Metascheduling and Heuristic Co-Allocation Strategies in Distributed Computing

In this paper, we address problems of efficient computing in distributed systems with non-dedicated resources including utility grid. There are global job flows from external users along with resource owner's local tasks upon the resource non-dedication condition. Competition for resource reservation between independent users, local and global job flows substantially complicates scheduling and the requirement to provide the necessary quality of service. A metascheduling concept, justified in this work, assumes a complex combination of job flow dispatching and application-level scheduling methods for parallel jobs, as well as resource sharing and consumption policies established in virtual organizations and based on economic principles. We introduce heuristic slot selection and co-allocation strategies for parallel jobs. They are formalized by given criteria and implemented by algorithms of linear complexity on an available slots number

Rare Freshwater Ciliate Paramecium chlorelligerum Kahl, 1935 and Its Macronuclear Symbiotic Bacterium "Candidatus Holospora parva"

Ciliated protists often form symbioses with many diverse microorganisms. In particular, symbiotic associations between ciliates and green algae, as well as between ciliates and intracellular bacteria, are rather wide-spread in nature. In this study, we describe the com- plex symbiotic system between a very rare ciliate, Paramecium chlorelligerum, unicellular algae inhabiting its cytoplasm, and novel bacteria colonizing the host macronucleus. Para- mecium chlorelligerum, previously found only twice in Germany, was retrieved from a novel location in vicinity of St. Petersburg in Russia. Species identification was based on both clas- sical morphological methods and analysis of the small subunit rDNA. Numerous algae occu- pying the cytoplasm of this ciliate were identified with ultrastructural and molecular methods as representatives of the Meyerella genus, which before was not considered among symbi- otic algae. In the same locality at least fifteen other species of “green” ciliates were found, thus it is indeed a biodiversity hot-spot for such protists. A novel species of bacterial symbi- onts living in the macronucleus of Paramecium chlorelligerum cells was morphologically and ultrastructurally investigated in detail with the description of its life cycle and infection capabilities. The new endosymbiont was molecularly characterized following the full-cycle rRNA approach. Furthermore, phylogenetic analysis confirmed that the novel bacterium is a member of Holospora genus branching basally but sharing all characteristics of the genus except inducing connecting piece formation during the infected host nucleus division. We propose the name “Candidatus Holospora parva” for this newly described species. The described complex system raises new questions on how these microorganisms evolve and interact in symbiosis

'Candidatus Sarmatiella mevalonica' endosymbiont of the ciliate Paramecium provides insights on evolutionary plasticity among Rickettsiales

Members of the bacterial order Rickettsiales are obligatorily associated with a wide range of eukaryotic hosts. Their evolutionary trajectories, in particular concerning the origin of shared or differential traits among distant sub-lineages, are still poorly understood. Here, we characterized a novel Rickettsiales bacterium associated with the ciliate Paramecium tredecaurelia and phylogenetically related to the Rickettsia genus. Its genome encodes significant lineage-specific features, chiefly the mevalonate pathway gene repertoire, involved in isoprenoid precursor biosynthesis. Not only this pathway has never been described in Rickettsiales, it also is very rare among bacteria, though typical in eukaryotes, thus likely representing a horizontally acquired trait. The presence of these genes could enable an efficient exploitation of host-derived intermediates for isoprenoid synthesis. Moreover, we hypothesize the reversed reactions could have replaced canonical pathways for producing acetyl-CoA, essential for phospholipid biosynthesis. Additionally, we detected phylogenetically unrelated mevalonate pathway genes in metagenome-derived Rickettsiales sequences, likely indicating evolutionary convergent effects of independent horizontal gene transfer events. Accordingly, convergence, involving both gene acquisitions and losses, is highlighted as a relevant evolutionary phenomenon in Rickettsiales, possibly favoured by plasticity and comparable lifestyles, representing a potentially hidden origin of other more nuanced similarities among sub-lineages.Peer reviewe

Paramecium Diversity and a New Member of the Paramecium aurelia Species Complex Described from Mexico

Paramecium (Ciliophora) is an ideal model organism to study the biogeography of protists. However, many regions of the world, such as Central America, are still neglected in understanding Paramecium diversity. We combined morphological and molecular approaches to identify paramecia isolated from more than 130 samples collected from different waterbodies in several states of Mexico. We found representatives of six Paramecium morphospecies, including the rare species Paramecium jenningsi, and Paramecium putrinum, which is the first report of this species in tropical regions. We also retrieved five species of the Paramecium aurelia complex, and describe one new member of the complex, Paramecium quindecaurelia n. sp., which appears to be a sister species of Paramecium biaurelia. We discuss criteria currently applied for differentiating between sibling species in Paramecium. Additionally, we detected diverse bacterial symbionts in some of the collected ciliates

Metascheduling Strategies in Distributed Computing with Non-dedicated Resources

In this chapter, we address problems of efficient computing in distributed systems with non-dedicated resources including utility Grid. There are global job flows from external users along with resource owner’s local tasks upon resource non-dedication condition. Competition for resource reservation between independent users, local and global job flows substantially complicates scheduling and the requirement to provide the necessary quality of service. A metascheduling concept, justified in this work, assumes a complex combination of job flow dispatching and application-level scheduling methods for parallel jobs, as well as resource sharing and consumption policies established in virtual organizations and based on economic principles

Species-Specific Duplication of Surface Antigen Genes in <i>Paramecium</i>

Paramecium is a free-living ciliate that undergoes antigenic variation and still the functions of these variable surface antigen coats in this non-pathogenic ciliate remain elusive. Only a few surface antigen genes have been described, mainly in the two model species P. tetraurelia strain 51 and P. primaurelia strain 156. Given the lack of suitable sequence data to allow for phylogenetics and deeper sequence comparisons, we screened the genomes of six different Paramecium species for serotype genes and isolated 548 candidates. Our approach identified the subfamilies of the isogenes of individual serotypes that were mostly represented by intrachromosomal gene duplicates. These showed different duplication levels, and chromosome synteny suggested rather young duplication events after the emergence of the P. aurelia species complex, indicating a rapid evolution of surface antigen genes. We were able to identify the different subfamilies of the surface antigen genes with internal tandem repeats, which showed consensus motifs across species. The individual isogene families showed additional consensus motifs, indicating that the selection pressure holds individual amino acids constant in these repeats. This may be a hint of the receptor function of these antigens rather than a presentation of random epitopes, generating the variability of these surface molecules

Job Flow Distribution and Ranked Jobs Scheduling in Grid Virtual Organizations

In this work, we consider the problems of job flow distribution and ranked job framework forming within a model of cycle scheduling in Grid virtual organizations. The problem of job flow distribution is solved in terms of jobs and computing resource domains compatibility. A coefficient estimating such compatibility is introduced and studied experimentally. Two distribution strategies are suggested. Job framework forming is justified with such quality of service indicators as an average job execution time, a number of required scheduling cycles, and a number of job execution declines. Two methods for job selection and scheduling are proposed and compared: the first one is based on the knapsack problem solution, while the second one utilizes the mentioned compatibility coefficient. Along with these methods we present experimental results demonstrating the efficiency of proposed approaches and compare them with random job selection

Preference-based Fair Resource Sharing and Scheduling Optimization in Grid VOs

AbstractIn this paper, we deal with problems of efficient resource management and scheduling in utility Grids. There are global job flows from external users along with resource owners’ local tasks upon resource non-dedication condition. Competition for resource reservation between independent users, local and global job flows substantially complicates scheduling and the requirement to provide the necessary quality of service. A meta-scheduling model, justified in this work, assumes a complex combination of job flow dispatching and application-level scheduling methods for jobs, as well as resource sharing and consumption policies established in virtual organizations (VOs) and based on economic principles. A solution to the problem of fair resource sharing among VO stakeholders with simulation studies is proposed