Implementing noncollective parallel I/O in cluster environments using Active Message communication

A costeffective secondary storage architecture for parallel computers is to distribute storage across all processors, which then engage in either computation or I/O, depending on the demands of the moment. A difficulty associated with this architecture is that access to storage on another processor typically requires the cooperation of that processor, which can be hard to arrange if the processor is engaged in other computation. One partial solution to this problem is to require that remote I/O operations occur only via collective calls. In this paper, we describe an alternative approach based on the use of singlesided communication operations such as Active Messages. We present an implementation of this basic approach called Distant I/O and present experimental results that quantify the lowlevel performance of DIO mechanisms. This technique is exploited to support noncollective parallel shared file model for a large outofcore scientific application with very high I/O bandwidth requirements. The achieved performance exceeds by a wide margin the performance of a well equipped PIOFS parallel filesystem on the IBM SP.     

Increased episomal replication accounts for the high rate of adaptive mutation in recD mutants of Escherichia coli

Adaptive mutation has been studied extensively in FC40, a strain of Escherichia coli that cannot metabolize lactose (Lac-) because of a frameshift mutation affecting the lacZ gene on its episome. recD mutants of FC40, in which the exonuclease activity of RecBCD (ExoV) is abolished but its helicase activity is retained, have an increased rate of adaptive mutation. The results presented here show that, in several respects, adaptive mutation to Lac+ involves different mechanisms in recD mutant cells than in wild-type cells. About half of the apparent increase in the adaptive mutation rate of recD mutant cells is due to a RecA-dependent increase in episomal copy number and to growth of the Lac- cells on the lactose plates. The remaining increase appears to be due to continued replication of the episome, with the extra copies being degraded or passed to recD+ recipients. In addition, the increase in adaptive mutation rate in recD mutant cells is (i) dependent on activities of the single-stranded exonucleases, RecJ and ExoI, which are not required for (in fact, slightly inhibit) adaptive mutation in wild-type cells, and (ii) enhanced by RecG, which opposes adaptive mutation in wild-type cells.     

Chemiluminescent detection of sequential DNA hybridizations to high-density, filter-arrayed cDNA libraries: a subtraction method for novel gene discovery.

A chemiluminescent approach for sequential DNA hybridizations to high-density filter arrays of cDNAs, using a biotin-based random priming method followed by a streptavidin/alkaline phosphatase/CDP-Star detection protocol, is presented. The method has been applied to the Brugia malayi genome project, wherein cDNA libraries, cosmid and bacterial artificial chromosome (BAC) libraries have been gridded at high density onto nylon filters for subsequent analysis by hybridization. Individual probes and pools of rRNA probes, ribosomal protein probes and expressed sequence tag probes show correct specificity and high signal-to-noise ratios even after ten rounds of hybridization, detection, stripping of the probes from the membranes and rehybridization with additional probe sets. This approach provides a subtraction method that leads to a reduction in redundant DNA sequencing, thus increasing the rate of novel gene discovery. The method is also applicable for detecting target sequences, which are present in one or only a few copies per cell; it has proven useful for physical mapping of BAC and cosmid high-density filter arrays, wherein multiple probes have been hybridized at one time (multiplexed) and subsequently "deplexed" into individual components for specific probe localizations.     

An Arabidopsis mutant with deregulated ABA gene expression: implications for negative regulator function

The physiological acclimation of plants to osmotic stresses involves a complex programme of gene regulation. In one signalling pathway, elevated levels of abscisic acid (ABA) activate a subset of stress genes. Because ABA responses lack a definable morphological phenotype, we have screened for mutants that exhibit deregulated ABA-responsive gene expression. To monitor this ABA response, a line of Arabidopsis thaliana carrying a transgene composed of the ABA-responsive Arabidopsis kin2 promoter fused to the coding sequence for the firefly luciferase gene, kin2::luc, was generated. Patterns of ABA-responsive luciferase activity were monitored by photon counting. In contrast to wild-type plants which display a transient activation of kin2::luc, an ABA deregulated gene expression mutant (ade1) exhibits both sustained and enhanced levels of transgene activity. Levels of kin2, cor47 and rab18 expression in ade1 plants are also enhanced and prolonged indicating that the molecular mechanism(s) altered in ade1 plants affects the regulation of other ABA-responsive genes. The mutant phenotype is specific for the ABA response as cold-inducible kin2 expression is unaltered in ade1 plants. Genetic analyses indicate that the ade1 mutant is a monogenic recessive trait. A role for negative regulator function in ABA signalling is discussed.     

A haplotype-based test of association using data from cohort and nested case-control epidemiologic studies

Haplotype-based risk models can lead to powerful methods for detecting the association of a disease with a genomic region of interest. In population-based studies of unrelated individuals, however, the haplotype status of some subjects may not be discernible without ambiguity from available locus-specific genotype data. A score test for detecting haplotype-based association using genotype data has been developed in the context of generalized linear models for analysis of data from cross-sectional and retrospective studies. In this article, we develop a test for association using genotype data from cohort and nested case-control studies where subjects are prospectively followed until disease incidence or censoring (end of follow-up) occurs. Assuming a proportional hazard model for the haplotype effects, we derive an induced hazard function of the disease given the genotype data, and hence propose a test statistic based on the associated partial likelihood. The proposed test procedure can account for differential follow-up of subjects, can adjust for possibly time-dependent environmental co-factors and can make efficient use of valuable age-at-onset information that is available on cases. We provide an algorithm for computing the test statistic using readily available statistical software. Utilizing simulated data in the context of two genomic regions GPX1 and GPX3, we evaluate the validity of the proposed test for small sample sizes and study its power in the presence and absence of missing genotype data.     

Genetic signatures of pre-expansion bottleneck in the Choctaw population of Oklahoma

Previous research showed that the Choctaw Indians of Oklahoma exhibit considerable linkage disequilibria (LD) in a number of regions of the genome that has allowed genetic fine mapping for potential susceptibility genes for the autoimmune connective tissue disease scleroderma, or systemic sclerosis (SSc). In principle, such enhanced background LD in the Choctaws could be caused by population bottleneck event(s) followed by recent population expansion. This investigation utilizes genome-scan data on 175 dinucleotide loci from 76 Choctaw individuals to seek genetic evidence of the demographic history of the Choctaw Nation. Of the 175 loci examined, 105 are in Hardy-Weinberg equilibrium. The average unbiased homozygosity over the 105 loci for the Choctaws (29.3%) is significantly higher than that in the European descent group (20.9%); and when adjusted for sample-size differences, the Choctaw also exhibit a significantly smaller number of segregating alleles (6.65 vs. 8.14) at these loci. Both of these observations are consistent with the trend expected in an isolated population. Comparison of the allele size variance and gene diversity yields an imbalance index (lnbeta) of 0.811 in the Choctaw. Of the 105 loci examined, 93 exhibit excess expected homozygosity in comparison to the expectations of a stepwise mutation model in a population of constant size. Taken together, these observations are consistent with a signature of the recent population size expansion of the Choctaws, preceded by bottleneck event(s).     

Large-scale expansion of cytomegalovirus-specific cytotoxic T cells in suspension culture

Clinical trials in recent years involving the adoptive transfer of antigen-specific cytotoxic T lymphocytes (CTL) have shown promise in restoring immunity against viral infection and reducing tumor burden in patients with solid and hematological malignancies. However, the large cell number required to achieve efficacy, 10(9) to 10(11), makes routine application of adoptive immunotherapy impractical. Investigation into new methods of CTL expansion may be useful in addressing this problem. Use of stirred suspension bioreactors are one such method that may allow large-scale T-cell expansion. Suspension cultures offer advantages over conventional static culture methods, including providing a homogeneous culture environment, and the potential for optimization and control of culture conditions. We generated cytomegalovirus (CMV)-specific CTL and investigated the potential of stirred bioreactor systems for expansion of large cell numbers. We found that CTL can be readily expanded ( > 200-fold) from cryopreserved stocks by nonspecific stimulation in the presence of allogeneic feeder cells and interleukin-2 (IL-2). Activated CTL inoculated into either suspension or static cultures could be subsequently expanded tenfold, and showed similar growth kinetics and metabolism independent of the culture vessel used. Furthermore, CTL remained specific for CMVpp65 peptide through the expansion phases, as demonstrated by pp65-tetramer staining ( > 95% tetramer(+)) and cytotoxicity assays. This study indicates that suspension reactor systems may be useful in large-scale expansion of antigen-specific CTL lines or clones, and may facilitate the advancement of routine adoptive immunotherapy.     

Clumping factor B, a fibrinogen-binding MSCRAMM (microbial surface components recognizing adhesive matrix molecules) adhesin of Staphylococcus aureus, also binds to the tail region of type I cytokeratin 10

The primary habitat of Staphylococcus aureus in humans is the moist squamous epithelium of the anterior nares. We showed previously that S. aureus adheres to desquamated epithelial cells and that clumping factor B (ClfB), a surface-located MSCRAMM (microbial surface components recognizing adhesive matrix molecules) known for its ability to bind to the alpha-chain of fibrinogen, is partly responsible (O'Brien, L. M., Walsh, E. J., Massey, R. C., Peacock, S. J., and Foster, T. J. (2002) Cell. Microbiol. 4, 759-770). We identified cytokeratin 10 (K10) as the ligand recognized by ClfB. Here we have shown that purified recombinant human and murine K10 immobilized on a plastic surface supports adherence of S. aureus in a ClfB-dependent manner. Furthermore, the recombinant A domain of ClfB (rClfB 45-542) bound to immobilized K10 dose-dependently and saturably. Subdomains of human and murine K10 were expressed and purified. The N-terminal head domain (residues 1-145) did not support the binding of rClfB or adherence of S. aureus ClfB+. In contrast, the C-terminal tail domains (human rHK10 452-593, mouse rMK10 454-570) promoted avid binding and adherence. Isothermal titration microcalorimetry and intrinsic tryptophan fluorescence experiments gave dissociation constants for rClfB 45-542 binding to rMK10 454-570 of 1.4 and 1.7 microM, respectively. The tail region of K10 is composed largely of quasi-repeats of Tyr-(Gly/Ser)n. A synthetic peptide corresponding to a typical glycine loop (YGGGSSGGGSSGGY; Y-Y loop peptide) inhibited the adherence of S. aureus ClfB+ to immobilized MK10 to a level of 80%, whereas control peptides had no effect. The KD of rClfB 45-542 for the Y-Y loop peptide was 5.3 microm by intrinsic tryptophan fluorescence. Thus ClfB binds to the glycine loop region of the tail domain of keratin 10 where there are probably multiple binding sites. Binding is discussed in the context of the dock-lock-latch model for MSCRAMM-ligand interactions. We provide an explanation for the molecular basis for S. aureus adherence to the squamous epithelium and suggest that nasal colonization might be prevented by reagents that inhibit this interaction.     

The Australian scincid lizard Menetia greyii: a new instance of widespread vertebrate parthenogenesis

Molecular data derived from allozymes and mitochondrial nucleotide sequences, in combination with karyotypes, sex ratios, and inheritance data, have revealed the widespread Australian lizard Menetia greyii to be a complex of sexual and triploid unisexual taxa. Three sexual species, three presumed parthenogenetic lineages, and one animal of uncertain status were detected amongst 145 animals examined from south-central Australia, an area representing less than one-seventh of the total distribution of the complex. Parthenogenesis appears to have originated via interspecific hybridization, although presumed sexual ancestors could only be identified in two cases. The allozyme and mtDNA data reveal the presence of many distinct clones within the presumed parthenogenetic lineages. This new instance of vertebrate parthenogenesis is a first for the Scincidae and only the second definitive case of unisexuality in an indigenous Australian vertebrate.