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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
}

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
}

Kirstin Meyer, Oleksandr Ostrenko, George Bourantas, Hernán Morales-Navarrete, Natalie Porat-Shliom, Fabián Segovia-Miranda, Hidenori Nonaka, Ali Ghaemi, Jean-Marc Verbavatz, Lutz Brusch, Ivo F. Sbalzarini, Yannis Kalaidzidis, Roberto Weigert, Marino Zerial
A Predictive 3D Multi-Scale Model of Biliary Fluid Dynamics in the Liver Lobule.
Cell Syst, 4(3) 277-290 (2017)
  PubMed   

Bile, the central metabolic product of the liver, is transported by the bile canaliculi network. The impairment of bile flow in cholestatic liver diseases has urged a demand for insights into its regulation. Here, we developed a predictive 3D multi-scale model that simulates fluid dynamic properties successively from the subcellular to the tissue level. The model integrates the structure of the bile canalicular network in the mouse liver lobule, as determined by high-resolution confocal and serial block-face scanning electron microscopy, with measurements of bile transport by intravital microscopy. The combined experiment-theory approach revealed spatial heterogeneities of biliary geometry and hepatocyte transport activity. Based on this, our model predicts gradients of bile velocity and pressure in the liver lobule. Validation of the model predictions by pharmacological inhibition of Rho kinase demonstrated a requirement of canaliculi contractility for bile flow in vivo. Our model can be applied to functionally characterize liver diseases and quantitatively estimate biliary transport upon drug-induced liver injury.
@article{Meyer6804,
author={Kirstin Meyer, Oleksandr Ostrenko, George Bourantas, Hernán Morales-Navarrete, Natalie Porat-Shliom, Fabián Segovia-Miranda, Hidenori Nonaka, Ali Ghaemi, Jean-Marc Verbavatz, Lutz Brusch, Ivo F. Sbalzarini, Yannis Kalaidzidis, Roberto Weigert, Marino Zerial},
title={A Predictive 3D Multi-Scale Model of Biliary Fluid Dynamics in the Liver Lobule.},
journal={Cell systems},
volume={4},
issue ={3},
pages={277--290},
year=2017
}

Sonja Kroschwald, Simon Alberti
Gel or Die: Phase Separation as a Survival Strategy.
Cell, 168(6) 947-948 (2017)
PubMed   

Stress conditions trigger protein assembly by demixing from the cytoplasm, but the biological significance is still unclear. In this issue of Cell, Riback et al. report that the yeast poly(A)-binding protein 1 (Pab1) is a phase-separating stress sensor that boosts organismal fitness under physiological stress conditions.
@article{Kroschwald6801,
author={Sonja Kroschwald, Simon Alberti},
title={Gel or Die: Phase Separation as a Survival Strategy.},
journal={Cell},
volume={168},
issue ={6},
pages={947--948},
year=2017
}

Sara N. Nagelberg, Lauren D. Zarzar, Natalie Nicolas, Kaushikaram Subramanian, Julia A Kalow, Vishnu Sresht, Daniel Blankschtein, George Barbastathis, Moritz Kreysing, Timothy M Swager, Mathias Kolle
Reconfigurable and responsive droplet-based compound micro-lenses.
Nat Commun, 8 Art. No. 14673 (2017)
  PubMed   

Micro-scale optical components play a crucial role in imaging and display technology, biosensing, beam shaping, optical switching, wavefront-analysis, and device miniaturization. Herein, we demonstrate liquid compound micro-lenses with dynamically tunable focal lengths. We employ bi-phase emulsion droplets fabricated from immiscible hydrocarbon and fluorocarbon liquids to form responsive micro-lenses that can be reconfigured to focus or scatter light, form real or virtual images, and display variable focal lengths. Experimental demonstrations of dynamic refractive control are complemented by theoretical analysis and wave-optical modelling. Additionally, we provide evidence of the micro-lenses' functionality for two potential applications-integral micro-scale imaging devices and light field display technology-thereby demonstrating both the fundamental characteristics and the promising opportunities for fluid-based dynamic refractive micro-scale compound lenses.
@article{Nagelberg6800,
author={Sara N. Nagelberg, Lauren D. Zarzar, Natalie Nicolas, Kaushikaram Subramanian, Julia A Kalow, Vishnu Sresht, Daniel Blankschtein, George Barbastathis, Moritz Kreysing, Timothy M Swager, Mathias Kolle},
title={Reconfigurable and responsive droplet-based compound micro-lenses.},
journal={Nature communications},
volume={8},
pages={null--null},
year=2017
}

Tomasz Sadowski, Christian Klose, Mathias J. Gerl, Anna Wójcik-Maciejewicz, Ronny Herzog, Kai Simons, Adam Reich, Michal Surma
Large-scale human skin lipidomics by quantitative, high-throughput shotgun mass spectrometry.
Sci Rep, 7 Art. No. 43761 (2017)
  PubMed   

The lipid composition of human skin is essential for its function; however the simultaneous quantification of a wide range of stratum corneum (SC) and sebaceous lipids is not trivial. We developed and validated a quantitative high-throughput shotgun mass spectrometry-based platform for lipid analysis of tape-stripped SC skin samples. It features coverage of 16 lipid classes; total quantification to the level of individual lipid molecules; high reproducibility and high-throughput capabilities. With this method we conducted a large lipidomic survey of 268 human SC samples, where we investigated the relationship between sampling depth and lipid composition, lipidome variability in samples from 14 different sampling sites on the human body and finally, we assessed the impact of age and sex on lipidome variability in 104 healthy subjects. We found sebaceous lipids to constitute an abundant component of the SC lipidome as they diffuse into the topmost SC layers forming a gradient. Lipidomic variability with respect to sampling depth, site and subject is considerable, and mainly accredited to sebaceous lipids, while stratum corneum lipids vary less. This stresses the importance of sampling design and the role of sebaceous lipids in skin studies.
@article{Sadowski6807,
author={Tomasz Sadowski, Christian Klose, Mathias J. Gerl, Anna Wójcik-Maciejewicz, Ronny Herzog, Kai Simons, Adam Reich, Michal Surma},
title={Large-scale human skin lipidomics by quantitative, high-throughput shotgun mass spectrometry.},
journal={Scientific reports},
volume={7},
pages={null--null},
year=2017
}

Edlyn Wu, Ajay A Vashisht, Clément Chapat, Mathieu N Flamand, Emiliano Cohen, Mihail Sarov, Yuval Tabach, Nahum Sonenberg, James Wohlschlegel, Thomas F Duchaine
A continuum of mRNP complexes in embryonic microRNA-mediated silencing.
Nucleic Acids Res, 45(4) 2081-2098 (2017)
  PubMed  

@article{Wu6704,
author={Edlyn Wu, Ajay A Vashisht, Clément Chapat, Mathieu N Flamand, Emiliano Cohen, Mihail Sarov, Yuval Tabach, Nahum Sonenberg, James Wohlschlegel, Thomas F Duchaine},
title={A continuum of mRNP complexes in embryonic microRNA-mediated silencing.},
journal={Nucleic acids research},
volume={45},
issue ={4},
pages={2081--2098},
year=2017
}

Salman F Banani, Hyun-Ok Kate Lee, Anthony Hyman, Michael K Rosen
Biomolecular condensates: organizers of cellular biochemistry.
Nat Rev Mol Cell Biol, Art. No. doi: 10.1038/nrm.2017.7 (2017)
PubMed   

Biomolecular condensates are micron-scale compartments in eukaryotic cells that lack surrounding membranes but function to concentrate proteins and nucleic acids. These condensates are involved in diverse processes, including RNA metabolism, ribosome biogenesis, the DNA damage response and signal transduction. Recent studies have shown that liquid-liquid phase separation driven by multivalent macromolecular interactions is an important organizing principle for biomolecular condensates. With this physical framework, it is now possible to explain how the assembly, composition, physical properties and biochemical and cellular functions of these important structures are regulated.
@article{Banani6797,
author={Salman F Banani, Hyun-Ok Kate Lee, Anthony Hyman, Michael K Rosen},
title={Biomolecular condensates: organizers of cellular biochemistry.},
journal={Nature reviews. Molecular cell biology},
volume={},
pages={null--null},
year=2017
}

Ana Lisica, Stephan W. Grill
Optical tweezers studies of transcription by eukaryotic RNA polymerases.
Biomol Concepts, Art. No. doi: 10.1515/bmc-2016-0028 (2017)
PubMed   

Transcription is the first step in the expression of genetic information and it is carried out by large macromolecular enzymes called RNA polymerases. Transcription has been studied for many years and with a myriad of experimental techniques, ranging from bulk studies to high-resolution transcript sequencing. In this review, we emphasise the advantages of using single-molecule techniques, particularly optical tweezers, to study transcription dynamics. We give an overview of the latest results in the single-molecule transcription field, focusing on transcription by eukaryotic RNA polymerases. Finally, we evaluate recent quantitative models that describe the biophysics of RNA polymerase translocation and backtracking dynamics.
@article{Lisica6798,
author={Ana Lisica, Stephan W. Grill},
title={Optical tweezers studies of transcription by eukaryotic RNA polymerases.},
journal={Biomolecular concepts},
volume={},
pages={null--null},
year=2017
}

Dmitrij Schlesinger, Florian Jug, Gene Myers, Carsten Rother, Dagmar Kainmueller
Crowd Sourcing Image Segmentation with iaSTAPLE
arXiv, Art. No. arXiv:1702.06461 [cs.CV] (2017)
   

@article{null6782,
author={Dmitrij Schlesinger, Florian Jug, Gene Myers, Carsten Rother, Dagmar Kainmueller},
title={Crowd Sourcing Image Segmentation with iaSTAPLE},
journal={arXiv},
volume={},
pages={null--null},
year=2017
}