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"The model of a network where no one is in charge is a model that can scale," said Douglas E. Van Houweling, the chairman of the Merit Network when the NSFnet backbone was constructed.
A third backbone was constructed, containing L SNPs that were segregating in all layers to fill the N + (I-I u ) + 1 gaps.
The vector backbone was constructed by cutting pRS400 with Pac I and Sac II, rendering the ends blunt with Klenow enzyme and circularizing the vector by T4 DNA ligase.
A second backbone was constructed consisting of I SNPs segregating in the inbred lines, which ensured that for these non-commercial lines there were N + I SNPs already in the candidate panel that were spread across the chromosomes providing a good coverage without big gaps.
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Recombinant vector backbones were constructed so that expression of all shRNAs was driven by the human H1 polymerase III promoter, while expression of the EGFP reporter or of α-synuclein was driven by the human synapsin 1 gene promoter [ 20], both expression cassettes being in a head-to-head arrangement.
A second set of 43 "backbone-specific PSSMs was constructed: one for each designed domain.
We then explored further models (Additional file 1: Table S3), partitioning sloth species into subgroups following a backbone phylogeny, which was constructed from the topologies of several recent phylogenetic analyses [ 1, 5, 10].
The lentiviral backbone plasmid FUW-TfROVA was constructed by insertion of cDNA consisting of the first 118 amino acids of the membrane-anchoring domain of murine transferrin receptor fused downstream with truncated chicken ovalbumin (OVA, amino acids 139 386) into FUW.
The backbone tree for time inference was constructed with RAxML v7.2.8 with the same settings as described above, further forcing monophyly for each of the nodes used for calibration (− g option), plus for the sequences belonging to the crowngroups Afrotheria, Laurasiatheria and Euarchontoglires within each of the clades A1, AICDA, A3Z1, A3Z2 and A3Z3, respectively.
A green fluorescence marker gene eGFP driven by ubiquitin promoter was constructed into pZP200 backbone (http://www.biotech.unl.edu/pzp200) containing the selection marker HptII gene that encodes hygromycin phosphotransferase, was driven by cauliflower mosaic virus (CaMV) 35S promoter (Fig. 2a).
Plasmid-bearing Myc-tagged rat galectin-8 coding sequence under the chicken beta-actin promoter was constructed on the backbone plasmid pQE-TrySystem.
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