Bacillus anthracis pXO1 Plasmid Sequence Conservation among Closely Related Bacterial Species

The complete sequencing and annotation of the 181.7-kb Bacillus anthracis virulence plasmid pXO1 predicted 143 genes but could only assign putative functions to 45. Hybridization assays, PCR amplification, and DNA sequencing were used to determine whether pXO1 open reading frame (ORF) sequences were present in other bacilli and more distantly related bacterial genera. Eighteen Bacillus species isolates and four other bacterial species were tested for the presence of 106 pXO1 ORFs. Three ORFs were conserved in most of the bacteria tested. Many of the pXO1 ORFs were detected in closely related Bacillus species, and some were detected only in B. anthracis isolates. Three isolates, Bacillus cereus D-17, B. cereus 43881, and Bacillus thuringiensis 33679, contained sequences that were similar to more than one-half of the pXO1 ORF sequences examined. The majority of the DNA fragments that were amplified by PCR from these organisms had DNA sequences between 80 and 98% similar to that of pXO1. Pulsed-field gel electrophoresis revealed large potential plasmids present in both B. cereus 43881 (341 kb) and B. thuringiensis ATCC 33679 (327 kb) that hybridized with a DNA probe composed of six pXO1 ORFs.     

Gene-specific contributions to mumps virus neurovirulence and neuroattenuation

Mumps virus (MuV) is highly neurotropic and was the leading cause of aseptic meningitis in the Western Hemisphere prior to widespread use of live attenuated MuV vaccines. Due to the absence of markers of virus neuroattenuation and neurovirulence, ensuring mumps vaccine safety has proven problematic, as demonstrated by the occurrence of aseptic meningitis in recipients of certain vaccine strains. Here we examined the genetic basis of MuV neuroattenuation and neurovirulence by generating a series of recombinant viruses consisting of combinations of genes derived from a cDNA clone of the neurovirulent wild-type 88-1961 strain (r88) and from a cDNA clone of the highly attenuated Jeryl Lynn vaccine strain (rJL). Testing of these viruses in rats demonstrated the ability of several individual rJL genes and gene combinations to significantly neuroattenuate r88, with the greatest effect imparted by the rJL nucleoprotein/matrix protein combination. Interestingly, no tested combination of r88 genes, including the nucleoprotein/matrix protein combination, was able to convert rJL into a highly neurovirulent virus, highlighting mechanistic differences between processes involved in neuroattenuation and neurovirulence.     

Sunlight and the survival of enteric bacteria in natural waters

Escherichia coli and some salmonellas were exposed in seawater and freshwater to natural sunlight, visible light of comparable intensity, and light containing a similar proportion of u.v. as natural sunlight but of a much lower intensity. Direct viable bacterial counts and culturable counts on selective and non-selective media were made at intervals. The rate of decrease in numbers of culturable bacteria was significantly faster in seawater than in freshwater when exposed to natural sunlight. No significant difference was found between the rates of decrease in numbers of culturable bacteria in seawater and those in freshwater when bacteria were exposed to light with a small u.v. component of similar intensity. The effect of salinity on loss of culturability is, therefore, more significant in the presence of u.v. radiation. Direct counts by the acridine orange direct viable count method decreased much more slowly than the culturable counts in seawater but comparably with culturable counts in freshwater in natural sunlight. Direct viable counts and culturable counts decreased at a similar rate in seawater and in freshwater in visible light. This may signify the evolution of enteric bacteria towards a viable but non-culturable form in seawater when exposed to natural sunlight. The presence of humic acids significantly reduced loss of culturability but only in low salinity conditions. Salinity appears to be an important factor influencing culturability in bacteria exposed to sunlight.     

A fault detection service for wide area distributed computations

The potential for faults in distributed computing systems is a significant complicating factor for application developers. While a variety of techniques exist for detecting and correcting faults, the implementation of these techniques in a particular context can be difficult. Hence, we propose a fault detection service designed to be incorporated, in a modular fashion, into distributed computing systems, tools, or applications. This service uses well-known techniques based on unreliable fault detectors to detect and report component failure, while allowing the user to trade off timeliness of reporting against false positive rates. We describe the architecture of this service, report on experimental results that quantify its cost and accuracy, and describe its use in two applications, monitoring the status of system components of the GUSTO computational grid testbed and as part of the NetSolve network-enabled numerical solver. This revised version was published online in July 2006 with corrections to the Cover Date.     

To strengthen consensus, consult the stakeholders

CIOMS has been criticised for not adequately consulting stakeholders about its revised ethical guidelines regarding medical research. Political and logistical issues that arise in democratic processes and open exchange of information probably contributed to this exclusion. What might CIOMS have done to be more inclusive and attain broader consensus on its proposed revisions? Consensus is dynamic, and evolves as a community digests new information and perspectives. Engaging the public (and particularly the stakeholders) in discussion about the revisions would have generated broader consensus. It would have encouraged more stakeholders (i.e. researchers, potential research participants, research institutions, or governments) to buy in. CIOMS needs a process to encourage dialogue and stakeholder input. The CIOMS guidelines themselves promote stakeholder consultation and capacity building, but CIOMS has done relatively little to distribute or promote its own guidelines. CIOMS should do more to promote its revised guidelines, and engage stakeholders in dialogue. This paper explores the bioethics debate about universal and relative values to illustrate the value of consultation and consensus building. It concludes that like research sponsors, CIOMS and similar organisations have an ethical responsibility to facilitate capacity building in less developed areas, and to participate more actively in consensus building.     

Genomewide linkage searches for Mendelian disease loci can be efficiently conducted using high-density SNP genotyping arrays

Genomewide linkage searches aimed at identifying disease susceptibility loci are generally conducted using 300–400 microsatellite markers. Genotyping bi-allelic single nucleotide polymorphisms (SNPs) provides an alternative strategy. The availability of dense SNP maps coupled with recent technological developments in highly paralleled SNP genotyping makes it practical to now consider the use of these markers for whole-genome genetic linkage analyses. Here, we report the findings from three successful genomewide linkage analyses of families segregating autosomal recessively inherited neonatal diabetes, craniosynostosis and dominantly inherited renal dysplasia using the Affymetrix 10K SNP array. A single locus was identified for each disease state, two of which are novel. The performance of the SNP array, both in terms of efficiency and precision, indicates that such platforms will become the dominant technology for performing genomewide linkage searches.