Enriched region

The characteristic example of Se-enriched regions is the San Joaquin Valley in California, USA (Figure 1). 

Detection and Definition of Enriched Regions in ChIP-on-Chip Experiments... 

Task General annotation of significantly enriched regions. 

Figure 7.3 Correlation between MAT and Chipinsector results. All enriched regions identified by MAT are aligned at the zero position and correlated by all enriched regions identified by Chipinspector within a window of -10000 to +10000 bp. The curve shows the correlation histogram. The two lines give the mean count (309) and the standard deviation of counts (713) in the entire window.

Results Table 7.1 shows the general statistic of the armotation for the enriched regions. It is obvious that only a small percentage of the ER binding occurs within known promoter regions. 

Table 7.1 Annotation and general statistics of enriched regions.

Result Transcription factor binding sites for the ER-enriched regions (calculated with RegionMiner and CEAS Tables 7.2 and 7.3). 

Erom the RegionMiner analysis it is clear that estrogen receptor elements (EREs) are strongly overrepresented in enriched regions. ER is found at 2116 sequences. The random expectation would be only 825 matches. This results in... 

Figure 7.4 Visualization of enrichment. Color code yellow = promoter green = exon gray= primary transcript orange = enriched region red=TSS red box = promoter prediction.

Method Use RegionMiner to compare the annotated TSR with the modifications in a window of —10 000 to +10 000 bp around the enriched regions (Figure 7.5). 

Figure 7.6 Correiation of open chromatin IP (DNasel hypersensitivity data) with H3K4me3 enrichment. All H3K4me3 enriched regions (symbolized as gray bars) are aligned at the zero position and correlated with the open chromatin...

The Pu-enriched region also contained Am, REE, Zr, and Ru however, americium and the REE were present at lower than expected levels. The depletion of REE and Am in the precipitated Pu-layer is interesting as these elements are usually considered to be good analogues for Pu chemistry. The chemistry of Pu has been recently complicated by the discovery of Pu02+JC (Haschke et al. 2000 Conradson et al. 

Software predictions suggest a number of potential phosphorylation sites in the coronin 7 protein. The highest E value predictions are for potential MAP kinase phosphorylation sites at serine residue 442 and threonines 497 and 733, cdc2 sites at S-450 and S-775, cdk5 at S-437, PKC sites at S-7, S-465 and T-654 and Src sites at tyrosine residues 288 and 758. Not surprisingly, many serine and threonine phosphorylation predictions concentrate in the low complexity PST-enriched region. Although it remains to be elucidated which of the predicted sites are relevant in vivo, at least some of them have been experimentally demonstrated to be phosphorylated in vitro (see below). 

Vacha, F., Sarafis, V., Benediktyova, B.L., Valenta, J., Vacha, M., Sheue, C.-R. and Nedbal, L. (2007) Identification of Photosystem I and Photosystem II enriched regions of thylakoid membrane by optical microimaging of cryo-fluorescence emission spectra and of variable fluorescence. Micron, 38, 170-175. 

Fig. 8 Illustration of the RSA computer simulations based on the model of heterogeneous surfaces. Annexin Al binds irreversibly with ki to circular POPS-rich domains in the membrane, while the adsorption of the protein to POPC-enriched regions is reversible and described by the two rate constants kon and fcoff- The mass transport to the surface is taken into account by the rate constant fctr...

Figure 23. (iXAFS results for Pu on tuff. Top The k1-weighted Pu-EXAFS spectra for one Pu-enriched region on the tuff. Bottom the complementary Fourier-transformed data of Pu-EXAFS spectra showing the pseudo-radial distribution of atoms around the Pu at the region examined (from Duff etal. 2001). 

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