Recombination and linkage disequilibrium in Arabidopsis thaliana

Linkage disequilibrium (LD) is a major aspect of the organization of genetic variation in natural populations. Here we describe the genome-wide pattern of LD in a sample of 19 Arabidopsis thaliana accessions using 341,602 non-singleton SNPs. LD decays within 10 kb on average, considerably faster than previously estimated. Tag SNP selection algorithms and 'hide-the-SNP' simulations suggest that genome-wide association mapping will require only 40%-50% of the observed SNPs, a reduction similar to estimates in a sample of African Americans. An Affymetrix genotyping array containing 250,000 SNPs has been designed based on these results; we demonstrate that it should have more than adequate coverage for genome-wide association mapping. The extent of LD is highly variable, and we find clear evidence of recombination hotspots, which seem to occur preferentially in intergenic regions. LD also reflects the action of selection, and it is more extensive between nonsynonymous polymorphisms than between synonymous polymorphisms.     

A single positively selected West Nile viral mutation confers increased virogenesis in American crows

West Nile virus (WNV), first recognized in North America in 1999, has been responsible for the largest arboviral epiornitic and epidemic of human encephalitis in recorded history. Despite the well-described epidemiological patterns of WNV in North America, the basis for the emergence of WNV-associated avian pathology, particularly in the American crow (AMCR) sentinel species, and the large scale of the North American epidemic and epiornitic is uncertain. We report here that the introduction of a T249P amino acid substitution in the NS3 helicase (found in North American WNV) in a low-virulence strain was sufficient to generate a phenotype highly virulent to AMCRs. Furthermore, comparative sequence analyses of full-length WNV genomes demonstrated that the same site (NS3-249) was subject to adaptive evolution. These phenotypic and evolutionary results provide compelling evidence for the positive selection of a mutation encoding increased viremia potential and virulence in the AMCR sentinel bird species.     

Saving the Strong Programme? A critique of David Bloor’s recent work

This article critically appraises David Bloor’s recent attempts to refute criticisms levelled at the Strong Programme’s social constructionist approach to scientific knowledge. Bloor has tried to argue, contrary to some critics, that the Strong Programme is not idealist in character, and it does not involve a challenge to the credibility of scientific knowledge. I argue that Bloor’s attempt to deflect the charge of idealism, which calls on the self-referential theory of social institutions, is partially successful. However, I suggest that although the Strong Programme should not be accused of ‘strong idealism’, it is still vulnerable to the criticism that it entails a form of ‘weak idealism’. The article moves on to argue that, contrary to Bloor, constructionist approaches do challenge the credibility of the scientific knowledge that they analyse. I conclude the article by arguing that sociological analyses of scientific knowledge can be conducted without the weak idealism and the credibility-challenging assumptions of the Strong Programme approach.     

Research fraud: false data confessed

Joseph Cort, a researcher at Mount Sinai Medical School in New York City from 1976 to 1980, has admitted fabricating data on the synthesis of hormone analogues. Cort's research at Mount Sinai was supported principally by a contract from Vega Biochemicals, though he received a small amount of support under a National Institutes of Health grant to his department.     

Genetic engineering: regulation issue is resurrected by EPA

The Environmental Protection Agency is asserting regulatory control over the commercial production of genetically-engineered microorganisms, such as oil-eating bacteria, intended for release into the environment. EPA's legally-complex claim that such organisms are "new chemical substances," and thus subject to the Toxic Substances Control Act (TSCA), raises a challenge to the adequacy of regulation by the National Institute of Health's Recombinant DNA Advisory Committee (RAC) over the commercial and ecological implications of environmental release. Industry, which has been voluntarily adhering to the RAC guidelines, is reluctant to challenge application of the relatively lenient TSCA requirements but eager to see the legal uncertainties resolved.     

Further snag with Stanford patent: filing error claimed in Cohen-Boyer

An attorney for Stanford and the University of California has conceded that there is a serious error in the second Cohen-Boyer genetic engineering patent, but he argues that the patent is still valid. In an August decision to reject the patent, the U.S. Patent Office cited the error as one of several potential flaws. The same potential flaws are found in the original Cohen-Boyer patent, as well. Also in question is whether Robert Helling of the University of Michigan should be included as a co-inventor. Further appeals could delay a final decision until the summer of 1984 or beyond.