Figs and compares the different dynamic

Figs. 1 and 2 compares the different dynamic of substrate and product as revealed by their distance profiles with the catalytic Ser221 (see Fig. 1) and the r.m.s.d. values as computed considering the ligand atoms only. Fig. 3 compares the pull force profiles along the x axis of the undocking processes for the two simulated complexes as derived by SMD simulations. The analysis of the interaction scores as computed during the SMD runs reveals that the undocking processes are mainly governed by Van der Waals and hydrophobic interactions as parameterized by CHARMM Lennard Jones (L–J) energies (see Fig. 4, [2]) and by MLP Interaction scores (MLPInS see Fig. 5, [3]), while ionic interactions were found to be negligible and roughly constant during the SMD runs (data not shown).
2. Experimental design, materials and methods
Data Affymetrix GeneChip microarray analyses of mRNA isolated from human microvascular endothelial adenylate cyclase (HMVEC) following 24h treatment with 10μM niacin revealed significantly (P<0.05) altered expression of only five protein coding genes at a fold change of greater than 1.3 (Table 1). Changes in the expression of EFCAB4B, NAP1L2, and OR13C8 in response to niacin treatment were confirmed by real time quantitative PCR. We also observed altered expression (>1.3 fold, P<0.05) of 3 non-coding sequences in HMVEC treated with niacin (Table 2), which appear to be small nuclear or nucleolar RNAs (snRNA and snoRNA). Our experiment was conducted using arrays consisting of predominantly coding transcripts (GeneChip Human Gene 1.0 ST, Affymetrix), and was not optimized to rigorously detect changes in the expression of small non-coding sequences.
Experimental design, materials and methods
Acknowledgments We thank David Carter of the London Regional Genomics Center (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca) for performing GeneChip assays and for expert advice regarding bioinformatics analyses of changes in gene expression. This study was funded by an operating Grant from the Canadian Diabetes Association (OG-3-11-3339-NB) to N.M.B.
Data, experimental design, materials and methods In order to disclose the mechanism of high efficient synthesis of silk proteins, in-depth proteomic analysis of the silkworm middle silk gland (MSG) was performed with shotgun LC–MS/MS. The silkworm MSGs at the 3rd day of the fifth instar were dissected and cut into anterior (MSG-A), middle (MSG-M), and posterior (MSG-P) sections. The proteins were separated by 1D SDS-PAGE followed by in-gel trypsin digestion. The digested peptides were analyzed using a Nano-LC–MS/MS system with a LTQ-Orbitrap mass spectrometer. The generated raw MS data were deposited to the ProteomeXchange Consortium [1] via the PRIDE partner repository [2] with the dataset identifier http://www.ebi.ac.uk/pride/archive/projects/PXD003371. We finally identified 643, 594, and 823 proteins from the MSG-A, -M, and -P, respectively, with a FDR of lower than 0.5% [3]. The differential expression of proteins was analyzed with a label-free quantification method. The differentially expressed proteins were further subjected to functional enrichment analysis (Fig. 1).
Acknowledgments This work was supported by the grants from the National Basic Research Program of China (No. 2012CB114601), and Projects of Zhejiang Provincial Science and Technology Plans (No. 2012C12910, and 2013C32048).
Data Next generation sequencing was done for retinoblastoma and medulloblastoma samples. These sequences or “reads” were mapped and compared to a human reference genome and low coverage was determined. This comparison allowed the construction of chromosomal maps with positions and association to cytogenetic bands for an overview of the data. An integrity score was used for a panoramic view of the sequencing data. Expression microarray was also done for the same samples and lists of over and under expressed genes are presented related to regions of gains and losses [1].