Mechanisms of Olfaction in Insects - ResearchSpace@Auckland ...
Mechanisms of Olfaction in Insects - ResearchSpace@Auckland ...
Mechanisms of Olfaction in Insects - ResearchSpace@Auckland ...
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Identification <strong>of</strong> putative odorant receptors from Epiphyas postvittana 98<br />
Table 4.4: Primers used for amplify<strong>in</strong>g 5‟ RACE products from the two candidate<br />
PRs identified from microarray screen<strong>in</strong>g and the three PR candidates identified from<br />
the 454 transcriptome sequenc<strong>in</strong>g <strong>of</strong> E. postvittana.<br />
EST Identified<br />
from:<br />
Microarray<br />
screen<strong>in</strong>g<br />
454<br />
Transcriptome<br />
sequenc<strong>in</strong>g<br />
Primer Nucleotide Sequence (5’ – 3’)<br />
25174 (outer) AGATTTCTCTGATTATTTACACAATGTATA<br />
25174 (nested) GTTGCACAGTGGCGACAGACCGGCACTTTT<br />
25214 (outer) TTATTACTAAAATTACCCTCGTAACAACAA<br />
25214 (nested) CCCGAATGATATTCCAAATGCTTACAAACT<br />
1032444 (outer) GTGGCCCAAAAGGCGCAAAGCCCGAAT<br />
1032444 (nested) GCCATAACTTCGATACCCACTGCCCTC<br />
1037459 (outer) GCGGGAACAGCGCGCAGTTCACACAAC<br />
1037459 (nested) GAAGTCATCCCCTTTATGTCGACAGCG<br />
1042257 (outer) GTATGAGTATTGTACCGTTTGTGCCCCG<br />
1042257 (nested) CTTCCAGGCAGACAGCCCTGAACACCG<br />
Abridged anchor primer (AAP) GGCCACGCGTCGACTAGTACGGGIIGGGIIGGGIIG<br />
Abridged universal amplification<br />
primer (AUAP)<br />
4.2.16 Bio<strong>in</strong>formatics<br />
GGCCACGCGTCGACTAGTAC<br />
The predicted OR prote<strong>in</strong>s from the low coverage genomic scaffolds were translated<br />
<strong>in</strong>to the six read<strong>in</strong>g frames and compared with the B. mori OR exons for determ<strong>in</strong><strong>in</strong>g<br />
the exons <strong>of</strong> the prote<strong>in</strong>s. The program SplicePredictor<br />
(http://deepc2.psi.iastate.edu/cgi-b<strong>in</strong>/sp.cgi) was also used for predict<strong>in</strong>g the<br />
exon/<strong>in</strong>tron boundaries. A phylogenetic tree was constructed us<strong>in</strong>g the PHYLIP3.6a3<br />
package (Felsenste<strong>in</strong>, 2005) <strong>of</strong> all the known and putative E. postvittana ORs together<br />
with the ORs from B. mori (Warren et al., 2007; Tanaka et al., 2009), H. virescens<br />
(Krieger et al., 2002; Krieger et al., 2004), P. xylostella, M. separata, and D. <strong>in</strong>dica<br />
(Mitsuno et al., 2008).<br />
The prote<strong>in</strong> sequence <strong>of</strong> EpOR34 was submitted to seven different transmembrane<br />
prediction programs <strong>in</strong>clud<strong>in</strong>g HMMTOP (Tusnady and Simon, 2001), TMPred<br />
(H<strong>of</strong>mann and St<strong>of</strong>fel, 1993), TMHMM (Krogh et al., 2001), DAS (Cserzo et al.,<br />
1997), SPLIT (Juretic et al., 1993), TMMOD (Kahsay et al., 2005) and TOPPRED<br />
(Claros and von Heijne, 1994). The predicted TM regions were compared and a