39 results on '"Jug F"'
Search Results
2. ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation
- Author
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Jiménez de la Morena, J., primary, Conesa, P., additional, Fonseca, Y.C., additional, de Isidro-Gómez, F.P., additional, Herreros, D., additional, Fernández-Giménez, E., additional, Strelak, D., additional, Moebel, E., additional, Buchholz, T.O., additional, Jug, F., additional, Martinez-Sanchez, A., additional, Harastani, M., additional, Jonic, S., additional, Conesa, J.J., additional, Cuervo, A., additional, Losana, P., additional, Sánchez, I., additional, Iceta, M., additional, del Cano, L., additional, Gragera, M., additional, Melero, R., additional, Sharov, G., additional, Castaño-Díez, D., additional, Koster, A., additional, Piccirillo, J.G., additional, Vilas, J.L., additional, Otón, J., additional, Marabini, R., additional, Sorzano, C.O.S., additional, and Carazo, J.M., additional
- Published
- 2022
- Full Text
- View/download PDF
3. Deep Learning für die Messzeitreduzierung bei FDG-PETs in der Demenzdiagnostik
- Author
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Schiller, F., additional, Thurow, J., additional, Deschamps, J., additional, Schmied, C., additional, Jug, F., additional, Brumberg, J., additional, Frings, L., additional, Meyer, P.T., additional, and Mix, M., additional
- Published
- 2022
- Full Text
- View/download PDF
4. 3D FIB-SEM reconstruction of microtubule-organelle interaction in whole primary mouse β cells
- Author
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Müller, A., Schmidt, D., Xu, C.S., Pang, S., D'Costa, J.V., Kretschmar, S., Münster, C., Kurth, T., Jug, F., Weigert, M., Hess, H.F., and Solimena, M.
- Subjects
Technology Platforms - Abstract
Microtubules play a major role in intracellular trafficking of vesicles in endocrine cells. Detailed knowledge of microtubule organization and their relation to other cell constituents is crucial for understanding cell function. However, their role in insulin transport and secretion is under debate. Here, we use FIB-SEM to image islet β cells in their entirety with unprecedented resolution. We reconstruct mitochondria, Golgi apparati, centrioles, insulin secretory granules, and microtubules of seven β cells, and generate a comprehensive spatial map of microtubule-organelle interactions. We find that microtubules form nonradial networks that are predominantly not connected to either centrioles or endomembranes. Microtubule number and length, but not microtubule polymer density, vary with glucose stimulation. Furthermore, insulin secretory granules are enriched near the plasma membrane, where they associate with microtubules. In summary, we provide the first 3D reconstructions of complete microtubule networks in primary mammalian cells together with evidence regarding their importance for insulin secretory granule positioning and thus their supportive role in insulin secretion.
- Published
- 2021
5. Regionalized tissue fluidization by an actomyosin cable is required for epithelial gap closure during insect gastrulation
- Author
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Jain, A., primary, Ulman, V., additional, Mukherjee, A., additional, Prakash, M., additional, Pimpale, L., additional, Muenster, S., additional, Haase, R., additional, Panfilio, K.A., additional, Jug, F., additional, Grill, S.W., additional, Tomancak, P., additional, and Pavlopoulos, A., additional
- Published
- 2019
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6. Deep-Learning für signifikante Messzeitreduzierung bei zerebralen FDG-PETs in der Demenzdiagnostik: Validierung und diagnostische Sicherheit
- Author
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Schiller, F., Brumberg, J., Frings, L., Deschamps, J., Schmied, C., Jug, F., Mix, M., and Meyer, P. T.
- Published
- 2024
- Full Text
- View/download PDF
7. Interacting maps for fast visual interpretation.
- Author
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Cook, M., Gugelmann, L., Jug, F., Krautz, C., and Steger, A.
- Published
- 2011
- Full Text
- View/download PDF
8. Sharpening projections
- Author
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Krautz Christoph, Jug Florian, and Cook Matthew
- Subjects
Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 ,Neurophysiology and neuropsychology ,QP351-495 - Published
- 2009
- Full Text
- View/download PDF
9. Mechanical and biochemical feedback combine to generate complex contractile oscillations in cytokinesis.
- Author
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Werner ME, Ray DD, Breen C, Staddon MF, Jug F, Banerjee S, and Maddox AS
- Subjects
- Animals, Biomechanical Phenomena, Caenorhabditis elegans Proteins metabolism, Caenorhabditis elegans Proteins genetics, Feedback, Physiological, rhoA GTP-Binding Protein metabolism, Embryo, Nonmammalian physiology, Cytokinesis physiology, Caenorhabditis elegans physiology, Actomyosin metabolism
- Abstract
The actomyosin cortex is an active material that generates force to drive shape changes via cytoskeletal remodeling. Cytokinesis is the essential cell division event during which a cortical actomyosin ring closes to separate two daughter cells. Our active gel theory predicted that actomyosin systems controlled by a biochemical oscillator and experiencing mechanical strain would exhibit complex spatiotemporal behavior. To test whether active materials in vivo exhibit spatiotemporally complex kinetics, we imaged the C. elegans embryo with unprecedented temporal resolution and discovered that sections of the cytokinetic cortex undergo periodic phases of acceleration and deceleration. Contractile oscillations exhibited a range of periodicities, including those much longer periods than the timescale of RhoA pulses, which was shorter in cytokinesis than in any other biological context. Modifying mechanical feedback in vivo or in silico revealed that the period of contractile oscillation is prolonged as a function of the intensity of mechanical feedback. Fast local ring ingression occurs where speed oscillations have long periods, likely due to increased local stresses and, therefore, mechanical feedback. Fast ingression also occurs where material turnover is high, in vivo and in silico. We propose that downstream of initiation by pulsed RhoA activity, mechanical feedback, including but not limited to material advection, extends the timescale of contractility beyond that of biochemical input and, therefore, makes it robust to fluctuations in activation. Circumferential propagation of contractility likely allows for sustained contractility despite cytoskeletal remodeling necessary to recover from compaction. Thus, like biochemical feedback, mechanical feedback affords active materials responsiveness and robustness., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Inc. All rights reserved.)
- Published
- 2024
- Full Text
- View/download PDF
10. Live-cell imaging powered by computation.
- Author
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Shroff H, Testa I, Jug F, and Manley S
- Subjects
- Humans, Animals, Image Processing, Computer-Assisted methods, Artificial Intelligence, Signal-To-Noise Ratio, Cell Survival, Microscopy, Fluorescence methods
- Abstract
The proliferation of microscopy methods for live-cell imaging offers many new possibilities for users but can also be challenging to navigate. The prevailing challenge in live-cell fluorescence microscopy is capturing intra-cellular dynamics while preserving cell viability. Computational methods can help to address this challenge and are now shifting the boundaries of what is possible to capture in living systems. In this Review, we discuss these computational methods focusing on artificial intelligence-based approaches that can be layered on top of commonly used existing microscopies as well as hybrid methods that integrate computation and microscope hardware. We specifically discuss how computational approaches can improve the signal-to-noise ratio, spatial resolution, temporal resolution and multi-colour capacity of live-cell imaging., (© 2024. Springer Nature Limited.)
- Published
- 2024
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11. Bioprinting Soft 3D Models of Hematopoiesis using Natural Silk Fibroin-Based Bioink Efficiently Supports Platelet Differentiation.
- Author
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Di Buduo CA, Lunghi M, Kuzmenko V, Laurent PA, Della Rosa G, Del Fante C, Dalle Nogare DE, Jug F, Perotti C, Eto K, Pecci A, Redwan IN, and Balduini A
- Subjects
- Humans, Ink, Hematopoietic Stem Cells metabolism, Hematopoietic Stem Cells cytology, Gelatin chemistry, Fibroins metabolism, Fibroins chemistry, Bioprinting methods, Printing, Three-Dimensional, Blood Platelets metabolism, Cell Differentiation, Hematopoiesis physiology
- Abstract
Hematopoietic stem and progenitor cells (HSPCs) continuously generate platelets throughout one's life. Inherited Platelet Disorders affect ≈ 3 million individuals worldwide and are characterized by defects in platelet formation or function. A critical challenge in the identification of these diseases lies in the absence of models that facilitate the study of hematopoiesis ex vivo. Here, a silk fibroin-based bioink is developed and designed for 3D bioprinting. This bioink replicates a soft and biomimetic environment, enabling the controlled differentiation of HSPCs into platelets. The formulation consisting of silk fibroin, gelatin, and alginate is fine-tuned to obtain a viscoelastic, shear-thinning, thixotropic bioink with the remarkable ability to rapidly recover after bioprinting and provide structural integrity and mechanical stability over long-term culture. Optical transparency allowed for high-resolution imaging of platelet generation, while the incorporation of enzymatic sensors allowed quantitative analysis of glycolytic metabolism during differentiation that is represented through measurable color changes. Bioprinting patient samples revealed a decrease in metabolic activity and platelet production in Inherited Platelet Disorders. These discoveries are instrumental in establishing reference ranges for classification and automating the assessment of treatment responses. This model has far-reaching implications for application in the research of blood-related diseases, prioritizing drug development strategies, and tailoring personalized therapies., (© 2024 The Authors. Advanced Science published by Wiley‐VCH GmbH.)
- Published
- 2024
- Full Text
- View/download PDF
12. Community-developed checklists for publishing images and image analyses.
- Author
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Schmied C, Nelson MS, Avilov S, Bakker GJ, Bertocchi C, Bischof J, Boehm U, Brocher J, Carvalho MT, Chiritescu C, Christopher J, Cimini BA, Conde-Sousa E, Ebner M, Ecker R, Eliceiri K, Fernandez-Rodriguez J, Gaudreault N, Gelman L, Grunwald D, Gu T, Halidi N, Hammer M, Hartley M, Held M, Jug F, Kapoor V, Koksoy AA, Lacoste J, Le Dévédec S, Le Guyader S, Liu P, Martins GG, Mathur A, Miura K, Montero Llopis P, Nitschke R, North A, Parslow AC, Payne-Dwyer A, Plantard L, Ali R, Schroth-Diez B, Schütz L, Scott RT, Seitz A, Selchow O, Sharma VP, Spitaler M, Srinivasan S, Strambio-De-Castillia C, Taatjes D, Tischer C, and Jambor HK
- Subjects
- Reproducibility of Results, Image Processing, Computer-Assisted, Microscopy, Checklist, Publishing
- Abstract
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., (© 2023. Springer Nature America, Inc.)
- Published
- 2024
- Full Text
- View/download PDF
13. Mechanical positive feedback and biochemical negative feedback combine to generate complex contractile oscillations in cytokinesis.
- Author
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Werner ME, Ray DD, Breen C, Staddon MF, Jug F, Banerjee S, and Maddox AS
- Abstract
Contractile force generation by the cortical actomyosin cytoskeleton is essential for a multitude of biological processes. The actomyosin cortex behaves as an active material that drives local and large-scale shape changes via cytoskeletal remodeling in response to biochemical cues and feedback loops. Cytokinesis is the essential cell division event during which a cortical actomyosin ring generates contractile force to change cell shape and separate two daughter cells. Our recent work with active gel theory predicts that actomyosin systems under the control of a biochemical oscillator and experiencing mechanical strain will exhibit complex spatiotemporal behavior, but cytokinetic contractility was thought to be kinetically simple. To test whether active materials in vivo exhibit spatiotemporally complex kinetics, we used 4-dimensional imaging with unprecedented temporal resolution and discovered sections of the cytokinetic cortex undergo periodic phases of acceleration and deceleration. Quantification of ingression speed oscillations revealed wide ranges of oscillation period and amplitude. In the cytokinetic ring, activity of the master regulator RhoA pulsed with a timescale of approximately 20 seconds, shorter than that reported for any other biological context. Contractility oscillated with 20-second periodicity and with much longer periods. A combination of in vivo and in silico approaches to modify mechanical feedback revealed that the period of contractile oscillation is prolonged as a function of the intensity of mechanical feedback. Effective local ring ingression is characterized by slower speed oscillations, likely due to increased local stresses and therefore mechanical feedback. Fast ingression also occurs where material turnover is high, in vivo and in silico . We propose that downstream of initiation by pulsed RhoA activity, mechanical positive feedback, including but not limited to material advection, extends the timescale of contractility beyond that of biochemical input and therefore makes it robust to fluctuations in activation. Circumferential propagation of contractility likely allows sustained contractility despite cytoskeletal remodeling necessary to recover from compaction. Our work demonstrates that while biochemical feedback loops afford systems responsiveness and robustness, mechanical feedback must also be considered to describe and understand the behaviors of active materials in vivo .
- Published
- 2023
- Full Text
- View/download PDF
14. Community-developed checklists for publishing images and image analyses.
- Author
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Schmied C, Nelson MS, Avilov S, Bakker GJ, Bertocchi C, Bischof J, Boehm U, Brocher J, Carvalho M, Chiritescu C, Christopher J, Cimini BA, Conde-Sousa E, Ebner M, Ecker R, Eliceiri K, Fernandez-Rodriguez J, Gaudreault N, Gelman L, Grunwald D, Gu T, Halidi N, Hammer M, Hartley M, Held M, Jug F, Kapoor V, Koksoy AA, Lacoste J, Dévédec SL, Guyader SL, Liu P, Martins GG, Mathur A, Miura K, Montero Llopis P, Nitschke R, North A, Parslow AC, Payne-Dwyer A, Plantard L, Ali R, Schroth-Diez B, Schütz L, Scott RT, Seitz A, Selchow O, Sharma VP, Spitaler M, Srinivasan S, Strambio-De-Castillia C, Taatjes D, Tischer C, and Jambor HK
- Abstract
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 the obtained images and image analyses results, there are to date no unified guidelines. 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 image analysis for publications. These checklists offer authors, readers, and publishers key recommendations for image formatting and annotation, color selection, data availability, and for reporting image analysis workflows. The goal of our guidelines is to increase the clarity and reproducibility of image figures and thereby heighten the quality and explanatory power of microscopy data is in publications.
- Published
- 2023
15. Better research software tools to elevate the rate of scientific discovery or why we need to invest in research software engineering.
- Author
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Deschamps J, Dalle Nogare D, and Jug F
- Abstract
Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
- Published
- 2023
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- View/download PDF
16. Using AI in bioimage analysis to elevate the rate of scientific discovery as a community.
- Author
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Nogare DD, Hartley M, Deschamps J, Ellenberg J, and Jug F
- Published
- 2023
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17. Zyxin contributes to coupling between cell junctions and contractile actomyosin networks during apical constriction.
- Author
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Slabodnick MM, Tintori SC, Prakash M, Zhang P, Higgins CD, Chen AH, Cupp TD, Wong T, Bowie E, Jug F, and Goldstein B
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- Animals, Zyxin genetics, Zyxin metabolism, Constriction, Proteomics, Intercellular Junctions genetics, Intercellular Junctions metabolism, Morphogenesis genetics, Actomyosin genetics, Actomyosin metabolism, Caenorhabditis elegans metabolism
- Abstract
One of the most common cell shape changes driving morphogenesis in diverse animals is the constriction of the apical cell surface. Apical constriction depends on contraction of an actomyosin network in the apical cell cortex, but such actomyosin networks have been shown to undergo continual, conveyor belt-like contractions before the shrinking of an apical surface begins. This finding suggests that apical constriction is not necessarily triggered by the contraction of actomyosin networks, but rather can be triggered by unidentified, temporally-regulated mechanical links between actomyosin and junctions. Here, we used C. elegans gastrulation as a model to seek genes that contribute to such dynamic linkage. We found that α-catenin and β-catenin initially failed to move centripetally with contracting cortical actomyosin networks, suggesting that linkage is regulated between intact cadherin-catenin complexes and actomyosin. We used proteomic and transcriptomic approaches to identify new players, including the candidate linkers AFD-1/afadin and ZYX-1/zyxin, as contributing to C. elegans gastrulation. We found that ZYX-1/zyxin is among a family of LIM domain proteins that have transcripts that become enriched in multiple cells just before they undergo apical constriction. We developed a semi-automated image analysis tool and used it to find that ZYX-1/zyxin contributes to cell-cell junctions' centripetal movement in concert with contracting actomyosin networks. These results identify several new genes that contribute to C. elegans gastrulation, and they identify zyxin as a key protein important for actomyosin networks to effectively pull cell-cell junctions inward during apical constriction. The transcriptional upregulation of ZYX-1/zyxin in specific cells in C. elegans points to one way that developmental patterning spatiotemporally regulates cell biological mechanisms in vivo. Because zyxin and related proteins contribute to membrane-cytoskeleton linkage in other systems, we anticipate that its roles in regulating apical constriction in this manner may be conserved., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Slabodnick et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
- Published
- 2023
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18. Nanog organizes transcription bodies.
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Kuznetsova K, Chabot NM, Ugolini M, Wu E, Lalit M, Oda H, Sato Y, Kimura H, Jug F, and Vastenhouw NL
- Subjects
- Animals, Nanog Homeobox Protein genetics, Nanog Homeobox Protein metabolism, Embryonic Development genetics, Zebrafish Proteins genetics, Zebrafish Proteins metabolism, Transcription, Genetic, Homeodomain Proteins genetics, Homeodomain Proteins metabolism, SOX Transcription Factors genetics, SOX Transcription Factors metabolism, Zebrafish genetics, Zebrafish metabolism, Transcription Factors genetics, Transcription Factors metabolism
- Abstract
The localization of transcriptional activity in specialized transcription bodies is a hallmark of gene expression in eukaryotic cells.
1 - 3 How proteins of the transcriptional machinery come together to form such bodies, however, is unclear. Here, we take advantage of two large, isolated, and long-lived transcription bodies that reproducibly form during early zebrafish embryogenesis to characterize the dynamics of transcription body formation. Once formed, these transcription bodies are enriched for initiating and elongating RNA polymerase II, as well as the transcription factors Nanog and Sox19b. Analyzing the events leading up to transcription, we find that Nanog and Sox19b cluster prior to transcription. The clustering of transcription factors is sequential; Nanog clusters first, and this is required for the clustering of Sox19b and the initiation of transcription. Mutant analysis revealed that both the DNA-binding domain as well as one of the two intrinsically disordered regions of Nanog are required to organize the two bodies of transcriptional activity. Taken together, our data suggest that the clustering of transcription factors dictates the formation of transcription bodies., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2022 Elsevier Inc. All rights reserved.)- Published
- 2023
- Full Text
- View/download PDF
19. Prediction of designer-recombinases for DNA editing with generative deep learning.
- Author
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Schmitt LT, Paszkowski-Rogacz M, Jug F, and Buchholz F
- Subjects
- DNA genetics, Directed Molecular Evolution, Recombinases genetics, Deep Learning
- Abstract
Site-specific tyrosine-type recombinases are effective tools for genome engineering, with the first engineered variants having demonstrated therapeutic potential. So far, adaptation to new DNA target site selectivity of designer-recombinases has been achieved mostly through iterative cycles of directed molecular evolution. While effective, directed molecular evolution methods are laborious and time consuming. Here we present RecGen (Recombinase Generator), an algorithm for the intelligent generation of designer-recombinases. We gather the sequence information of over one million Cre-like recombinase sequences evolved for 89 different target sites with which we train Conditional Variational Autoencoders for recombinase generation. Experimental validation demonstrates that the algorithm can predict recombinase sequences with activity on novel target-sites, indicating that RecGen is useful to accelerate the development of future designer-recombinases., (© 2022. The Author(s).)
- Published
- 2022
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20. EmbedSeg: Embedding-based Instance Segmentation for Biomedical Microscopy Data.
- Author
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Lalit M, Tomancak P, and Jug F
- Subjects
- Humans, Image Processing, Computer-Assisted methods, Imaging, Three-Dimensional methods, Algorithms, Microscopy methods
- Abstract
Automatic detection and segmentation of biological objects in 2D and 3D image data is central for countless biomedical research questions to be answered. While many existing computational methods are used to reduce manual labeling time, there is still a huge demand for further quality improvements of automated solutions. In the natural image domain, spatial embedding-based instance segmentation methods are known to yield high-quality results, but their utility to biomedical data is largely unexplored. Here we introduce EmbedSeg, an embedding-based instance segmentation method designed to segment instances of desired objects visible in 2D or 3D biomedical image data. We apply our method to four 2D and seven 3D benchmark datasets, showing that we either match or outperform existing state-of-the-art methods. While the 2D datasets and three of the 3D datasets are well known, we have created the required training data for four new 3D datasets, which we make publicly available online. Next to performance, also usability is important for a method to be useful. Hence, EmbedSeg is fully open source (https://github.com/juglab/EmbedSeg), offering (i) tutorial notebooks to train EmbedSeg models and use them to segment object instances in new data, and (ii) a napari plugin that can also be used for training and segmentation without requiring any programming experience. We believe that this renders EmbedSeg accessible to virtually everyone who requires high-quality instance segmentations in 2D or 3D biomedical image data., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022. Published by Elsevier B.V.)
- Published
- 2022
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21. Conversion of anterograde into retrograde trains is an intrinsic property of intraflagellar transport.
- Author
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Nievergelt AP, Zykov I, Diener D, Chhatre A, Buchholz TO, Delling M, Diez S, Jug F, Štěpánek L, and Pigino G
- Subjects
- Biological Transport, Calcium metabolism, Cilia metabolism, Cytoplasmic Dyneins metabolism, Flagella physiology, Dyneins metabolism, Kinesins
- Abstract
Cilia or eukaryotic flagella are microtubule-based organelles found across the eukaryotic tree of life. Their very high aspect ratio and crowded interior are unfavorable to diffusive transport of most components required for their assembly and maintenance. Instead, a system of intraflagellar transport (IFT) trains moves cargo rapidly up and down the cilium (Figure 1A).
1-3 Anterograde IFT, from the cell body to the ciliary tip, is driven by kinesin-II motors, whereas retrograde IFT is powered by cytoplasmic dynein-1b motors.4 Both motors are associated with long chains of IFT protein complexes, known as IFT trains, and their cargoes.5-8 The conversion from anterograde to retrograde motility at the ciliary tip involves (1) the dissociation of kinesin motors from trains,9 (2) a fundamental restructuring of the train from the anterograde to the retrograde architecture,8 , 10 , 11 (3) the unloading and reloading of cargo,2 and (4) the activation of the dynein motors.8 , 12 A prominent hypothesis is that there is dedicated calcium-dependent protein-based machinery at the ciliary tip to mediate these processes.4 , 13 However, the mechanisms of IFT turnaround have remained elusive. In this study, we use mechanical and chemical methods to block IFT at intermediate positions along the cilia of the green algae Chlamydomonas reinhardtii, in normal and calcium-depleted conditions. We show that IFT turnaround, kinesin dissociation, and dynein-1b activation can consistently be induced at arbitrary distances from the ciliary tip, with no stationary tip machinery being required. Instead, we demonstrate that the anterograde-to-retrograde conversion is a calcium-independent intrinsic ability of IFT., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)- Published
- 2022
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22. Extracellular mechanical forces drive endocardial cell volume decrease during zebrafish cardiac valve morphogenesis.
- Author
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Vignes H, Vagena-Pantoula C, Prakash M, Fukui H, Norden C, Mochizuki N, Jug F, and Vermot J
- Subjects
- Animals, Cell Size, Heart Valves metabolism, Mechanotransduction, Cellular, Morphogenesis, TRPV Cation Channels metabolism, Zebrafish metabolism, Zebrafish Proteins metabolism
- Abstract
Organ morphogenesis involves dynamic changes of tissue properties while cells adapt to their mechanical environment through mechanosensitive pathways. How mechanical cues influence cell behaviors during morphogenesis remains unclear. Here, we studied the formation of the zebrafish atrioventricular canal (AVC) where cardiac valves develop. We show that the AVC forms within a zone of tissue convergence associated with the increased activation of the actomyosin meshwork and cell-orientation changes. We demonstrate that tissue convergence occurs with a reduction of cell volume triggered by mechanical forces and the mechanosensitive channel TRPP2/TRPV4. Finally, we show that the extracellular matrix component hyaluronic acid controls cell volume changes. Together, our data suggest that multiple force-sensitive signaling pathways converge to modulate cell volume. We conclude that cell volume reduction is a key cellular feature activated by mechanotransduction during cardiovascular morphogenesis. This work further identifies how mechanical forces and extracellular matrix influence tissue remodeling in developing organs., Competing Interests: Declaration of interests The authors declare no competing or financial interests., (Copyright © 2022. Published by Elsevier Inc.)
- Published
- 2022
- Full Text
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23. Dynamic cell contacts between periportal mesenchyme and ductal epithelium act as a rheostat for liver cell proliferation.
- Author
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Cordero-Espinoza L, Dowbaj AM, Kohler TN, Strauss B, Sarlidou O, Belenguer G, Pacini C, Martins NP, Dobie R, Wilson-Kanamori JR, Butler R, Prior N, Serup P, Jug F, Henderson NC, Hollfelder F, and Huch M
- Subjects
- Animals, Cell Proliferation, Epithelium, Liver, Mice, Epithelial Cells, Mesoderm
- Abstract
In the liver, ductal cells rarely proliferate during homeostasis but do so transiently after tissue injury. These cells can be expanded as organoids that recapitulate several of the cell-autonomous mechanisms of regeneration but lack the stromal interactions of the native tissue. Here, using organoid co-cultures that recapitulate the ductal-to-mesenchymal cell architecture of the portal tract, we demonstrate that a subpopulation of mouse periportal mesenchymal cells exerts dual control on proliferation of the epithelium. Ductal cell proliferation is either induced and sustained or, conversely, completely abolished, depending on the number of direct mesenchymal cell contacts, through a mechanism mediated, at least in part, by Notch signaling. Our findings expand the concept of the cellular niche in epithelial tissues, whereby not only soluble factors but also cell-cell contacts are the key regulatory cues involved in the control of cellular behaviors, suggesting a critical role for cell-cell contacts during regeneration., Competing Interests: Declaration of interests M.H. is inventor in a patent on liver organoids and is on the advisory board of the journal Cell Stem Cell., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2021
- Full Text
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24. Democratising deep learning for microscopy with ZeroCostDL4Mic.
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von Chamier L, Laine RF, Jukkala J, Spahn C, Krentzel D, Nehme E, Lerche M, Hernández-Pérez S, Mattila PK, Karinou E, Holden S, Solak AC, Krull A, Buchholz TO, Jones ML, Royer LA, Leterrier C, Shechtman Y, Jug F, Heilemann M, Jacquemet G, and Henriques R
- Subjects
- Animals, Cell Line, Tumor, Cloud Computing, Datasets as Topic, Humans, Primary Cell Culture, Rats, Software, Deep Learning, Image Processing, Computer-Assisted methods, Microscopy methods
- Abstract
Deep Learning (DL) methods are powerful analytical tools for microscopy and can outperform conventional image processing pipelines. Despite the enthusiasm and innovations fuelled by DL technology, the need to access powerful and compatible resources to train DL networks leads to an accessibility barrier that novice users often find difficult to overcome. Here, we present ZeroCostDL4Mic, an entry-level platform simplifying DL access by leveraging the free, cloud-based computational resources of Google Colab. ZeroCostDL4Mic allows researchers with no coding expertise to train and apply key DL networks to perform tasks including segmentation (using U-Net and StarDist), object detection (using YOLOv2), denoising (using CARE and Noise2Void), super-resolution microscopy (using Deep-STORM), and image-to-image translation (using Label-free prediction - fnet, pix2pix and CycleGAN). Importantly, we provide suitable quantitative tools for each network to evaluate model performance, allowing model optimisation. We demonstrate the application of the platform to study multiple biological processes.
- Published
- 2021
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25. 3D FIB-SEM reconstruction of microtubule-organelle interaction in whole primary mouse β cells.
- Author
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Müller A, Schmidt D, Xu CS, Pang S, D'Costa JV, Kretschmar S, Münster C, Kurth T, Jug F, Weigert M, Hess HF, and Solimena M
- Subjects
- Animals, Cell Membrane drug effects, Cell Membrane metabolism, Cell Nucleus drug effects, Cell Nucleus metabolism, Cells, Cultured, Glucose pharmacology, Insulin metabolism, Insulin-Secreting Cells drug effects, Mice, Inbred C57BL, Microtubules drug effects, Microtubules metabolism, Secretory Vesicles drug effects, Secretory Vesicles metabolism, Mice, Imaging, Three-Dimensional, Insulin-Secreting Cells metabolism, Microscopy, Electron, Scanning, Microtubules ultrastructure, Organelles metabolism
- Abstract
Microtubules play a major role in intracellular trafficking of vesicles in endocrine cells. Detailed knowledge of microtubule organization and their relation to other cell constituents is crucial for understanding cell function. However, their role in insulin transport and secretion is under debate. Here, we use FIB-SEM to image islet β cells in their entirety with unprecedented resolution. We reconstruct mitochondria, Golgi apparati, centrioles, insulin secretory granules, and microtubules of seven β cells, and generate a comprehensive spatial map of microtubule-organelle interactions. We find that microtubules form nonradial networks that are predominantly not connected to either centrioles or endomembranes. Microtubule number and length, but not microtubule polymer density, vary with glucose stimulation. Furthermore, insulin secretory granules are enriched near the plasma membrane, where they associate with microtubules. In summary, we provide the first 3D reconstructions of complete microtubule networks in primary mammalian cells together with evidence regarding their importance for insulin secretory granule positioning and thus their supportive role in insulin secretion., (© 2020 Müller et al.)
- Published
- 2021
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26. The ImageJ ecosystem: Open-source software for image visualization, processing, and analysis.
- Author
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Schroeder AB, Dobson ETA, Rueden CT, Tomancak P, Jug F, and Eliceiri KW
- Subjects
- Artificial Intelligence, Image Processing, Computer-Assisted, Software
- Abstract
For decades, biologists have relied on software to visualize and interpret imaging data. As techniques for acquiring images increase in complexity, resulting in larger multidimensional datasets, imaging software must adapt. ImageJ is an open-source image analysis software platform that has aided researchers with a variety of image analysis applications, driven mainly by engaged and collaborative user and developer communities. The close collaboration between programmers and users has resulted in adaptations to accommodate new challenges in image analysis that address the needs of ImageJ's diverse user base. ImageJ consists of many components, some relevant primarily for developers and a vast collection of user-centric plugins. It is available in many forms, including the widely used Fiji distribution. We refer to this entire ImageJ codebase and community as the ImageJ ecosystem. Here we review the core features of this ecosystem and highlight how ImageJ has responded to imaging technology advancements with new plugins and tools in recent years. These plugins and tools have been developed to address user needs in several areas such as visualization, segmentation, and tracking of biological entities in large, complex datasets. Moreover, new capabilities for deep learning are being added to ImageJ, reflecting a shift in the bioimage analysis community towards exploiting artificial intelligence. These new tools have been facilitated by profound architectural changes to the ImageJ core brought about by the ImageJ2 project. Therefore, we also discuss the contributions of ImageJ2 to enhancing multidimensional image processing and interoperability in the ImageJ ecosystem., (© 2020 The Protein Society.)
- Published
- 2021
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27. Regionalized tissue fluidization is required for epithelial gap closure during insect gastrulation.
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Jain A, Ulman V, Mukherjee A, Prakash M, Cuenca MB, Pimpale LG, Münster S, Haase R, Panfilio KA, Jug F, Grill SW, Tomancak P, and Pavlopoulos A
- Subjects
- Actomyosin metabolism, Animals, Biomechanical Phenomena, Cell Movement, Epithelium metabolism, Insect Proteins metabolism, Morphogenesis, Serous Membrane embryology, Serous Membrane metabolism, Tribolium embryology, Wound Healing, Epithelium embryology, Gastrulation physiology, Insecta embryology
- Abstract
Many animal embryos pull and close an epithelial sheet around the ellipsoidal egg surface during a gastrulation process known as epiboly. The ovoidal geometry dictates that the epithelial sheet first expands and subsequently compacts. Moreover, the spreading epithelium is mechanically stressed and this stress needs to be released. Here we show that during extraembryonic tissue (serosa) epiboly in the insect Tribolium castaneum, the non-proliferative serosa becomes regionalized into a solid-like dorsal region with larger non-rearranging cells, and a more fluid-like ventral region surrounding the leading edge with smaller cells undergoing intercalations. Our results suggest that a heterogeneous actomyosin cable contributes to the fluidization of the leading edge by driving sequential eviction and intercalation of individual cells away from the serosa margin. Since this developmental solution utilized during epiboly resembles the mechanism of wound healing, we propose actomyosin cable-driven local tissue fluidization as a conserved morphogenetic module for closure of epithelial gaps.
- Published
- 2020
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28. CLIJ: GPU-accelerated image processing for everyone.
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Haase R, Royer LA, Steinbach P, Schmidt D, Dibrov A, Schmidt U, Weigert M, Maghelli N, Tomancak P, Jug F, and Myers EW
- Subjects
- Humans, Algorithms, Computer Graphics instrumentation, Computer Graphics trends, Image Interpretation, Computer-Assisted instrumentation, Image Interpretation, Computer-Assisted methods, Molecular Imaging methods, Signal Processing, Computer-Assisted instrumentation
- Published
- 2020
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- View/download PDF
29. Cell segmentation methods for label-free contrast microscopy: review and comprehensive comparison.
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Vicar T, Balvan J, Jaros J, Jug F, Kolar R, Masarik M, and Gumulec J
- Subjects
- Algorithms, Humans, Image Processing, Computer-Assisted, Cell Fractionation methods, Microscopy methods
- Abstract
Background: Because of its non-destructive nature, label-free imaging is an important strategy for studying biological processes. However, routine microscopic techniques like phase contrast or DIC suffer from shadow-cast artifacts making automatic segmentation challenging. The aim of this study was to compare the segmentation efficacy of published steps of segmentation work-flow (image reconstruction, foreground segmentation, cell detection (seed-point extraction) and cell (instance) segmentation) on a dataset of the same cells from multiple contrast microscopic modalities., Results: We built a collection of routines aimed at image segmentation of viable adherent cells grown on the culture dish acquired by phase contrast, differential interference contrast, Hoffman modulation contrast and quantitative phase imaging, and we performed a comprehensive comparison of available segmentation methods applicable for label-free data. We demonstrated that it is crucial to perform the image reconstruction step, enabling the use of segmentation methods originally not applicable on label-free images. Further we compared foreground segmentation methods (thresholding, feature-extraction, level-set, graph-cut, learning-based), seed-point extraction methods (Laplacian of Gaussians, radial symmetry and distance transform, iterative radial voting, maximally stable extremal region and learning-based) and single cell segmentation methods. We validated suitable set of methods for each microscopy modality and published them online., Conclusions: We demonstrate that image reconstruction step allows the use of segmentation methods not originally intended for label-free imaging. In addition to the comprehensive comparison of methods, raw and reconstructed annotated data and Matlab codes are provided.
- Published
- 2019
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- View/download PDF
30. Content-aware image restoration for electron microscopy.
- Author
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Buchholz TO, Krull A, Shahidi R, Pigino G, Jékely G, and Jug F
- Subjects
- Image Processing, Computer-Assisted methods, Microscopy, Fluorescence methods, Neural Networks, Computer, Microscopy, Electron methods
- Abstract
Multiple approaches to use deep neural networks for image restoration have recently been proposed. Training such networks requires well registered pairs of high and low-quality images. While this is easily achievable for many imaging modalities, e.g., fluorescence light microscopy, for others it is not. Here we summarize on a number of recent developments in the fast-paced field of Content-Aware Image Restoration (CARE), in particular, and the associated area of neural network training, more in general. We then give specific examples how electron microscopy data can benefit from these new technologies., (© 2019 Elsevier Inc. All rights reserved.)
- Published
- 2019
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- View/download PDF
31. Content-aware image restoration: pushing the limits of fluorescence microscopy.
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Weigert M, Schmidt U, Boothe T, Müller A, Dibrov A, Jain A, Wilhelm B, Schmidt D, Broaddus C, Culley S, Rocha-Martins M, Segovia-Miranda F, Norden C, Henriques R, Zerial M, Solimena M, Rink J, Tomancak P, Royer L, Jug F, and Myers EW
- Subjects
- Animals, Drosophila melanogaster metabolism, Drosophila melanogaster ultrastructure, HeLa Cells, Humans, Liver metabolism, Liver ultrastructure, Photons, Planarians metabolism, Planarians ultrastructure, Retina metabolism, Retina ultrastructure, Tribolium metabolism, Tribolium ultrastructure, Zebrafish metabolism, Fluorescent Dyes chemistry, Image Processing, Computer-Assisted methods, Microscopy, Fluorescence methods, Software
- Abstract
Fluorescence microscopy is a key driver of discoveries in the life sciences, with observable phenomena being limited by the optics of the microscope, the chemistry of the fluorophores, and the maximum photon exposure tolerated by the sample. These limits necessitate trade-offs between imaging speed, spatial resolution, light exposure, and imaging depth. In this work we show how content-aware image restoration based on deep learning extends the range of biological phenomena observable by microscopy. We demonstrate on eight concrete examples how microscopy images can be restored even if 60-fold fewer photons are used during acquisition, how near isotropic resolution can be achieved with up to tenfold under-sampling along the axial direction, and how tubular and granular structures smaller than the diffraction limit can be resolved at 20-times-higher frame rates compared to state-of-the-art methods. All developed image restoration methods are freely available as open source software in Python, FIJI, and KNIME.
- Published
- 2018
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32. Differential lateral and basal tension drive folding of Drosophila wing discs through two distinct mechanisms.
- Author
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Sui L, Alt S, Weigert M, Dye N, Eaton S, Jug F, Myers EW, Jülicher F, Salbreux G, and Dahmann C
- Subjects
- Actins metabolism, Actomyosin, Amides antagonists & inhibitors, Animals, Biomechanical Phenomena, Body Patterning genetics, Cell Division, Cell Proliferation, Cell Shape, Cell Size, Drosophila anatomy & histology, Drosophila embryology, Drosophila genetics, Drosophila Proteins genetics, Drosophila Proteins metabolism, Epithelial Cells drug effects, Epithelium drug effects, Extracellular Matrix, Imaginal Discs growth & development, Larva cytology, Larva metabolism, Laser Therapy, Models, Anatomic, Models, Biological, Pyridines antagonists & inhibitors, Drosophila growth & development, Epithelial Cells cytology, Epithelium anatomy & histology, Epithelium embryology, Morphogenesis, Stress, Mechanical
- Abstract
Epithelial folding transforms simple sheets of cells into complex three-dimensional tissues and organs during animal development. Epithelial folding has mainly been attributed to mechanical forces generated by an apically localized actomyosin network, however, contributions of forces generated at basal and lateral cell surfaces remain largely unknown. Here we show that a local decrease of basal tension and an increased lateral tension, but not apical constriction, drive the formation of two neighboring folds in developing Drosophila wing imaginal discs. Spatially defined reduction of extracellular matrix density results in local decrease of basal tension in the first fold; fluctuations in F-actin lead to increased lateral tension in the second fold. Simulations using a 3D vertex model show that the two distinct mechanisms can drive epithelial folding. Our combination of lateral and basal tension measurements with a mechanical tissue model reveals how simple modulations of surface and edge tension drive complex three-dimensional morphological changes.
- Published
- 2018
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33. Monitoring single-cell gene regulation under dynamically controllable conditions with integrated microfluidics and software.
- Author
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Kaiser M, Jug F, Julou T, Deshpande S, Pfohl T, Silander OK, Myers G, and van Nimwegen E
- Subjects
- Algorithms, Cell Tracking instrumentation, Cell Tracking methods, Escherichia coli cytology, Escherichia coli drug effects, Escherichia coli genetics, Glucose pharmacology, Lac Operon genetics, Lactose pharmacology, Single-Cell Analysis instrumentation, Gene Expression Regulation, Bacterial, Microfluidic Analytical Techniques methods, Single-Cell Analysis methods, Software
- Abstract
Much is still not understood about how gene regulatory interactions control cell fate decisions in single cells, in part due to the difficulty of directly observing gene regulatory processes in vivo. We introduce here a novel integrated setup consisting of a microfluidic chip and accompanying analysis software that enable long-term quantitative tracking of growth and gene expression in single cells. The dual-input Mother Machine (DIMM) chip enables controlled and continuous variation of external conditions, allowing direct observation of gene regulatory responses to changing conditions in single cells. The Mother Machine Analyzer (MoMA) software achieves unprecedented accuracy in segmenting and tracking cells, and streamlines high-throughput curation with a novel leveraged editing procedure. We demonstrate the power of the method by uncovering several novel features of an iconic gene regulatory program: the induction of Escherichia coli's lac operon in response to a switch from glucose to lactose.
- Published
- 2018
- Full Text
- View/download PDF
34. An objective comparison of cell-tracking algorithms.
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Ulman V, Maška M, Magnusson KEG, Ronneberger O, Haubold C, Harder N, Matula P, Matula P, Svoboda D, Radojevic M, Smal I, Rohr K, Jaldén J, Blau HM, Dzyubachyk O, Lelieveldt B, Xiao P, Li Y, Cho SY, Dufour AC, Olivo-Marin JC, Reyes-Aldasoro CC, Solis-Lemus JA, Bensch R, Brox T, Stegmaier J, Mikut R, Wolf S, Hamprecht FA, Esteves T, Quelhas P, Demirel Ö, Malmström L, Jug F, Tomancak P, Meijering E, Muñoz-Barrutia A, Kozubek M, and Ortiz-de-Solorzano C
- Subjects
- Benchmarking, Cell Line, Humans, Algorithms, Cell Tracking methods, Image Interpretation, Computer-Assisted
- Abstract
We present a combined report on the results of three editions of the Cell Tracking Challenge, an ongoing initiative aimed at promoting the development and objective evaluation of cell segmentation and tracking algorithms. With 21 participating algorithms and a data repository consisting of 13 data sets from various microscopy modalities, the challenge displays today's state-of-the-art methodology in the field. We analyzed the challenge results using performance measures for segmentation and tracking that rank all participating methods. We also analyzed the performance of all of the algorithms in terms of biological measures and practical usability. Although some methods scored high in all technical aspects, none obtained fully correct solutions. We found that methods that either take prior information into account using learning strategies or analyze cells in a global spatiotemporal video context performed better than other methods under the segmentation and tracking scenarios included in the challenge.
- Published
- 2017
- Full Text
- View/download PDF
35. Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos.
- Author
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Stapel LC, Lombardot B, Broaddus C, Kainmueller D, Jug F, Myers EW, and Vastenhouw NL
- Subjects
- Animals, Automation, Cell Membrane metabolism, Gene Expression Regulation, Developmental, In Situ Hybridization, Fluorescence methods, RNA genetics, RNA, Messenger genetics, RNA, Messenger metabolism, Subcellular Fractions metabolism, Transcription, Genetic, Embryo, Nonmammalian metabolism, RNA metabolism, Zebrafish embryology, Zebrafish genetics
- Abstract
Analysis of differential gene expression is crucial for the study of cell fate and behavior during embryonic development. However, automated methods for the sensitive detection and quantification of RNAs at cellular resolution in embryos are lacking. With the advent of single-molecule fluorescence in situ hybridization (smFISH), gene expression can be analyzed at single-molecule resolution. However, the limited availability of protocols for smFISH in embryos and the lack of efficient image analysis pipelines have hampered quantification at the (sub)cellular level in complex samples such as tissues and embryos. Here, we present a protocol for smFISH on zebrafish embryo sections in combination with an image analysis pipeline for automated transcript detection and cell segmentation. We use this strategy to quantify gene expression differences between different cell types and identify differences in subcellular transcript localization between genes. The combination of our smFISH protocol and custom-made, freely available, analysis pipeline will enable researchers to fully exploit the benefits of quantitative transcript analysis at cellular and subcellular resolution in tissues and embryos., (© 2016. Published by The Company of Biologists Ltd.)
- Published
- 2016
- Full Text
- View/download PDF
36. ClearVolume: open-source live 3D visualization for light-sheet microscopy.
- Author
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Royer LA, Weigert M, Günther U, Maghelli N, Jug F, Sbalzarini IF, and Myers EW
- Subjects
- Computer Graphics, Databases, Factual, Information Storage and Retrieval methods, Imaging, Three-Dimensional methods, Microscopy methods, Software
- Published
- 2015
- Full Text
- View/download PDF
37. Bioimage Informatics in the context of Drosophila research.
- Author
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Jug F, Pietzsch T, Preibisch S, and Tomancak P
- Subjects
- Algorithms, Animals, Computational Biology methods, Drosophila melanogaster, Image Processing, Computer-Assisted methods, Molecular Imaging methods
- Abstract
Modern biological research relies heavily on microscopic imaging. The advanced genetic toolkit of Drosophila makes it possible to label molecular and cellular components with unprecedented level of specificity necessitating the application of the most sophisticated imaging technologies. Imaging in Drosophila spans all scales from single molecules to the entire populations of adult organisms, from electron microscopy to live imaging of developmental processes. As the imaging approaches become more complex and ambitious, there is an increasing need for quantitative, computer-mediated image processing and analysis to make sense of the imagery. Bioimage Informatics is an emerging research field that covers all aspects of biological image analysis from data handling, through processing, to quantitative measurements, analysis and data presentation. Some of the most advanced, large scale projects, combining cutting edge imaging with complex bioimage informatics pipelines, are realized in the Drosophila research community. In this review, we discuss the current research in biological image analysis specifically relevant to the type of systems level image datasets that are uniquely available for the Drosophila model system. We focus on how state-of-the-art computer vision algorithms are impacting the ability of Drosophila researchers to analyze biological systems in space and time. We pay particular attention to how these algorithmic advances from computer science are made usable to practicing biologists through open source platforms and how biologists can themselves participate in their further development., (Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2014
- Full Text
- View/download PDF
38. Active graph matching for automatic joint segmentation and annotation of C. elegans.
- Author
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Kainmueller D, Jug F, Rother C, and Myers G
- Subjects
- Animals, Image Enhancement methods, Reproducibility of Results, Sensitivity and Specificity, Algorithms, Caenorhabditis elegans cytology, Cell Nucleus ultrastructure, Image Interpretation, Computer-Assisted methods, Microscopy methods, Pattern Recognition, Automated methods, Subtraction Technique
- Abstract
In this work we present a novel technique we term active graph matching, which integrates the popular active shape model into a sparse graph matching problem. This way we are able to combine the benefits of a global, statistical deformation model with the benefits of a local deformation model in form of a second-order random field. We present a new iterative energy minimization technique which achieves empirically good results. This enables us to exceed state-of-the art results for the task of annotating nuclei in 3D microscopic images of C. elegans. Furthermore with the help of the generalized Hough transform we are able to jointly segment and annotate a large set of nuclei in a fully automatic fashion for the first time.
- Published
- 2014
- Full Text
- View/download PDF
39. Reliable neuronal systems: the importance of heterogeneity.
- Author
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Lengler J, Jug F, and Steger A
- Subjects
- Animals, Brain physiology, Computer Simulation, Excitatory Postsynaptic Potentials physiology, Humans, Learning physiology, Neurons cytology, Poisson Distribution, Receptors, AMPA genetics, Receptors, AMPA metabolism, Receptors, N-Methyl-D-Aspartate genetics, Receptors, N-Methyl-D-Aspartate metabolism, Synapses physiology, Synaptic Transmission physiology, alpha-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid metabolism, gamma-Aminobutyric Acid metabolism, Genetic Heterogeneity, Models, Neurological, Nerve Net physiology, Neuronal Plasticity genetics, Neurons metabolism
- Abstract
For every engineer it goes without saying: in order to build a reliable system we need components that consistently behave precisely as they should. It is also well known that neurons, the building blocks of brains, do not satisfy this constraint. Even neurons of the same type come with huge variances in their properties and these properties also vary over time. Synapses, the connections between neurons, are highly unreliable in forwarding signals. In this paper we argue that both these fact add variance to neuronal processes, and that this variance is not a handicap of neural systems, but that instead predictable and reliable functional behavior of neural systems depends crucially on this variability. In particular, we show that higher variance allows a recurrently connected neural population to react more sensitively to incoming signals, and processes them faster and more energy efficient. This, for example, challenges the general assumption that the intrinsic variability of neurons in the brain is a defect that has to be overcome by synaptic plasticity in the process of learning.
- Published
- 2013
- Full Text
- View/download PDF
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