Arne Seitz

École Polytechnique Fédérale de Lausanne

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Olivier Burri

École Polytechnique Fédérale de Lausanne

Romain Guiet

École Polytechnique Fédérale de Lausanne

Thierry Laroche

Soitec (France)

Nicolas Chiaruttini

École Polytechnique Fédérale de Lausanne

Ulrike Boehm

Janelia Research Campus

Johanna Bischof

European Molecular Biology Laboratory

Julia Fernández-Rodrı́guez

University of Gothenburg

Roland Nitschke

University of Freiburg

Daniel Sage

École Polytechnique Fédérale de Lausanne

Olivier Hagens

École Polytechnique Fédérale de Lausanne

Cooperative Institutions

École Polytechnique Fédérale de Lausanne

European Molecular Biology Organization

University of Lausanne

Centre National de la Recherche Scientifique

Inserm

Heidelberg University

University of Geneva

University Hospital of Lausanne

European Molecular Biology Laboratory

Johannes Gutenberg University Mainz

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ABBA, a novel tool for whole-brain mapping, reveals brain-wide differences in immediate early genes induction following learning

bioRxiv (Cold Spring Harbor Laboratory) (2024)

Nicolas Chiaruttini Carlo Castoldi Linda Maria Requie Carmen Camarena-Delgado B Bianco

Abstract Unbiased characterization of whole-brain cytoarchitecture represents an invaluable tool for understanding brain function. For this, precise mapping of histological markers from 2D sections onto 3D brain atlases is pivotal. Here, we present two novel software tools facilitating this process: Aligning Big Brains and Atlases (ABBA), designed to streamline the precise and efficient registration of 2D sections to 3D reference atlases, and BraiAn, an integrated suite for multi-marker automated segmentation, whole-brain statistical analysis, and data visualisation. Combining these tools, we performed a comprehensive comparative study of the whole-brain expression of three of the most widely used immediate early genes (IEGs). Thanks to their neural activity-dependent expression, IEGs have been used for decades as a proxy of neural activity to generate unbiased mapping of activity following behaviour, but their respective induction in response to neuronal activation across the entire brain remains unclear. To address this question, we systematically compared the brain-wide expression cFos, Arc and NPAS4, three abundantly used IEGs, across three different behavioural conditions related to memory. Our results highlight major differences in both their distribution and induction patterns, indicating that they do not represent equivalent markers across brain areas or activity states, but can provide instead complementary information.

Cytoarchitecture

10.1101/2024.09.06.611625

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Citations (2)

High-Throughput Microscopy Using Live Mammalian Cells

Cold Spring Harbor Protocols (2010)

Stefan Terjung Thomas Walter Arne Seitz Beate Neumann Rainer Pepperkok

INTRODUCTION Since the complete sequencing of several genomes, the systematic understanding of protein function and interaction has become one of the most important tasks in current molecular biology. Recent advances in light microscopy equipment regarding automation and acquisition speed offer the possibility to perform hundreds of experiments in parallel to study protein function and interaction in intact cells. In this context, live cell imaging is an excellent tool that may be used to investigate dynamic or rarely occurring cellular processes, to distinguish between primary and secondary phenotypes, and to study the phenotype kinetics. In this article, we present a guideline for high-throughput microscopy for functional screening in living cells. We shall examine each aspect of the general screening process and consider specific examples in the processing of time-lapse experiments. Although this article is largely based on examples from cultured mammalian cells, many of its considerations apply to cultured cells from other species such as Drosophila and to some extent to microscopy-based screening in small organisms such as Caenorhabditis elegans .

High-Content Screening

Live cell imaging

High-Throughput Screening

10.1101/pdb.top84

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Citations (5)

<title>Large-diameter bacteriorhodopsin films for applications in nondestructive testing</title>

Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE (1999)

Norbert Hampp Arne Seitz Thorsten Juchem Dieter Oesterhelt

Bacteriorhodopsin (BR) films with dimension of 100 mm X 100 mm have been developed for applications in non- destructive testing. Films made from the photochromic retinal protein BR have been successfully employed in a variety of optical applications. Among them holographic interferometry for non-destructive testing which is one of the applications where the aperture of the BR-films used for recording plays an important role. The BR-films available earlier had an aperture of about 2/3 inch. Due to this limit size it was necessary to focus the light scattered from the object under investigation to the BR-film by means of lenses which in turn limit the optical resolution of the whole system. Now BR-films with a more than 50-fold larger are have been developed which allow lensless recording of the holograms. The optical quality of the films, in particular the spatial homogeneity of their optical density and their light sensitivity, is constant over the full aperture within a few percent. Applications of this new type of BR-films in non-destructive testing of ceramic parts are presented.

10.1117/12.348404

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Citations (4)

An Open-Source Whole Slide Image Registration Workflow at Cellular Precision Using Fiji, QuPath and Elastix

Frontiers in Computer Science (2022)

Nicolas Chiaruttini Olivier Burri Peter Haub Romain Guiet Jessica Sordet‐Dessimoz

Image analysis workflows for Histology increasingly require the correlation and combination of measurements across several whole slide images. Indeed, for multiplexing, as well as multimodal imaging, it is indispensable that the same sample is imaged multiple times, either through various systems for multimodal imaging, or using the same system but throughout rounds of sample manipulation (e.g. multiple staining sessions). In both cases slight deformations from one image to another are unavoidable, leading to an imperfect superimposition Redundant and thus a loss of accuracy making it difficult to link measurements, in particular at the cellular level. Using pre-existing software components and developing missing ones, we propose a user-friendly workflow which facilitates the nonlinear registration of whole slide images in order to reach sub-cellular resolution level. The set of whole slide images to register and analyze is at first defined as a QuPath project. Fiji is then used to open the QuPath project and perform the registrations. Each registration is automated by using an elastix backend, or semi-automated by using BigWarp in order to interactively correct the results of the automated registration. These transformations can then be retrieved in QuPath to transfer any regions of interest from an image to the corresponding registered images. In addition, the transformations can be applied in QuPath to produce on-the-fly transformed images that can be displayed on top of the reference image. Thus, relevant data can be combined and analyzed throughout all registered slides, facilitating the analysis of correlative results for multiplexed and multimodal imaging.

Image registration

Sample (material)

Superimposition

Semi automatic

10.3389/fcomp.2021.780026

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Citations (36)

<title>Printing inks containing the photochromic protein bacteriorhodopsin</title>

Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE (2000)

Norbert Hampp Martin Neebe Arne Seitz

The biological photo chrome bacteriorhodopsin occurs in nature in the form of a 2D crystalline lattice. In this form, the so-called purple membranes, it is astonishingly stable towards chemical and thermal degradation. Variants of the naturally occurring bacteriorhodopsin can be switched between a purple and a yellowish state with yellow and blue light - no UV light is required. The application of bacteriorhodopsin in the form of a photochromic ink is described. In addition to the optical effect, which can be checked easily without instrumentation, additional optional security elements can be hidden in the material which are very hard to detect and to copy. Among them is the alteration of the aminoacid sequence of bacteriorhodopsin in positions which do not interact with its photochemical properties. By this and related methods even single production batches may be identified. The price of the material to date is too high for a broad commercial application but current efforts to reduce the production costs by several orders of magnitude look promising.

Degradation

10.1117/12.382181

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Citations (3)

Measuring Secretory Membrane Traffic

Methods in molecular biology (2008)

Vytaute Starkuviene Arne Seitz Holger Erfle Rainer Pepperkok

10.1007/978-1-59745-261-8_14

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Citations (4)

Open Source Tools for Biological Image Analysis

Methods in molecular biology (2019)

Romain Guiet Olivier Burri Arne Seitz

Sketch

10.1007/978-1-4939-9686-5_2

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Citations (11)

Hookworms Evade Host Immunity by Secreting a Deoxyribonuclease to Degrade Neutrophil Extracellular Traps

Cell Host & Microbe (2020)

Tiffany Bouchery Mati Moyat Javier Sotillo Solomon Silverstein Beatrice Volpe

Hookworms cause a major neglected tropical disease, occurring after larvae penetrate the host skin. Neutrophils are phagocytes that kill large pathogens by releasing neutrophil extracellular traps (NETs), but whether they target hookworms during skin infection is unknown. Using a murine hookworm, Nippostrongylus brasiliensis, we observed neutrophils being rapidly recruited and deploying NETs around skin-penetrating larvae. Neutrophils depletion or NET inhibition altered larvae behavior and enhanced the number of adult worms following murine infection. Nevertheless, larvae were able to mitigate the effect of NETs by secreting a deoxyribonuclease (Nb-DNase II) to degrade the DNA backbone. Critically, neutrophils were able to kill larvae in vitro, which was enhanced by neutralizing Nb-DNase II. Homologs of Nb-DNase II are present in other nematodes, including the human hookworm, Necator americanus, which also evaded NETs in vitro. These findings highlight the importance of neutrophils in hookworm infection and a potential conserved mechanism of immune evasion.

Neutrophil Extracellular Traps

Nippostrongylus brasiliensis

Deoxyribonucleases

10.1016/j.chom.2020.01.011

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Citations (68)

A novel transmembrane domain mediating retention of a highly motile herpesvirus glycoprotein in the endoplasmic reticulum

Journal of General Virology (2010)

Torsten Däubner Annette Fink Arne Seitz Stefan Tenzer Jonas Müller

Gene m164 of murine cytomegalovirus belongs to the large group of 'private' genes that show no homology to those of other cytomegalovirus species and are thought to represent 'host adaptation' genes involved in virus–host interaction. Previous interest in the m164 gene product was based on the presence of an immunodominant CD8 T-cell epitope presented at the surface of infected cells, despite interference by viral immune-evasion proteins. Here, we provide data to reveal that the m164 gene product shows unusual features in its cell biology. A novel strategy of mass-spectrometric analysis was employed to map the N terminus of the mature protein, 107 aa downstream of the start site of the predicted open reading frame. The resulting 36.5 kDa m164 gene product is identified here as an integral type-I membrane glycoprotein with exceptional intracellular trafficking dynamics, moving within the endoplasmic reticulum (ER) and outer nuclear membrane with an outstandingly high lateral membrane motility, actually 100 times higher than those published for cellular ER-resident proteins. Notably, gp36.5/m164 does not contain any typical ER-retention/retrieval signals, such as the C-terminal motifs KKXX or KXKXX, and does not pass the Golgi apparatus. Instead, it belongs to the rare group of viral glycoproteins in which the transmembrane domain (TMD) itself mediates direct ER retention. This is the first report relating TMD usage of an ER-resident transmembrane protein to its lateral membrane motility as a paradigm in cell biology. We propose that TMD usage for ER retention facilitates free and fast floating in ER-related membranes and between ER subdomains.

ER retention

Membrane glycoproteins

10.1099/vir.0.018580-0

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Citations (20)

Community-developed checklists for publishing images and image analyses

Nature Methods (2023)

Christopher Schmied Michael S. Nelson Sergiy Avilov Gert‐Jan Bakker Cristina Bertocchi

Images document scientific discoveries and are prevalent in modern biomedical research. Microscopy imaging in particular is currently undergoing rapid technological advancements. However, for scientists wishing to publish obtained images and image-analysis results, there are currently no unified guidelines for best practices. Consequently, microscopy images and image data in publications may be unclear or difficult to interpret. Here, we present community-developed checklists for preparing light microscopy images and describing image analyses for publications. These checklists offer authors, readers and publishers key recommendations for image formatting and annotation, color selection, data availability and reporting image-analysis workflows. The goal of our guidelines is to increase the clarity and reproducibility of image figures and thereby to heighten the quality and explanatory power of microscopy data.

Disk formatting

Publication

CLARITY

10.1038/s41592-023-01987-9

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Citations (36)