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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 Source   

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
}

Sven Karol, Tobias Nett, Pietro Incardona, Nesrine Khouzami, Jeronimo Castrillon, Ivo F. Sbalzarini
A Language and Development Environment for Parallel Particle Methods
In: V. International Conference on Particle-based Methods - Fundamentals and Applications (2017)(Eds.) Peter Wriggers, Barcelona, International Center for Numerical Methods in Engineering (CIMNE) (2017), 1-10
   

@proceedings{Karol6891,
title = {A Language and Development Environment for Parallel Particle Methods},
year = 2017,
editor = {Sven Karol, Tobias Nett, Pietro Incardona, Nesrine Khouzami, Jeronimo Castrillon, Ivo F. Sbalzarini},
volume = {V. International Conference on Particle-based Methods - Fundamentals and Applications},
series = {},
publisher = {International Center for Numerical Methods in Engineering (CIMNE)}
}

Kamran Rizzolo, Jennifer Huen, Ashwani Kumar, Sadhna Phanse, James Vlasblom, Yoshito Kakihara, Hussein A Zeineddine, Zoran Minic, Jamie Snider, Wen Wang, Carles Pons, Thiago V Seraphim, Edgar Boczek, Simon Alberti, Michael Costanzo, Chad L Myers, Igor Stagljar, Charles Boone, Mohan Babu, Walid A Houry
Features of the Chaperone Cellular Network Revealed through Systematic Interaction Mapping.
Cell Rep, 20(11) 2735-2748 (2017)
PubMed Source   

A comprehensive view of molecular chaperone function in the cell was obtained through a systematic global integrative network approach based on physical (protein-protein) and genetic (gene-gene or epistatic) interaction mapping. This allowed us to decipher interactions involving all core chaperones (67) and cochaperones (15) of Saccharomyces cerevisiae. Our analysis revealed the presence of a large chaperone functional supercomplex, which we named the naturally joined (NAJ) chaperone complex, encompassing Hsp40, Hsp70, Hsp90, AAA+, CCT, and small Hsps. We further found that many chaperones interact with proteins that form foci or condensates under stress conditions. Using an in vitro reconstitution approach, we demonstrate condensate formation for the highly conserved AAA+ ATPases Rvb1 and Rvb2, which are part of the R2TP complex that interacts with Hsp90. This expanded view of the chaperone network in the cell clearly demonstrates the distinction between chaperones having broad versus narrow substrate specificities in protein homeostasis.
@article{Rizzolo6932,
author={Kamran Rizzolo, Jennifer Huen, Ashwani Kumar, Sadhna Phanse, James Vlasblom, Yoshito Kakihara, Hussein A Zeineddine, Zoran Minic, Jamie Snider, Wen Wang, Carles Pons, Thiago V Seraphim, Edgar Boczek, Simon Alberti, Michael Costanzo, Chad L Myers, Igor Stagljar, Charles Boone, Mohan Babu, Walid A Houry},
title={Features of the Chaperone Cellular Network Revealed through Systematic Interaction Mapping.},
journal={Cell reports},
volume={20},
issue ={11},
pages={2735--2748},
year=2017
}

Amayra Hernández-Vega, Marcus Braun, Lara Scharrel, Marcus Jahnel, Susanne Wegmann, Bradley T Hyman, Simon Alberti, Stefan Diez, Anthony Hyman
Local Nucleation of Microtubule Bundles through Tubulin Concentration into a Condensed Tau Phase.
Cell Rep, 20(10) 2304-2312 (2017)
PubMed Source   

Non-centrosomal microtubule bundles play important roles in cellular organization and function. Although many diverse proteins are known that can bundle microtubules, biochemical mechanisms by which cells could locally control the nucleation and formation of microtubule bundles are understudied. Here, we demonstrate that the concentration of tubulin into a condensed, liquid-like compartment composed of the unstructured neuronal protein tau is sufficient to nucleate microtubule bundles. We show that, under conditions of macro-molecular crowding, tau forms liquid-like drops. Tubulin partitions into these drops, efficiently increasing tubulin concentration and driving the nucleation of microtubules. These growing microtubules form bundles, which deform the drops while remaining enclosed by diffusible tau molecules exhibiting a liquid-like behavior. Our data suggest that condensed compartments of microtubule bundling proteins could promote the local formation of microtubule bundles in neurons by acting as non-centrosomal microtubule nucleation centers and that liquid-like tau encapsulation could provide both stability and plasticity to long axonal microtubule bundles.
@article{Hernández-Vega6933,
author={Amayra Hernández-Vega, Marcus Braun, Lara Scharrel, Marcus Jahnel, Susanne Wegmann, Bradley T Hyman, Simon Alberti, Stefan Diez, Anthony Hyman},
title={Local Nucleation of Microtubule Bundles through Tubulin Concentration into a Condensed Tau Phase.},
journal={Cell reports},
volume={20},
issue ={10},
pages={2304--2312},
year=2017
}

Barbara Tavares, Raquel Jacinto, Pedro Sampaio, Sara Pestana, Andreia Pinto, Andreia Vaz, Mónica Roxo-Rosa, Rui Gardner, Telma Lopes, Britta Schilling, Ian Henry, Leonor Saúde, Susana Lopes
Notch/Her12 signalling modulates motile/immotile cilia ratio downstream of Foxj1a in zebrafish left-right organizer.
Elife, 6 1-1 (2017)
PubMed Source   

Foxj1a is necessary and sufficient to specify motile cilia. Using transcriptional studies and slow-scan two-photon live imaging capable of identifying the number of motile and immotile cilia, we now established that the final number of motile cilia depends on Notch signalling (NS). We found that despite all left-right organizer (LRO) cells express foxj1a and the ciliary axonemes of these cells have dynein arms some cilia remain immotile. We identified that this decision is taken early in development in the Kupffer's Vesicle (KV) precursors the readout being her12 transcription. We demonstrate that overexpression of either her12 or Notch intracellular domain (NICD) increases the number of immotile cilia at the expense of motile cilia, and leads to an accumulation of immotile cilia at the anterior half of the KV. This disrupts the normal fluid flow intensity and pattern, with consequent impact on dand5 expression pattern and left-right (L-R) axis establishment.
@article{Tavares6931,
author={Barbara Tavares, Raquel Jacinto, Pedro Sampaio, Sara Pestana, Andreia Pinto, Andreia Vaz, Mónica Roxo-Rosa, Rui Gardner, Telma Lopes, Britta Schilling, Ian Henry, Leonor Saúde, Susana Lopes},
title={Notch/Her12 signalling modulates motile/immotile cilia ratio downstream of Foxj1a in zebrafish left-right organizer.},
journal={eLife},
volume={6},
pages={1--1},
year=2017
}

Simon Alberti
The wisdom of crowds: regulating cell function through condensed states of living matter.
J Cell Sci, 130(17) 2789-2796 (2017)
PubMed Source   

Our understanding of cells has progressed rapidly in recent years, mainly because of technological advances. Modern technology now allows us to observe molecular processes in living cells with high spatial and temporal resolution. At the same time, we are beginning to compile the molecular parts list of cells. However, how all these parts work together to yield complex cellular behavior is still unclear. In addition, the established paradigm of molecular biology, which sees proteins as well-folded enzymes that undergo specific lock-and-key type interactions, is increasingly being challenged. In fact, it is now becoming clear that many proteins do not fold into three-dimensional structures and additionally show highly promiscuous binding behavior. Furthermore, proteins function in collectives and form condensed phases with different material properties, such as liquids, gels, glasses or filaments. Here, I examine emerging evidence that the formation of macromolecular condensates is a fundamental principle in cell biology. I further discuss how different condensed states of living matter regulate cellular functions and decision-making and ensure adaptive behavior and survival in times of cellular crisis.
@article{Alberti6934,
author={Simon Alberti},
title={The wisdom of crowds: regulating cell function through condensed states of living matter.},
journal={Journal of cell science},
volume={130},
issue ={17},
pages={2789--2796},
year=2017
}

Federica F Morelli, Dineke S Verbeek, Jessika Bertacchini, Jonathan Vinet, Laura Mediani, Sandra Marmiroli, Giovanna Cenacchi, Milena Nasi, Sara De Biasi, Jeanette F Brunsting, Jan Lammerding, Elena Pegoraro, Corrado Angelini, Rossella Tupler, Simon Alberti, Serena Carra
Aberrant Compartment Formation by HSPB2 Mislocalizes Lamin A and Compromises Nuclear Integrity and Function.
Cell Rep, 20(9) 2100-2115 (2017)
PubMed Source   

Small heat shock proteins (HSPBs) contain intrinsically disordered regions (IDRs), but the functions of these IDRs are still unknown. Here, we report that, in mammalian cells, HSPB2 phase separates to form nuclear compartments with liquid-like properties. We show that phase separation requires the disordered C-terminal domain of HSPB2. We further demonstrate that, in differentiating myoblasts, nuclear HSPB2 compartments sequester lamin A. Increasing the nuclear concentration of HSPB2 causes the formation of aberrant nuclear compartments that mislocalize lamin A and chromatin, with detrimental consequences for nuclear function and integrity. Importantly, phase separation of HSPB2 is regulated by HSPB3, but this ability is lost in two identified HSPB3 mutants that are associated with myopathy. Our results suggest that HSPB2 phase separation is involved in reorganizing the nucleoplasm during myoblast differentiation. Furthermore, these findings support the idea that aberrant HSPB2 phase separation, due to HSPB3 loss-of-function mutations, contributes to myopathy.
@article{Morelli6935,
author={Federica F Morelli, Dineke S Verbeek, Jessika Bertacchini, Jonathan Vinet, Laura Mediani, Sandra Marmiroli, Giovanna Cenacchi, Milena Nasi, Sara De Biasi, Jeanette F Brunsting, Jan Lammerding, Elena Pegoraro, Corrado Angelini, Rossella Tupler, Simon Alberti, Serena Carra},
title={Aberrant Compartment Formation by HSPB2 Mislocalizes Lamin A and Compromises Nuclear Integrity and Function.},
journal={Cell reports},
volume={20},
issue ={9},
pages={2100--2115},
year=2017
}

Virag Sharma, Peter Schwede, Michael Hiller
CESAR 2.0 substantially improves speed and accuracy of comparative gene annotation
Bioinformatics, 1-3 (2017)
  Source  

@article{Sharma6922,
author={Virag Sharma, Peter Schwede, Michael Hiller},
title={CESAR 2.0 substantially improves speed and accuracy of comparative gene annotation},
journal={Bioinformatics (Oxford, England)},
volume={},
pages={1--3},
year=2017
}

Corinna Blasse, Stephan Saalfeld, Raphael Etournay, Andreas Sagner, Suzanne Eaton, Eugene W Myers
PreMosa: extracting 2D surfaces from 3D microscopy mosaics.
Bioinformatics, 33(16) 2563-2569 (2017)
PubMed Source   

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: (i) extracting and mapping the stained manifold in each stack into a single 2D projection plane, (ii) correcting uneven illumination artifacts, (iii) stitching the mosaic planes into a single, large 2D image and (iv) 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={33},
issue ={16},
pages={2563--2569},
year=2017
}

Shambaditya Saha, Anthony Hyman
RNA gets in phase.
J Cell Biol, 216(8) 2235-2237 (2017)
PubMed Source   

Several neurological disorders are linked to tandem nucleotide repeat expansion in the mutated gene. Jain and Vale (2017. Nature. https://doi.org/10.1038/nature22386) show that, above a pathological threshold repeat number, base pairing interactions drive phase separation of RNA into membrane-less gels, suggesting that RNA can scaffold the assembly of phase-separated compartments that sequester proteins/RNAs causing toxicity.
@article{Saha6925,
author={Shambaditya Saha, Anthony Hyman},
title={RNA gets in phase.},
journal={The Journal of cell biology},
volume={216},
issue ={8},
pages={2235--2237},
year=2017
}