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The SH3 domain mutations were prepared using the Quikchange protocol (Statagene) and verified by DNA sequencing.
Recombinant infectious clones of HIV-1 carrying various mutations were prepared using standard site-directed mutagenesis protocols as described previously [38].
All mutations were prepared by PCR-based mutagenesis of the 0.21 kb promoter region in pcDNA3.1Luc plasmid, using the QuickChange II XL Site-directed mutagenesis kit (Stratagene) according to manufacturer's procedures and oligonucleotide primers as in supplementary Table 1.
To test the functional relevance of the candidate transcription factor binding sites, point mutations were prepared to inactivate each of the identified conserved motifs in the context of the −219/+114 FSCN1 luciferase reporter plasmid (Fig. 4A, Fig. 5A).
ErbB2 exon 20 insertion mutations were prepared using the method described above.
Site-specific point mutations were prepared with the QuikChange site-directed mutagenesis kit (Stratagene) and expressed and purified following the same protocol as described for wild-type crammer.
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By comparing the sets from 12 M2' plants to each other, a variant filter to distinguish unrelated variation from mutations was prepared based on a common frequency threshold of 20%%.
To examine the effect of Met → Val or Met → Leu substitution on amyloidogenesis and seeding efficiency, four single-mutation peptides were prepared; these were bPrPM109V, bPrPM129V, bPrPM134V, and bPrPM129L, with the respective mutations M109 → V, M129 → V, M134 → V, and M129 → L.
To compare the effects of mutating V/L/I at these positions into M, three single-mutation peptides were prepared: these were bPrPV112M, bPrPL138M, and bPrPI139M, containing, respectively, V112 → M, L138 → M, and I139 → M.
The mutation matrices were prepared using the same procedure described in [ 11].
One-day-old protonemal tissue for repair and mutation experiments were prepared from one-week-old tissue scraped from plates, suspended in 8 mL of BCD medium, and sheared by a T25 homogenizer (IKA, Germany) at 10 000 rpm for two 1-minute cycles and let 24 hours to recover in cultivation chamber with gentle shaking at 100 rpm.
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mutations were genotyped
mutations were described
mutations were detected
mutations were eliminated
mutations were analyzed
mutations were verified
mutations were inherited
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