A BAC-based physical map of the apple genome

Genome-wide physical mapping is an essential step toward investigating the genetic basis of complex traits as well as pursuing genomics research of virtually all plant and animal species. We have constructed a physical map of the apple genome from a total of 74,281 BAC clones representing approximately 10.5x haploid genome equivalents. The physical map consists of 2702 contigs, and it is estimated to span approximately 927 Mb in physical length. The reliability of contig assembly was evaluated by several methods, including assembling contigs using variable stringencies, assembling contigs using fingerprints from individual libraries, checking consensus maps of contigs, and using DNA markers. Altogether, the results demonstrated that the contigs were properly assembled. The apple genome-wide BAC-based physical map represents the first draft genome sequence not only for any member of the large Rosaceae family, but also for all tree species. This map will play a critical role in advanced genomics research for apple and other tree species, including marker development in targeted chromosome regions, fine-mapping and isolation of genes/QTL, conducting comparative genomics analyses of plant chromosomes, and large-scale genomics sequencing.     

Linking the concept of scale to studies of biological diversity: evolving approaches and tools

Although the concepts of scale and biological diversity independently have received rapidly increasing attention in the scientific literature since the 1980s, the rate at which the two concepts have been investigated jointly has grown much more slowly. We find that scale considerations have been incorporated explicitly into six broad areas of investigation related to biological diversity: (1) heterogeneity within and among ecosystems, (2) disturbance ecology, (3) conservation and restoration, (4) invasion biology, (5) importance of temporal scale for understanding processes, and (6) species responses to environmental heterogeneity. In addition to placing the papers of this Special Feature within the context of brief summaries of the expanding literature on these six topics, we provide an overview of tools useful for integrating scale considerations into studies of biological diversity. Such tools include hierarchical and structural-equation modelling, kriging, variable-width buffers, k -fold cross-validation, and cascading graph diagrams, among others. Finally, we address some of the major challenges and research frontiers that remain, and conclude with a look to the future.     

Bioethics of public commenting: Manipulation,data risk,and public participation in E-Rulemaking

Little scholarly attention has been given to the ethics of public commenting as part of the online federal rule-making process. This essay argues the process of public commenting on federal regulations in the digital era threatens both the integrity of those regulations and the integrity of the individuals they are meant to protect. The ongoing risk is anonymous public commenting is open to manipulation. This risk is particularly salient for eRulemaking with implications for human subjects as was shown in the completed revision process to the Common Rule. Guarding against physical and informational harms requires at least some verification of the identities of public commenters. The burdens of verification access are outweighed by the benefits to authentic participation in e-Rulemaking.     

Development of persistent lymphocytosis in cattle is closely associated with DRB2

Correspondence to: H. A. Lewin.