ALBERT

Description: The Cambrian inlier at Beaver Harbour, southern New Brunswick, is now confidently referred to the marginal platform of the late Proterozoic–Early Paleozoic Avalon microcontinent. The sub-trilobitic Lower Cambrian Chapel Island and Random Formations are unconformably overlain by the mafic volcanic-dominated Wade's Lane Formation (new). Late Early Cambrian trilobites and small shelly taxa in the lowest Wade's Lane demonstrate a long Random–Wade's Lane hiatus (middle Terreneuvian–early Branchian). Latest Early–middle Middle Cambrian pyroclastic volcanism produced a volcanic edifice at Beaver Harbour that is one of three known volcanic centers that extended 550 km along the northwest margin of Avalon. Middle Middle Cambrian sea-level rise, probably in the Paradoxides eteminicus Chron, mantled the extinct volcanics with gray-green mudstone and limestone of the Fossil Brook Member. Black, dysoxic mudstone of the upper Manuels River Formation (upper Middle Cambrian, P. davidis Zone) is the youngest Cambrian unit in the Beaver Harbour inlier. Lapworthella cornu (Wiman, 1903) emend., a senior synonym of the genotype L. nigra (Cobbold, 1921), Hyolithellus sinuosus Cobbold, 1921, and probably Acrothyra sera Matthew, 1902a, range through the ca. 8 m.y. of the trilobite-bearing upper Lower Cambrian, and H. sinuosus and A. sera persist into the middle Middle Cambrian. Lapworthella cornu and H. sinuosus replaced the tropical taxa L. schodackensis (Lochman, 1956) and H. micans Billings, 1872, in cool-water Avalon.

Description: Background With multiple strains of various pathogens being sequenced, it is necessary to develop high-throughput methods that can simultaneously process multiple bacterial or viral genomes to find common fingerprints as well as fingerprints that are unique to each individual genome. We present algorithmic enhancements to an existing single-genome pipeline that allows for efficient design of microarray probes common to groups of target genomes. The enhanced pipeline takes advantage of the similarities in the input genomes to narrow the search to short, nonredundant regions of the target genomes and, thereby, significantly reduces the computation time. The pipeline also computes a three-state hybridization matrix, which gives the expected hybridization of each probe with each target. Results Design of microarray probes for eight pathogenic Burkholderia genomes shows that the multiple-genome pipeline is nearly four-times faster than the single-genome pipeline for this application. The probes designed for these eight genomes were experimentally tested with one non-target and three target genomes. Hybridization experiments show that less than 10% of the designed probes cross hybridize with non-targets. Also, more than 65% of the probes designed to identify all Burkholderia mallei and B. pseudomallei strains successfully hybridize with a B. pseudomallei strain not used for probe design. Conclusion The savings in runtime suggest that the enhanced pipeline can be used to design fingerprints for tens or even hundreds of related genomes in a single run. Hybridization results with an unsequenced B. pseudomallei strain indicate that the designed probes might be useful in identifying unsequenced strains of B. mallei and B. pseudomallei.