Publications and Acknowledgements

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List of publications

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Holst, M. R., Richner, M., Arenshøj, P. O., Alam, P., Hyldig, K. & Nielsen, M. S. (2024). Ex vivo nanoscale abluminal mapping of putative cargo receptors at the blood-brain barrier of expanded brain capillaries. Fluids and Barriers of the CNS, 21(1), Article 80. https://doi.org/10.1186/s12987-024-00585-x

Pløen, G. G., Sørensen, C. B. & Bentzon, J. F. (2024). Smooth muscle cells clonally expand in a murine carotid allograft model complicated by immune reactions to reporter transgenes. Transplant Immunology, 87, Article 102129. https://doi.org/10.1016/j.trim.2024.102129

Jespersen, J. H., Harazin, A., Bohn, A. B., Christensen, A., Lorentzen, E. & Lorentzen, A. (2023). Analysis of cortical cell polarity by imaging flow cytometry. Journal of Cellular Biochemistry, 124(11), 1685-1694. https://doi.org/10.1002/jcb.30476

Maimaitili, M., Chen, M., Febbraro, F., Ucuncu, E., Kelly, R., Niclis, J. C., Christiansen, J. R., Mermet-Joret, N., Niculescu, D., Lauritsen, J., Iannielli, A., Klæstrup, I. H., Jensen, U. B., Qvist, P., Nabavi, S., Broccoli, V., Nykjær, A., Romero-Ramos, M. & Denham, M. (2023). Enhanced production of mesencephalic dopaminergic neurons from lineage-restricted human undifferentiated stem cells. Nature Communications, 14(1), Article 7871. https://doi.org/10.1038/s41467-023-43471-0

Sardella, D., Kristensen, A. M., Bordoni, L., Kidmose, H., Shahrokhtash, A., Sutherland, D. S., Frische, S. & Schiessl, I. M. (2023). Serial intravital 2-photon microscopy and analysis of the kidney using upright microscopes. Frontiers in Physiology, 14, Article 1176409. https://doi.org/10.3389/fphys.2023.1176409

Pløen, G. G., Sørensen, C. B. & Bentzon, J. F. (2023). Severe arterial injury heals with a complex clonal structure involving a large fraction of surviving smooth muscle cells. Atherosclerosis, 387, Article 117341. https://doi.org/10.1016/j.atherosclerosis.2023.117341

Fruhwürth, S., Reinert, L. S., Öberg, C., Sakr, M., Henricsson, M., Zetterberg, H. & Paludan, S. R. (2023). TREM2 is down-regulated by HSV1 in microglia and involved in antiviral defense in the brain. Science Advances, 9(33), eadf5808. Article eadf5808. https://doi.org/10.1126/sciadv.adf5808

Fonager, S. V., Winther, G., Wittenborn, T. R., Jensen, L., Fahlquist-Hagert, C., Hansen, L. A., Füchtbauer, E.-M., Romero-Ramos, M. & Degn, S. E. (2022). Increased maternofoetal transfer of antibodies in a murine model of systemic lupus erythematosus, but no immune activation and neuroimmune sequelae in offspring. Journal of Neuroimmunology, 370, Article 577927. https://doi.org/10.1016/j.jneuroim.2022.577927

Katzilieris-Petras, G., Lai, X., Rashidi, A. S., Verjans, G. M. G. M., Reinert, L. S. & Paludan, S. R. (2022). Microglia Activate Early Antiviral Responses upon Herpes Simplex Virus 1 Entry into the Brain to Counteract Development of Encephalitis-Like Disease in Mice. Journal of Virology, 96(6), Article e01311-21. https://doi.org/10.1128/jvi.01311-21

Richner, M., Gonçalves, N. P., Jensen, P. H., Nyengaard, J. R., Vægter, C. B. & Jan, A. (2022). Recombinant adeno-associated virus mediated gene delivery in the extracranial nervous system of adult mice by direct nerve immersion. STAR Protocols, 3(1), Article 101181. https://doi.org/10.1016/j.xpro.2022.101181

Van Den Berge, N., Ferreira, N., Mikkelsen, T. W., Alstrup, A. K. O., Tamgüney, G., Karlsson, P., Terkelsen, A. J., Nyengaard, J. R., Jensen, P. H. & Borghammer, P. (2021). Ageing promotes pathological alpha-synuclein propagation and autonomic dysfunction in wild-type rats. Brain : a journal of neurology, 144(6), 1853–1868. https://doi.org/10.1093/brain/awab061

Reinert, L. S., Rashidi, A. S., Tran, D. N., Katzilieris-Petras, G., Hvidt, A. K., Gohr, M., Fruhwürth, S., Bodda, C., Thomsen, M. K., Vendelbo, M. H., Khan, A. R., Hansen, B., Bergström, P., Agholme, L., Mogensen, T. H., Christensen, M. H., Nyengaard, J. R., Sen, G. C., Zetterberg, H. ... Paludan, S. R. (2021). Brain immune cells undergo cGAS/STING-dependent apoptosis during herpes simplex virus type 1 infection to limit type I IFN production. Journal of Clinical Investigation, 131(1), Article e136824. https://doi.org/10.1172/JCI136824

Ferreira, N., Richner, M., van der Laan, A., Bergholdt Jul Christiansen, I., Vægter, C. B., Nyengaard, J. R., Halliday, G. M., Weiss, J., Giasson, B. I., Mackenzie, I. R., Jensen, P. H. & Jan, A. (2021). Prodromal neuroinvasion of pathological α-synuclein in brainstem reticular nuclei and white matter lesions in a model of α-synucleinopathy. Brain Communications, 3(2), Article fcab104. https://doi.org/10.1093/braincomms/fcab104

Ferreira, N., Gonçalves, N. P., Jan, A., Jensen, N. M., van der Laan, A., Mohseni, S., Vægter, C. B. & Jensen, P. H. (2021). Trans-synaptic spreading of alpha-synuclein pathology through sensory afferents leads to sensory nerve degeneration and neuropathic pain. Acta Neuropathologica Communications, 9(1), Article 31. https://doi.org/10.1186/s40478-021-01131-8

Delaidelli, A., Richner, M., Jiang, L., van der Laan, A., Bergholdt Jul Christiansen, I., Ferreira, N., Nyengaard, J. R., Vægter, C. B., Jensen, P. H., Mackenzie, I. R., Sorensen, P. H. & Jan, A. (2021). α-Synuclein pathology in Parkinson disease activates homeostatic NRF2 anti-oxidant response. Acta Neuropathologica Communications, 9(1), Article 105. https://doi.org/10.1186/s40478-021-01209-3

Hudecz, D., Khire, T., Chung, H. L., Adumeau, L., Glavin, D., Luke, E., Nielsen, M. S., Dawson, K. A., McGrath, J. L. & Yan, Y. (2020). Ultrathin Silicon Membranes for in Situ Optical Analysis of Nanoparticle Translocation across a Human Blood-Brain Barrier Model. ACS Nano, 14(1), 1111-1122. https://doi.org/10.1021/acsnano.9b08870

Asad, J., Richner, M., Vægter, C. B., Nyengaard, J. R. & Jensen, P. H. (2019). Gene Transfer in Rodent Nervous Tissue Following Hindlimb Intramuscular Delivery of Recombinant Adeno-Associated Virus Serotypes AAV2/6, AAV2/8, and AAV2/9. Neuroscience Insights, 14(November-December), 1-12. https://doi.org/10.1177/1179069519889022

Toth, A. E., Siupka, P., P Augustine, T. J., Venø, S. T., Thomsen, L. B., Moos, T., Lohi, H. T., Madsen, P., Lykke-Hartmann, K. & Nielsen, M. S. (2018). The Endo-Lysosomal System of Brain Endothelial Cells Is Influenced by Astrocytes In Vitro. Molecular Neurobiology, 55(11), 8522-8537. https://doi.org/10.1007/s12035-018-0988-x

Reinert, L. S., Lopušná, K., Winther, H., Sun, C., Thomsen, M. K., Nandakumar, R., Mogensen, T. H., Meyer, M., Vægter, C., Nyengaard, J. R., Fitzgerald, K. A. & Paludan, S. R. (2016). Sensing of HSV-1 by the cGAS-STING pathway in microglia orchestrates antiviral defence in the CNS. Nature Communications, 7, Article 13348. https://doi.org/10.1038/ncomms13348

Acknowledgement

Always mention the Bioimaging Core Facility in your acknowledgements and if relevant also in your Materials and Methods section. This is critical for the facility e.g. for better visibility of the facility and for fundraising purposes - and it increases credibility of your work.

Acknowledgments: The authors acknowledge the Bioimaging Core Facility, Health, Aarhus University, Denmark, for the use of equipment and support.

Materials and Methods: Image acquisition and analyses were performed at the Bioimaging Core Facility, Health, Aarhus University, Denmark.

If requested by the journal, our Research Resource Identification (RRID) number is: RRID:SCR_023876
What is an RRID number?

Material and methods section

If requested by your journal, you may include the following information (where relevant) in your Materials and Methods section, to accurately describe the way in which you did your imaging:
Microscope model and manufacturer, e.g. 710 laser scanning confocal microscope, Zeiss objective lens magnification, NA, and correction for abberation, e.g. 63x/1.4 oil Plan-Apochromat wavelengths of excitation and emission camera model and manufacturer software programme(s) and version, e.g. Zeiss Zen Desk image acquisition settings, e.g. focus step size (for z-series), exposure time, binning, time between images (for time lapse) details of any image processing or analysis procedures

Example of microscopy section:
Microscopy Slides were imaged with the Olympus VS120 slide scanner equipped with Spectra X light engine and Semrock pentafilter (DAPI/FITC/Cy3/Cy5/Cy7 Penta LED HC Filter Set #F68-050) with Hamamatsu ORCA-FLASH4.0 V2 (QE 82%) camera. Overview images were taken with the 2x Air NA 0.08 objective and higher magnification images with the 40x Air NA 0.95 objective. Fluorophore 1 was excited with bandpass filter 395/25 and 295mW and emission was filtered with bandpass filter 425/50, Fluorophore2 with ... Images were processed with software XX and (describe image analysis workflow e.g. display range or similar).

Revised 29.04.2025

Nina Glöckner Burmeister