Journal: Frontiers in Cell and Developmental Biology

Article Title: Stable knockdown of Drp1 improves retinoic acid-BDNF-induced neuronal differentiation through global transcriptomic changes and results in reduced phosphorylation of ERK1/2 independently of DUSP1 and 6

doi: 10.3389/fcell.2024.1342741

Figure Lengend Snippet: Generating a stably depleted human neuroblastoma cell line for Drp1 using lentiviral technology. Using lentiviral technology, DNM1L/Drp1 expression was downregulated in the SH-SY5Y human neuroblastoma cell line. HEK293T cells were transfected with the mixture of packaging-enveloping vectors and the plasmid pGIPZ-GFP containing the shRNA target sequence to produce the virus. Cells stably expressing empty pGIPZ-GFP were used as a control. Transduction of SH-SY5Y neuroblastoma cells was conducted using 8 μg/mL polybrene, and cells were maintained in media containing 1.25 μg/mL puromycin for selection. (A) The qPCR analysis shows successful silencing of DNM1L in shDrp1 cells. The sequences of primer #1 and #2 are listed in . (B) Total cell lysates from control and shDrp1 cells were separated by SDS-PAGE to analyze Drp1 protein levels. Actin was used as the loading control. (C) Representative transmission electron microscopy images of mitochondria in control (upper panel) and shDrp1 cells (lower panel). Cell and mitochondria contours were manually segmented. Only mitochondria with visible and intact internal membranes were considered for consecutive analyses (insets). Mitochondria were displayed using a default shared colormaps option of Amira 3D with 8 distinct colors. Colors are independent of values; their purpose is to show the mitochondria used for further analyses. Amira 3D (version 2022.1; ThermoFischer Scientific) image analysis software was used to analyze the numerical parameters of the segmented structures. The clustering of mitochondria was quantified as a measure of the closest neighbor of each mitochondrion. Mitochondria were color-coded based on their distance from the closest neighbor. Distance values in μm were extracted using the Label Analysis module of Amira 3D. These distance values were displayed using the Colorize by Measure module of Amira 3D, which colored the mitochondria according to the values. Color scales were added using the Colormap Legend module from Amira 3D. A scale bar was added by the software to the upper right corner of each image. Quantitative analyses of average inside mitochondrial length (μm) (D) , total inside mitochondrial length (μm) (E) , average (F) and total (G) mitochondrial area (μm 2 ), and average mitochondrial distance (μm) (H) . Mann-Whitney test was used for statistical analyses. Only p values p < 0.05 are considered statistically significant.

Article Snippet: Color scales were added using the Colormap Legend module from Amira 3D.

Techniques: Stable Transfection, Expressing, Transfection, Plasmid Preparation, shRNA, Sequencing, Virus, Control, Transduction, Selection, SDS Page, Transmission Assay, Electron Microscopy, Software, MANN-WHITNEY

Journal: Cognitive Research: Principles and Implications

Article Title: More of what? Dissociating effects of conceptual and numeric mappings on interpreting colormap data visualizations

doi: 10.1186/s41235-023-00482-1

Figure Lengend Snippet: Example colormaps representing A congruent and B incongruent domain concepts. A Colormap of the Universal Health Coverage Index featuring a dark-more encoding (darker colors encode larger index values, which correspond to more coverage). Figure from Ortiz-Ospina and Roser . B Two colormaps representing country ranks based on the Economic Complexity Index. In B , left (original figure), darker colors encode for more complexity (lower ranks, which are smaller numbers). In B , right, the color scale has been inverted, such that darker colors encode for less complexity (higher ranks, which are larger numbers). Figures adapted from Ortiz-Ospina and Beltekian ; Simoes and Hidalgo

Article Snippet: Other known relational associations for colormaps include the opaque-is-more bias (Schloss et al., ) and the hotspot-is-more bias (Schott, ; Sibrel et al., ).

Techniques:

Journal: Communications Biology

Article Title: Scanning single molecule localization microscopy (scanSMLM) for super-resolution volume imaging

doi: 10.1038/s42003-023-05364-2

Figure Lengend Snippet: a Fluorescence image of a typical NIH3T3 cells transfected with Dendra2-Actin plasmid DNA. b A small section of the cell is imaged using scanSMLM and 3D super-resolved volume is reconstructed, where colormap represents the depth. c Few 3D sections are displayed that show Actin filaments at different depths in a single cell. d , e Volume views along with the diagonal views (along lines Q1, Q2 and Q3) showing the arrangement of single Dendra2-Actin molecules. Scale = 1 μm. Additional details can be found in Supplementary note .

Article Snippet: The depth is represented by colormap (see colorbar scale). c Few chosen single mitochondria (R1, R2, R3) are resolved that shows the distribution of single molecules (Meos-Tom20). d The corresponding line intensity plots suggests the distribution of single molecules on mitochondria (L1, L2, L3). e , f Volume views and the corresponding diagonal views (along lines, Q1, Q2, Q3) display the organization of single molecules across cell depths in a single mitochondria.

Techniques: Fluorescence, Transfection, Plasmid Preparation

Journal: Communications Biology

Article Title: Scanning single molecule localization microscopy (scanSMLM) for super-resolution volume imaging

doi: 10.1038/s42003-023-05364-2

Figure Lengend Snippet: a A high-resolution fluorescence image of mitochondria in a NIH3T3 cell (transfected with mEos-Tom20 plasmid DNA). b A section of the mitochondrial network is super-resolved and the volume is reconstructed. The depth is represented by colormap (see colorbar scale). c Few chosen single mitochondria (R1, R2, R3) are resolved that shows the distribution of single molecules (Meos-Tom20). d The corresponding line intensity plots suggests the distribution of single molecules on mitochondria (L1, L2, L3). e , f Volume views and the corresponding diagonal views (along lines, Q1, Q2, Q3) display the organization of single molecules across cell depths in a single mitochondria. Additional details can be found in Supplementary note .

Article Snippet: The depth is represented by colormap (see colorbar scale). c Few chosen single mitochondria (R1, R2, R3) are resolved that shows the distribution of single molecules (Meos-Tom20). d The corresponding line intensity plots suggests the distribution of single molecules on mitochondria (L1, L2, L3). e , f Volume views and the corresponding diagonal views (along lines, Q1, Q2, Q3) display the organization of single molecules across cell depths in a single mitochondria.

Techniques: Fluorescence, Transfection, Plasmid Preparation