Journal: Frontiers in Oncology

Article Title: Progression-Mediated Changes in Mitochondrial Morphology Promotes Adaptation to Hypoxic Peritoneal Conditions in Serous Ovarian Cancer

doi: 10.3389/fonc.2020.600113

Figure Lengend Snippet: Mitochondrial fragmentation is enhanced during aggregation. (A) Representative images of mitochondria in MOSE-L and MOSE-L TIC v spheroids obtained by confocal fluorescent microscopy (scale bar set at 20µm) indicating MitoTracker deep red (MTDR) staining was retained during aggregation and after 48 h incubation prior to MeOH fixation. (B) STORM imaging (scale bar set at 1µm.) with cluster representations of assigned localizations (right) from super resolution images. (C) Mitochondrial fragmentation was quantified using the image-based cluster analysis module with the SRX software. # p < 0.05 different from MOSE-L in normoxia, *p < 0.05 different from MOSE-L in hypoxia.

Article Snippet: Mitochondrial fragmentation was assessed and compared between different cell types and media conditions using the image-based cluster analysis module within the Vutara SRX software.

Techniques: Microscopy, Staining, Incubation, Imaging, Software

Journal: Frontiers in Oncology

Article Title: Progression-Mediated Changes in Mitochondrial Morphology Promotes Adaptation to Hypoxic Peritoneal Conditions in Serous Ovarian Cancer

doi: 10.3389/fonc.2020.600113

Figure Lengend Snippet: Mitochondrial fragmentation is regionally altered in ovarian cancer spheroids. (A) Regional super resolution stochastic optical reconstruction microscopy (STORM) imaging of MOSE-L and MOSE-L TIC v spheroids and cluster representations of assigned localizations. Localizations colored by depth (darker indicates increasing spheroid depth) scale bar set at 1µm. (B, C) Quantitation of mitochondrial fragmentation and morphological structure using the image-based cluster analysis module with the Vutara SRX software system for cluster particle count and surface area. *p < 0.05.

Article Snippet: Mitochondrial fragmentation was assessed and compared between different cell types and media conditions using the image-based cluster analysis module within the Vutara SRX software.

Techniques: Microscopy, Imaging, Quantitation Assay, Software

Journal: Developmental cell

Article Title: Casein kinase 1δ stabilizes mature axons by inhibiting transcription termination of Ankyrin

doi: 10.1016/j.devcel.2019.12.005

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: For a full list of strains and mutations used in this work, see . table ft1 table-wrap mode="anchored" t5 caption a7 REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies N/A Bacterial and Virus Strains BL21 Lab stock TOP 10 Lab stock Biological Samples N/A Chemicals, Peptides, and Recombinant Proteins CK1 delta NEB P6030 Critical Commercial Assays N/A Deposited Data N/A Experimental Models: Cell Lines N/A Experimental Models: Organisms/Strains See KEY RESOURCES TABLE Oligonucleotides See KEY RESOURCES TABLE Recombinant DNA N/A Software and Algorithms SNP filtering This paper: https://github.com/jorgensenlab/WGS-variant-filtering GraphPad prism https://www.graphpad.com/scientific-software/prism/ STAR aligner https://github.com/alexdobin/STAR DESeq2 https://bioconductor.org/packages/release/bioc/html/DESeq2.html DEXseq https://bioconductor.org/packages/release/bioc/html/DEXSeq.html Burrows-Wheeler Aligner http://bio-bwa.sourceforge.net/ Unified genotyper GATK https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8–0/org_broadinstitute_gatk_tools_walkers_genotyper_UnifiedGenotyper.php SNPEff http://snpeff.sourceforge.net/ ApE A plasmid Editor https://jorgensen.biology.utah.edu/wayned/ape/ Fiji – Fiji is just imageJ https://fiji.sc/ SapTrap builder https://www.micropublication.org/journals/biology/m4qq-2x02/ Primer3Plus http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi WormLab https://www.mbfbioscience.com/wormlab Vutara SRX https://www.bruker.com/products/fluorescence-microscopes/vutara-super-resolution-microscopy/overview/srx-software-vutara-super-resolution.html Zeiss LSM5 Pascal No longer supported Zeiss LSM510 No longer supported Zeiss ZEN black https://www.zeiss.com/microscopy/us/products/microscope-software/zen-lite.html Nikon I series https://www.nikon.com/products/microscope-solutions/support/download/software/biological/90i_v24432.htm Other Open in a separate window KEY RESOURCES TABLE kin-20(ox423) and wild-type axon quantification C. elegans hermaphrodites were immobilized for microscopy on a 2% agarose pad in M9 + 25mM sodium azide solution on a glass slide.

Techniques: Recombinant, Software, Plasmid Preparation

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: Two polymorphic cholesterol monohydrate crystal structures form in macrophage culture models of atherosclerosis

doi: 10.1073/pnas.1803119115

Figure Lengend Snippet: Time evolution of plasma membrane crystalline cholesterol domains. (A) Time course of segregated cholesterol domain growth. Data were analyzed for average pixel intensity from the wide-field fluorescence images. The starting point (t = 0) corresponds to cells that were not incubated with acLDL. The fluorescence level at t = 0 was assigned to 1, and the subsequent measurements were normalized to this level. Data are normalized mean (n = 10) ± SE. (B) Average cluster area after different incubation times with acLDL (mean ± SE; n = 3–6). Data were analyzed by using the Vutara SRX statistical package. (C–F) Resolved superresolution localization map after different incubation times with acLDL (C, 10 h; D, 18 h; E, 24 h; F, 36 h). Insets show high magnifications of representative clusters in the STORM data from a top view. [Scale bars (Insets): 100 nm.] The color scales indicate the heights of the domains in the cell: blue, top of the cell; red, bottom of the cell.

Article Snippet: The domain areas were then analyzed for each incubation time point by using the Vutara SRX cluster analysis software (more details are in SI Appendix , SI Materials and Methods ).

Techniques: Clinical Proteomics, Membrane, Fluorescence, Incubation