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The existence and duration of a free-swimming phase during larval development is one of the important factors in determining the linkage of impaired reproductive ability caused by imposex to population decline (Bryan et al. 1986; Gibbs and Bryan 1986; Gibbs et al. 1988 , 1990 , 1991
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The key feature of ContigScape is to determine the linkage of two contigs assembled from 454 or Illumina reads.
To determine the linkage of a mutation to a chromosome, we initially relied on the visual inspection of DNA band intensities on Ethidium bromide-stained agarose gels.
However, in their work, various ubiquitin mutants such as 63K-only or K63R, whose lysine residue is replaced by an arginine residue, were over-expressed to determine the linkage of Parkin-catalyzed ubiquitylation.
Maliepaard et al. [ 8] derived numerous formulas for estimating the linkage between different types of markers by correctly determining the linkage phase of markers.
A Multiplex double ARMS reaction on solid phase (Trans-Cistor) was used to determine the linkage phase of each pair of polymorphic sites and to resolve complex genotypes into constituent haplotypes.
A LOD score of at least 6.0 was used to determine the linkage groups, of which the marker orders were verified at LOD score 3.0.
Because the fate of ubiquitylated proteins is determined by which lysine(s) within ubiquitin is covalently linked via an isopeptide bond to the C terminus of an adjacent ubiquitin (Weissman 2001), we next tried to determine the linkage mode of ubiquitylation catalyzed by Parkin.
Adjudicators were unable to determine the linkage status of 3 pairs, described below, in which sequencing was completed (Supplementary Table S1).
We used JoinMap 4.0 (Van Ooijen 2006) to determine the linkage map of the population (N= 204 markers).
In contrast to RING E3 ligases, HECT ligases determine the linkage specificity of the ubiquitin chain formed in a reaction that proceeds via a thioester intermediate.
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