DOCSLIB.ORG

Supplementary Material: Human Adaptation to Arsenic-Rich Environments

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Supplementary Material: Human Adaptation to Arsenic-Rich Environments Supplementary material: Human Adaptation to Arsenic-Rich Environments 1 15 Total SAC Sub SAC 10 density 5 0 0.0 0.2 0.4 0.6 iAs/AsAdj 25 20 15 density 10 5 0 0.00 0.05 0.10 0.15 0.20 MMA/AsAdj 3.0 2.0 density 1.0 0.0 0.0 0.5 1.0 1.5 2.0 DMA/AsAdj Figure S1: Phenotype density comparisons between the entire study population (385 women, in green) and the sample used for the association study and selection study (124 women, in blue), for 3 types of metabolites: inorganic arsenic (top panel), MMA (middle panel) and DMA (bottom panel), adjusted for the total arsenic content in urine. 2 Figure S2: Manhattan plots (FDR-corrected q-values) for %MMA (upper panel), %DMA (middle panel) and %inorganic arsenic from GWAS analyses. 3 Figure S3: Zoom-in of chromosome 10 region associated with %MMA and %DMA. 4 MMA Chr 3 MMA Chr 6 8 8 LOC440970 CADM2 LAMA2 BC035400 ARHGAP18C6orf191 L3MBTL3 SAMD3 TMEM200A 6 6 ● ● ● ● ● ● ● ● ● (P − value) ●●● ● (P − value) 4 ●● ●● ● 4 ● 10 ●● 10 ● ●●●●● ● ● ● ●●●●●●●●●●● ● ● ●●●● ● ●●●● ● ●●● ● ●●● ● ● ● ●●●● ●●● ● ● ●●●●● ● ●●●●● ● −log ● ● −log ● ●● ● ●● ●● ● ●●● ● ● ● ●●● ●●● ● ● ● ● ●●●●● ●●● ● ●● ● ● ● ● ●●● ●● ● ● ● ● ●●●●●●● ●● ● ●● ● ●●● ●● ● ●●● ● ● ● ● ●●● ● ●●● ●● ● ● ● ● ● ● ● ● 2 ● 2 ●●● ●●● ●●● ● ● ● ● ●●●●● ● ● ●● ● ● ●●● ● ●●● ●● ●●●●●●●●●● ● ● ●●● ●●● ●● ● ●●● ● ●● ●● ● ● ● ●●●●●●●● ● ●● ● ●● ● ●●● ●●●● ●●● ●● ● ●●● ● ● ● ● ● ● ●●●● ●● ●●●●● ●●● ● ● ● ● ● ● ●● ● ● ● ● ●●●● ● ●● ●● ● ● ●● ● ●●●● ● ●● ● ● ● ● ● ●● ● ● ● ● ● ●●●● ●●●● ● ●● ●● ●●●●●● ● ● ●●●●● ● ●●● ●● ● ● ● ● ●● ● ●● ●● ● ● ● ●●● ● ●●●● ●● ●● ● ● ● ● ● ● ● ● ●● ●●●●● ●●●●● ● ● ●●●●●● ●●●●● ●●● ● ● ● ● ●● ● ●● ● ●●● ●●●● ● ●● ●● ● ● ● ●● ●● ●● ● ●●● ●●●● ●● ●●●●●●●● ●●●● ● ●● ●● ●●● ● ●●● ● ●● ● ●● ●● ● ● ● ● ●●●●● ● ● ● ● ● ●●●● ●●● ●● ●●● ● ●● ● ● ● ● ●●●●●● ●●● ●●● ● ● ● ●● ●●●●● ● ●● ● ●●●●● ● ●● ● ● ● ● ●●●● ● ● ● ● ● ● ●●● ●●●● ●●● ●●●● ● ●●●●●●● ● ● ● ●●●●●● ● ●●● ●●● ● ● ● ● ● ● ●●●● ●● ● ●●●●●●●● ● ●●● ● ● ● ● ●● ● ●●●● ● ●●● ●●●●● ●● ●●● ●●● ● ● ● ●● ●● ● ● ●●●●●●●●●●●●●● ● ●● ●● ●●●●●●● ● ● ●●●●●●●●● ● ●●● ● ●●● ●● ●●● ●● ● ●●● ●● ● ● ● ●● ● ● ● ●●● ● ● ●●● ●●●● ●●●●●●● ● ● ●● ●●● ● ●● ● ● ● ●●● ● ● ●●●● ●● ●● ● ●●● ●●● ● ●●●● ●●● ●● ●●●●● ● ● ●●●●●● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●● ●●●●●●●●●●● ● ●●● ● ●●●●●●● ●●●●●●●● ●●●● ● ●●●●● ● ● ● ●●●●●●●●●●●●●●●●●●● ●● ● ●●● ● ●●●●●●●● ●●●●●●●● ●● ●●●●●●● ● ● ●● ●●●●● ●●●●●●● ●● ● ● ●●●●●● ●●● ●●● ●● ●●● ●●● ●● ● ● ●●● ●●●●●●●●● ●●●●●●●●●●●●●●● ● ●●●●●●● ●●●●●●●●● ●●●●●● ● ●● ●●●●●●●●●● ● ● ●● ●●●●●● ●●●●●●●●●●●●● ●●●●●●●●●●●●● ●●● ●●●●●●● ●●●●●● ●●●●●●●●●●●●●●●●●●●● ● ● ●●● ● ●●● ●●● ●●●●●● ●●●●● ● ● ● ●●● ●●●●●● ●● ●● ●●● ●●● ●● ●●● ●●●●●●●● ●● ●● ● ●●● ●●● ●●● ● ●●● ●●●●●● ●●● ●●●●●●●● ●● ●●●●●●●●●●●●●● ●● ● ●● ● ●●●●● ●●●●●●● ●●●●●●●●●●●●●●●● ●● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ● ●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●● ●●●● ●●●●● ●●●●●●●● ●●●●●●●●●●●●● ● ●●● ●● ●●●●●●●● ●●●● ● ●●●●●●●● ●●● ●●●●●●● ●●●●●●● ●● ●●●●● ●● ●●● ● ●●●●●●● ●●● ●●● ●●●●● ●● ● ●●●●● ●●●●●● ●●●●●●●●●●●●● ● ●●●●●●●●●●●●●●●● ●●● ●●●●●●●●●●● ●●● ●●●●●●●●●●●●● ●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●● ●●●●●●●●●●●●●●●●●●● ● ● ●●●●●●●●●●●●●●●●●●●●●●●● ● ●●●●● ● ●●●●●●●● ●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●● ● ●●● ●● ●●●● ● ●●●●●● ●●●● ●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●● ●●●●● ●●●●●●●● ●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●● ●●●● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●● ●●●●●●●●●●●●● ●●●●● ●●●● ●●●●●●●●●●●●●●● ●● ●●●●●●●●●●●●●●●●● ●●●●●●●● ● ●●●●●●●● ● ●●●●●●● ●● ●●● ● ●●●●●●●●●●●●●●●● ● ● ●●●●● ●●●●●●●●●●●●●●●●●●● ● ● ●●●●●●●●●●● ●●●● ● ●●●● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●● ●●●●●●●●●●●●● ●●●●●●● ●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● 0 0 83.5 84.0 84.5 85.0 85.5 86.0 129.5 130.0 130.5 Position in Mb Position in Mb MMA Chr 13 MMA Chr 21 8 8 MZT1BORAPIBF1 KLF5 KLF12AX748190AK056689 COL6A1 COL6A2DKFZp586E1322FTCDC21orf56LSS MCM3AP−AS1MCM3APYBEYC21orf58BC031638PCNT DIP2A S100B PRMT2 6 6 ● ● ● ● ●●● ●● ● ● ●●●● ● ● ● ● ● ●● (P − value) (P − value) ● ● ●● ● ● ●●● 4 ● 4 ●● ● 10 10 ● ● ●● ● ● ● ● ● ●● ● ●● ● ● ●●● −log −log ● ● ● ● ● ● ●● ●●● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ●● ● ● ●●● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● 2 ● 2 ●●● ●●●● ● ● ● ● ● ●● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ●●● ●● ● ● ●● ●●● ●●●● ●●●● ● ● ● ● ● ● ●●●● ● ● ● ● ● ● ●● ● ●●● ●●●●● ● ● ● ●● ● ●● ● ● ●● ●● ● ● ●● ● ● ● ●● ●●●●●●●●● ● ● ● ●● ● ● ● ●●●●● ●● ● ●●● ● ● ● ● ● ●● ● ● ●●●●● ● ● ● ●●●● ●●● ● ● ●●● ●● ●● ● ● ●● ● ●●●●●●●●●●●●● ●● ● ● ● ● ●●● ● ●●●● ● ● ●●● ● ●● ● ●●●● ● ● ● ● ●●● ●● ●●●● ● ● ●●●●●●●●●●● ● ●●● ● ●● ● ● ● ●● ●● ● ● ● ● ● ●● ●● ●● ● ● ●●●● ●● ● ●●●●● ●●● ● ●● ● ● ●●●● ●● ● ● ●●● ● ●●●● ● ●●● ● ● ● ● ● ● ●●●●● ●● ● ●● ● ● ● ● ●● ● ● ● ● ●● ●●● ●● ●●● ●●●●● ●●●●● ●●● ●●●●●●●● ●● ●●●● ●● ● ● ●●●●● ●●● ●● ● ●●●● ●● ●●●● ●●●●●●● ● ● ●● ●● ● ●● ● ● ● ● ● ● ● ●● ● ● ●● ●● ●●●●● ●●● ●●●●● ●● ●● ●● ●●● ● ●● ●●● ● ● ●● ● ●●●●●●● ●● ● ●●●● ●●●●● ●●● ●●● ● ● ●●● ●●●●● ● ● ● ●● ●● ● ● ● ●● ● ●●● ●●●●●● ●● ● ● ●●● ● ●● ●●●● ● ●● ●● ●● ● ● ●● ●●● ● ● ●●●● ● ● ● ●●●●● ●●●●●● ●● ●●●● ● ● ●●●●●● ●● ●● ●● ●● ● ● ●●●●●● ● ● ● ● ● ● ●● ● ● ●●●●●● ●●● ●● ● ● ● ● ●●●●● ●●●●●●●●●●●●●● ●●●●● ● ●●●●●● ●●●● ●●● ●●●●●●● ● ●●●● ● ● ●●●●●● ● ●●● ●● ●●● ●●●●●● ●● ●●●● ●● ● ●●●● ● ●●●●●●●● ● ● ● ●● ●●● ● ● ●●●●● ●●●●●● ●●●●●●● ● ● ●● ●● ●●●●●● ●●● ●●● ● ●●●● ●● ●●●●●● ● ●● ●● ● ●●● ●●●● ●●●●●●● ● ●●●●●●●● ● ●●●●●● ●●● ●● ●●● ●● ●●● ●●● ●● ● ●●●●● ●●●● ●●● ● ●● ●● ●●●●●●●●●●●●●●●●●● ●●● ● ●●●●●●●●●●●●● ● ●●●●● ●●●●●●● ● ●●●● ●●●●●●●● ● ● ●●● ● ● ● ●●●● ●●● ●●● ●● ●●●● ● ●●●●● ● ● ● ●●●●●●●●●●●●●●●●●● ●●●●●●● ● ● ●●●●●●●● ●●●●●●●●●●●●● ● ● ● ●● ● ● ●● ●●● ●●● ● ● ● ●●● ●●●●●●●●●●●●●●●●●●●●●●● ●● ●● ●●●●●●●●● ● ● ● ● ●●● ●●●●●● ●●●●●● ● ● ●● ●●●●●●● ●●● ● ●●●●●●●●●●●●●●● ●●●●●●●● ●●●● ●● ●●● ●●●●● ● ● ●● ●● ●●●●●●●● ● ● ● ●●●●●●●●●● ●●● ●●●●●●● ●●●●●● ●●●●●●●● ●●●●●●● ●● ● ● ●●● ● ●●● ●●● ● ●●●●●●●● ● ●●● ●●●●●●●●●●●●●●●●●●● ●●●●●● ●●●●●●●●●●●●●●● ●●●●●●●●●●●● ●●●●●●● ● ● ● ● ● ●●●●●●●●●●●●●●● ● ●●●●●●●●●●●●●●●●●●● ●●●● ●●●●●●●●● ●●●●●●●●●●●●●● ● ● ● ●●●●●●●●● ●●●●●●●● ●●●● ●●●●●●●● ●●● ● ● ●●●● ●●●●●●●●● ●●● ●●●●● ●●●●●●●●●●●● ●●●● ●●●● ●● ●●●●●●●●●● ●●● ● ●●● ●●●● ●●● ●●● ●●● ● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●● ●● ● ●● ● ● ●●●●● ●●●●●●●●●●● ●●●●●●●●●●●●●●●● ●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●● ●●● ●●●●●●● ●●●●●● ●●●● ●● ●●●●●●● ●● ●●●●●● ●●●● ●●●●●●●●●●● ● ● ●● ●●●●●●●●●●●●●●●●●●● ●●●●●●● ●● ● ●●● ● ● ● ●● ●● ●● ● ●●●●●●● ●●●●●●● ●●●● ●●●●●●●●●●●●● ● ●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●● ● ● ● ● ● ●● ●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●● ●●●● ●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●● ● ●●●●●●●●●●●● ●●●●●●●●● ●● ●●●●●●●●●●●●●●● ● ●●●●●●●●●● ●●●●●●●●●●● ●●●●●●●●●●●●●● ●●●● ● ●●●●●●● ●●●●●● ● ● ●●●●●●●●● ●● ● ●●●●●●●●●●●●●●●●●● ●●●●●●●● ●● ●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ● ●● ● ● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ● ●●●●● ●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●● ●●●●●●●●●●●●●● ●●●●●●●●●●●●●●● ●●●●●●●●● ●●●●●●●●●●● ● ●●●●●●●●● ● ●●●● ●●●● ●● ● ●●●●●● ●● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ● ● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●● ●●●●●●●●●● ●●●●●●●● ● ●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●● ●●●●● ●●●●●● ● ● ● ● ● ● ●●●●●●●●●●● ●●●●●● ●● ● 0 0 72.5 73.0 73.5 74.0 74.5 75.0 47.4 47.5 47.6 47.7 47.8 47.9 48.0 48.1 Position in Mb Position in Mb Figure S4: Zoom-in of regions associated with %MMA. 5 DMA Chr 12 DMA Chr 13 8 8 MUCL1 KIAA0748NEUROD4 OR9K2 OR10A7OR6C74OR6C1OR6C3OR6C75OR6C6OR6C65OR6C76OR6C2OR6C70OR6C68OR6C4 OR10P1METTL7BITGA7BLOC1S1RDH5CD63GDF11SARNPDNAJC14ORMDL2 MZT1BORAPIBF1 KLF5 KLF12AX748190AK056689AX747962LINC00347 6 6 ● ● ● ● ● ● ● ● ●●●● ● ● ● (P − value) (P − value) ● 4 4 10 ●● ● 10 ● ● ● ●●● ● ●● ● ● ● ● ● ● ● ●● −log ●●● ● ● ● −log ● ● ●● ●●●● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ● ● ● ● ●● ● ● ● ● ● ● ● ●●●●●●●●● ●● ● ● ●● ●● ● ● ●● ● ●● ●● ● ●●●●●● ●● ● ● ● ● ● ●●● ● ● ● 2 ● ● ● ● ●● ● ● ● ● 2 ● ●● ● ●● ●●● ● ● ● ● ●● ●● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ●● ● ●● ● ● ● ●● ● ● ●● ● ● ● ●● ●●●●●●●● ● ● ● ● ● ● ● ● ● ●● ● ●●●● ●● ●● ●● ●● ● ●● ● ●●●● ● ●● ● ●●● ● ● ● ●●●●● ●●●●● ● ● ● ●●●● ●● ● ● ● ●●● ● ● ● ●●●● ● ● ● ● ●●● ● ● ● ●●●●● ●●● ● ●● ●●● ● ● ● ●● ● ●●● ●●● ●● ● ●● ● ●●●● ● ● ● ●● ●● ● ● ● ● ● ●● ● ● ●● ● ●● ● ● ● ●● ●● ●● ●● ● ● ● ● ● ●● ● ● ● ●● ● ● ● ●●● ●● ● ● ● ● ● ●●●● ●●● ● ●● ●● ● ● ● ●●● ●●● ●● ●●●● ● ● ●● ● ● ●● ● ●●●● ●●● ● ●●●● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ●● ●● ●● ●● ● ● ●●●● ●●● ●●● ● ● ●● ● ●● ●● ●●● ●● ●●●● ●●●●● ●● ●● ● ● ●●● ●●● ● ● ●●● ● ● ●●●● ● ● ● ●● ● ● ●●● ● ● ● ●● ● ●● ●●●● ●●●●● ● ● ● ● ●●● ● ●●● ● ● ●●●●●● ● ●● ●● ●● ●● ● ●●●●● ● ● ● ● ● ● ● ● ●●● ● ●● ●●●●●●● ● ● ●●●● ●●●●●●● ●●● ●● ● ●●●●● ● ●●●●●●● ● ●●● ●● ● ●●●●●● ●●●●●●●●● ●● ● ● ● ●● ● ● ●● ● ● ●●●● ●●● ●●●● ● ● ●● ●●●●●●●● ● ●●● ● ●●●●● ●●● ●●● ● ● ●● ●● ● ●●●●●●● ●●●●●●●●● ●●● ●● ● ● ●●●●●● ●●● ●●●● ●● ● ●●● ●●● ●●● ●●●●●●●●●●●●●●● ● ● ●● ●● ● ●●● ● ● ● ●●●● ●● ●●● ●● ● ●●●● ● ●●● ●● ● ●●● ●● ●● ●●● ●●●●●●● ● ● ● ●●●●●● ●●●●● ● ●●● ●●●● ● ●●●●●● ●●●●●●●●●● ● ●●●● ●●●● ●● ● ● ●●●●●●●●●● ● ● ●●● ● ●●● ●●● ● ●●●●●●●●●●●●●●●● ●●●●●●● ●● ● ●● ●●●● ●●● ● ●● ●●●●●●●●● ● ●● ●●●● ●● ●●●●●●●●●●●●●●●● ●●● ●●● ●●●● ● ● ●●●● ●● ● ●●●●● ●●●●● ●●●
Load more

Recommended publications
  • Sean Raspet – Molecules
    1. Commercial name: Fructaplex© IUPAC Name: 2-(3,3-dimethylcyclohexyl)-2,5,5-trimethyl-1,3-dioxane SMILES: CC1(C)CCCC(C1)C2(C)OCC(C)(C)CO2 Molecular weight: 240.39 g/mol Volume (cubic Angstroems): 258.88 Atoms number (non-hydrogen): 17 miLogP: 4.43 Structure: Biological Properties: Predicted Druglikenessi: GPCR ligand -0.23 Ion channel modulator -0.03 Kinase inhibitor -0.6 Nuclear receptor ligand 0.15 Protease inhibitor -0.28 Enzyme inhibitor 0.15 Commercial name: Fructaplex© IUPAC Name: 2-(3,3-dimethylcyclohexyl)-2,5,5-trimethyl-1,3-dioxane SMILES: CC1(C)CCCC(C1)C2(C)OCC(C)(C)CO2 Predicted Olfactory Receptor Activityii: OR2L13 83.715% OR1G1 82.761% OR10J5 80.569% OR2W1 78.180% OR7A2 77.696% 2. Commercial name: Sylvoxime© IUPAC Name: N-[4-(1-ethoxyethenyl)-3,3,5,5tetramethylcyclohexylidene]hydroxylamine SMILES: CCOC(=C)C1C(C)(C)CC(CC1(C)C)=NO Molecular weight: 239.36 Volume (cubic Angstroems): 252.83 Atoms number (non-hydrogen): 17 miLogP: 4.33 Structure: Biological Properties: Predicted Druglikeness: GPCR ligand -0.6 Ion channel modulator -0.41 Kinase inhibitor -0.93 Nuclear receptor ligand -0.17 Protease inhibitor -0.39 Enzyme inhibitor 0.01 Commercial name: Sylvoxime© IUPAC Name: N-[4-(1-ethoxyethenyl)-3,3,5,5tetramethylcyclohexylidene]hydroxylamine SMILES: CCOC(=C)C1C(C)(C)CC(CC1(C)C)=NO Predicted Olfactory Receptor Activity: OR52D1 71.900% OR1G1 70.394% 0R52I2 70.392% OR52I1 70.390% OR2Y1 70.378% 3. Commercial name: Hyperflor© IUPAC Name: 2-benzyl-1,3-dioxan-5-one SMILES: O=C1COC(CC2=CC=CC=C2)OC1 Molecular weight: 192.21 g/mol Volume
    [Show full text]
  • The Hypothalamus As a Hub for SARS-Cov-2 Brain Infection and Pathogenesis
    bioRxiv preprint doi: https://doi.org/10.1101/2020.06.08.139329; this version posted June 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. The hypothalamus as a hub for SARS-CoV-2 brain infection and pathogenesis Sreekala Nampoothiri1,2#, Florent Sauve1,2#, Gaëtan Ternier1,2ƒ, Daniela Fernandois1,2 ƒ, Caio Coelho1,2, Monica ImBernon1,2, Eleonora Deligia1,2, Romain PerBet1, Vincent Florent1,2,3, Marc Baroncini1,2, Florence Pasquier1,4, François Trottein5, Claude-Alain Maurage1,2, Virginie Mattot1,2‡, Paolo GiacoBini1,2‡, S. Rasika1,2‡*, Vincent Prevot1,2‡* 1 Univ. Lille, Inserm, CHU Lille, Lille Neuroscience & Cognition, DistAlz, UMR-S 1172, Lille, France 2 LaBoratorY of Development and PlasticitY of the Neuroendocrine Brain, FHU 1000 daYs for health, EGID, School of Medicine, Lille, France 3 Nutrition, Arras General Hospital, Arras, France 4 Centre mémoire ressources et recherche, CHU Lille, LiCEND, Lille, France 5 Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and ImmunitY of Lille (CIIL), Lille, France. # and ƒ These authors contriButed equallY to this work. ‡ These authors directed this work *Correspondence to: [email protected] and [email protected] Short title: Covid-19: the hypothalamic hypothesis 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.08.139329; this version posted June 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
    [Show full text]
  • Lupus Nephritis Supp Table 5
    Supplementary Table 5 : Transcripts and DAVID pathways correlating with the expression of CD4 in lupus kidney biopsies Positive correlation Negative correlation Transcripts Pathways Transcripts Pathways Identifier Gene Symbol Correlation coefficient with CD4 Annotation Cluster 1 Enrichment Score: 26.47 Count P_Value Benjamini Identifier Gene Symbol Correlation coefficient with CD4 Annotation Cluster 1 Enrichment Score: 3.16 Count P_Value Benjamini ILMN_1727284 CD4 1 GOTERM_BP_FAT translational elongation 74 2.50E-42 1.00E-38 ILMN_1681389 C2H2 zinc finger protein-0.40001984 INTERPRO Ubiquitin-conjugating enzyme/RWD-like 17 2.00E-05 4.20E-02 ILMN_1772218 HLA-DPA1 0.934229063 SP_PIR_KEYWORDS ribosome 60 2.00E-41 4.60E-39 ILMN_1768954 RIBC1 -0.400186083 SMART UBCc 14 1.00E-04 3.50E-02 ILMN_1778977 TYROBP 0.933302249 KEGG_PATHWAY Ribosome 65 3.80E-35 6.60E-33 ILMN_1699190 SORCS1 -0.400223681 SP_PIR_KEYWORDS ubl conjugation pathway 81 1.30E-04 2.30E-02 ILMN_1689655 HLA-DRA 0.915891173 SP_PIR_KEYWORDS protein biosynthesis 91 4.10E-34 7.20E-32 ILMN_3249088 LOC93432 -0.400285215 GOTERM_MF_FAT small conjugating protein ligase activity 35 1.40E-04 4.40E-02 ILMN_3228688 HLA-DRB1 0.906190291 SP_PIR_KEYWORDS ribonucleoprotein 114 4.80E-34 6.70E-32 ILMN_1680436 CSH2 -0.400299744 SP_PIR_KEYWORDS ligase 54 1.50E-04 2.00E-02 ILMN_2157441 HLA-DRA 0.902996561 GOTERM_CC_FAT cytosolic ribosome 59 3.20E-33 2.30E-30 ILMN_1722755 KRTAP6-2 -0.400334007 GOTERM_MF_FAT acid-amino acid ligase activity 40 1.60E-04 4.00E-02 ILMN_2066066 HLA-DRB6 0.901531942 SP_PIR_KEYWORDS
    [Show full text]
  • Supplementary Data
    SUPPLEMENTARY METHODS 1) Characterisation of OCCC cell line gene expression profiles using Prediction Analysis for Microarrays (PAM) The ovarian cancer dataset from Hendrix et al (25) was used to predict the phenotypes of the cell lines used in this study. Hendrix et al (25) analysed a series of 103 ovarian samples using the Affymetrix U133A array platform (GEO: GSE6008). This dataset comprises clear cell (n=8), endometrioid (n=37), mucinous (n=13) and serous epithelial (n=41) primary ovarian carcinomas and samples from 4 normal ovaries. To build the predictor, the Prediction Analysis of Microarrays (PAM) package in R environment was employed (http://rss.acs.unt.edu/Rdoc/library/pamr/html/00Index.html). When more than one probe described the expression of a given gene, we used the probe with the highest median absolute deviation across the samples. The dataset from Hendrix et al. (25) and the dataset of OCCC cell lines described in this manuscript were then overlaid on the basis of 11536 common unique HGNC gene symbols. Only the 99 primary ovarian cancers samples and the four normal ovary samples were used to build the predictor. Following leave one out cross-validation, a predictor based upon 126 genes was able to identify correctly the four distinct phenotypes of primary ovarian tumour samples with a misclassification rate of 18.3%. This predictor was subsequently applied to the expression data from the 12 OCCC cell lines to determine the likeliest phenotype of the OCCC cell lines compared to primary ovarian cancers. Posterior probabilities were estimated for each cell line in comparison to the following phenotypes: clear cell, endometrioid, mucinous and serous epithelial.
    [Show full text]
  • Us 2018 / 0305689 A1
    US 20180305689A1 ( 19 ) United States (12 ) Patent Application Publication ( 10) Pub . No. : US 2018 /0305689 A1 Sætrom et al. ( 43 ) Pub . Date: Oct. 25 , 2018 ( 54 ) SARNA COMPOSITIONS AND METHODS OF plication No . 62 /150 , 895 , filed on Apr. 22 , 2015 , USE provisional application No . 62/ 150 ,904 , filed on Apr. 22 , 2015 , provisional application No. 62 / 150 , 908 , (71 ) Applicant: MINA THERAPEUTICS LIMITED , filed on Apr. 22 , 2015 , provisional application No. LONDON (GB ) 62 / 150 , 900 , filed on Apr. 22 , 2015 . (72 ) Inventors : Pål Sætrom , Trondheim (NO ) ; Endre Publication Classification Bakken Stovner , Trondheim (NO ) (51 ) Int . CI. C12N 15 / 113 (2006 .01 ) (21 ) Appl. No. : 15 /568 , 046 (52 ) U . S . CI. (22 ) PCT Filed : Apr. 21 , 2016 CPC .. .. .. C12N 15 / 113 ( 2013 .01 ) ; C12N 2310 / 34 ( 2013. 01 ) ; C12N 2310 /14 (2013 . 01 ) ; C12N ( 86 ) PCT No .: PCT/ GB2016 /051116 2310 / 11 (2013 .01 ) $ 371 ( c ) ( 1 ) , ( 2 ) Date : Oct . 20 , 2017 (57 ) ABSTRACT The invention relates to oligonucleotides , e . g . , saRNAS Related U . S . Application Data useful in upregulating the expression of a target gene and (60 ) Provisional application No . 62 / 150 ,892 , filed on Apr. therapeutic compositions comprising such oligonucleotides . 22 , 2015 , provisional application No . 62 / 150 ,893 , Methods of using the oligonucleotides and the therapeutic filed on Apr. 22 , 2015 , provisional application No . compositions are also provided . 62 / 150 ,897 , filed on Apr. 22 , 2015 , provisional ap Specification includes a Sequence Listing . SARNA sense strand (Fessenger 3 ' SARNA antisense strand (Guide ) Mathew, Si Target antisense RNA transcript, e . g . NAT Target Coding strand Gene Transcription start site ( T55 ) TY{ { ? ? Targeted Target transcript , e .
    [Show full text]
  • University of Copenhagen, Grønnegårdsvej 7, 1870 Frederiksberg, Denmark Cesses Covered Were Related to Each Other
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Copenhagen University Research Information System Copy number variations and genome-wide associations reveal putative genes and metabolic pathways involved with feed conversion ratio in beef cattle Satana, Miguel Henrique de Almedia ; Junior, Gerson Antônio Oliveira ; Cesar, Aline Silva Mello; Freua, Mateus Castelani; Gomes, Rodrigo da Costra ; Silva, Saulo da Luz e ; Leme, Paulo Roberto; Fukumasu, Heidge; Carvalho, Minos Esperandio; Ventura, Ricardo Vierira; Coutinho, Luiz Lehmann; Kadarmideen, Haja; Ferraz, José Bento Sterman Published in: Journal of Applied Genetics DOI: 10.1007/s13353-016-0344-7 Publication date: 2016 Document license: Other Citation for published version (APA): Satana, M. H. D. A., Junior, G. A. O., Cesar, A. S. M., Freua, M. C., Gomes, R. D. C., Silva, S. D. L. E., ... Ferraz, J. B. S. (2016). Copy number variations and genome-wide associations reveal putative genes and metabolic pathways involved with feed conversion ratio in beef cattle. Journal of Applied Genetics, 57(4), 495- 504. https://doi.org/10.1007/s13353-016-0344-7 Download date: 08. apr.. 2020 J Appl Genetics DOI 10.1007/s13353-016-0344-7 ANIMAL GENETICS • ORIGINAL PAPER Copy number variations and genome-wide associations reveal putative genes and metabolic pathways involved with the feed conversion ratio in beef cattle Miguel Henrique de Almeida Santana1,2 & Gerson Antônio Oliveira Junior3 & Aline Silva Mello Cesar3 & Mateus Castelani Freua2 & Rodrigo da Costa Gomes4 & Saulo da Luz e Silva2 & Paulo Roberto Leme2 & Heidge Fukumasu2 & Minos Esperândio Carvalho2 & Ricardo Vieira Ventura2,5 & Luiz Lehmann Coutinho6 & Haja N.
    [Show full text]
  • Explorations in Olfactory Receptor Structure and Function by Jianghai
    Explorations in Olfactory Receptor Structure and Function by Jianghai Ho Department of Neurobiology Duke University Date:_______________________ Approved: ___________________________ Hiroaki Matsunami, Supervisor ___________________________ Jorg Grandl, Chair ___________________________ Marc Caron ___________________________ Sid Simon ___________________________ [Committee Member Name] Dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Neurobiology in the Graduate School of Duke University 2014 ABSTRACT Explorations in Olfactory Receptor Structure and Function by Jianghai Ho Department of Neurobiology Duke University Date:_______________________ Approved: ___________________________ Hiroaki Matsunami, Supervisor ___________________________ Jorg Grandl, Chair ___________________________ Marc Caron ___________________________ Sid Simon ___________________________ [Committee Member Name] An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Neurobiology in the Graduate School of Duke University 2014 Copyright by Jianghai Ho 2014 Abstract Olfaction is one of the most primitive of our senses, and the olfactory receptors that mediate this very important chemical sense comprise the largest family of genes in the mammalian genome. It is therefore surprising that we understand so little of how olfactory receptors work. In particular we have a poor idea of what chemicals are detected by most of the olfactory receptors in the genome, and for those receptors which we have paired with ligands, we know relatively little about how the structure of these ligands can either activate or inhibit the activation of these receptors. Furthermore the large repertoire of olfactory receptors, which belong to the G protein coupled receptor (GPCR) superfamily, can serve as a model to contribute to our broader understanding of GPCR-ligand binding, especially since GPCRs are important pharmaceutical targets.
    [Show full text]
  • Supplementary Materialsupplementary Material
    DOI:10.1071/AN20275_AC CSIRO 2021 Animal Production Science 2021, 61, 731–744 Genome-wide association study between copy number variation regions and carcass and meat quality traits in Nellore cattle Mariana Piatto Berton1,5, Marcos Vinícius de Antunes Lemos1, Tatiane Cristina Seleguim Chud2, Nedenia Bonvino Stafuzza1, Sabrina Kluska1, Sabrina Thaise Amorim1, Lucas Silva Ferlin Lopes1, Angélica Simone Cravo Pereira3, Derek Bickhart4, George Liu4, Lúcia Galvão de Albuquerque1 and Fernando Baldi1 1Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no, CEP 14884-900 Jaboticabal, SP, Brazil 2Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada N1G 2W1 3 Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Rua Duque de Caxias Norte, 225, CEP 13635-900 Pirassununga, SP, Brazil 4 USDA-ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, Maryland 20705, USA; 2Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742, USA 5Corresponding author. E-mail: [email protected] Table S1. Description of significant (P value<0.05) CNVRs associated with beef tenderness (BT) and candidate genes within the CNVRs. CNVR ID BTA Type* Start (bp) End (bp) Size (bp) Low** High** P value FDR CNVR_gain_3 1 Gain 1374155 3404571 2030417 27 45 0.026 0.36 CNVR_gain_644 2 Gain 81291862 83154452 1862591 32 15 0.015 0.40 CNVR_loss_936 5 Loss 22514133 22563988 49856 233
    [Show full text]
  • Online Supporting Information S1: Proteins in Each Positive Regulatory Pathway
    Online Supporting Information S1: Proteins in each positive regulatory pathway Index Proteins DLD,GCK,GPI,HK1,HK2,HK3,ACSS1,ACSS2,ADH1A,ADH1B,ADH4,ADH5,ADH6,ADH7,AK R1A1,ALDH1A3,ALDH1B1,ALDH2,ALDH3A1,ALDH3A2,ALDH3B1,ALDH3B2,ALDH7A1,ALD Positive_1 H9A1,ALDOA,ALDOB,ALDOC,BPGM,DLAT,ENO1,ENO2,ENO3,FBP1,FBP2,G6PC,G6PC2,G ALM,GAPDH,LDHA,LDHAL6A,LDHAL6B,LDHB,LDHC,PCK1,PCK2,PDHA1,PDHA2,PDHB,PF KL,PFKM,PFKP,PGAM1,PGAM2,PGAM4,PGK1,PGK2,PGM1,PGM3,PKLR,PKM2,TPI1 CS,DLD,FH,PC,ACLY,ACO1,ACO2,DLAT,DLST,IDH1,IDH2,IDH3A,IDH3B,IDH3G,MDH1 Positive_2 ,MDH2,OGDH,OGDHL,PCK1,PCK2,PDHA1,PDHA2,PDHB,SDHA,SDHB,SDHC,SDHD,SUCLA2 ,SUCLG1,SUCLG2 GPI,PGD,RPE,TKT,ALDOA,ALDOB,ALDOC,DERA,FBP1,FBP2,G6PD,H6PD,PFKL,PFKM,P Positive_3 FKP,PGLS,PGM1,PGM3,PRPS1,PRPS2,RBKS,RPIA,TALDO1,TKTL1,TKTL2 RPE,AKR1B1,DCXR,GUSB,UGDH,UGP2,UGT1A10,UGT2A1,UGT2A3,UGT2B10,UGT2B11,U Positive_4 GT2B17,UGT2B28,UGT2B4,UGT2B7,XYLB FUK,GCK,HK1,HK2,HK3,KHK,MPI,AKR1B1,ALDOA,ALDOB,ALDOC,FBP1,FBP2,FPGT,GM Positive_5 DS,GMPPA,GMPPB,MTMR1,MTMR2,MTMR6,PFKFB1,PFKFB2,PFKFB3,PFKFB4,PFKL,PFKM ,PFKP,PGM2,PHPT1,PMM1,PMM2,SORD,TPI1,TSTA3,UGCGL1,UGCGL2 GAA,GCK,GLA,HK1,HK2,HK3,LCT,AKR1B1,B4GALT1,B4GALT2,G6PC,G6PC2,GALE,GAL Positive_6 K1,GALK2,GALT,GANC,GLB1,LALBA,MGAM,PGM1,PGM3,UGP2 Positive_7 ACACA,ACACB,FASN,MCAT,OLAH,OXSM Positive_8 ACAA2,ECHS1,HADH,HADHA,HADHB,HSD17B4,MECR,PPT1,HSD17B10 ACAA1,ACAA2,ACADL,ACADM,ACADS,ACADSB,ACADVL,ACAT1,ACAT2,ACOX1,ACOX3,AC SL1,ACSL3,ACSL4,ACSL5,ACSL6,ADH1A,ADH1B,ADH4,ADH5,ADH6,ADH7,ALDH1A3,AL Positive_9 DH1B1,ALDH2,ALDH3A1,ALDH3A2,ALDH7A1,ALDH9A1,CPT1A,CPT1B,CPT1C,CPT2,CYP 4A11,CYP4A22,ECHS1,EHHADH,GCDH,HADH,HADHA,HADHB,HSD17B4,HSD17B10
    [Show full text]
  • Dermal Olfactory Receptor OR51B5 Is Essential for Survival and Collagen Synthesis in Human Dermal Fibroblast (Hs68 Cells)
    International Journal of Molecular Sciences Article Dermal Olfactory Receptor OR51B5 Is Essential for Survival and Collagen Synthesis in Human Dermal Fibroblast (Hs68 Cells) Bomin Son †, Wesuk Kang †, Soyoon Park, Dabin Choi and Taesun Park * Department of Food and Nutrition, BK21 FOUR, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Korea; [email protected] (B.S.); [email protected] (W.K.); [email protected] (S.P.); [email protected] (D.C.) * Correspondence: [email protected]; Tel.: +82-2-2123-3123; Fax: +82-2-365-3118 † These authors contributed equally to this work. Abstract: Skin dermis comprises extracellular matrix components, mainly collagen fibers. A decrease in collagen synthesis caused by several factors, including ultraviolet (UV) irradiation and stress, eventually causes extrinsic skin aging. Olfactory receptors (ORs) were initially considered to be specifically expressed in nasal tissue, but several ORs have been reported to be present in other tissues, and their biological roles have recently received increasing attention. In this study, we aimed to characterize the role of ORs in cell survival and collagen synthesis in dermal fibroblasts. We confirmed that UVB irradiation and dexamethasone exposure significantly decreased cell survival and collagen synthesis in Hs68 dermal fibroblasts. Moreover, we demonstrated that the mRNA expression of 10 ORs detectable in Hs68 cells was significantly downregulated in aged conditions compared with that in normal conditions. Thereafter, by individual knockdown of the 10 candidate Citation: Son, B.; Kang, W.; Park, S.; ORs, we identified that only OR51B5 knockdown leads to a reduction of cell survival and collagen Choi, D.; Park, T. Dermal Olfactory synthesis.
    [Show full text]
  • Investigating the Role of Epigenetics in Scar Maintenance Andrew William
    Investigating the role of epigenetics in scar maintenance Andrew William Stevenson BSc. (Hons.) School of Surgery This thesis is presented for the degree of Doctor of Philosophy at the University of Western Australia 2016 A I II DECLARATION FOR THESES CONTAINING PUBLISHED WORK AND/OR WORK PREPARED FOR PUBLICATION The examination of the thesis is an examination of the work of the student. The work must have been substantially conducted by the student during enrolment in the degree. Where the thesis includes work to which others have contributed, the thesis must include a statement that makes the student’s contribution clear to the examiners. This may be in the form of a description of the precise contribution of the student to the work presented for examination and/or a statement of the percentage of the work that was done by the student. In addition, in the case of co-authored publications included in the thesis, each author must give their signed permission for the work to be included. If signatures from all the authors cannot be obtained, the statement detailing the student’s contribution to the work must be signed by the coordinating supervisor. Please sign one of the statements below. 1. This thesis does not contain work that I have published, nor work under review for publication. Student Signature .................. 2. This thesis contains only sole-authored work, some of which has been published and/or prepared for publication under sole authorship. The bibliographical details of the work and where it appears in the thesis are outlined below. Student Signature ...................
    [Show full text]
  • Supplementary Methods
    doi: 10.1038/nature06162 SUPPLEMENTARY INFORMATION Supplementary Methods Cloning of human odorant receptors 423 human odorant receptors were cloned with sequence information from The Olfactory Receptor Database (http://senselab.med.yale.edu/senselab/ORDB/default.asp). Of these, 335 were predicted to encode functional receptors, 45 were predicted to encode pseudogenes, 29 were putative variant pairs of the same genes, and 14 were duplicates. We adopted the nomenclature proposed by Doron Lancet 1. OR7D4 and the six intact odorant receptor genes in the OR7D4 gene cluster (OR1M1, OR7G2, OR7G1, OR7G3, OR7D2, and OR7E24) were used for functional analyses. SNPs in these odorant receptors were identified from the NCBI dbSNP database (http://www.ncbi.nlm.nih.gov/projects/SNP) or through genotyping. OR7D4 single nucleotide variants were generated by cloning the reference sequence from a subject or by inducing polymorphic SNPs by site-directed mutagenesis using overlap extension PCR. Single nucleotide and frameshift variants for the six intact odorant receptors in the same gene cluster as OR7D4 were generated by cloning the respective genes from the genomic DNA of each subject. The chimpanzee OR7D4 orthologue was amplified from chimpanzee genomic DNA (Coriell Cell Repositories). Odorant receptors that contain the first 20 amino acids of human rhodopsin tag 2 in pCI (Promega) were expressed in the Hana3A cell line along with a short form of mRTP1 called RTP1S, (M37 to the C-terminal end), which enhances functional expression of the odorant receptors 3. For experiments with untagged odorant receptors, OR7D4 RT and S84N variants without the Rho tag were cloned into pCI.
    [Show full text]