Transparent mediation-based access to multiple yeast data sources using an ontology driven interface

Background

Over the past decade the workflow system paradigm has evolved as an efficient and user-friendly approach for developing complex bioinformatics applications. Two popular workflow systems that have gained acceptance by the bioinformatics community are Taverna and Galaxy. Each system has a large user-base and supports an ever-growing repository of application workflows. However, workflows developed for one system cannot be imported and executed easily on the other. The lack of interoperability is due to differences in the models of computation, workflow languages, and architectures of both systems. This lack of interoperability limits sharing of workflows between the user communities and leads to duplication of development efforts.

Results

In this paper, we present Tavaxy, a stand-alone system for creating and executing workflows based on using an extensible set of re-usable workflow patterns. Tavaxy offers a set of new features that simplify and enhance the development of sequence analysis applications: It allows the integration of existing Taverna and Galaxy workflows in a single environment, and supports the use of cloud computing capabilities. The integration of existing Taverna and Galaxy workflows is supported seamlessly at both run-time and design-time levels, based on the concepts of hierarchical workflows and workflow patterns. The use of cloud computing in Tavaxy is flexible, where the users can either instantiate the whole system on the cloud, or delegate the execution of certain sub-workflows to the cloud infrastructure.

Conclusions

Tavaxy reduces the workflow development cycle by introducing the use of workflow patterns to simplify workflow creation. It enables the re-use and integration of existing (sub-) workflows from Taverna and Galaxy, and allows the creation of hybrid workflows. Its additional features exploit recent advances in high performance cloud computing to cope with the increasing data size and complexity of analysis. The system can be accessed either through a cloud-enabled web-interface or downloaded and installed to run within the user's local environment. All resources related to Tavaxy are available at http://www.tavaxy.org.     

A model to calculate cardiac output in hemodialysis patients by thermodilution

ABSTRACT: The Blood Temperature Monitor module (BTM) is used to measure recirculation by thermodilution in dialysis. Numerous studies have confirmed its interest in the measuring of the vascular access flow. In this letter we describe a model to calculate cardiac output in dialysis by the BTM.     

Adaptation to Oxygen: ROLE OF TERMINAL OXIDASES IN PHOTOSYNTHESIS INITIATION IN THE PURPLE PHOTOSYNTHETIC BACTERIUM,RUBRIVIVAX GELATINOSUS*

The appearance of oxygen in the Earth''s atmosphere via oxygenic photosynthesis required strict anaerobes and obligate phototrophs to cope with the presence of this toxic molecule. Here we show that in the anoxygenic phototroph Rubrivivax gelatinosus, the terminal oxidases (cbb₃, bd, and caa₃) expand the range of ambient oxygen tensions under which the organism can initiate photosynthesis. Unlike the wild type, the cbb₃⁻/bd⁻ double mutant can start photosynthesis only in deoxygenated medium or when oxygen is removed, either by sparging cultures with nitrogen or by co-inoculation with strict aerobes bacteria. In oxygenated environments, this mutant survives nonphotosynthetically until the O₂ tension is reduced. The cbb₃ and bd oxidases are therefore required not only for respiration but also for reduction of the environmental O₂ pressure prior to anaerobic photosynthesis. Suppressor mutations that restore respiration simultaneously restore photosynthesis in nondeoxygenated medium. Furthermore, induction of photosystem in the cbb₃⁻ mutant led to a highly unstable strain. These results demonstrate that photosynthetic metabolism in environments exposed to oxygen is critically dependent on the O₂-detoxifying action of terminal oxidases.     

Cytogenetic analysis of hybrids derived from wheat and <Emphasis Type="Italic">Tritipyrum</Emphasis> using conventional staining and genomic <Emphasis Type="Italic">in situ</Emphasis> hybridization

The new salt tolerant cereal, Tritipyrum (2n=6x=42, AABBE^bE^b) offers potential to introduce desirable characters for wheat improvements. This study was aimed to generate a segregating population from Iranian local wheat cultivars (2n=6x=42, AABBDD) and Tritipyrum crosses, study of the meiotic behaviour in F₂ hybrids and identification of E^b chromosomes in F₃ individuals. Results showed meiotic abnormalities in F₂ plants and different pairing frequency in the meiosis among F₂ plants. Genomic in situ hybridization revealed that total and E^b chromosome number of F₃ seeds ranged from 39 to 45 and 0 to 10, respectively. A significant prevalence of hyper-aneuploidy was observed among F₃ genotypes. C-banding patterns identified E^b chromosomes in Tritipyrum, indicating that it also can be useful to study wheat-Tritipyrum derivatives.     

Biochemical,physiological and molecular evaluation of rice cultivars differing in salt tolerance at the seedling stage

Changes in the antioxidant enzymes, lipid peroxidation, sodium and potassium, chlorophyll, H₂O₂ and proline content were monitored in the leaves of 42 rice varieties which were not yet well-documented for the salinity tolerance under different salinity levels. The tolerant varieties (FL478, Hassani, Shahpasand, Gharib and Nemat) showed signs of tolerance (lower Na⁺/K⁺ ratio, high proline accumulation, less membrane damage, lower H₂O₂ production, and higher superoxide dismutase and catalase activity) very well. The positive relationship between the level of salt tolerance and the amount of proline accumulation in the rice varieties support the important role of proline under the salt stress. The varieties were genotyped for 12 microsatellite markers that were closely linked to SalTol QTL. The results of association analysis indicated that RM1287, RM8094, RM3412 and AP3206 markers had the high value of R² for the regression models of the studied traits. It shows the important role of SalTol in controlling physio-biochemical traits. The results can be used in the future marker assisted selection (MAS) directly, if the results are confirmed.     

Salmonella contamination of vegetables irrigated with untreated wastewater

The irrigation of vegetables with raw wastewater has been practised in El Azzouzia, the wastewater-spreading field of Marrakesh city (Morocco), for many years. This water was found to be contaminated with different serogroups of Salmonella. B and C were the most frequently isolated groups. These same serogroups were detected on vegetables irrigated with these wastewater effluents. The crops whose edible product develops on the ground surface, such as lettuce and parsley, were more contaminated than those which grow, above the soil surface, like tomatoes and pimento. Except on lettuce, Salmonella on crops did not persist beyond 3 days after irrigation.     

Solar inactivation of mesophilic Aeromonas by exogenous photooxidation in high-rate algal pond treating waste water

AIMS: Investigations were carried out to observe the effect of sunlight on the survival of mesophilic Aeromonas (A. caviae, A. hydrophila and A. sobria) in high-rate algal pond. METHODS AND RESULTS: Light damage was estimated by loss of bacterial culturability, using simple beaker experiments. Survival of the strains studied under illuminated conditions was highly affected by the physico-chemical conditions within the microcosms. The inactivation of Aeromonas increased strongly as dissolved oxygen was increased, and was dependent on exogenous sensitizers. This process was enhanced by the high pH of water. Die-off of bacteria was prevented by adding catalase and pyruvate (H2O2 scavengers) into the microcosms. CONCLUSIONS: The damage of Aeromonas was mainly due to exogenous photooxidation. Hydrogen peroxide at least was involved in light-induced damage of bacteria. Aeromonas sobria appeared to be slightly less sensitive to photooxidation than A. hydrophila and A. caviae. SIGNIFICANCE AND IMPACT OF STUDY: The present study could explain the relative resistance of A. sobria to treatment in wastewater stabilization ponds.