TY  - JOUR
A1  - Kaltdorf, Kristin Verena
A1  - Schulze, Katja
A1  - Helmprobst, Frederik
A1  - Kollmannsberger, Philip
A1  - Dandekar, Thomas
A1  - Stigloher, Christian
T1  - Fiji macro 3D ART VeSElecT: 3D automated reconstruction tool for vesicle structures of electron tomograms
JF  - PLoS Computational Biology
N2  - Automatic image reconstruction is critical to cope with steadily increasing data from advanced microscopy. We describe here the Fiji macro 3D ART VeSElecT which we developed to study synaptic vesicles in electron tomograms. We apply this tool to quantify vesicle properties (i) in embryonic Danio rerio 4 and 8 days past fertilization (dpf) and (ii) to compare Caenorhabditis elegans N2 neuromuscular junctions (NMJ) wild-type and its septin mutant (unc-59(e261)). We demonstrate development-specific and mutant-specific changes in synaptic vesicle pools in both models. We confirm the functionality of our macro by applying our 3D ART VeSElecT on zebrafish NMJ showing smaller vesicles in 8 dpf embryos then 4 dpf, which was validated by manual reconstruction of the vesicle pool. Furthermore, we analyze the impact of C. elegans septin mutant unc-59(e261) on vesicle pool formation and vesicle size. Automated vesicle registration and characterization was implemented in Fiji as two macros (registration and measurement). This flexible arrangement allows in particular reducing false positives by an optional manual revision step. Preprocessing and contrast enhancement work on image-stacks of 1nm/pixel in x and y direction. Semi-automated cell selection was integrated. 3D ART VeSElecT removes interfering components, detects vesicles by 3D segmentation and calculates vesicle volume and diameter (spherical approximation, inner/outer diameter). Results are collected in color using the RoiManager plugin including the possibility of manual removal of non-matching confounder vesicles. Detailed evaluation considered performance (detected vesicles) and specificity (true vesicles) as well as precision and recall. We furthermore show gain in segmentation and morphological filtering compared to learning based methods and a large time gain compared to manual segmentation. 3D ART VeSElecT shows small error rates and its speed gain can be up to 68 times faster in comparison to manual annotation. Both automatic and semi-automatic modes are explained including a tutorial.
KW  - Biology
KW  - Vesicles
KW  - Caenorhabditis elegans
KW  - Zebrafish
KW  - Septins
KW  - Synaptic vesicles
KW  - Neuromuscular junctions
KW  - Computer software
KW  - Synapses
Y1  - 2017
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-172112
VL  - 13
IS  - 1
ER  - 
TY  - JOUR
A1  - Dütting, Sebastian
A1  - Gaits-Iacovoni, Frederique
A1  - Stegner, David
A1  - Popp, Michael
A1  - Antkowiak, Adrien
A1  - van Eeuwijk, Judith M.M.
A1  - Nurden, Paquita
A1  - Stritt, Simon
A1  - Heib, Tobias
A1  - Aurbach, Katja
A1  - Angay, Oguzhan
A1  - Cherpokova, Deya
A1  - Heinz, Niels
A1  - Baig, Ayesha A.
A1  - Gorelashvili, Maximilian G.
A1  - Gerner, Frank
A1  - Heinze, Katrin G.
A1  - Ware, Jerry
A1  - Krohne, Georg
A1  - Ruggeri, Zaverio M.
A1  - Nurden, Alan T.
A1  - Schulze, Harald
A1  - Modlich, Ute
A1  - Pleines, Irina
A1  - Brakebusch, Cord
A1  - Nieswandt, Bernhard
T1  - A Cdc42/RhoA regulatory circuit downstream of glycoprotein Ib guides transendothelial platelet biogenesis
JF  - Nature Communications
N2  - Blood platelets are produced by large bone marrow (BM) precursor cells, megakaryocytes (MKs), which extend cytoplasmic protrusions (proplatelets) into BM sinusoids. The molecular cues that control MK polarization towards sinusoids and limit transendothelial crossing to proplatelets remain unknown. Here, we show that the small GTPases Cdc42 and RhoA act as a regulatory circuit downstream of the MK-specific mechanoreceptor GPIb to coordinate polarized transendothelial platelet biogenesis. Functional deficiency of either GPIb or Cdc42 impairs transendothelial proplatelet formation. In the absence of RhoA, increased Cdc42 activity and MK hyperpolarization triggers GPIb-dependent transmigration of entire MKs into BM sinusoids. These findings position Cdc42 (go-signal) and RhoA (stop-signal) at the centre of a molecular checkpoint downstream of GPIb that controls transendothelial platelet biogenesis. Our results may open new avenues for the treatment of platelet production disorders and help to explain the thrombocytopenia in patients with Bernard–Soulier syndrome, a bleeding disorder caused by defects in GPIb-IX-V.
KW  - megakaryocytes
KW  - blood platelets
KW  - regulatory circuit downstream
KW  - glycoprotein Ib
Y1  - 2017
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-170797
VL  - 8
IS  - 15838
ER  -