Automated, Reliable, and Efficient Continental-Scale Replication of 7.3 Petabytes of Climate Simulation Data: A Case Study

We report on our experiences replicating 7.3 petabytes (PB) of Earth System Grid Federation (ESGF) climate simulation data from Lawrence Livermore National Laboratory (LLNL) in California to Argonne National Laboratory (ANL) in Illinois and Oak Ridge National Laboratory (ORNL) in Tennessee. This movement of some 29 million files, twice, undertaken in order to establish new ESGF nodes at ANL and ORNL, was performed largely automatically by a simple replication tool, a script that invoked Globus to transfer large bundles of files while tracking progress in a database. Under the covers, Globus organized transfers to make efficient use of the high-speed Energy Sciences network (ESnet) and the data transfer nodes deployed at participating sites, and also addressed security, integrity checking, and recovery from a variety of transient failures. This success demonstrates the considerable benefits that can accrue from the adoption of performant data replication infrastructure

Pleiotropic control of five eucaryotic genes by multiple regulatory elements

We have previously shown that allophanate acts as an inducer for five structural genes whose products participate in the degradation of allantoin by Saccharomyces cerevisiae. This observation led us to hypothesize that these genes might be controlled in common and to test the hypothesis by searching for mutants unable to induce production of the allantoin-degrading enzymes. Such mutants have been found. These strains grew poorly when provided with any of the allantoin pathway intermediates, but used other nitrogen sources normally. The mutations carried in these strains were recessive to wild-type alleles and complemented mutations in all known loci associated with the allantoin pathway. The locus containing the most thoroughly studied mutation (dal81-1) was not fund to be tightly linked to any of the allantoin pathway structural genes. The low basal levels of allantoin pathway enzymes observed in Dal81- strains remained the same whether or not the inducer was present in the growth medium. However, the levels of enzyme increased moderately when mutants were grown on poor nitrogen sources. From these observations, we conclude that dal81 mutant strains possess a defect in the induction of enzyme synthesis; enzyme production due to relief of nitrogen catabolite repression, however, appears normal. The observed epistatic relationships of mutations in the DAL80 and DAL81 loci suggest that their products may possess a reasonable degree of functional independence.</jats:p

Allantoate transport in Saccharomyces cerevisiae

Allantoate uptake appears to be mediated by an energy-dependent active transport system with an apparent Michaelis constant of about 50 microM. Cells were able to accumulate allantoate to greater than 3,000 times the extracellular concentration. The rate of accumulation was maximum at pH 5.7 to 5.8. The energy source for allantoate uptake is probably different from that for uptake of the other allantoin pathway intermediates. The latter systems are inhibited by arsenate, fluoride, dinitrophenol, and carboxyl cyanide-m-chlorophenyl hydrazone, whereas allantoate accumulation was sensitive to only dinitrophenol and carboxyl cyanide-m-chlorophenyl hydrazone. Efflux of preloaded allanotate did not occur at detectable levels. However, exchange of intra- and extracellular allantoate was found to occur very slowly. The latter two characteristics are shared with the allantoin uptake system and may result from the sequestering of intracellular allantoate within the cell vacuole. During the course of these studies, we found that, contrary to earlier reports, the reaction catalyzed by allantoinase is freely reversible.</jats:p

STRUCTURAL ANALYSIS OF THE <i>dur</i> LOCI IN <i>S. CEREVISIAE</i>: TWO DOMAINS OF A SINGLE MULTIFUNCTIONAL GENE

ABSTRACT In Saccharomyces cerevisiae, the degradation of urea to carbon dioxide and ammonia is catalyzed byurea carboxylase and albphanate hydrolase. The loci coding for these enzymes (dur1 and dur2) are very tightly linked an the right arm of chromosome II between pet11 and met8. Pleiotropic mutations that fail to complement mutations in either of the dur loci were found to be predominantly located in or near the dur2 locus. We interpret these data as suggesting that the two dur loci might in reality be domains of a single gene that codes fora multifunctional polypeptide. In view OIthis conclusion, we have renamed the dur loci as the durl,2 locus.</jats:p

A CLUSTER OF THREE GENES RESPONSIBLE FOR ALLANTOIN DEGRADATION IN <i>SACCHAROMYCES CEREVISIAE</i>

ABSTRACT Mutant strains of Saccharomyces cerevisiae unable to utilize allantoin as sole nitrogen murce were isolated and divided into three groups on the basis of their biochemical and genetic characteristics. The three loci associated with these mutant classes were designated dall (allantoinase minus), da12 (allantoicase minus) and da14 (allantoin transport minus). All three loci are located in a cluster that is proximal to the lysl locus on the right arm of chromosome IX. The gene order and intergenic distances were estimated to be: dall—2.5 cM—dal4—1.9cM—dal2—4.6cM—lysl.</jats:p