SR-Tesseler: a method to segment and quantify localization-based super-resolution microscopy data

2015 ◽  
Vol 12 (11) ◽  
pp. 1065-1071 ◽  
Author(s):  
Florian Levet ◽  
Eric Hosy ◽  
Adel Kechkar ◽  
Corey Butler ◽  
Anne Beghin ◽  
...  
Keyword(s):  
Super Resolution ◽  
Microscopy Data ◽  
Super Resolution Microscopy

Adrenergically induced translocation of red blood cell β-adrenergic sodium-proton exchangers has ecological relevance for hypoxic and hypercapnic white seabass

2021 ◽  
Author(s):  
Till S Harter ◽  
Alexander M Clifford ◽  
Martin Tresguerres
Keyword(s):  
Cellular Response ◽  
Functional Characterization ◽  
Super Resolution ◽  
Adrenergic Stimulation ◽  
Low Oxygen ◽  
Root Effect ◽  
Binding Characteristics ◽  
Atractoscion Nobilis ◽  
Microscopy Data ◽  
Super Resolution Microscopy

White seabass (Atractoscion nobilis) increasingly experience periods of low oxygen (O2; hypoxia) and high carbon dioxide (CO2, hypercapnia) due to climate change and eutrophication of the coastal waters of California. Hemoglobin (Hb) is the principal O2 carrier in the blood and in many teleost fishes Hb-O2 binding is compromised at low pH; however, the red blood cells (RBC) of some species regulate intracellular pH with adrenergically-stimulated sodium-proton-exchangers (β-NHE). We hypothesized that RBC β-NHEs in white seabass are an important mechanism that can protect the blood O2-carrying capacity during hypoxia and hypercapnia. We determined the O2-binding characteristics of white seabass blood, the cellular and sub-cellular response of RBCs to adrenergic stimulation, and quantified the protective effect of β-NHE activity on Hb-O2 saturation. White seabass had typical teleost Hb characteristics, with a moderate O2 affinity (PO2 at half-saturation; P50 2.9 kPa) that was highly pH-sensitive (Bohr coefficient -0.92; Root effect 52%). Novel findings from super-resolution microscopy revealed β-NHE protein in vesicle-like structures and its translocation into the membrane after adrenergic stimulation. Microscopy data were corroborated by molecular and phylogenetic results, and a functional characterization of β-NHE activity. The activation of RBC β-NHEs increased Hb-O2 saturation by ~8% in normoxic hypercapnia, and by up to ~20% in hypoxic normocapnia. Our results provide novel insight into the cellular mechanism of adrenergic RBC stimulation within an ecologically relevant context. β-NHE activity in white seabass has great potential to protect arterial O2 transport during hypoxia and hypercapnia but is less effective during combinations of these stressors.

scholarly journals 3DClusterViSu: 3D clustering analysis of super-resolution microscopy data by 3D Voronoi tessellations

2018 ◽  
Vol 34 (17) ◽  
pp. 3004-3012 ◽  
Author(s):  
Leonid Andronov ◽  
Jonathan Michalon ◽  
Khalid Ouararhni ◽  
Igor Orlov ◽  
Ali Hamiche ◽  
...  
Keyword(s):  
Clustering Analysis ◽  
Super Resolution ◽  
Voronoi Tessellations ◽  
Microscopy Data ◽  
Super Resolution Microscopy

scholarly journals SharpViSu: integrated analysis and segmentation of super-resolution microscopy data

2016 ◽  
Vol 32 (14) ◽  
pp. 2239-2241 ◽  
Author(s):  
Leonid Andronov ◽  
Yves Lutz ◽  
Jean-Luc Vonesch ◽  
Bruno P. Klaholz
Keyword(s):  
Super Resolution ◽  
Integrated Analysis ◽  
Microscopy Data ◽  
Super Resolution Microscopy

scholarly journals Extracting Organelle Membrane Topology from Super-Resolution Microscopy Data

2021 ◽  
Vol 120 (3) ◽  
pp. 279a
Author(s):  
Zach Marin ◽  
Lukas A. Fuentes ◽  
Joerg Bewersdorf ◽  
David Baddeley
Keyword(s):  
Super Resolution ◽  
Membrane Topology ◽  
Microscopy Data ◽  
Organelle Membrane ◽  
Super Resolution Microscopy

scholarly journals Registration and Visualization of Correlative Super-Resolution Microscopy Data

2019 ◽  
Vol 116 (11) ◽  
pp. 2073-2078 ◽  
Author(s):  
Sebastian Reinhard ◽  
Sarah Aufmkolk ◽  
Markus Sauer ◽  
Sören Doose
Keyword(s):  
Super Resolution ◽  
Microscopy Data ◽  
Super Resolution Microscopy

scholarly journals FALCON: fast and unbiased reconstruction of high-density super-resolution microscopy data

2014 ◽  
Vol 4 (1) ◽  
Author(s):  
Junhong Min ◽  
Cédric Vonesch ◽  
Hagai Kirshner ◽  
Lina Carlini ◽  
Nicolas Olivier ◽  
...  
Keyword(s):  
Super Resolution ◽  
High Density ◽  
Microscopy Data ◽  
Super Resolution Microscopy

Super-Resolution Microscopy in Studying the Structure and Function of the Cell Nucleus

Acta Naturae ◽  
2017 ◽  
Vol 9 (4) ◽  
pp. 42-51
Author(s):  
S. S. Ryabichko ◽  
◽  
A. N. Ibragimov ◽  
L. A. Lebedeva ◽  
E. N. Kozlov ◽  
...  
Keyword(s):  
Cell Nucleus ◽  
Super Resolution ◽  
Structure And Function ◽  
And Function ◽  
Super Resolution Microscopy

Structural Evidence of Photoisomerization Pathways in Fluorescent Proteins

2019 ◽  
Author(s):  
Jeffrey Chang ◽  
Matthew Romei ◽  
Steven Boxer
Keyword(s):  
Rational Design ◽  
Fluorescent Protein ◽  
Fluorescent Proteins ◽  
Super Resolution ◽  
Unit Cell Size ◽  
Chlorine Substituent ◽  
Gfp Chromophore ◽  
The One ◽  
Green Fluorescent ◽  
Super Resolution Microscopy

<p>Double-bond photoisomerization in molecules such as the green fluorescent protein (GFP) chromophore can occur either via a volume-demanding one-bond-flip pathway or via a volume-conserving hula-twist pathway. Understanding the factors that determine the pathway of photoisomerization would inform the rational design of photoswitchable GFPs as improved tools for super-resolution microscopy. In this communication, we reveal the photoisomerization pathway of a photoswitchable GFP, rsEGFP2, by solving crystal structures of <i>cis</i> and <i>trans</i> rsEGFP2 containing a monochlorinated chromophore. The position of the chlorine substituent in the <i>trans</i> state breaks the symmetry of the phenolate ring of the chromophore and allows us to distinguish the two pathways. Surprisingly, we find that the pathway depends on the arrangement of protein monomers within the crystal lattice: in a looser packing, the one-bond-flip occurs, whereas in a tighter packing (7% smaller unit cell size), the hula-twist occurs.</p><p> </p><p> </p><p> </p><p> </p><p> </p><p> </p> <p> </p>

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