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Andreas Müller, Martin Neukam, Anna Ivanova, Anke Sönmez, Carla Münster, Susanne Kretschmar, Yannis Kalaidzidis, Thomas Kurth, Jean-Marc Verbavatz, Michele Solimena
A Global Approach for Quantitative Super Resolution and Electron Microscopy on Cryo and Epoxy Sections Using Self-labeling Protein Tags.
Sci Rep, 7 Art. No. 23 (2017)
  PubMed   

Correlative light and electron microscopy (CLEM) is a powerful approach to investigate the molecular ultrastructure of labeled cell compartments. However, quantitative CLEM studies are rare, mainly due to small sample sizes and the sensitivity of fluorescent proteins to strong fixatives and contrasting reagents for EM. Here, we show that fusion of a self-labeling protein to insulin allows for the quantification of age-distinct insulin granule pools in pancreatic beta cells by a combination of super resolution and transmission electron microscopy on Tokuyasu cryosections. In contrast to fluorescent proteins like GFP organic dyes covalently bound to self-labeling proteins retain their fluorescence also in epoxy resin following high pressure freezing and freeze substitution, or remarkably even after strong chemical fixation. This enables for the assessment of age-defined granule morphology and degradation. Finally, we demonstrate that this CLEM protocol is highly versatile, being suitable for single and dual fluorescent labeling and detection of different proteins with optimal ultrastructure preservation and contrast.
@article{Müller6796,
author={Andreas Müller, Martin Neukam, Anna Ivanova, Anke Sönmez, Carla Münster, Susanne Kretschmar, Yannis Kalaidzidis, Thomas Kurth, Jean-Marc Verbavatz, Michele Solimena},
title={A Global Approach for Quantitative Super Resolution and Electron Microscopy on Cryo and Epoxy Sections Using Self-labeling Protein Tags.},
journal={Scientific reports},
volume={7},
pages={null--null},
year=2017
}

Martin Weigert, Loic Royer, Florian Jug, Gene Myers
Isotropic reconstruction of 3D fluorescence microscopy images using convolutional neural networks
arXiv, Art. No. arXiv:1704.01510 [cs.CV] (2017)
    

Fluorescence microscopy images usually show severe anisotropy in axial versus lateral resolution. This hampers downstream processing, i.e. the automatic extraction of quantitative biological data. While deconvolution methods and other techniques to address this problem exist, they are either time consuming to apply or limited in their ability to remove anisotropy. We propose a method to recover isotropic resolution from readily acquired anisotropic data. We achieve this using a convolutional neural network that is trained end-to-end from the same anisotropic body of data we later apply the network to. The network effectively learns to restore the full isotropic resolution by restoring the image under a trained, sample specific image prior. We apply our method to 3 synthetic and 3 real datasets and show that our results improve on results from deconvolution and state-of-the-art super-resolution techniques. Finally, we demonstrate that a standard 3D segmentation pipeline performs on the output of our network with comparable accuracy as on the full isotropic data.
@article{null6812,
author={Martin Weigert, Loic Royer, Florian Jug, Gene Myers},
title={Isotropic reconstruction of 3D fluorescence microscopy images using convolutional neural networks},
journal={arXiv},
volume={},
pages={null--null},
year=2017
}

Corinna Blasse, Stephan Saalfeld, Raphael Etournay, Andreas Sagner, Suzanne Eaton, Eugene W Myers
PreMosa: Extracting 2D surfaces from 3D microscopy mosaics.
Bioinformatics, Art. No. doi: 10.1093/bioinformatics/btx195 (2017)
PubMed   

A significant focus of biological research is to understand the development, organization and function of tissues. A particularly productive area of study is on single layer epithelial tissues in which the adherence junctions of cells form a 2D manifold that is fluorescently labeled. Given the size of the tissue, a microscope must collect a mosaic of overlapping 3D stacks encompassing the stained surface. Downstream interpretation is greatly simplified by preprocessing such a dataset as follows: (a) extracting and mapping the stained manifold in each stack into a single 2D projection plane, (b) correcting uneven illumination artifacts, (c) stitching the mosaic planes into a single, large 2D image, and (d) adjusting the contrast.
@article{Blasse6824,
author={Corinna Blasse, Stephan Saalfeld, Raphael Etournay, Andreas Sagner, Suzanne Eaton, Eugene W Myers},
title={PreMosa: Extracting 2D surfaces from 3D microscopy mosaics.},
journal={Bioinformatics (Oxford, England)},
volume={},
pages={1--1},
year=2017
}

Philipp von Hundelshausen, Stijn M Agten, Veit Eckardt, Xavier Blanchet, Martin M Schmitt, Hans Ippel, Carlos Neideck, Kiril Bidzhekov, Julian Leberzammer, Kanin Wichapong, Alexander Faussner, Maik Drechsler, Jochen Grommes, Johanna P van Geffen, He Li, Almudena Ortega-Gomez, Remco T A Megens, Ronald Naumann, Ingrid Dijkgraaf, Gerry A F Nicolaes, Yvonne Döring, Oliver Soehnlein, Esther Lutgens, Johan W M Heemskerk, Rory R Koenen, Kevin H Mayo, Tilman M Hackeng, Christian Weber
Chemokine interactome mapping enables tailored intervention in acute and chronic inflammation.
Sci Transl Med, 9(384) Art. No. eaah6650 (2017)
PubMed   

Chemokines orchestrate leukocyte trafficking and function in health and disease. Heterophilic interactions between chemokines in a given microenvironment may amplify, inhibit, or modulate their activity; however, a systematic evaluation of the chemokine interactome has not been performed. We used immunoligand blotting and surface plasmon resonance to obtain a comprehensive map of chemokine-chemokine interactions and to confirm their specificity. Structure-function analyses revealed that chemokine activity can be enhanced by CC-type heterodimers but inhibited by CXC-type heterodimers. Functional synergism was achieved through receptor heteromerization induced by CCL5-CCL17 or receptor retention at the cell surface via auxiliary proteoglycan binding of CCL5-CXCL4. In contrast, inhibitory activity relied on conformational changes (in CXCL12), affecting receptor signaling. Obligate CC-type heterodimers showed high efficacy and potency and drove acute lung injury and atherosclerosis, processes abrogated by specific CCL5-derived peptide inhibitors or knock-in of an interaction-deficient CXCL4 variant. Atheroprotective effects of CCL17 deficiency were phenocopied by a CCL5-derived peptide disrupting CCL5-CCL17 heterodimers, whereas a CCL5 α-helix peptide mimicked inhibitory effects on CXCL12-driven platelet aggregation. Thus, formation of specific chemokine heterodimers differentially dictates functional activity and can be exploited for therapeutic targeting.
@article{Hundelshausen6820,
author={Philipp von Hundelshausen, Stijn M Agten, Veit Eckardt, Xavier Blanchet, Martin M Schmitt, Hans Ippel, Carlos Neideck, Kiril Bidzhekov, Julian Leberzammer, Kanin Wichapong, Alexander Faussner, Maik Drechsler, Jochen Grommes, Johanna P van Geffen, He Li, Almudena Ortega-Gomez, Remco T A Megens, Ronald Naumann, Ingrid Dijkgraaf, Gerry A F Nicolaes, Yvonne Döring, Oliver Soehnlein, Esther Lutgens, Johan W M Heemskerk, Rory R Koenen, Kevin H Mayo, Tilman M Hackeng, Christian Weber},
title={Chemokine interactome mapping enables tailored intervention in acute and chronic inflammation.},
journal={Science translational medicine},
volume={9},
issue ={384},
pages={null--null},
year=2017
}

Daniel Mateju, Titus Franzmann, Avinash Patel, Andrii Kopach, Edgar Boczek, Shovamayee Maharana, Hyun-Ok Kate Lee, Serena Carra, Anthony Hyman, Simon Alberti
An aberrant phase transition of stress granules triggered by misfolded protein and prevented by chaperone function.
EMBO J, Art. No. doi: 10.15252/embj.201695957 (2017)
  PubMed   

Stress granules (SG) are membrane-less compartments involved in regulating mRNAs during stress. Aberrant forms of SGs have been implicated in age-related diseases, such as amyotrophic lateral sclerosis (ALS), but the molecular events triggering their formation are still unknown. Here, we find that misfolded proteins, such as ALS-linked variants of SOD1, specifically accumulate and aggregate within SGs in human cells. This decreases the dynamics of SGs, changes SG composition, and triggers an aberrant liquid-to-solid transition of in vitro reconstituted compartments. We show that chaperone recruitment prevents the formation of aberrant SGs and promotes SG disassembly when the stress subsides. Moreover, we identify a backup system for SG clearance, which involves transport of aberrant SGs to the aggresome and their degradation by autophagy. Thus, cells employ a system of SG quality control to prevent accumulation of misfolded proteins and maintain the dynamic state of SGs, which may have relevance for ALS and related diseases.
@article{Mateju6825,
author={Daniel Mateju, Titus Franzmann, Avinash Patel, Andrii Kopach, Edgar Boczek, Shovamayee Maharana, Hyun-Ok Kate Lee, Serena Carra, Anthony Hyman, Simon Alberti},
title={An aberrant phase transition of stress granules triggered by misfolded protein and prevented by chaperone function.},
journal={The EMBO journal},
volume={},
pages={1--1},
year=2017
}

Jaydeep Sidhaye, Caren Norden
Concerted action of neuroepithelial basal shrinkage and active epithelial migration ensures efficient optic cup morphogenesis
Elife, Art. No. eLife 2017;6:e22689 (2017)
    

Organ formation is a multi-scale event that involves changes at the intracellular, cellular and tissue level. Organogenesis often starts with the formation of characteristically shaped organ precursors. However, the cellular mechanisms driving organ precursor formation are often not clear. Here, using zebrafish, we investigate the epithelial rearrangements responsible for the development of the hemispherical retinal neuroepithelium (RNE), a part of the optic cup. We show that in addition to basal shrinkage of RNE cells, active migration of connected epithelial cells into the RNE is a crucial player in its formation. This cellular movement is driven by progressive cell-matrix contacts and actively translocates prospective RNE cells to their correct location before they adopt neuroepithelial fate. Failure of this migration during neuroepithelium formation leads to ectopic determination of RNE cells and consequently impairs optic cup formation. Overall, this study illustrates how spatiotemporal coordination between morphogenic movements and fate determination critically influences organogenesis.
@article{Sidhaye6810,
author={Jaydeep Sidhaye, Caren Norden},
title={Concerted action of neuroepithelial basal shrinkage and active epithelial migration ensures efficient optic cup morphogenesis},
journal={eLife},
volume={},
pages={1--29},
year=2017
}

Jan Brugués
Cytoskeleton Dynamics: Mind the Gap!
Curr Biol, 27(7) 279-281 (2017)
PubMed   

A new study presents a quantitative biophysical model of microtubule aster growth with autocatalytic microtubule nucleation. The model accounts for asters that grow indefinitely, even when their microtubules are unstable.
@article{Brugués6830,
author={Jan Brugués},
title={Cytoskeleton Dynamics: Mind the Gap!},
journal={Current biology : CB},
volume={27},
issue ={7},
pages={279--281},
year=2017
}

Yuanhao Gong, Ivo F. Sbalzarini
Curvature Filters Efficiently Reduce Certain Variational Energies.
IEEE Trans Image Process, 26(4) 1786-1798 (2017)
  PubMed   

In image processing, the rapid approximate solution of variational problems involving generic data-fitting terms is often of practical relevance, for example in real-time applications. Variational solvers based on diffusion schemes or the Euler-Lagrange equations are too slow and restricted in the types of data-fitting terms. Here, we present a filter-based approach to reduce variational energies that contain generic data-fitting terms, but are restricted to specific regularizations. Our approach is based on reducing the regularization part of the variational energy, while guaranteeing non-increasing total energy. This is applicable to regularization-dominated models, where the data-fitting energy initially increases, while the regularization energy initially decreases. We present fast discrete filters for regularizers based on Gaussian curvature, mean curvature, and total variation. These pixel-local filters can be used to rapidly reduce the energy of the full model. We prove the convergence of the resulting iterative scheme in a greedy sense, and we show several experiments to demonstrate applications in image-processing problems involving regularization-dominated variational models.
@article{Gong6799,
author={Yuanhao Gong, Ivo F. Sbalzarini},
title={Curvature Filters Efficiently Reduce Certain Variational Energies.},
journal={IEEE transactions on image processing : a publication of the IEEE Signal Processing Society},
volume={26},
issue ={4},
pages={1786--1798},
year=2017
}

John J Reynolds, Louise S Bicknell, Paula Carroll, Martin R Higgs, Ranad Shaheen, Jennie E Murray, Dimitrios Papadopoulos, Andrea Leitch, Olga Murina, Žygimantė Tarnauskaitė, Sarah R Wessel, Anastasia Zlatanou, Audrey Vernet, Alex von Kriegsheim, Rachel M A Mottram, Clare V Logan, Hannah Bye, Yun Li, Alexander Brean, Sateesh Maddirevula, Rachel C Challis, Kassiani Skouloudaki, Agaadir Almoisheer, Hessa S Alsaif, Ariella Amar, Natalie J Prescott, Michael B Bober, Angela Duker, Eissa Faqeih, Mohammed Zain Seidahmed, Saeed Al Tala, Abdulrahman Alswaid, Saleem Ahmed, Jumana Yousuf Al-Aama, Janine Altmüller, Mohammed Al Balwi, Angela F Brady, Luciana Chessa, Helen Cox, Rita Fischetto, Raoul Heller, Bertram D Henderson, Emma Hobson, Peter Nürnberg, E Ferda Percin, Angela Peron, Luigina Spaccini, Alan J Quigley, Seema Thakur, Carol A Wise, Grace Yoon, Maha Alnemer, Pavel Tomancak, Gökhan Yigit, A Malcolm R Taylor, Martin A M Reijns, Michael A Simpson, David Cortez, Fowzan Sami Alkuraya, Christopher G Mathew, Andrew P Jackson, Grant S Stewart
Mutations in DONSON disrupt replication fork stability and cause microcephalic dwarfism.
Nat Genet, 49(4) 537-549 (2017)
PubMed   

To ensure efficient genome duplication, cells have evolved numerous factors that promote unperturbed DNA replication and protect, repair and restart damaged forks. Here we identify downstream neighbor of SON (DONSON) as a novel fork protection factor and report biallelic DONSON mutations in 29 individuals with microcephalic dwarfism. We demonstrate that DONSON is a replisome component that stabilizes forks during genome replication. Loss of DONSON leads to severe replication-associated DNA damage arising from nucleolytic cleavage of stalled replication forks. Furthermore, ATM- and Rad3-related (ATR)-dependent signaling in response to replication stress is impaired in DONSON-deficient cells, resulting in decreased checkpoint activity and the potentiation of chromosomal instability. Hypomorphic mutations in DONSON substantially reduce DONSON protein levels and impair fork stability in cells from patients, consistent with defective DNA replication underlying the disease phenotype. In summary, we have identified mutations in DONSON as a common cause of microcephalic dwarfism and established DONSON as a critical replication fork protein required for mammalian DNA replication and genome stability.
@article{Reynolds6781,
author={John J Reynolds, Louise S Bicknell, Paula Carroll, Martin R Higgs, Ranad Shaheen, Jennie E Murray, Dimitrios Papadopoulos, Andrea Leitch, Olga Murina, Žygimantė Tarnauskaitė, Sarah R Wessel, Anastasia Zlatanou, Audrey Vernet, Alex von Kriegsheim, Rachel M A Mottram, Clare V Logan, Hannah Bye, Yun Li, Alexander Brean, Sateesh Maddirevula, Rachel C Challis, Kassiani Skouloudaki, Agaadir Almoisheer, Hessa S Alsaif, Ariella Amar, Natalie J Prescott, Michael B Bober, Angela Duker, Eissa Faqeih, Mohammed Zain Seidahmed, Saeed Al Tala, Abdulrahman Alswaid, Saleem Ahmed, Jumana Yousuf Al-Aama, Janine Altmüller, Mohammed Al Balwi, Angela F Brady, Luciana Chessa, Helen Cox, Rita Fischetto, Raoul Heller, Bertram D Henderson, Emma Hobson, Peter Nürnberg, E Ferda Percin, Angela Peron, Luigina Spaccini, Alan J Quigley, Seema Thakur, Carol A Wise, Grace Yoon, Maha Alnemer, Pavel Tomancak, Gökhan Yigit, A Malcolm R Taylor, Martin A M Reijns, Michael A Simpson, David Cortez, Fowzan Sami Alkuraya, Christopher G Mathew, Andrew P Jackson, Grant S Stewart},
title={Mutations in DONSON disrupt replication fork stability and cause microcephalic dwarfism.},
journal={Nature genetics},
volume={49},
issue ={4},
pages={537--549},
year=2017
}

David Zwicker, Rabea Seyboldt, Christoph A. Weber, Anthony A. Hyman, Frank Jülicher
Growth and division of active droplets provides a model for protocells
Nat. Phys., 13(4) 408-413 (2017)
  

Nature Physics | Article Print Share/bookmark Growth and division of active droplets provides a model for protocells David Zwicker, Rabea Seyboldt, Christoph A. Weber, Anthony A. Hyman & Frank Jülicher Affiliations Contributions Corresponding author Nature Physics 13, 408–413 (2017) doi:10.1038/nphys3984 Received 29 April 2016 Accepted 10 November 2016 Published online 12 December 2016 Article tools PDF Citation Reprints Rights & permissions Article metrics Abstract Abstract• Introduction• Division of active droplets• Chemically active droplets as a model for protocells• Methods• References• Acknowledgements• Author information• Supplementary information It has been proposed that during the early steps in the origin of life, small droplets could have formed via the segregation of molecules from complex mixtures by phase separation. These droplets could have provided chemical reaction centres. However, whether these droplets could divide and propagate is unclear. Here we examine the behaviour of droplets in systems that are maintained away from thermodynamic equilibrium by an external supply of energy. In these systems, droplets grow by the addition of droplet material generated by chemical reactions. Surprisingly, we find that chemically driven droplet growth can lead to shape instabilities that trigger the division of droplets into two smaller daughters. Therefore, chemically active droplets can exhibit cycles of growth and division that resemble the proliferation of living cells. Dividing active droplets could serve as a model for prebiotic protocells, where chemical reactions in the droplet play the role of a prebiotic metabolism.
@article{Zwicker6828,
author={David Zwicker, Rabea Seyboldt, Christoph A. Weber, Anthony A. Hyman, Frank Jülicher},
title={Growth and division of active droplets provides a model for protocells},
journal={Nature Physics},
volume={13},
issue ={4},
pages={408--413},
year=2017
}