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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
}

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)}
}

Sara Carvalhal, Michelle Stevense, Katrin Koehler, Ronald Naumann, Angela Huebner, Rolf Jessberger, Eric R Griffis
ALADIN is Required for the Production of Fertile Mouse Oocytes.
Mol Biol Cell, 1-1 (2017)
PubMed   

Asymmetric cell divisions depend upon the precise placement of the spindle apparatus. In mammalian oocytes, spindles assemble close to the cell's center but chromosome segregation takes place at the cell periphery where half of the chromosomes are expelled into small, non-developing polar bodies at anaphase. By dividing so asymmetrically, most of the cytoplasmic content within the oocyte is preserved, which is critical for successful fertilization and early development. Recently, we determined that the nucleoporin ALADIN participates in spindle assembly in somatic cells, and we have also shown that female mice homozygously null for ALADIN are sterile. In this study we show that this protein is involved in specific meiotic stages including meiotic resumption, spindle assembly, and spindle positioning. In the absence of ALADIN, polar body extrusion is compromised due to problems in spindle orientation and anchoring at the first meiotic anaphase. ALADIN null oocytes that mature far enough to be fertilized in vitro are unable to support embryonic development beyond the two-cell stage. Overall, we find that ALADIN is critical for oocyte maturation and appears to be far more essential for this process than for somatic cell divisions.
@article{Carvalhal6921,
author={Sara Carvalhal, Michelle Stevense, Katrin Koehler, Ronald Naumann, Angela Huebner, Rolf Jessberger, Eric R Griffis},
title={ALADIN is Required for the Production of Fertile Mouse Oocytes.},
journal={Molecular biology of the cell},
volume={},
pages={1--1},
year=2017
}

Jaroslav Icha, Michael Weber, Jennifer Waters, Caren Norden
Phototoxicity in live fluorescence microscopy, and how to avoid it.
Bioessays, 39(8) Art. No. doi: 10.1002/bies.201700003 (2017)
  PubMed   

Phototoxicity frequently occurs during live fluorescence microscopy, and its consequences are often underestimated. Damage to cellular macromolecules upon excitation light illumination can impair sample physiology, and even lead to sample death. In this review, we explain how phototoxicity influences live samples, and we highlight that, besides the obvious effects of phototoxicity, there are often subtler consequences of illumination that are imperceptible when only the morphology of samples is examined. Such less apparent manifestations of phototoxicity are equally problematic, and can change the conclusions drawn from an experiment. Thus, limiting phototoxicity is a prerequisite for obtaining reproducible quantitative data on biological processes. We present strategies to reduce phototoxicity, e.g. limiting the illumination to the focal plane and suggest controls for phototoxicity effects. Overall, we argue that phototoxicity needs increased attention from researchers when designing experiments, and when evaluating research findings.
@article{Icha6914,
author={Jaroslav Icha, Michael Weber, Jennifer Waters, Caren Norden},
title={Phototoxicity in live fluorescence microscopy, and how to avoid it.},
journal={BioEssays : news and reviews in molecular, cellular and developmental biology},
volume={39},
issue ={8},
pages={null--null},
year=2017
}

Josefine Asmus, Christian L Müller, Ivo F. Sbalzarini
Lp-Adaptation: Simultaneous Design Centering and Robustness Estimation of Electronic and Biological Systems.
Sci Rep, 7(1) Art. No. 6660 (2017)
  PubMed   

The design of systems or models that work robustly under uncertainty and environmental fluctuations is a key challenge in both engineering and science. This is formalized in the design-centering problem, which is defined as finding a design that fulfills given specifications and has a high probability of still doing so if the system parameters or the specifications fluctuate randomly. Design centering is often accompanied by the problem of quantifying the robustness of a system. Here we present a novel adaptive statistical method to simultaneously address both problems. Our method, L p -Adaptation, is inspired by the evolution of robustness in biological systems and by randomized schemes for convex volume computation. It is able to address both problems in the general, non-convex case and at low computational cost. We describe the concept and the algorithm, test it on known benchmarks, and demonstrate its real-world applicability in electronic and biological systems. In all cases, the present method outperforms the previous state of the art. This enables re-formulating optimization problems in engineering and biology as design centering problems, taking global system robustness into account.
@article{Asmus6915,
author={Josefine Asmus, Christian L Müller, Ivo F. Sbalzarini},
title={Lp-Adaptation: Simultaneous Design Centering and Robustness Estimation of Electronic and Biological Systems.},
journal={Scientific reports},
volume={7},
issue ={1},
pages={null--null},
year=2017
}

Sabine Stopp, Marco Gründl, Marc Fackler, Jonas Malkmus, Marina Leone, Ronald Naumann, Stefan Frantz, Elmar Wolf, Björn von Eyss, Felix B Engel, Stefan Gaubatz
Deletion of Gas2l3 in mice leads to specific defects in cardiomyocyte cytokinesis during development.
Proc Natl Acad Sci U.S.A., 114(30) 8029-8034 (2017)
PubMed   

GAS2L3 is a recently identified cytoskeleton-associated protein that interacts with actin filaments and tubulin. The in vivo function of GAS2L3 in mammals remains unknown. Here, we show that mice deficient in GAS2L3 die shortly after birth because of heart failure. Mammalian cardiomyocytes lose the ability to proliferate shortly after birth, and further increase in cardiac mass is achieved by hypertrophy. The proliferation arrest of cardiomyocytes is accompanied by binucleation through incomplete cytokinesis. We observed that GAS2L3 deficiency leads to inhibition of cardiomyocyte proliferation and to cardiomyocyte hypertrophy during embryonic development. Cardiomyocyte-specific deletion of GAS2L3 confirmed that the phenotype results from the loss of GAS2L3 in cardiomyocytes. Cardiomyocytes from Gas2l3-deficient mice exhibit increased expression of a p53-transcriptional program including the cell cycle inhibitor p21. Furthermore, loss of GAS2L3 results in premature binucleation of cardiomyocytes accompanied by unresolved midbody structures. Together these results suggest that GAS2L3 plays a specific role in cardiomyocyte cytokinesis and proliferation during heart development.
@article{Stopp6920,
author={Sabine Stopp, Marco Gründl, Marc Fackler, Jonas Malkmus, Marina Leone, Ronald Naumann, Stefan Frantz, Elmar Wolf, Björn von Eyss, Felix B Engel, Stefan Gaubatz},
title={Deletion of Gas2l3 in mice leads to specific defects in cardiomyocyte cytokinesis during development.},
journal={Proceedings of the National Academy of Sciences of the United States of America},
volume={114},
issue ={30},
pages={8029--8034},
year=2017
}

Adam Klosin, Anthony Hyman
Molecular biology: A liquid reservoir for silent chromatin.
Nature, 547(7662) 168-170 (2017)
PubMed  

@article{Klosin6909,
author={Adam Klosin, Anthony Hyman},
title={Molecular biology: A liquid reservoir for silent chromatin.},
journal={Nature},
volume={547},
issue ={7662},
pages={168--170},
year=2017
}

Gaia Pigino, Stephen M King
Switching dynein motors on and off.
Nat Struct Mol Biol, 24(7) 557-559 (2017)
PubMed  

@article{Pigino6906,
author={Gaia Pigino, Stephen M King},
title={Switching dynein motors on and off.},
journal={Nature structural & molecular biology},
volume={24},
issue ={7},
pages={557--559},
year=2017
}

Kai Schuhmann, Henrik Thomas, Jacobo Miranda Ackerman, Konstantin O Nagornov, Yury O Tsybin, Andrej Shevchenko
Intensity-Independent Noise Filtering in FT MS and FT MS/MS Spectra for Shotgun Lipidomics.
Anal Chem, 89(13) 7046-7052 (2017)
PubMed   

Shotgun lipidomics relies on the direct infusion of total lipid extracts into a high resolution tandem mass spectrometer. A single shotgun analysis produces several hundred of densely populated FT MS and FT MS/MS spectra, each of which might comprise thousands of peaks although a very small percentage of those belong to lipids. Eliminating noise by adjusting a minimal peak intensity threshold is biased and inefficient since lipid species and classes vary in their natural abundance and ionization capacity. We developed a method of peak intensity-independent noise filtering in shotgun FT MS and FT MS/MS spectra that capitalizes on a stable composition of the infused analyte leading to consistent time-independent detection of its bona fide components. Repetition rate filtering relies on a single quantitative measure of peaks detection reproducibility irrespectively of their absolute intensities, masses, or assumed elemental compositions. In comparative experiments, it removed more than 95% of signals detectable in shotgun spectra without compromising the accuracy and scope of lipid identification and quantification. It also accelerated spectra processing by 15-fold and increased the number of simultaneously processed spectra by ∼500-fold hence eliminating the major bottleneck in high-throughput bottom-up shotgun lipidomics.
@article{Schuhmann6896,
author={Kai Schuhmann, Henrik Thomas, Jacobo Miranda Ackerman, Konstantin O Nagornov, Yury O Tsybin, Andrej Shevchenko},
title={Intensity-Independent Noise Filtering in FT MS and FT MS/MS Spectra for Shotgun Lipidomics.},
journal={Analytical chemistry},
volume={89},
issue ={13},
pages={7046--7052},
year=2017
}

Valentina Botti, François McNicoll, Michaela Steiner, Florian M Richter, Anfisa Solovyeva, Marius Wegener, Oliver D Schwich, Ina Poser, Kathi Zarnack, Ilka Wittig, Karla M. Neugebauer, Michaela Müller-McNicoll
Cellular differentiation state modulates the mRNA export activity of SR proteins.
J Cell Biol, 216(7) 1993-2009 (2017)
PubMed   

SR proteins function in nuclear pre-mRNA processing, mRNA export, and translation. To investigate their cellular dynamics, we developed a quantitative assay, which detects differences in nucleocytoplasmic shuttling among seven canonical SR protein family members. As expected, SRSF2 and SRSF5 shuttle poorly in HeLa cells but surprisingly display considerable shuttling in pluripotent murine P19 cells. Combining individual-resolution cross-linking and immunoprecipitation (iCLIP) and mass spectrometry, we show that elevated arginine methylation of SRSF5 and lower phosphorylation levels of cobound SRSF2 enhance shuttling of SRSF5 in P19 cells by modulating protein-protein and protein-RNA interactions. Moreover, SRSF5 is bound to pluripotency-specific transcripts such as Lin28a and Pou5f1/Oct4 in the cytoplasm. SRSF5 depletion reduces and overexpression increases their cytoplasmic mRNA levels, suggesting that enhanced mRNA export by SRSF5 is required for the expression of pluripotency factors. Remarkably, neural differentiation of P19 cells leads to dramatically reduced SRSF5 shuttling. Our findings indicate that posttranslational modification of SR proteins underlies the regulation of their mRNA export activities and distinguishes pluripotent from differentiated cells.
@article{Botti6900,
author={Valentina Botti, François McNicoll, Michaela Steiner, Florian M Richter, Anfisa Solovyeva, Marius Wegener, Oliver D Schwich, Ina Poser, Kathi Zarnack, Ilka Wittig, Karla M. Neugebauer, Michaela Müller-McNicoll},
title={Cellular differentiation state modulates the mRNA export activity of SR proteins.},
journal={The Journal of cell biology},
volume={216},
issue ={7},
pages={1993--2009},
year=2017
}