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1. Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data

Author

Bialy, Nikki, Alber, Frank, Andrews, Brenda, Angelo, Michael, Beliveau, Brian, Bintu, Lacramioara, Boettiger, Alistair, Boehm, Ulrike, Brown, Claire M., Maina, Mahmoud Bukar, Chambers, James J., Cimini, Beth A., Eliceiri, Kevin, Errington, Rachel, Faklaris, Orestis, Gaudreault, Nathalie, Germain, Ronald N., Goscinski, Wojtek, Grunwald, David, Halter, Michael, Hanein, Dorit, Hickey, John W., Lacoste, Judith, Laude, Alex, Lundberg, Emma, Ma, Jian, Malacrida, Leonel, Moore, Josh, Nelson, Glyn, Neumann, Elizabeth Kathleen, Nitschke, Roland, Onami, Shuichi, Pimentel, Jaime A., Plant, Anne L., Radtke, Andrea J., Sabata, Bikash, Schapiro, Denis, Schöneberg, Johannes, Spraggins, Jeffrey M., Sudar, Damir, Vierdag, Wouter-Michiel Adrien Maria, Volkmann, Niels, Wählby, Carolina, Siyuan, Wang, Yaniv, Ziv, and Strambio-De-Castillia, Caterina

Subjects
Quantitative Biology - Other Quantitative Biology
Abstract

Together with the molecular knowledge of genes and proteins, biological images promise to significantly enhance the scientific understanding of complex cellular systems and to advance predictive and personalized therapeutic products for human health. For this potential to be realized, quality-assured image data must be shared among labs at a global scale to be compared, pooled, and reanalyzed, thus unleashing untold potential beyond the original purpose for which the data was generated. There are two broad sets of requirements to enable image data sharing in the life sciences. One set of requirements is articulated in the companion White Paper entitled Enabling Global Image Data Sharing in the Life Sciences, which is published in parallel and addresses the need to build the cyberinfrastructure for sharing the digital array data. In this White Paper, we detail a broad set of requirements, which involves collecting, managing, presenting, and propagating contextual information essential to assess the quality, understand the content, interpret the scientific implications, and reuse image data in the context of the experimental details. We start by providing an overview of the main lessons learned to date through international community activities, which have recently made considerable progress toward generating community standard practices for imaging Quality Control (QC) and metadata. We then provide a clear set of recommendations for amplifying this work. The driving goal is to address remaining challenges and democratize access to everyday practices and tools for a spectrum of biomedical researchers, regardless of their expertise, access to resources, and geographical location., Comment: This manuscript is published with a closely related companion entitled, Enabling Global Image Data Sharing in the Life Sciences, which can be found at the following link, arXiv:2401.13023 [q-bio.OT]

Published
2024

2. Suppressed basal mitophagy drives cellular aging phenotypes that can be reversed by a p62-targeting small molecule

Author

Kelly, George, Kataura, Tetsushi, Panek, Johan, Ma, Gailing, Salmonowicz, Hanna, Davis, Ashley, Kendall, Hannah, Brookes, Charlotte, Ayine-Tora, Daniel Moscoh, Banks, Peter, Nelson, Glyn, Dobby, Laura, Pitrez, Patricia R., Booth, Laura, Costello, Lydia, Richardson, Gavin D., Lovat, Penny, Przyborski, Stefan, Ferreira, Lino, Greaves, Laura, Szczepanowska, Karolina, von Zglinicki, Thomas, Miwa, Satomi, Brown, Max, Flagler, Michael, Oblong, John E., Bascom, Charles C., Carroll, Bernadette, Reynisson, Jóhannes, and Korolchuk, Viktor I.

Published
2024
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3. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy

Author

Nelson, Glyn, Boehm, Ulrike, Bagley, Steve, Bajcsy, Peter, Bischof, Johanna, Brown, Claire M, Dauphin, Aurelien, Dobbie, Ian M, Eriksson, John E, Faklaris, Orestis, Fernandez-Rodriguez, Julia, Ferrand, Alexia, Gelman, Laurent, Gheisari, Ali, Hartmann, Hella, Kukat, Christian, Laude, Alex, Mitkovski, Miso, Munck, Sebastian, North, Alison J, Rasse, Tobias M, Resch-Genger, Ute, Schuetz, Lucas C, Seitz, Arne, Strambio-De-Castillia, Caterina, Swedlow, Jason R, Alexopoulos, Ioannis, Aumayr, Karin, Avilov, Sergiy, Bakker, Gert-Jan, Bammann, Rodrigo R, Bassi, Andrea, Beckert, Hannes, Beer, Sebastian, Belyaev, Yury, Bierwagen, Jakob, Birngruber, Konstantin A, Bosch, Manel, Breitlow, Juergen, Cameron, Lisa A, Chalfoun, Joe, Chambers, James J, Chen, Chieh-Li, Conde-Sousa, Eduardo, Corbett, Alexander D, Cordelieres, Fabrice P, Del Nery, Elaine, Dietzel, Ralf, Eismann, Frank, Fazeli, Elnaz, Felscher, Andreas, Fried, Hans, Gaudreault, Nathalie, Goh, Wah Ing, Guilbert, Thomas, Hadleigh, Roland, Hemmerich, Peter, Holst, Gerhard A, Itano, Michelle S, Jaffe, Claudia B, Jambor, Helena K, Jarvis, Stuart C, Keppler, Antje, Kirchenbuechler, David, Kirchner, Marcel, Kobayashi, Norio, Krens, Gabriel, Kunis, Susanne, Lacoste, Judith, Marcello, Marco, Martins, Gabriel G, Metcalf, Daniel J, Mitchell, Claire A, Moore, Joshua, Mueller, Tobias, Nelson, Michael S, Ogg, Stephen, Onami, Shuichi, Palmer, Alexandra L, Paul-Gilloteaux, Perrine, Pimentel, Jaime A, Plantard, Laure, Podder, Santosh, Rexhepaj, Elton, Royon, Arnaud, Saari, Markku A, Schapman, Damien, Schoonderwoert, Vincent, Schroth-Diez, Britta, Schwartz, Stanley, Shaw, Michael, Spitaler, Martin, Stoeckl, Martin T, Sudar, Damir, Teillon, Jeremie, Terjung, Stefan, Thuenauer, Roland, Wilms, Christian D, Wright, Graham D, and Nitschke, Roland

Subjects
Quantitative Biology - Other Quantitative Biology, Physics - Instrumentation and Detectors
Abstract

In April 2020, the QUality Assessment and REProducibility for Instruments and Images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models, and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper 1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; 2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers, and observers of such; 3) outlines the current actions of the QUAREP-LiMi initiative, and 4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics., Comment: 17 pages, 3 figures, shortened abstract, Co-Lead Authors: Glyn Nelson and Ulrike Boehm, Corresponding author: Roland Nitschke

Published
2021
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4. Interpretation of Confocal ISO 21073: 2019 confocal microscopes: Optical data of fluorescence confocal microscopes for biological imaging- Recommended Methodology for Quality Control

Author

Nelson, Glyn, Gelman, Laurent, Faklaris, Orestis, Nitschke, Roland, and Laude, Alex

Subjects
Quantitative Biology - Other Quantitative Biology
Abstract

The performance of a confocal imaging system may be no better than a general-purpose widefield system if it is not properly maintained or quality controlled. The publication of ISO 21073, 'Confocal microscopes- Optical data of fluorescence confocal microscopes for biological imaging', set a standard for the minimal Quality Control (QC) that should be performed for Confocal Microscopes. Here we describe methodology for performing the QC requirements to satisfy ISO 21073, as well as suggesting other QC methods that should be performed to obtain a minimum level of information about the microscope system., Comment: When drawing up this document, it became apparent that further work was required to determine best methodology and further minimal QC tests, as well as extend to other common imaging modalities. As a consequence, QUAREP-LiMi (https://quarep.org) was established to produce a more definitive and expansive QC Methodology manual for light microscopy to supersede this document

Published
2020

5. A perspective on Microscopy Metadata: data provenance and quality control

Author

Huisman, Maximiliaan, Hammer, Mathias, Rigano, Alex, Boehm, Ulrike, Chambers, James J., Gaudreault, Nathalie, North, Alison J., Pimentel, Jaime A., Sudar, Damir, Bajcsy, Peter, Brown, Claire M., Corbett, Alexander D., Faklaris, Orestis, Lacoste, Judith, Laude, Alex, Nelson, Glyn, Nitschke, Roland, Grunwald, David, and Strambio-De-Castillia, Caterina

Subjects
Quantitative Biology - Quantitative Methods, Computer Science - Databases
Abstract

The application of microscopy in biomedical research has come a long way since Antonie van Leeuwenhoek discovered unicellular organisms. Countless innovations have positioned light microscopy as a cornerstone of modern biology and a method of choice for connecting omics datasets to their biological and clinical correlates. Still, regardless of how convincing published imaging data looks, it does not always convey meaningful information about the conditions in which it was acquired, processed, and analyzed. Adequate record-keeping, reporting, and quality control are therefore essential to ensure experimental rigor and data fidelity, allow experiments to be reproducibly repeated, and promote the proper evaluation, interpretation, comparison, and re-use. To this end, microscopy images should be accompanied by complete descriptions detailing experimental procedures, biological samples, microscope hardware specifications, image acquisition parameters, and image analysis procedures, as well as metrics accounting for instrument performance and calibration. However, universal, community-accepted Microscopy Metadata standards and reporting specifications that would result in Findable Accessible Interoperable and Reproducible (FAIR) microscopy data have not yet been established. To understand this shortcoming and to propose a way forward, here we provide an overview of the nature of microscopy metadata and its importance for fostering data quality, reproducibility, scientific rigor, and sharing value in light microscopy. The proposal for tiered Microscopy Metadata Specifications that extend the OME Data Model put forth by the 4D Nucleome Initiative and by Bioimaging North America [1-3] as well as a suite of three complementary and interoperable tools are being developed to facilitate the process of image data documentation and are presented in related manuscripts [4-6].

Published
2019

6. Sublethal necroptosis signaling promotes inflammation and liver cancer

Author

Vucur, Mihael, Ghallab, Ahmed, Schneider, Anne T., Adili, Arlind, Cheng, Mingbo, Castoldi, Mirco, Singer, Michael T., Büttner, Veronika, Keysberg, Leonie S., Küsgens, Lena, Kohlhepp, Marlene, Görg, Boris, Gallage, Suchira, Barragan Avila, Jose Efren, Unger, Kristian, Kordes, Claus, Leblond, Anne-Laure, Albrecht, Wiebke, Loosen, Sven H., Lohr, Carolin, Jördens, Markus S., Babler, Anne, Hayat, Sikander, Schumacher, David, Koenen, Maria T., Govaere, Olivier, Boekschoten, Mark V., Jörs, Simone, Villacorta-Martin, Carlos, Mazzaferro, Vincenzo, Llovet, Josep M., Weiskirchen, Ralf, Kather, Jakob N., Starlinger, Patrick, Trauner, Michael, Luedde, Mark, Heij, Lara R., Neumann, Ulf P., Keitel, Verena, Bode, Johannes G., Schneider, Rebekka K., Tacke, Frank, Levkau, Bodo, Lammers, Twan, Fluegen, Georg, Alexandrov, Theodore, Collins, Amy L., Nelson, Glyn, Oakley, Fiona, Mann, Derek A., Roderburg, Christoph, Longerich, Thomas, Weber, Achim, Villanueva, Augusto, Samson, Andre L., Murphy, James M., Kramann, Rafael, Geisler, Fabian, Costa, Ivan G., Hengstler, Jan G., Heikenwalder, Mathias, and Luedde, Tom

Published
2023
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7. Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications

Author

Rigano, Alessandro, Ehmsen, Shannon, Öztürk, Serkan Utku, Ryan, Joel, Balashov, Alexander, Hammer, Mathias, Kirli, Koray, Boehm, Ulrike, Brown, Claire M., Bellve, Karl, Chambers, James J., Cosolo, Andrea, Coleman, Robert A., Faklaris, Orestis, Fogarty, Kevin E., Guilbert, Thomas, Hamacher, Anna B., Itano, Michelle S., Keeley, Daniel P., Kunis, Susanne, Lacoste, Judith, Laude, Alex, Ma, Willa Y., Marcello, Marco, Montero-Llopis, Paula, Nelson, Glyn, Nitschke, Roland, Pimentel, Jaime A., Weidtkamp-Peters, Stefanie, Park, Peter J., Alver, Burak H., Grunwald, David, and Strambio-De-Castillia, Caterina

Published
2021
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8. Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model

Author

Hammer, Mathias, Huisman, Maximiliaan, Rigano, Alessandro, Boehm, Ulrike, Chambers, James J., Gaudreault, Nathalie, North, Alison J., Pimentel, Jaime A., Sudar, Damir, Bajcsy, Peter, Brown, Claire M., Corbett, Alexander D., Faklaris, Orestis, Lacoste, Judith, Laude, Alex, Nelson, Glyn, Nitschke, Roland, Farzam, Farzin, Smith, Carlas S., Grunwald, David, and Strambio-De-Castillia, Caterina

Published
2021
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9. QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy

Author

Boehm, Ulrike, Nelson, Glyn, Brown, Claire M., Bagley, Steve, Bajcsy, Peter, Bischof, Johanna, Dauphin, Aurelien, Dobbie, Ian M., Eriksson, John E., Faklaris, Orestis, Fernandez-Rodriguez, Julia, Ferrand, Alexia, Gelman, Laurent, Gheisari, Ali, Hartmann, Hella, Kukat, Christian, Laude, Alex, Mitkovski, Miso, Munck, Sebastian, North, Alison J., Rasse, Tobias M., Resch-Genger, Ute, Schuetz, Lucas C., Seitz, Arne, Strambio-De-Castillia, Caterina, Swedlow, Jason R., and Nitschke, Roland

Published
2021
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10. The ageing cell

Author

Wordsworth, James, primary, Nelson, Glyn, additional, and von Zglinicki, Thomas, additional

Published
2022
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14. Author Correction: Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model

Author

Hammer, Mathias, Huisman, Maximiliaan, Rigano, Alessandro, Boehm, Ulrike, Chambers, James J., Gaudreault, Nathalie, North, Alison J., Pimentel, Jaime A., Sudar, Damir, Bajcsy, Peter, Brown, Claire M., Corbett, Alexander D., Faklaris, Orestis, Lacoste, Judith, Laude, Alex, Nelson, Glyn, Nitschke, Roland, Farzam, Farzin, Smith, Carlas S., Grunwald, David, and Strambio-De-Castillia, Caterina

Published
2022
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15. Author Correction: Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications

Author

Rigano, Alessandro, Ehmsen, Shannon, Öztürk, Serkan Utku, Ryan, Joel, Balashov, Alexander, Hammer, Mathias, Kirli, Koray, Boehm, Ulrike, Brown, Claire M., Bellve, Karl, Chambers, James J., Cosolo, Andrea, Coleman, Robert A., Faklaris, Orestis, Fogarty, Kevin E., Guilbert, Thomas, Hamacher, Anna B., Itano, Michelle S., Keeley, Daniel P., Kunis, Susanne, Lacoste, Judith, Laude, Alex, Ma, Willa Y., Marcello, Marco, Montero-Llopis, Paula, Nelson, Glyn, Nitschke, Roland, Pimentel, Jaime A., Weidtkamp-Peters, Stefanie, Park, Peter J., Alver, Burak H., Grunwald, David, and Strambio-De-Castillia, Caterina

Published
2022
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16. Author Correction: QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy

Author

Boehm, Ulrike, Nelson, Glyn, Brown, Claire M., Bagley, Steve, Bajcsy, Peter, Bischof, Johanna, Dauphin, Aurelien, Dobbie, Ian M., Eriksson, John E., Faklaris, Orestis, Fernandez-Rodriguez, Julia, Ferrand, Alexia, Gelman, Laurent, Gheisari, Ali, Hartmann, Hella, Kukat, Christian, Laude, Alex, Mitkovski, Miso, Munck, Sebastian, North, Alison J., Rasse, Tobias M., Resch-Genger, Ute, Schuetz, Lucas C., Seitz, Arne, Strambio-De-Castillia, Caterina, Swedlow, Jason R., and Nitschke, Roland

Published
2022
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18. Development of the recombinant aequorin method and its evaluation for calcium measurement in filamentous fungi

Author

Nelson, Glyn

Subjects
572.8
Abstract

The aim of this work was to express the Ca2+ sensitive photoprotein, apoaequorin, in filamentous fungi to a high level in order to allow routine and simple measurement of changes in cytosolic Ca2+ ([Ca2+]c) concentration in living hyphae. Analysis of the codon bias of the available apoaequorin genes showed a large discrepancy with the codon usage of the target fungi, Neurospora crassa, Aspergillus niger and A. awamori. To overcome this discrepancy, a synthetic apoaequorin gene with optimal codon usage for Neurospora and Aspergillus was designed and synthesised. An expression vector was generated for the production of apoaequorin from the synthetic gene using a constitutive Aspergillus promoter and suitable selectable markers for transformation. An expression vector was also produced for use in N. crassa to allow comparison of the aequorin levels obtained between the synthetic gene and the native gene. Strains of A. niger and A. awamori were transformed with the Aspergillus apoaequorin expression vector, and transformants expressing large amounts of active aequorin were selected and purified. Transformants of N. crassa were also produced using the Neurospora expression vector, and the highest expression transformants isolated and purified. Comparisons of the aequorin expression levels obtained in these transformants showed a 200-fold higher level of expression in A. awamori compared with that obtained in N. crassa. Also, the comparison between native and synthetic aequorin production showed a 280-fold higher level in the synthetic aequorin transformant. One high expression transformant from each Aspergillus species was chosen for investigation of [Ca2+]c responses to a variety of external stimuli. A successful method of growing cultures in small volume, still liquid culture in 96-well microtitre plates was developed which allowed efficient analysis of [Ca2+]c in growing cultures. Using such cultures, [Ca2+]c was monitored during germination, growth and conidiation. A suitable age of culture (18-36 h) was determined for investigation of changes in [Ca2+]c in response to external stimuli. The first stimulus investigated was the application of high extracellular concentration (50 mM) of Ca2+, which elicited a large [Ca2+]c increase.

Published
1999

20. Dynamic regulation of airway surface liquid pH by TMEM16A and SLC26A4 in cystic fibrosis nasal epithelia with rare mutations

Author

Longziekten onderzoek 2, Child Health, Onderzoek, Regenerative Medicine and Stem Cells, Delpiano, Livia, Rodenburg, Lisa W., Burke, Matthew, Nelson, Glyn, Amatngalim, Gimano D., Beekman, Jeffrey M., Gray, Michael A., Longziekten onderzoek 2, Child Health, Onderzoek, Regenerative Medicine and Stem Cells, Delpiano, Livia, Rodenburg, Lisa W., Burke, Matthew, Nelson, Glyn, Amatngalim, Gimano D., Beekman, Jeffrey M., and Gray, Michael A.

Published
2023

22. Mitochondria are required for pro‐ageing features of the senescent phenotype

Author

Correia‐Melo, Clara, Marques, Francisco DM, Anderson, Rhys, Hewitt, Graeme, Hewitt, Rachael, Cole, John, Carroll, Bernadette M, Miwa, Satomi, Birch, Jodie, Merz, Alina, Rushton, Michael D, Charles, Michelle, Jurk, Diana, Tait, Stephen WG, Czapiewski, Rafal, Greaves, Laura, Nelson, Glyn, Bohlooly‐Y, Mohammad, Rodriguez‐Cuenca, Sergio, Vidal‐Puig, Antonio, Mann, Derek, Saretzki, Gabriele, Quarato, Giovanni, Green, Douglas R, Adams, Peter D, von Zglinicki, Thomas, Korolchuk, Viktor I, and Passos, João F

Published
2016
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25. Results of community surveys organized by the members of the BioImaging North America – Quality Control and Data Management Working Group to understand the microscopy reporting and reproducibility needs of the bioimaging community

Author

Bilay, Nikki, Orr, Vanessar, Boehm, Ulrike, Chambers, James, Gaudreault, Nathalie, North, Alison J., Pimentel, Jaime A., Sudar, Damir, Bajcsy, Peter, Brown, Claire M., Corbett, Alexander D., Faklaris, Orestis, Halter, Michael, Lacoste, Judith, Laude, Alex, Nelson, Glyn, Nitschke, Roland, Miller, Caroline, and Strambio-De-Castillia, Caterina

Subjects
Quality Control, Microscopy, Metadata, Data Sharing, Reporting, Data Provenance, Calibration, Research Data Management, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), ComputingMilieux_MISCELLANEOUS, Reproducibility, Imaging
Abstract

In January 2022, members of the BioImaging North America (BINA) Quality Control and Data Management Working Group, held a Community Conversation to introduce a series of articles that had been featured in the FOCUS on Microscopy Reporting and Reproducibility published in the December 2021 issue of Nature Methods. During this event, the authors of the papers featured on the FOCUS issue were invited to present their work and interact with members of the BINA community. A series of community surveys were conducted during this Community Conversation to better understand the audience, their current reporting and reproducibility practices, and their interest in tools and resources to help them better take advantage of these practices. While the results of these polls are limited by the small sample size, this document is published in the hope that these results could be useful to the community to guide the future development of Research Data Management metadata specifications and software tools., Additional support: -- Chan Zuckerberg Initiative DAF (Silicon Valley Community Foundation) grant #2019-198155 (5022) awarded to C.S.D.C. as part of the Imaging Scientist Program. -- Chan Zuckerberg Initiative DAF (Silicon Valley Community Foundation) grant ##2020-225398 awarded to C.M.B. as part of the Imaging Scientist Program, {"references":["https://www.bioimagingnorthamerica.org/","https://www.bioimagingnorthamerica.org/qc-dm-wg/","https://doi.org/10.1038/s41592-021-01327-9","https://doi.org/10.1038/s41592-021-01315-z","https://doi.org/10.1038/s41592-021-01290-5"]}

Published
2022
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27. Basal Mitophagy is Suppressed in Cellular Senescence and Mediates Senescence Phenotypes

Author

Kelly, George, primary, Kataura, Tetsushi, additional, Banks, Peter, additional, Nelson, Glyn, additional, Ayine-Tora, Daniel Moscoh, additional, Dobby, Laura, additional, Ma, Gailing, additional, Costello, Lydia, additional, Carroll, Bernadette, additional, Lovat, Penny, additional, Salmonowicz, Hanna, additional, Ferreira, Lino, additional, Przyborski, Stefan, additional, von Zglinicki, Thomas, additional, Miwa, Satomi, additional, Reynisson, Jóhannes, additional, Oblong, John E., additional, Bascom, Charles C., additional, and Korolchuk, Viktor, additional

Published
2022
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28. Author Correction: Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications

Author

Rigano, Alessandro, primary, Ehmsen, Shannon, additional, Öztürk, Serkan Utku, additional, Ryan, Joel, additional, Balashov, Alexander, additional, Hammer, Mathias, additional, Kirli, Koray, additional, Boehm, Ulrike, additional, Brown, Claire M., additional, Bellve, Karl, additional, Chambers, James J., additional, Cosolo, Andrea, additional, Coleman, Robert A., additional, Faklaris, Orestis, additional, Fogarty, Kevin E., additional, Guilbert, Thomas, additional, Hamacher, Anna B., additional, Itano, Michelle S., additional, Keeley, Daniel P., additional, Kunis, Susanne, additional, Lacoste, Judith, additional, Laude, Alex, additional, Ma, Willa Y., additional, Marcello, Marco, additional, Montero-Llopis, Paula, additional, Nelson, Glyn, additional, Nitschke, Roland, additional, Pimentel, Jaime A., additional, Weidtkamp-Peters, Stefanie, additional, Park, Peter J., additional, Alver, Burak H., additional, Grunwald, David, additional, and Strambio-De-Castillia, Caterina, additional

Published
2021
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31. QUAREP‐LiMi: A community‐driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy

Author

Nelson, Glyn, primary, Boehm, Ulrike, additional, Bagley, Steve, additional, Bajcsy, Peter, additional, Bischof, Johanna, additional, Brown, Claire M., additional, Dauphin, Aurélien, additional, Dobbie, Ian M., additional, Eriksson, John E., additional, Faklaris, Orestis, additional, Fernandez‐Rodriguez, Julia, additional, Ferrand, Alexia, additional, Gelman, Laurent, additional, Gheisari, Ali, additional, Hartmann, Hella, additional, Kukat, Christian, additional, Laude, Alex, additional, Mitkovski, Miso, additional, Munck, Sebastian, additional, North, Alison J., additional, Rasse, Tobias M., additional, Resch‐Genger, Ute, additional, Schuetz, Lucas C., additional, Seitz, Arne, additional, Strambio‐De‐Castillia, Caterina, additional, Swedlow, Jason R., additional, Alexopoulos, Ioannis, additional, Aumayr, Karin, additional, Avilov, Sergiy, additional, Bakker, Gert‐Jan, additional, Bammann, Rodrigo R., additional, Bassi, Andrea, additional, Beckert, Hannes, additional, Beer, Sebastian, additional, Belyaev, Yury, additional, Bierwagen, Jakob, additional, Birngruber, Konstantin A., additional, Bosch, Manel, additional, Breitlow, Juergen, additional, Cameron, Lisa A., additional, Chalfoun, Joe, additional, Chambers, James J., additional, Chen, Chieh‐Li, additional, Conde‐Sousa, Eduardo, additional, Corbett, Alexander D., additional, Cordelieres, Fabrice P., additional, Nery, Elaine Del, additional, Dietzel, Ralf, additional, Eismann, Frank, additional, Fazeli, Elnaz, additional, Felscher, Andreas, additional, Fried, Hans, additional, Gaudreault, Nathalie, additional, Goh, Wah Ing, additional, Guilbert, Thomas, additional, Hadleigh, Roland, additional, Hemmerich, Peter, additional, Holst, Gerhard A., additional, Itano, Michelle S., additional, Jaffe, Claudia B., additional, Jambor, Helena K., additional, Jarvis, Stuart C., additional, Keppler, Antje, additional, Kirchenbuechler, David, additional, Kirchner, Marcel, additional, Kobayashi, Norio, additional, Krens, Gabriel, additional, Kunis, Susanne, additional, Lacoste, Judith, additional, Marcello, Marco, additional, Martins, Gabriel G., additional, Metcalf, Daniel J., additional, Mitchell, Claire A., additional, Moore, Joshua, additional, Mueller, Tobias, additional, Nelson, Michael S., additional, Ogg, Stephen, additional, Onami, Shuichi, additional, Palmer, Alexandra L., additional, Paul‐Gilloteaux, Perrine, additional, Pimentel, Jaime A., additional, Plantard, Laure, additional, Podder, Santosh, additional, Rexhepaj, Elton, additional, Royon, Arnaud, additional, Saari, Markku A., additional, Schapman, Damien, additional, Schoonderwoert, Vincent, additional, Schroth‐Diez, Britta, additional, Schwartz, Stanley, additional, Shaw, Michael, additional, Spitaler, Martin, additional, Stoeckl, Martin T., additional, Sudar, Damir, additional, Teillon, Jeremie, additional, Terjung, Stefan, additional, Thuenauer, Roland, additional, Wilms, Christian D., additional, Wright, Graham D., additional, and Nitschke, Roland, additional

Published
2021
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33. Micro-Meta App: an interactive software tool to facilitate the collection of microscopy metadata based on community-driven specifications

Author

Rigano, Alex, primary, Ehmsen, Shannon, additional, Ozturk, Serkan Utku, additional, Ryan, Joel, additional, Balashov, Alexander, additional, Hammer, Mathias, additional, Kirli, Koray, additional, Bellve, Karl, additional, Boehm, Ulrike, additional, Brown, Claire M., additional, Chambers, James J., additional, Coleman, Robert A., additional, Cosolo, Andrea, additional, Faklaris, Orestis, additional, Fogarty, Kevin, additional, Guilbert, Thomas, additional, Hamacher, Anna B., additional, Itano, Michelle S., additional, Keeley, Daniel P., additional, Kunis, Susanne, additional, Lacoste, Judith, additional, Laude, Alex, additional, Ma, Willa, additional, Marcello, Marco, additional, Montero-Llopis, Paula, additional, Nelson, Glyn, additional, Nitschke, Roland, additional, Pimentel, Jaime A., additional, Weidtkamp-Peters, Stefanie, additional, Park, Peter J., additional, Alver, Burak, additional, Grunwald, David, additional, and Strambio-De-Castillia, Caterina, additional

Published
2021
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34. Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model

Author

Hammer, Mathias, primary, Huisman, Maximiliaan, additional, Rigano, Alex, additional, Boehm, Ulrike, additional, Chambers, James J., additional, Gaudreault, Nathalie, additional, North, Alison J., additional, Pimentel, Jaime A., additional, Sudar, Damir, additional, Bajcsy, Peter, additional, Brown, Claire M., additional, Corbett, Alexander D., additional, Faklaris, Orestis, additional, Lacoste, Judith, additional, Laude, Alex, additional, Nelson, Glyn, additional, Nitschke, Roland, additional, Farzam, Farzin, additional, Smith, Carlas S., additional, Grunwald, David, additional, and Strambio-De-Castillia, Caterina, additional

Published
2021
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39. mTORC1 activity is supported by spatial association with focal adhesions

Author

Rabanal-Ruiz, Yoana, primary, Byron, Adam, additional, Wirth, Alexander, additional, Madsen, Ralitsa, additional, Sedlackova, Lucia, additional, Hewitt, Graeme, additional, Nelson, Glyn, additional, Stingele, Julian, additional, Wills, Jimi C., additional, Zhang, Tong, additional, Zeug, André, additional, Fässler, Reinhard, additional, Vanhaesebroeck, Bart, additional, Maddocks, Oliver D.K., additional, Ponimaskin, Evgeni, additional, Carroll, Bernadette, additional, and Korolchuk, Viktor I., additional

Published
2021
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40. mTORC1 activity is supported by spatial association with focal adhesions

Author

Rabanal-Ruiz, Yoana, primary, Byron, Adam, additional, Wirth, Alexander, additional, Madsen, Ralitsa, additional, Sedlackova, Lucia, additional, Hewitt, Graeme, additional, Nelson, Glyn, additional, Stingele, Julian, additional, Wills, Jimi C., additional, Zhang, Tong, additional, Zeug, André, additional, Fässler, Reinhard, additional, Vanhaesebroeck, Bart, additional, Maddocks, Oliver D.K., additional, Ponimaskin, Evgeni, additional, Carroll, Bernadette, additional, and Korolchuk, Viktor I., additional

Published
2020
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41. Metabolic dysfunction in human skin: Restoration of mitochondrial integrity and metabolic output by nicotinamide (niacinamide) in primary dermal fibroblasts from older aged donors

Author

Oblong, John E., primary, Bowman, Amy, additional, Rovito, Holly A., additional, Jarrold, Bradley B., additional, Sherrill, Joseph D., additional, Black, Markaisa R., additional, Nelson, Glyn, additional, Kimball, Alexa B., additional, and Birch‐Machin, Mark A., additional

Published
2020
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44. Bioengineering the microanatomy of human skin

Author

Roger, Mathilde, Fullard, Nicola, Costello, Lydia, Bradbury, Steven, Markiewicz, Ewa, O'Reilly, Steven, Darling, Nicole, Ritchie, Pamela, Määttä, Arto, Karakesisoglou, Iakowos, Nelson, Glyn, von Zglinicki, Thomas, Dicolandrea, Teresa, Isfort, Robert, Bascom, Charles, and Przyborski, Stefan

Subjects
integumentary system, C100
Abstract

Recreating the structure of human tissues in the laboratory is valuable for fundamental research, testing interventions, and reducing the use of animals. Critical to the use of such technology is the ability to produce tissue models that accurately reproduce the microanatomy of the native tissue. Current artificial cell‐based skin systems lack thorough characterisation, are not representative of human skin, and can show variation. In this study, we have developed a novel full thickness model of human skin comprised of epidermal and dermal compartments. Using an inert porous scaffold, we created a dermal construct using human fibroblasts that secrete their own extracellular matrix proteins, which avoids the use of animal‐derived materials. The dermal construct acts as a foundation upon which epidermal keratinocytes were seeded and differentiated into a stratified keratinised epithelium. In‐depth morphological analyses of the model demonstrated very close similarities with native human skin. Extensive immunostaining and electron microscopy analysis revealed ultrastructural details such as keratohyalin granules and lamellar bodies within the stratum granulosum, specialised junctional complexes, and the presence of a basal lamina. These features reflect the functional characteristics and barrier properties of the skin equivalent. Robustness and reproducibility of in vitro models are important attributes in experimental practice, and we demonstrate the consistency of the skin construct between different users. In summary, a new model of full thickness human skin has been developed that possesses microanatomical features reminiscent of native tissue. This skin model platform will be of significant interest to scientists researching the structure and function of human skin.

Published
2019

47. The influence of artificial water canals on residential sale prices

Author

Nelson, Glyn, Hansz, J. Andrew, and Cypher, Matthew L.

Subjects
Environment -- Research, Architectural firms -- Environmental aspects -- Models, Architectural practice -- Environmental aspects -- Models, Business, Real estate industry, Models, Environmental aspects
Abstract

abstract Research in the fields of environmental psychology and landscape architecture demonstrates that humans have an innate preference for natural water settings. Where other real estate pricing studies have focused [...]

Published
2005

49. SQSTM1/p62 mediates crosstalk between autophagy and the UPS in DNA repair

Author

Hewitt, Graeme, Carroll, Bernadette, Sarallah, Rezazadeh, Correia-Melo, Clara, Ogrodnik, Mikolaj, Nelson, Glyn, Otten, Elsje G, Manni, Diego, Antrobus, Robin, Morgan, Brian A, von Zglinicki, Thomas, Jurk, Diana, Seluanov, Andrei, Gorbunova, Vera, Johansen, Terje, Passos, João F, and Korolchuk, Viktor I

Subjects
Cell Nucleus, autophagy, Proteasome Endopeptidase Complex, Basic Research Papers, DNA Repair, Ubiquitin, Filamins, aging, homologous recombination, Models, Biological, nonhomologous end joining, Mice, Inbred C57BL, Kinetics, Protein Transport, Proteolysis, Sequestosome-1 Protein, DNA damage, Animals, SQSTM1, Rad51 Recombinase
Abstract

SQSTM1/p62 (sequestosome 1) selectively targets polyubiquitinated proteins for degradation via macroautophagy and the proteasome. Additionally, SQSTM1 shuttles between the cytoplasmic and nuclear compartments, although its role in the nucleus is relatively unknown. Here, we report that SQSTM1 dynamically associates with DNA damage foci (DDF) and regulates DNA repair. Upon induction of DNA damage SQSTM1 interacts with FLNA (filamin A), which has previously been shown to recruit DNA repair protein RAD51 (RAD51 recombinase) to double-strand breaks and facilitate homologous recombination (HR). SQSTM1 promotes proteasomal degradation of FLNA and RAD51 within the nucleus, resulting in reduced levels of nuclear RAD51 and slower DNA repair. SQSTM1 regulates the ratio between HR and nonhomologous end joining (NHEJ) by promoting the latter at the expense of the former. This SQSTM1-dependent mechanism mediates the effect of macroautophagy on DNA repair. Moreover, nuclear localization of SQSTM1 and its association with DDF increase with aging and are prevented by life-span-extending dietary restriction, suggesting that an imbalance in the mechanism identified here may contribute to aging and age-related diseases.

Published
2016
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50. The bystander effect contributes to the accumulation of senescent cells in vivo

Author

da Silva, Paulo F. L., Ogrodnik, Mikolaj, Kucheryavenko, Olena, Glibert, Julien, Miwa, Satomi, Cameron, Kerry, Ishaq, Abbas, Saretzki, Gabriele, Nagaraja-Grellscheid, Sushma, Nelson, Glyn, and von Zglinicki, Thomas

Abstract

Senescent cells accumulate with age in multiple tissues and may cause age‐associated disease and functional decline. In vitro, senescent cells induce senescence in bystander cells. To see how important this bystander effect may be for accumulation of senescent cells in vivo, we xenotransplanted senescent cells into skeletal muscle and skin of immunocompromised NSG mice. 3 weeks after the last transplantation, mouse dermal fibroblasts and myofibres displayed multiple senescence markers in the vicinity of transplanted senescent cells, but not where non‐senescent or no cells were injected. Adjacent to injected senescent cells, the magnitude of the bystander effect was similar to the increase in senescence markers in myofibres between 8 and 32 months of age. The age‐associated increase of senescence markers in muscle correlated with fibre thinning, a widely used marker of muscle aging and sarcopenia. Senescent cell transplantation resulted in borderline induction of centrally nucleated fibres and no significant thinning, suggesting that myofibre aging might be a delayed consequence of senescence‐like signalling. To assess the relative importance of the bystander effect versus cell‐autonomous senescence, we compared senescent hepatocyte frequencies in livers of wild‐type and NSG mice under ad libitum and dietary restricted feeding. This enabled us to approximate cell‐autonomous and bystander‐driven senescent cell accumulation as well as the impact of immunosurveillance separately. The results suggest a significant impact of the bystander effect for accumulation of senescent hepatocytes in liver and indicate that senostatic interventions like dietary restriction may act as senolytics in immunocompetent animals.

Published
2019
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