Journal: Nature

Article Title: Multiple Dynamin family members collaborate to drive mitochondrial division

doi: 10.1038/nature20555

Figure Lengend Snippet: Dynamin-2 is required for mitochondrial division a , Representative images of HeLa cells expressing mito-BFP that were transfected with scrambled control, Drp1, or Dyn2 siRNA. n = 36 cells for each siRNA treatment. Scale bars = 10 μm. b , Immuno-blots with antibodies against Dyn2, Drp1, and GAPDH in siRNA-treated cells. c, The effect on mitochondrial morphology was quantitated within a 230 μm 2 region of interest (ROI) for mean area per mitochondria (left graph), and mean mitochondria per ROI (right graph). Similar to COS-7 cells, Drp1 or Dyn2–depleted cells had larger mitochondria and less mitochondrion per ROI compared to control cells. These data were obtained from three biological replicate experiments; each for scrambled siRNA, Drp1 siRNA, Dyn2 siRNA treatments. Error bars represent the the standard error of the mean (s.e.m). *p

Article Snippet: COS-7 cells (ATCC-CRL-1651), HeLa cells (ATCC-CCL-2), PtK1 cells (ATCC-CRL-6493) were verified by cytochrome c oxidase subunit I (CO1) interspecies assay, whereas CCL-2-HeLa cells were further verified by short tandem repeat (STR) testing.

Techniques: Expressing, Transfection, Western Blot

Journal: Genome Biology

Article Title: An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar

doi: 10.1186/s13059-018-1618-7

Figure Lengend Snippet: PrimalSeq can be used to measure intrahost variants from a variety of sample types. a We sequenced technical duplicates of Zika virus populations (1000 virus RNA copies each) to identify intrahost single-nucleotide variants (iSNVs) > 3% within each sample. In vitro and in vivo samples were generated using Zika virus strain PRVABC59 (isolated from Puerto Rico, 2015) during infection of Ae. aegypti Aag2 cells (derived from embryos), human HeLa cells (derived from cervical epithelial cells), Ae. aegypti mosquitoes (orally infected), and Indian origin rhesus macaques (subcutaneously infected). For the in vitro and in vivo samples, where the reference population sequence is known, the iSNV frequencies were calculated by change in frequency from pre- to post-infection. Field Zika virus samples from pooled Ae. aegypti and human clinical samples were collected from Florida during the 2016 Zika virus outbreak. b Culex mosquitoes and dead American crows were collected from San Diego County, CA, during 2015 to sequence West Nile virus from field samples (10,000 virus RNA copies each). The iSNV frequencies from the field samples are the minor allele frequencies (maximum frequency = 0.5) because the reference virus sequence was not known. For both ( a and b ), analysis was limited to regions of the genome with > 400× coverage depth in the protein coding sequence and we masked amplicons with primer mismatches from our analysis (gray regions) for direct comparisons of intrahost genetic diversity

Article Snippet: Aag2 (derived from Ae. aegypti embryos [ ]) and HeLa (derived from human cervical epithelial cells, ATCC CCL-2) cells were infected using a multiplicity of infection of 0.01 and supernatant was harvested 5 days post infection.

Techniques: In Vitro, In Vivo, Generated, Isolation, Infection, Derivative Assay, Sequencing