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T1- and T2-weighted SE scan sequences were used to detect Gd on the nanoparticles inside the cells.
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The SE scans the input image where the SE centre matches the input image pixel; all pixels within SE shape dimensions are sampled and morphologically evaluated in relation to each other to determine the output pixel.
Detection and annotation of tRNA genes was done making use of ARWEN [ 48] and tRNA scan SE [ 49].
Prior to data collection, Se absorption edge scans were performed to determine the peak, the inflection point and the remote wavelengths.
The MRI was performed on spiral echo (SE) sequence, with scanning directions of cross section, sagittal plane, and coronal plane.
Data from the submitted recording sheets were manually entered into an Access database (DK and SE) or electronically scanned (FI and NO).
Sixteen of the 22 tRNAs were identified by tRNA-scan SE [ 98] with a cove cutoff score of 0.1 and the tRNA-model set to "nematode mito".
The annotation of the cp genome was based on two online available programs: DOGMA (http://dogma.ccbb.utexas.edu/) and tRNA-Scan SE (http://lowelab.ucsc.edu/tRNAscan-SE/) using the default settings.
tRNA genes were identified using tRNA-scan SE 1.21 (lowelab.ucsc.edu/tRNAscan-SE/, last accessed June 30 , 2014 (Lowe and Eddy 1997) and ARWEN 1.2 (http://130.235.46.10/ARWEN/, last accessed June 30 , 2014 (Laslett and Canbäck 2008).
Genomic position and secondary structure from 20 out of 22 transfer RNAs were identified by tRNA-scan SE [ 62], the remaining two by eye inspection of the regions under suspect.
We detected 47 tRNAs in O. tauri using tRNA-scan SE (Lowe and Eddy 1997) and SPLITS (Sugahara et al. 2006), which enabled the identification of six permuted tRNAs (supplementary table S4, Supplementary Material online).
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