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All analyses of the MD simulations were carried out using the PTRAJ modules of AMBER 9.0.
Consequently, the analyses of the MD data are based on the behaviors of individual protomers rather than the octomer as a whole.
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As expected from earlier analyses of the M and M' segments [12], M' alone was inactive.
1) Whereas a FACs analysis of the G2 sample is provided in Figure 1B, what do representative analyses of the M and G1 samples look like?
Reviewer #1: 1) Whereas a FACs analysis of the G2 sample is provided in Figure 1B, what do representative analyses of the M and G1 samples look like?
Structural analyses of the M domain show that it contains a large hydrophobic groove (Keenan et al., 1998) capable of housing a hydrophobic signal (Janda et al., 2010).
Sequence analyses of the M, N1, and hemagglutinin genes were performed (GenBank accession nos. HMO12479, HMO 12480, and HMO12481) and confirmed the initial diagnostic detection of pandemic (H1N1) 2009 virus.
In order to asses proliferation rate of TCam-2 seminoma cells, maintained at 1 g or in RPM culture conditions for 24 and 48 hours, we performed immunofluorescence analyses of the M-phase marker p-histone H3.
Our molecular sequence analyses of the M COX2e region indicate (1) relatively high rates of primary and secondary structure evolution, (2) potential instances of site-specific positive selection and (3) an overall pattern of purifying selection leading to the preservation of the TMH/IHL and C-terminus tail sub-regions of M COX2e.
Analyses of the 250 m and 1 km grids with zip-code areas and towns also produced significant associations (HR 1.12, 95% CI 0.99 to 1.26 for 250 m grid, and 1.12, 95% CI 0.97 to 1.29 for town).
Furthermore, secondary structure analyses of the two complete M cox2 sequences available in the GenBank (Anodonta woodiana [GenBank accession no. AB055626] and Inversidens japanensis [GenBank accession no. AB055624]) confirm the presence of two TMHs near the N-terminus of the protein (i.e., the standard metazoan COX2 TMH number and location).
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