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Computational synthesis of cortical dendritic morphologies
<p>Neuronal morphologies provide the foundation for the electrical behavior of neurons, the connectomes they form, and the dynamical properties of the brain. Comprehensive neuron models are essential for defining cell types, discerning their functional roles, and investigating brain disease related dendritic alterations. However, a lack of understanding of the principles underlying neuron morphologies has hindered attempts to computationally synthesize morphologies for decades. We introduce a synthesis algorithm based on a topological descriptor of neurons, which enables the rapid digital reconstruction of entire brain regions from few reference cells. This topology-guided synthesis generates dendrites that are statistically similar to biological reconstructions in terms of morpho-electrical and connectivity properties and offers a significant opportunity to investigate the links between neuronal morphology and brain function across different spatio-temporal scales. Synthesized cortical networks based on structurally altered dendrites associated with diverse brain pathologies, revealed principles linking branching properties to the structure of large-scale networks.</p> <p> </p> <p>We provide here the original biological reconstructions, the artificially generated cells and related data (electrical traces, connectivity of artificial networks) that were used for the analysis of the paper "Computational synthesis of cortical dendritic morphologies" to appear in Cell Reports.</p>
Correlative microscopy of rat cultured hippocampal pyramidal cell from 40x confocal imaging to super-resolution 93x 3D STED of dendritic spines
<p>This dataset contain multi-scale image of rat hippocampal pyramidal cell related to our paper "<em>From tissues to segmentation: a modular framework for multi-scale neuron isolation</em>" by Cauzzo et al. <strong>Nature Comm (2024).</strong></p>
Interferon-induced activation of dendritic cells and monocytes by yellow fever vaccination correlates with early antibody responses
<p>Bulk RNA-seq analysis of sorted subpopulations isolated from PBMC of yellow fever vaccinees from before and 3, 7, 14 and 28 days after vaccination and single cell RNA-seq analysis of sorted DC and monocytes fractions isolated from PBMC of of yellow fever vaccinees from before and 3 and 7 days after vaccination.</p>
Table 1 in Taming an ichnotaxonomical Pandora's box: revision of dendritic and rosetted microborings (ichnofamily: Dendrinidae)
<p><b>Table 1.</b> Studied material, listed by original ichnotaxon nomen and in order of publication date, with specification of collection, inventory number and investigation methods. Present type assignments: H = holotype, P = paratype, L = lectotype, PL = paralectotype(s), S = syntype(s), N = neotype. Inventory numbers from the Institut für Geowissenschaften, Goethe-Universität, Frankfurt include the sample code on the stub in brackets. Continued on next page.</p><table><thead><tr><th><b>Publication</b></th><th><b>Ichnotaxon</b></th><th><b>Inventory numbers</b></th><th><b>Collection</b></th><th><b>Comments</b></th></tr></thead><tbody><tr><th>von Hagenow</th><td><i>Talpina ramosa</i></td><td>MB.Po 2128.1 (L)</td><td>Museum für Naturkunde, Berlin,</td><td>loaned for</td></tr><tr><th>(1840)</th><td>T. solitaria Talpina ramosa</td><td>MB.W. 0864 (L+PL) MMG: MvK 530 (PL)</td><td>Germany Senckenberg Naturhistorische</td><td><i>macrophotography and microscopy</i></td></tr><tr><th></th><td><i>T. solitaria</i></td><td>MMG: MvK 532 (PL)</td><td>Sammlungen, Dresden, Germany</td><td></td></tr><tr><th>von Hagenow</th><td><i>Talpina foliacea</i></td><td>MB.Po 2130.1–3 (S)</td><td>Museum für Naturkunde, Berlin,</td><td>loaned for</td></tr><tr><th>(unpubl.)</th><td>T. sentiformis Talpina foliacea</td><td>MB.W. 0866 (S) MMG: MvK 529 (S)</td><td>Germany Senckenberg Naturhistorische</td><td><i>macrophotography and microscopy</i></td></tr><tr><th></th><td><i>T. sentiformis</i></td><td>MMG: MvK 530 (S)</td><td>Sammlungen, Dresden, Germany</td><td></td></tr><tr><th>Morris (1851)</th><td><i>Talpina dendrina</i></td><td>PI A 559 (L+PL)</td><td>Natural History Museum,</td><td>loaned for</td></tr><tr><th></th><td></td><td></td><td>London, UK</td><td>macrophotography, microscopy and μCT</td></tr><tr><th>Clarke (1908)</th><td><i>Clionolithes radicans</i></td><td>6702 (L+PL) 6700 (PL) 6701</td><td>New York State Museum, New York, USA</td><td>series of images provided by collection manager</td></tr><tr><th></th><td><i>C. palmatus</i></td><td>6697 (L)</td><td></td><td></td></tr><tr><th></th><td></td><td>6698 (PL)</td><td></td><td></td></tr><tr><th>Thomas (1911)</th><td><i>Clionolithes hackberryensis</i></td><td>2807, 2808, 2809, 2810 (S)</td><td>Palaeontology depository, University of Iowa, Iowa City, USA</td><td>loaned for microscopy</td></tr><tr><th>Lees & Thomas (1918)</th><td><i>Clionolithes lizardensis</i></td><td>2811, 2812, 2813 (S)</td><td>Palaeontology depository, University of Iowa, Iowa City, USA</td><td>loaned for microscopy</td></tr><tr><th>Ruedemann (1925)</th><td><i>Clionolithes quaerens</i></td><td>6699 (H)</td><td>New York State Museum, Albany, USA</td><td>series of images provided by collection manager</td></tr><tr><th>Fenton & Fenton</th><td><i>Clionolithes fossiger</i></td><td>4811 (H)</td><td>Carnegie Museum of Natural</td><td>series of images</td></tr><tr><th>(1932)</th><td><i>C. hackberryensis</i></td><td>4810, 4812 (P) 4804, 4805, 4806, 4807, 4808, 4809</td><td>History, Pittsburgh, USA</td><td>provided by collection manager</td></tr><tr><th></th><td><i>Clionolithes irregularis</i></td><td>PAL 84693 (H)</td><td>Smithsonian Institution, National Museum of Natural History, Washington DC, USA</td><td>loaned for microscopy</td></tr><tr><th>Mägdefrau</th><td><i>Dendrina belemniticola</i></td><td>MLU.Mäg1937.IV.1 (L)</td><td>Institut für Geowissenschaften</td><td>loaned for</td></tr><tr><th>(1937)</th><td></td><td>MLU.Mäg1937.IV.6 MLU.Mäg1937.IV.8</td><td>und Geographie, Halle, Germany</td><td>macrophotography, microscopy and scans of glass negatives</td></tr><tr><th></th><td><i>D. anomala</i></td><td>MLU.Mäg1937.IV. 5 (H) (glass negative only)</td><td></td><td></td></tr><tr><th></th><td></td><td>MLU.Mäg1937.IV.10 (N)</td><td></td><td></td></tr><tr><th></th><td><i>D. incomposita</i></td><td>MLU.Mäg1937.IV.2 (L+PL)</td><td></td><td></td></tr><tr><th></th><td><i>D. minor</i></td><td>MLU.Mäg1937.IV.3 (S)</td><td></td><td></td></tr><tr><th></th><td><i>Calcideletrix flexuosa</i></td><td>MLU.Mäg1937.IV.4 (H)</td><td></td><td></td></tr><tr><th></th><td><i>C. breviramosa</i></td><td>MLU.Mäg1937.IV.9 (H)</td><td></td><td></td></tr><tr><th></th><td><i>Dictyoporus nodosus</i></td><td>MLU.Mäg1937.IV.10 (H)</td><td></td><td></td></tr><tr><th></th><td><i>Abeliella riccioides</i></td><td>MLU.Mäg1937.V.1 (L+PL)</td><td></td><td></td></tr><tr><th></th><td><i>A. procera</i></td><td>MLU.Mäg1937.V.2 (L+PL)</td><td></td><td></td></tr><tr><th>Solle (1938)</th><td><i>Olkenbachia hirsuta</i></td><td>XXVI 165 a, d, e, f, i (3x), n (4x), s (3x) (P)</td><td>Senckenberg, Frankfurt, Germany</td><td>photographed at collection and/or loaned</td></tr><tr><th></th><td>O. pannosa O. simplex</td><td>XXVI 166a (H) XXVI 167a (H)</td><td></td><td><i>for microscopy and SEM</i></td></tr><tr><th></th><td><i>" Chondrites " symmetricus</i></td><td>XXX 415a (H)</td><td></td><td></td></tr><tr><th></th><td></td><td>XXX 415b (P)</td><td></td><td></td></tr><tr><th></th><td><i>"C." multifilum</i></td><td>XXX 414b (P)</td><td></td><td></td></tr><tr><th>Talent (1963)</th><td><i>Clionolithes sollei</i></td><td>P60575 (H+P)</td><td>Museum Victoria, Melbourne, Australia</td><td>series of images provided by collection manager</td></tr></tbody></table>
Table 4 in Taming an ichnotaxonomical Pandora's box: revision of dendritic and rosetted microborings (ichnofamily: Dendrinidae)
<p><b>Table 4.</b> Compilation of informally named records of dendrinid microborings (in order of publication), together with the identifications based on the revised dendrinid ichnotaxonomy.? = uncertain; p = partim. Continued on next page.</p><table><thead><tr><th><b>Informal name</b></th><th><b>Publication</b></th><th><b>Identification</b></th></tr></thead><tbody><tr><th>Spinate Microborings</th><td>Edwards & Perkins (1974)</td><td>? <i>Rhopalondendrina contra</i> isp. nov.</td></tr><tr><th>Spinate boring form</th><td>Zeff & Perkins (1979)</td><td>? <i>Rhopalondendrina acanthina</i> isp. nov.</td></tr><tr><th>Algal form B</th><td>Budd & Perkins (1980)</td><td>? <i>Calcideletrix fastigata</i> comb. nov.</td></tr><tr><th>Sponge form B</th><td>Budd & Perkins (1980)</td><td>? <i>Rhopalondendrina acanthina</i> isp. nov.</td></tr><tr><th>Morfotipo B2</th><td>Mayoral (1988)</td><td>? <i>Calcideletrix fastigata</i> comb. nov.</td></tr><tr><th>Morfotipo B3</th><td>Mayoral (1988)</td><td>? <i>Calcideletrix fastigata</i> comb. nov.</td></tr><tr><th>Morfotipo B4</th><td>Mayoral (1988)</td><td>? <i>Pyrodendrina villosa</i> isp. nov.</td></tr><tr><th>Morfotipo B5</th><td>Mayoral (1988)</td><td><i>= Nododendrina europaea</i> comb. nov.</td></tr><tr><th>J-Form C-1</th><td>Glaub (1988)</td><td><i>= Nododendrina europaea</i> comb. nov.</td></tr><tr><th>J-Form C-2</th><td>Glaub (1988)</td><td>? <i>Entobia</i> isp.</td></tr><tr><th>J-Form F-4</th><td>Glaub (1988)</td><td><i>= Rhopalondendrina avis</i> isp. nov.</td></tr><tr><th>Sponge, Form 1</th><td>Günther (1990)</td><td>= <i>Rhopalondendrina tigris</i> isp. nov.</td></tr><tr><th>Rosetten-Form B</th><td>Hofmann & Vogel (1992)</td><td>= <i>Calcideletrix anomala</i> comb. nov.</td></tr><tr><th>Rosetten-Form D</th><td>Hofmann & Vogel (1992)</td><td>= <i>Dendrina belemniticola</i></td></tr><tr><th>Rosetten-Form E</th><td>Hofmann & Vogel (1992)</td><td>= <i>Dendrina belemniticola</i></td></tr><tr><th>Rosetten-Form G</th><td>Hofmann & Vogel (1992)</td><td>= <i>Calcideletrix flexuosa</i></td></tr><tr><th>Dendroid-Form I</th><td>Schmidt (1992)</td><td>? <i>Entobia</i> isp.</td></tr><tr><th>Dendroid-Form II</th><td>Schmidt (1992)</td><td>? <i>Clionolithes radicans</i></td></tr><tr><th>Dendroid-Form III</th><td>Schmidt (1992)</td><td>? <i>Rhopalondendrina acanthina</i> isp. nov.</td></tr><tr><th>Echinoid form</th><td>Radtke (1993)</td><td>= <i>Rhopalondendrina tigris</i> isp. nov.</td></tr><tr><th><i>Cliona</i> sp. 1</th><td>Schmidt & Freiwald (1993)</td><td><i>= Nododendrina europaea</i> comb. nov.</td></tr><tr><th>Semidendrina-Form</th><td>Glaub (1994)</td><td><i>= Nododendrina europaea</i> comb. nov.</td></tr><tr><th>Fastigatdendrina-Form</th><td>Glaub (1994)</td><td>?</td></tr><tr><th>Rhopalondendrina-Form</th><td>Glaub (1994)</td><td>= <i>Rhopalondendrina avis</i> isp. nov.</td></tr><tr><th><i>Entobia</i> -Form 2</th><td>Glaub (1994)</td><td>?</td></tr><tr><th>J-Form C-2</th><td>Glaub & Schmidt (1994)</td><td>? <i>Entobia</i> isp.</td></tr><tr><th>Dendroid-Form II</th><td>Glaub & Schmidt (1994)</td><td>? <i>Clionolithes radicans</i></td></tr><tr><th>Dendroid-Form III</th><td>Glaub & Schmidt (1994)</td><td>? <i>Rhopalondendrina acanthina</i> isp. nov.</td></tr><tr><th>Rosetten-Form</th><td>Glaub & Schmidt (1994)</td><td>?</td></tr><tr><th>Rosetten-Form A</th><td>Hofmann (1996)</td><td>? (p) <i>Dendrina dendrina</i></td></tr><tr><th>Fastigatdendrina-Form</th><td>Bundschuh (2000)</td><td>?</td></tr><tr><th>Dendroid-Form A</th><td>Bundschuh (2000)</td><td>= <i>Dictyoporus nodosus</i></td></tr><tr><th>Dendroid-Form B</th><td>Bundschuh (2000)</td><td>? <i>Clionolithes radicans</i></td></tr><tr><th>Dendroid-Form C</th><td>Bundschuh (2000)</td><td>= <i>Dictyoporus nodosus</i></td></tr><tr><th>Dendroid-Form D</th><td>Bundschuh (2000)</td><td>?</td></tr><tr><th>Piatella-Form</th><td>Bundschuh (2000)</td><td>? <i>Dendrina lacerata</i></td></tr><tr><th>Rhopalodendrina form</th><td>Vogel & Marincovich (2004)</td><td>? <i>Rhopalondendrina avis</i> isp. nov.</td></tr><tr><th>Echinoid Form</th><td>Glaub (2004)</td><td>= <i>Rhopalondendrina tigris</i> isp. nov.</td></tr><tr><th><i>Semidendrina</i> Form</th><td>Beuck & Freiwald (2005)</td><td><i>= Nododendrina europaea</i> comb. nov.</td></tr><tr><th>Foraminiferan trace</th><td>Försterra <i>et al.</i> (2005)</td><td><i>= Pyrodendrina villosa</i> isp. nov.</td></tr><tr><th>Rosette A</th><td>Tapanila (2005)</td><td><i>= Pyrodendrina cupra</i></td></tr><tr><th><i>Semidendrina</i> -form</th><td>Bromley (2005)</td><td><i>= Nododendrina europaea</i> comb. nov.</td></tr><tr><th>Non-camerate radiating form</th><td>Bromley (2005)</td><td>= <i>Pyrodendrina villosa</i> isp. nov.</td></tr><tr><th>Hirsute camerate form</th><td>Bromley (2005)</td><td>? <i>Pyrodendrina villosa</i> isp. nov.</td></tr><tr><th><i>Semidendrina</i> Form</th><td>Wisshak <i>et al.</i> (2005a)</td><td>= <i>Pyrodendrina villosa</i> isp. nov.</td></tr><tr><th><i>Semidendrina</i> -form</th><td>Wisshak <i>et al.</i> (2005b)</td><td><i>= Nododendrina europaea</i> comb. nov.</td></tr><tr><th>Sponge form II</th><td>Wisshak <i>et al.</i> (2005a)</td><td>= <i>Pyrodendrina villosa</i> isp. nov.</td></tr><tr><th>Sponge form VI</th><td>Wisshak <i>et al.</i> (2005a)</td><td>? <i>Pyrodendrina arctica</i> isp. nov.</td></tr><tr><th>Rosette-shaped borings</th><td>Botquelen & Mayoral (2005)</td><td>? Clionolithes radicans</td></tr><tr><th><i>Semidendrina</i> -form</th><td>Wisshak (2006)</td><td><i>=</i> (p) <i>Nododendrina europaea</i> comb. nov.</td></tr><tr><th>Microsponge-form 2</th><td>Wisshak (2006)</td><td>= <i>Pyrodendrina villosa</i> isp. nov.</td></tr><tr><th>Microsponge-form 6</th><td>Wisshak (2006)</td><td>? <i>Pyrodendrina arctica</i> isp. nov.</td></tr><tr><th><i>Semidendrina</i> -form</th><td>Wisshak & Rüggeberg (2006)</td><td><i>= Nododendrina europaea</i> comb. nov.</td></tr><tr><th><i>Semidendrina</i> -form</th><td>Santos & Mayoral (2008)</td><td><i>= Nododendrina europaea</i> comb. nov.</td></tr><tr><th><i>Semidendrina</i> -form</th><td>Pereira <i>et al.</i> (2009)</td><td>? <i>Nododendrina europaea</i> comb. nov.</td></tr><tr><th>Dendroid Form 1</th><td>Vogel & Brett (2009)</td><td>? <i>Clionolithes cervicornis</i></td></tr><tr><th>Dendroid Form 2</th><td>Vogel & Brett (2009)</td><td>?</td></tr><tr><th>Mini-Meander Form</th><td>Vogel & Brett (2009)</td><td>?</td></tr><tr><th>Foraminiferan Form</th><td>Beuck <i>et al.</i> (2010)</td><td>= (p) <i>Pyrodendrina villosa</i> isp. nov.</td></tr><tr><th>Bunched whips form</th><td>Wisshak <i>et al.</i> (2011)</td><td>?</td></tr><tr><th>Dendroid form 1</th><td>Wisshak <i>et al.</i> (2011)</td><td>?</td></tr><tr><th>Dendroid form 2</th><td>Wisshak <i>et al.</i> (2011)</td><td>= <i>Rhopalondendrina acanthina</i> isp. nov.</td></tr><tr><th>Morphotype 4</th><td>Seuss <i>et al.</i> (2015)</td><td>?</td></tr></tbody></table>
Table 3 in Taming an ichnotaxonomical Pandora's box: revision of dendritic and rosetted microborings (ichnofamily: Dendrinidae)
<p><b>Table 3.</b> Revised suite of ichnotaxa (in order of original ichnogenus and ichnospecies establishment; type ichnospecies marked by asterisk) comprised within the ichnofamily Dendrinidae, and the most relevant diagnostic ichnogeneric feature(s).</p><table><thead><tr><th><b>Ichnotaxon</b></th><th><b>Most relevant diagnostic features</b></th></tr></thead><tbody><tr><th><i>Dendrina</i> Quenstedt, 1849</th><td>Thin inlet tunnel leads to substrate parallel, circumradial, rosetted cavity</td></tr><tr><th><i>D. dendrina</i> (Morris, 1851) comb. nov. *</th><td></td></tr><tr><th><i>D. belemniticola</i> Mägdefrau, 1937</th><td></td></tr><tr><th><i>D. lacerata</i> Hofmann, 1996</th><td></td></tr><tr><th><i>Clionolithes</i> Clarke, 1908</th><td>Tapering, ramified galleries radiating from dome-shaped central cavity</td></tr><tr><th><i>C. radicans</i> Clarke, 1908 *</th><td></td></tr><tr><th><i>C. palmatus</i> Clarke, 1908</th><td></td></tr><tr><th><i>C. pannosus</i> (Solle, 1938) comb. nov.</th><td></td></tr><tr><th><i>C. cervicornis</i> (Vogel <i>et al.</i>, 1987)</th><td></td></tr><tr><th><i>C. alcicornis</i> (Vogel <i>et al.</i>, 1987) comb. nov.</th><td></td></tr><tr><th><i>C. convexus</i> (Hofmann, 1996) comb. nov.</th><td></td></tr><tr><th><i>Calcideletrix</i> Mägdefrau, 1937</th><td>Strongly ramified with prostrate, tapering, rarely anastomosing galleries</td></tr><tr><th><i>C. flexuosa</i> Mägdefrau, 1937 *</th><td></td></tr><tr><th><i>C. breviramosa</i> Mägdefrau, 1937</th><td></td></tr><tr><th><i>C. anomala</i> (Mägdefrau, 1937) comb. nov.</th><td></td></tr><tr><th><i>C. fastigata</i> (Radtke, 1991) comb. nov.</th><td></td></tr><tr><th><i>Dictyoporus</i> Mägdefrau, 1937</th><td>Reticulate channel or tunnel network with high degree of anastomosis</td></tr><tr><th><i>D. nodosus</i> Mägdefrau, 1937 *</th><td></td></tr><tr><th><i>D. balani</i> (Tavernier <i>et al.</i>, 1992) comb. nov.</th><td></td></tr><tr><th><i>Abeliella</i> Mägdefrau, 1937</th><td>Strictly dichotomously ramifying prostrate trace in osteic substrates</td></tr><tr><th colspan="2"><i>A. riccioides</i> Mägdefrau, 1937 *</th></tr><tr><th><i>A. procera</i> Mägdefrau, 1937</th><td></td></tr><tr><th><i>Nododendrina</i> Vogel <i>et al.</i>, 1987</th><td>Vertical node with one or several anastomosing and prostrate plexuses</td></tr><tr><th><i>N. europaea</i> (Fischer, 1875) comb. nov.</th><td></td></tr><tr><th><i>N. incomposita</i> (Mägdefrau, 1937) comb. nov.</th><td></td></tr><tr><th><i>N. paleodendrica</i> (Elias, 1957) comb. nov.</th><td></td></tr><tr><th><i>N. nodosa</i> Vogel <i>et al.</i>, 1987 *</th><td></td></tr><tr><th><i>Pyrodendrina</i> Tapanila, 2008</th><td>Vertically tapering galleries emerging from a prostrate, ramifying cavity</td></tr><tr><th><i>P. cupra</i> Tapanila, 2008 *</th><td></td></tr><tr><th><i>P. arctica</i> isp. nov.</th><td></td></tr><tr><th><i>P. belua</i> isp. nov.</th><td></td></tr><tr><th><i>P. villosa</i> isp. nov.</th><td></td></tr><tr><th><i>Rhopalondendrina</i> igen. nov.</th><td>Oblique–arcuate inlet tunnel leading to semi-circular, prostrate plexus</td></tr><tr><th><i>R. avis</i> isp. nov. *</th><td></td></tr><tr><th><i>R. acanthina</i> isp. nov.</th><td></td></tr><tr><th><i>P. contra</i> isp. nov.</th><td></td></tr><tr><th><i>P. tigris</i> isp. nov.</th><td></td></tr><tr><th><i>Antodendrina</i> igen. nov.</th><td>Distinctly widening lobes radiating from a central cavity or depression</td></tr><tr><th colspan="2"><i>A. ligula</i> isp. nov. *</th></tr></tbody></table>
Dataset part one to the publication "CAL-1 as Cellular Model System to Study CCR7-Guided Human Dendritic Cell Migration"
<p>This study was supported in parts by research funding from the Swiss National Science Foundation (grant number 310030_189144), the Thurgauische Stiftung für Wissenschaft und Forschung, and the State Secretariat for Education, Research and Innovation to DFL.</p>
Climbing fiber multi-innervation of mouse Purkinje dendrites with arborization common to human
<p>Canonically, each Purkinje cell in the adult cerebellum receives only one climbing fiber from the inferior olive. Underlying current theories of cerebellar function is the notion that this highly conserved one-to-one relationship renders Purkinje dendrites into a single computational compartment. However, we show that multiple primary dendrites are a near-universal morphological feature in humans. Using tract-tracing, immunolabeling, and in vitro electrophysiology, we demonstrate in mice that ~25% of mature polydendritic cells receive more than one climbing fiber input. Two-photon calcium imaging in vivo reveals that separate dendrites can exhibit distinct response properties to sensory stimulation, indicating some polydendritic cells integrate functionally independent climbing fiber receptive fields. These findings reveal that Purkinje cells are morphologically and functionally more diverse than previously thought.</p>
Climbing fiber multi-innervation of mouse Purkinje dendrites with arborization common to human
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Data from: Learning enhances behaviorally relevant representations in apical dendrites
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Action potential evoked dendritic calcium signals in the medial superior olive (MSO) during development
<p>Dataset underlying the analysis of dendritic calcium signals evoked by somatic action potentials in MSO neurons during development (postnatal day 10 - 60). The data includes recordings from Mongolian gerbils (<em>Meriones unguiculatus</em>) raised in a normal acoustic environment and in omnidirectional white noise.</p> <p><strong>Linked paper:</strong> Franzen DL, Gleiss SA, Kellner CJ, Kladisios N, Felmy F. Activity-Dependent Calcium Signaling in Neurons of the Medial Superior Olive during Late Postnatal Development. J Neurosci. 2020 Feb 19;40(8):1689–700. <a href="https://doi.org/10.1523/JNEUROSCI.1545-19.2020">https://doi.org/10.1523/JNEUROSCI.1545-19.2020</a>.</p> <p><strong>Files included:</strong></p> <ul> <li> <p>A folder entitiled <em>data</em> containing:</p> <ul> <li>The imaging files (<code>.nix</code>) (1 file per imaged neuron). NIX files contain the kymograph data extracted from a ROI in the raw images along with the metadata. The imaging kymographs and associated <code>.nix</code> files were created with the <a href="https://zenodo.org/record/2575542#.XiYdAS2ZNo4">CaManager: ImageJ Plugin For Ca²⁺ Imaging</a>.</li> <li>An <code>excludes.csv</code> file that contains cells/trials to be excluded (e.g. recording error, movement, difficulty in tracing)</li> <li>A <code>Megatable_C.csv</code> file containing the electrophysiological data corresponding to imaged cells</li> </ul> </li> <li> <p>A <code>.nix</code> intermediate analysis file for <em>default parameters</em></p> </li> <li> <p>A <code>.csv</code> file with the combined electrophysiological and imaging data for <em>default parameters</em></p> </li> <li> <p>Several <code>.xlsx</code> files with the single cell data in Figures 2C, 2D, 2F.</p> </li> </ul> <p><strong>Jupyter notebook:</strong></p> <p>The <a href="https://github.com/delwen/CaJupyter">CaJupyter</a> GitHub repository contains a Jupyter notebook with a step-by-step guide of the analysis. It also allows for further exploration of the data.</p> <p><strong>See also:</strong></p> <ul> <li> <p>The original analysis code (without adaptations for the Jupyter notebook and Python 3) can be found at <a href="https://zenodo.org/record/2575675#.Xi%E2%80%A6">CaAnalysis: Analysis Toolbox for Ca²⁺ Imaging</a>.</p> </li> <li> <p>More information on NIX can be found at this <a href="https://g-node.github.io/nix/">link</a>.</p> </li> </ul>
Raw data related to: "Resiquimod-Mediated Activation of Plasmacytoid Dendritic Cells Is Amplified in Multiple Sclerosis"
<p><strong>Introduction</strong></p> <p>Multiple sclerosis (MS) is a chronic inflammatory autoimmune disease of the central nervous system. The cause of multiple sclerosis is unknown but there are several evidences that associate the genetic basis of the disease with environmental causes. An important association between viral infection and development of MS is clearly demonstrated. Viruses have a strong impact on innate immune cells. In particular, myeloid dendritic cells (mDCs) and plasmacytoid dendritic cells (pDCs), are able to respond to viruses and to activate the adaptive immune response.</p> <p><strong>Methods</strong></p> <p> In this study we mimic viral infection using synthetic single-strand RNA, Resiquimod, and we compared the response of both DC subsets derived from healthy donors and MS patients by characterizing the expression of costimulatory molecules on the DC surface.</p> <p><strong>Results</strong></p> <p>We found that pDCs from MS patients express higher levels of OX40-L. Moreover, we found that blood cells from MS patients and healthy donors upon Resiquimod-stimulation are enriched in a subpopulation of pDCs, characterized by a high amount of costimulatory molecules.</p> <p><strong>Conclusion</strong></p> <p>Overall, these results indicate that activation of pDCs is enhanced in MS, likely due to a latent viral infection, and that costimulatory molecules expressed on pDCs could mediate a protective response against the viral trigger of autoimmunity.</p>
Dataset for: Generation of model tissues with dendritic vascular networks via sacrificial laser-sintered carbohydrate templates
<p>Published in:<br> Nature Biomedical Engineering. doi: 10.1038/s41551-020-0566-1.</p> <p>Generation of model tissues with dendritic vascular networks via sacrificial laser-sintered carbohydrate templates</p> <p>Ian S. Kinstlinger (1), Sarah H. Saxton (2), Gisele A. Calderon (1), Karen Vasquez Ruiz (1), David R. Yalacki (1), Palvasha R. Deme (1), Jessica E. Rosenkrantz (3), Jesse D. Louis-Rosenberg (3), Fredrik Johansson (2), Kevin D. Janson (1), Daniel W. Sazer (1), Saarang S. Panchavati (1), Karl-Dimiter Bissig (4), Kelly R. Stevens (2,5), and Jordan S. Miller (1)</p> <p>1 Department of Bioengineering, Rice University, Houston, TX, USA.<br> 2 Department of Bioengineering, University of Washington, Seattle, WA, USA.<br> 3 Nervous System, Palenville, NY, USA.<br> 4 Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.<br> 5 Department of Pathology, University of Washington, Seattle, WA, USA</p> <p>Sacrificial templates for patterning perfusable vascular networks in engineered tissues have been constrained in architectural complexity, owing to the limitations of extrusion-based 3D-printing techniques. Here we show that cell-laden hydrogels can be patterned with algorithmically generated dendritic vessel networks and other complex hierarchical networks by using sacrificial templates made from laser-sintered carbohydrate powders. We quantified and modulated gradients of cell proliferation and cell metabolism emerging as a result of fluid convection through these networks and of diffusion of oxygen and metabolites out of them. We also show scalable strategies for the fabrication, perfusion culture and volumetric analysis of large tissue-like constructs with complex and heterogeneous internal vascular architectures. Perfusable dendritic networks in cell-laden hydrogels may help sustain thick and densely cellularized engineered tissues, and assist interrogations of the interplay between mass transport and tissue function.</p>
Statistical Laws of Protein Motion in Neuronal Dendritic Trees
<p>Across their dendritic trees, neurons distribute thousands of protein species that are necessary for maintaining synaptic function and plasticity and that need to be produced continuously and trafficked to their final destination. As each dendritic branchpoint splits the protein flow, increasing branchpoints decreases the total protein number downstream. Consequently, a neuron needs to produce more proteins to maintain a minimal protein number at distal synapses. Combining in vitro experiments and a theoretical framework, we show that proteins that diffuse within the cell plasma membrane are, on average, 35% more effective at reaching downstream locations than proteins that diffuse in the cytoplasm. This advantage emerges from a bias for forward motion at branchpoints when proteins diffuse within the plasma membrane. Using 3D electron microscopy (EM) data, we show that pyramidal branching statistics and the diffusion lengths of common proteins fall into a region that minimizes the overall protein need.</p>
Dendritic cell subsets in oral mucosa of allergic and healthy subjects
<p><strong>Abstract</strong></p> <p>Immunohistochemistry was used to identify, enumerate, and describe the tissue distribution of Langerhans type (CD1a and CD207), myeloid (CD1c and CD141), and plasmacytoid (CD303 and CD304) dendritic cell subsets in oral mucosa of allergic and non-allergic individuals. Allergic individuals have more CD141+ myeloid cells in epithelium and more CD1a+ Langerhans cells in the lamina propria compared to healthy controls, but similar numbers for the other DC subtypes. Our data are the first to describe the presence of CD303+ plasmacytoid DCs in human oral mucosa and a dense intraepithelial network of CD141+ DCs. The number of Langerhans type DCs (CD1a and CD207) and myeloid DCs (CD1c), was higher in the oral mucosa than in the nasal mucosa of the same individual independent of the atopic status.</p>
Pan-cancer analyses refine the single-cell portrait of tumor-infiltrating dendritic cells
<p>This is the dataset for "Pan-cancer Analyses Refine the Single-Cell Portrait of Tumor-Infiltrating Dendritic Cells".</p> <p>File "panDC_all_h5ad.gz" contains processed expression .h5ad data.</p> <p>File "panDC_metadata.csv" contains the meta data for this study.</p>
Data from: Illuminating T cell-dendritic cell interactions in vivo by FlAsHing antigens
<p>Delineating the complex network of interactions between antigen-specific T cells and antigen presenting cells (APCs) is crucial for effective precision therapies against cancer, chronic infections, and autoimmunity. However, the existing arsenal for examining antigen-specific T cell interactions is restricted to a select few antigen-T cell receptor pairs, with limited in situ utility. This lack of versatility is largely due to the disruptive effects of reagents on the immune synapse, which hinder real-time monitoring of antigen-specific interactions. To address this limitation, we have developed a novel and versatile immune monitoring strategy by adding a short cysteine-rich tag to antigenic peptides that emits fluorescence upon binding to thiol-reactive biarsenical hairpin compounds. Our findings demonstrate the specificity and durability of the novel antigen-targeting probes during dynamic immune monitoring in vitro and in vivo. This strategy opens new avenues for biological validation of T-cell receptors with newly identified epitopes by revealing the behavior of previously unrecognized antigen-receptor pairs, expanding our understanding of T cell responses.</p>
Respiratory Complex I Regulates Dendritic Cell Maturation in Explant Model of Human Tumor Immune Microenvironment
<p>Source data for the paper, "Respiratory Complex I Regulates Dendritic Cell Maturation in Explant Model of Human Tumor Immune Microenvironment."<br><br>This includes nanostring gene expression profiling of primary human tumor material ("fresh" in the data, these samples are taken directly after enzymatic digestion) and the corresponding 3D Patient-Derived Explant Culture (PDEC). <br><br>transfer_257851_files_0a119f4d.zip refers to the mouse spatial transcriptomics data.<br><br>DE_results_Metformin/LPS files refer to differentially expressed genes of human monocyte-derived dendritic cells of 6 individual donors to control untreated dendritic cells after 24hr treatment. <br><br> Also includes the original Seurat.rds file for the scSEQ of primary tumor material (fresh) vs. PDEC<br><br><br><br><br> </p>
A 3D dendrite microstructure database of a Ni-base SX based on relational geometric ontology (RGO)
<p>Material: Nickel-base superalloy ERBO/1 (more details: Parsa, A. B., et al. Advanced scale bridging microstructure analysis of single crystal Ni-base superalloys. Adv. Eng. Mater. 2015, 17 (2), 216-230, <a href="https://doi.org/10.1002/adem.201400136">https://doi.org/10.1002/adem.201400136</a>)</p> <p>Casting: Bridgman seed technique; Withdrawal rate: 180 mm/h, Thermal gradient 13.3 K/mm (more details: Hallensleben, P., et al. On the evolution of cast microstructures during processing of single crystal Ni-base superalloys using a Bridgman seed technique, Mat. Des. 2017, 128, 98–111, <a href="https://doi.org/10.1016/j.matdes.2017.05.001">https://doi.org/10.1016/j.matdes.2017.05.001</a>)</p> <p>Sample: Cross sectional slices extracted perpendicular to the growth direction of a single crystal superalloy cylinder (diameter 12mm, length 120 mm).</p> <p>Preperation: Each slice was individually mounted, grinded, polished and etched 6 seconds with an etching solution consisting of 100ml H2O, 100ml HCl, 100ml HNO3 and 3g MoO3. </p> <p>Image acquisition: Optical microscope of type Axio (Carl Zeiss GmbH) equipped with a high-resolution CCD-camera of type Leica DFC320 and stepper-motor driven sample stage of type Tango Desktop (Märzhäuser)</p> <p>--------------------------------------</p> <p>The published data is a compilation of 20 serial sectioned optical micrographs resolving the dendritic microstructure of the sample described above. They show a central region of the specimen at different heights of the cylindrical sample. The names of those micrographs correspond to the z-coordinate in millimeters, i.e. micrograph "012.tif" was extracted at 12mm. For each micrograph, an object detector based on a neural network was used to identify the dendrite core positions. Afterwards, registration algorithms were used to determine the growth directions together with branching and extinction events of all dendrites. Neighboring dendrites were identified by calculating a triangulation for each micrograph.</p> <p>This quantitative data was transformed into a microstructure database stored as a .JSON file using the "Relational Geometric Ontology" approach described in:</p> <p>A.R. Richter, F. Scholz, G. Eggeler, J. Frenzel, P. Thome, Microstructure informatics: Using computer vision for the characterization of dendrite growth phenomena in Ni-base single crystal Superalloys, Materials Characterization, Volume 223, 2025, <a href="https://doi.org/10.1016/j.matchar.2025.114878">https://doi.org/10.1016/j.matchar.2025.114878 </a></p> <p> </p>
Harnessing single cell RNA sequencing to identify dendritic cell types, characterize their biological states and infer their activation trajectory
<p><strong>Summary: </strong>Dendritic cells (DCs) orchestrate innate and adaptive immunity, by translating the sensing of distinct danger signals into the induction of different effector lymphocyte responses, to induce different defense mechanisms suited to face distinct types of threats. Hence, DCs are very plastic, which results from two key characteristics. First, DCs encompass distinct cell types specialized in different functions. Second, each DC type can undergo different activation states, fine-tuning its functions depending on its tissue microenvironment and the pathophysiological context, by adapting the output signals it delivers to the input signals it receives. Hence, to better understand DC biology and harness it in the clinic, we must determine which combinations of DC types and activation states mediate which functions, and how.<br> To decipher the nature, functions and regulation of DC types and their physiological activation states, one of the methods that can be harnessed most successfully is ex vivo single cell RNA sequencing (scRNAseq). However, for new users of this approach, determining which analytics strategy and computational tools to choose can be quite challenging, considering the rapid evolution and broad burgeoning of the field. In addition, awareness must be raised on the need for specific, robust and tractable strategies to annotate cells for cell type identity and activation states. It is also important to emphasize the necessity of examining whether similar cell activation trajectories are inferred by using different, complementary methods. In this chapter, we take these issues into account for providing a pipeline for scRNAseq analysis and illustrating it with a tutorial reanalyzing a public dataset of mononuclear phagocytes isolated from the lungs of naïve or tumor-bearing mice. We describe this pipeline step-by-step, including data quality controls, dimensionality reduction, cell clustering, cell cluster annotation, inference of the cell activation trajectories and investigation of the underpinning molecular regulation. It is accompanied with a more complete tutorial on Github. We anticipate that this method will be helpful for both wet lab and bioinformatics researchers interested in harnessing scRNAseq data for deciphering the biology of DCs or other cell types, and that it will contribute to establishing high standards in the field.</p> <p><strong>Data : </strong></p> <p>1. Table1_full_version.docx : Marker genes for cell clusters of global Seurat analysis<br> 2. Table2_full_version.docx : List of the Immgen samples used to generate the reference compendium for CMAP signature generation<br> 3. Table5_full_version.docx : Top 20 marker genes for cell clusters of the Seurat analysis on selected cDC1s</p> <p> </p> <p> </p>
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