabidopsis

Understanding the mechanisms plants utilize for seed storage protein (SSP) synthesis, transport and deposition have the potential rewards of enabling high yields of modified or foreign proteins. Hayashi et al. (1999) indicated that the machinery devoted to the synthesis of protein storage vacuoles in cotyledon cells can be induced in vegetative tissue by the constitutive expression of a pumpkin 2S albumin phosphinothricin-acetyl-transferase gene fusion (pumpkin 2S-PAT) resulting in the biogenesis of precursor-accumulating (PAC) vesicles in Arabidopsis leaves. This discovery was the impetus behind the work described which sought to examine this phenomenon further by ectopically evoking SSP trafficking and vesicle biogenesis machinery in leaves. With the aim of elucidating the mechanisms necessary to evoke PAC vesicle biogenesis, a suite of constructs including the pumpkin 2S-PAT and analogous napin-PAT and napin-GFP variants were synthesized. Analysis of these transgenes in Arabidopsis revealed that the pumpkin 2S albumin has a capacity unique from napin peptides to result in fusion protein accumulation. Further, the truncated pumpkin 2S albumin peptide and the pumpkin 2S albumin C-terminus were found to direct deposition to vesicles; however, the C-terminus alone was not enough to direct deposition to vesicles unless combined with a significantly shortened napin peptide. An increased ER protein throughput was correlated to trafficking of the fusion protein by Golgi-independent mechanisms resulting in stable accumulation of the unprocessed protein whereas less ER throughput indicated passage through the Golgi-dependent pathway resulting in accumulation of a processed variant. At the level of gene expression, as examined by a microarray study, both inducible and constitutive ectopic expression of pumpkin 2S-PAT resulted in substantial perturbations of the endomembrane system affecting protein folding, flowering time and ER-associated biosynthetic functions which indicated that modulation of flowering time and photoperiodism are highly dependent on protein trafficking and vacuolar biogenesis mechanisms and that high ER protein throughput occurs at the expense of biosynthesis and cessation of ER functioning

A simple method for integrating a complex model into an ensemble data assimilation system using MPI

This paper details a strategy for modifying the source code of a complex model so that the model may be used in a data assimilation context, {and gives the standards for implementing a data assimilation code to use such a model}. The strategy relies on keeping the model separate from any data assimilation code, and coupling the two through the use of Message Passing Interface (MPI) {functionality}. This strategy limits the changes necessary to the model and as such is rapid to program, at the expense of ultimate performance. The implementation technique is applied in different models with state dimension up to $2.7 \times 10^8$. The overheads added by using this implementation strategy in a coupled ocean-atmosphere climate model are shown to be an order of magnitude smaller than the addition of correlated stochastic random errors necessary for some nonlinear data assimilation techniques

The biotransformation of canola meal

Canola meal was obtained from each of two oil seed crushing plants in the Prairies. One type of meal was derived predominantly from the seeds of Brassica napus, whereas the other was derived predominantly from the seeds of Brassica rapa. Proximate, amino acid, and protein electrophoresis analyses were conducted on each type of canola meal. It was found that the two types of canola meal resembled one another with respect to the components analyzed. The composition of the two canola meals was studied further by examining the indigenous microflora of the meals. The microbiological load of the meals was found to be relatively low and comparable to vegetable products which are processed. Twenty ­one species of filamentous fungi were isolated from the meal samples and identified at least to the genus level. Four species were found in both types of meal and were from the genera Aspergillus, Eurotian, Moniliella and Mucor. Strains unique to the Brassica napus meal occurred among the genera Aspergillus, Cladosporium, Hadrotrichum, Mucor and Penicillium. Strains unique to the Brassica rapa meal occurred among the genera Cladosporium, Monoascus, Paecilomyces, Penicillium, Phoma, Polyscytalum, Rhizopus, and Rhizomucor. Several of the fungal strains isolated from the meal are known to be toxigenic and/or pathogenic to humans or livestock. The indigenous filamentous fungi of the meals were examined for their capacity to produce extracellular enzymes. A number of these species produced the enzymes necessary for the biotransformation of canola meal. In particular, Cladosporium sp., Mucor sp. M1, Penicillium fellutanum, and Rhizopus stolonifer showed the capacity to degrade lignin or cellulose. The growth of the indigenous microflora in the meals resulted in a reduced nutritional quality of the meal. Canola meal biotransformed by its indigenous microorganisms had an elevated content of ash, total dietary fibre, and non-protein nitrogen. It was found that the dominant species resulting from the growth of the microbial population could be influenced by the use of differing levels of moisture in the meal. Furthermore, the enzymatic activity residing in the biotransformed meal samples was found to be correlated with the dominant species which resulted from the growth of the microflora. Two species of filamentous fungi know to have the capacity to degrade plant cell walls, Chaetomium cellulolyticum and Ganoderma colossus, were grown on the meal in a solid substrate fermentation process. It was found that C. cellulolyticum grew rapidly on the meal. The meal end product possessed less total dietary fibre and protein, and more ash and non-protein nitrogen than the untreated meal. Further examination revealed that C. cellulolyticum has a high capacity for rapid proteolysis of canola meal protein. The white-rot fungus G. colossus was also found to grow on canola meal and degrade meal fibre, but had less capacity to degrade meal protein than C. cellulolyticum. In relation to its control, incubation of G. colossus at 37°C resulted in an increase in the essential amino acids lysine and valine, whereas incubation at 45°C resulted in less proteolysis of meal proteins and encouraged ligninase activity

Beowulf cluster computing with Linux

Comprehensive guides to the latest Beowulf tools and methodologies

The nonexistence of a (K6-e)-decomposition of the complete graph K29

We show via an exhaustive computer search that there does not exist a (K-6 - e)-decomposition of K-29. This is the first example of a non-complete graph G for which a G-decomposition of K2|E(G)|+1 does not exist. (C) 2009 Wiley Periodicals, Inc. J Combin Designs 18: 94-104, 201

Multicore Scheduling for Lightweight Communicating Processes

Process-oriented programming is a design methodology in which software applications are constructed from communicating concurrent processes. A process-oriented design is typically composed of a large number of small isolated concurrent components. These components allow for the scalable parallel execution of the resulting application on both shared-memory and distributed-memory architectures. In this paper we present a runtime designed to support process-oriented programming by providing lightweight processes and communication primitives. Our run-time scheduler, implemented using lock-free algorithms, automatically executes concurrent components in parallel on multicore systems. Run-time heuristics dynamically group processes into cache-affine work units based on communication patterns. Work units are then distributed via wait-free work-stealing. Initial performance analysis shows that, using the algorithms presented in this paper, process-oriented software can execute with an efficiency approaching that of optimised sequential and coarse-grain threaded designs