Merge branch 'polish-arc-DB' into 'main'

Polish arc db

See merge request hhu_molphys_frommer/Schladt_et_al_2024!2

README.md

+# Identification of nuclear pore proteins at plasmodesmata
+
+## Abstract
+
 Here we used bioinformatics, proteomics and fluorescence imaging to identify proteins with similarities to phase separating FG-NUPs at PD. We identified 20 NUPs in PD fractions, and validated dual localization to NPC and PD for 7 NUPs. Structured illumination microscopy detected the transmembrane anchor NUP CPR5 at both orifices of PD. cpr5 mutants showed reduced intercellular transport of SHR from stele to endodermis. The identification of FG-NUPs at PD is consistent with the recruitment of NUPs in the green lineage to form a PD pore gating complex consistent with liquid phase separation domains as diffusion barriers at PD.
 
-Raw and meta data can be found in "assays":
-NUP localization when transiently and stably expressed, topolgy of CPR5, structured illumination microscopy transiently expressing CPR5 and PDLP5, transport assays: bombardment, DropANdSee, short root SHR-GFP.
+![](_publication/biorxiv-preprint/Figure1.png)
+<figcaption>Figure 1. Identification of NUPs at plasmodesmata.</figcaption>
+
+## Preprint
+
+A bioRxiv preprint of the associated publication is available at https://doi.org/10.1101/2024.09.02.610746 and [here](_publication/biorxiv-preprint/2024.09.02.610746v2.full.pdf)
+
+
+## Raw data and metadata can be found in "assays"
+
+- NUP localization
+  - [transiently expressed](assays/transient_localization)
+  - [stably expressed](assays/stable_localization_in_reporter_line)
+- [topology of CPR5](assays/topology)
+- [structured illumination microscopy (SIM)](assays/SIM) transiently expressing CPR5 and PDLP5
+- transport assays
+  - [bombardment](assays/bombardment)
+  - [DropANdSee (DANS)](assays/DANS)
+  - [short root SHR-GFP](assays/SHR-GFP)
+- [sequencing results for cpr5G420D](assays/sequencing_of_Arabidopsis_cpr5-1)
+
+## Contributors
 
-Sequencing results for cpr5G420D can be found in 
+- Till Moritz Schladt
\ No newline at end of file
+  - email: till.schladt@hhu.de
+  - Affiliation: Heinrich Heine Univeryity, Düsseldorf
+  - ORCID: [0000-0002-9160-4664](https://orcid.org/0000-0002-9160-4664)
+- Miras Manuel
+  - Affiliation: CEBAS-CSIC, Heinrich-Heine-Universität Düsseldorf Mathematisch-Naturwissenschaftliche Fakultät, Insitute of Molecular Physiology Heinrich-Heine-Universität Düsseldorf Mathematisch-Naturwissenschaftliche Fakultät, Institute Molecular Physiology;Abiopep SL, ;Centro de Edafología y Biología Aplicada del Segura, Plant Virology;Centro de Edafología y Biología Aplicada del Segura, Plant Virology
+  - ORCID: [0000-0002-3636-0265](https://orcid.org/0000-0002-3636-0265)
+- Jona Obinna Ejike
+  - Affiliation: Heinrich Heine Universität, Düsseldorf
+  - ORCID: [0000-0002-4601-8551](https://orcid.org/0000-0002-4601-8551)
+- Mathieu Pottier
+  - Affiliation: Université de Lorraine, UMR 1136 Université de Lorraine/INRAE Interactions Arbres Microorganismes (IAM);Heinrich-Heine-Universität Düsseldorf, Institute for Molecular Physiology;University of Liège, Integrative Biological Sciences (InBioS);Université catholique de Louvain, Louvain Institute of Biomolecular Science and Technology (LIBST);CNRS Délégation Ile-de-France Sud, Institut des Sciences du Végétal (ISV)
+  - ORCID: [0000-0003-1551-4699](https://orcid.org/0000-0003-1551-4699)
+- Lin Xi
+  - Affiliation: University of Hohenheim
+  - ORCID: [0000-0002-6811-9505](https://orcid.org/0000-0002-6811-9505)
+- Andrea Restrepo
+  - Affiliation: Heinrich-Heine-Universität Düsseldorf, Institute for Molecular Physiology
+  - ORCID: [0000-0003-2870-394X](https://orcid.org/0000-0003-2870-394X)
+- Masayoshi Nakamura
+  - Affiliation: Nagoya University, Institute of Transformative Bio-Molecules;Nagoya University, Institute of Transformative Bio-Molecules;Carnegie Institution for Science, Department of Plant Biology;Nara Institute of Science and Technology, Department of Biological Science
+  - ORCID: [0000-0002-7107-4942](https://orcid.org/0000-0002-7107-4942)
+- Niklas Pütz
+  - Affiliation: Heinrich Heine Universität, Düsseldorf
+  - ORCID: [0009-0006-1153-5918](https://orcid.org/0009-0006-1153-5918)
+- Sebastian Hänsch
+  - Affiliation: Heinrich Heine University Düsseldorf, Center for Advanced Imaging;Heinrich Heine University Düsseldorf, Center for Advanced Imaging
+  - ORCID: [0000-0002-7762-2516](https://orcid.org/0000-0002-7762-2516)
+- Chen Gao
+  - Affiliation: University of Copenhagen, Department of Plant and Environmental Sciences
+  - ORCID: [0000-0003-4750-3900](https://orcid.org/0000-0003-4750-3900)
+- Julia Engelhorn
+  - Affiliation: University of Montpellier, IRD;Heinrich Heine University Düsseldorf, Institute for Molecular Physiology;University of Warwick, School of Life Sciences;CEA Grenoble, Cell & Plant Physiology Laboratory
+  - ORCID: [0000-0002-6680-3012](https://orcid.org/0000-0002-6680-3012)
+- Marcel Dickmanns
+  - Affiliation: Heinrich-Heine-Universität Düsseldorf, ;Max Planck Institute of Biochemistry, 
+  - ORCID: [0000-0003-4001-707X](https://orcid.org/0000-0003-4001-707X)
+- Gwendolyn Davis
+  - Affiliation: University of Warwick, Life Sciences;University of Cambridge, Plant Sciences
+  - ORCID: [0000-0003-4704-4863](https://orcid.org/0000-0003-4704-4863)
+- Ahan Dalal
+  - Affiliation: Hebrew University of Jerusalem, Plant Science;Tel Aviv University, Plant Science
+  - ORCID: [0000-0003-1876-1484](https://orcid.org/0000-0003-1876-1484)
+- Sven Gombos
+  - Affiliation: University of Hohenheim, Plant Systems Biology
+  - ORCID: [0000-0003-4177-526X](https://orcid.org/0000-0003-4177-526X)
+- Ronja Lange
+  - Affiliation: Heinrich Heine Universität, Düsseldorf
+  - ORCID: [0009-0009-2475-2438](https://orcid.org/0009-0009-2475-2438)
+- Rüdiger Simon
+  - Affiliation: Heinrich Heine University, Biology
+  - ORCID: [0000-0002-1317-7716](https://orcid.org/0000-0002-1317-7716)
+- Waltraud Schulze
+  - Affiliation: University of Hohenheim
+  - ORCID: [0000-0001-9957-7245](https://orcid.org/0000-0001-9957-7245)
+- Wolf B. Frommer
+  - Affiliation: Heinrich-Heine-Universitat Düsseldorf, Institute for Molecular Physiology;ITbM, ;Carnegie Institution for Science, Plant Biology;Stanford University, Biology;Carnegie Institution for Science, Plant Biology;Stanford University, Biology;Carnegie Institution for Science, Plant Biology;University of Tübingen, Biology
+  - ORCID: [0000-0001-6465-0115](https://orcid.org/0000-0001-6465-0115)
\ No newline at end of file

_publication/README.md

+
+# Publication files
+
+## bioRxiv preprint
+
+See [2024.09.02.610746v2.full.pdf](biorxiv-preprint/2024.09.02.610746v2.full.pdf)
+
+### Citation
+
+**Identification of nuclear pore proteins at plasmodesmata**
+
+T. Moritz Schladt, Manuel Miras, Jona Obinna Ejike, Mathieu Pottier, Lin Xi, Andrea Restrepo-Escobar, Masayoshi Nakamura, Niklas Pütz, Sebastian Hänsch, Chen Gao, Julia Engelhorn, Marcel Dickmanns, Gwendolyn V. Davis, Ahan Dalal, Sven Gombos, Ronja Lange, Rüdiger Simon, Waltraud X. Schulze, Wolf B. Frommer
+bioRxiv 2024.09.02.610746; doi: https://doi.org/10.1101/2024.09.02.610746
+
+### Copyright
+
+The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a [CC-BY-NC-ND 4.0 International license](http://creativecommons.org/licenses/by-nc-nd/4.0/).