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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
}

Nikolai Hecker, Virag Sharma, Michael Hiller
Transition to an aquatic habitat permitted the repeated loss of the pleiotropic KLK8 gene in mammals.
Genome Biol Evol, 1-1 (2017)
PubMed Source   

KLK8 (also called neuropsin) is a serine protease that plays distinct roles in the skin and hippocampus. In the skin, KLK8 influences keratinocyte proliferation and desquamation, and activates antimicrobial peptides in sweat. In the hippocampus, KLK8 affects memory acquisition. Here, we examined the evolution of KLK8 in mammals and discovered that, out of 70 placental mammals, KLK8 is exclusively lost in three independent fully-aquatic lineages, comprising dolphin, killer whale, minke whale and manatee. In addition, while the sperm whale has an intact KLK8 reading frame, the gene evolves neutrally in this species. We suggest that the distinct functions of KLK8 likely became obsolete in the aquatic environment, leading to the subsequent loss of KLK8 in several fully-aquatic mammalian lineages. First, the cetacean and manatee skin lacks sweat glands as an adaptation to the aquatic environment, which likely made the epidermal function of KLK8 obsolete. Second, cetaceans and manatees exhibit a proportionally small hippocampus, which may have rendered the hippocampal functions of KLK8 obsolete. Together, our results shed light on the genomic changes that correlate with skin and neuroanatomical differences of aquatic mammals, and show that even pleiotropic genes can be lost during evolution if an environmental change nullifies the need for the different functions of such genes.
@article{Hecker6970,
author={Nikolai Hecker, Virag Sharma, Michael Hiller},
title={Transition to an aquatic habitat permitted the repeated loss of the pleiotropic KLK8 gene in mammals.},
journal={Genome biology and evolution},
volume={},
pages={1--1},
year=2017
}

Jovan Mircetic, Antje Dietrich, Maciej Paszkowski-Rogacz, Mechthild Krause, Frank Buchholz
Development of a genetic sensor that eliminates p53 deficient cells.
Nat Commun, 8(1) Art. No. 1463 (2017)
PubMed Source   

The TP53 gene fulfills a central role in protecting cells from genetic insult. Given this crucial role it might be surprising that p53 itself is not essential for cell survival. Indeed, TP53 is the single most mutated gene across different cancer types. Thus, both a theoretical and a question of significant practical applicability arise: can cells be programmed to make TP53 an essential gene? Here we present a genetic p53 sensor, in which the loss of p53 is coupled to the rise of HSV-TK expression. We show that the sensor can distinguish both p53 knockout and cells expressing a common TP53 cancer mutation from otherwise isogenic TP53 wild-type cells. Importantly, the system is sensitive enough to specifically target TP53 loss-of-function cells with the HSV-TK pro-drug Ganciclovir both in vitro and in vivo. Our work opens new ways to programming cell intrinsic transformation protection systems that rely on endogenous components.
@article{Mircetic6978,
author={Jovan Mircetic, Antje Dietrich, Maciej Paszkowski-Rogacz, Mechthild Krause, Frank Buchholz},
title={Development of a genetic sensor that eliminates p53 deficient cells.},
journal={Nature communications},
volume={8},
issue ={1},
pages={null--null},
year=2017
}

Dominik Schwudke, Anna Shevchenko, N Hoffmann, R Ahrends
Lipidomics informatics for life-science.
J Biotechnol, 261 Art. No. doi: 10.1016/j.jbiotec.2017.08.010 (2017)
PubMed Source   

Lipidomics encompasses analytical approaches that aim to identify and quantify the complete set of lipids, defined as lipidome in a given cell, tissue or organism as well as their interactions with other molecules. The majority of lipidomics workflows is based on mass spectrometry and has been proven as a powerful tool in system biology in concert with other Omics disciplines. Unfortunately, bioinformatics infrastructures for this relatively young discipline are limited only to some specialists. Search engines, quantification algorithms, visualization tools and databases developed by the 'Lipidomics Informatics for Life-Science' (LIFS) partners will be restructured and standardized to provide broad access to these specialized bioinformatics pipelines. There are many medical challenges related to lipid metabolic alterations that will be fostered by capacity building suggested by LIFS. LIFS as member of the 'German Network for Bioinformatics' (de.NBI) node for 'Bioinformatics for Proteomics' (BioInfra.Prot) and will provide access to the described software as well as to tutorials and consulting services via a unified web-portal.
@article{Schwudke6940,
author={Dominik Schwudke, Anna Shevchenko, N Hoffmann, R Ahrends},
title={Lipidomics informatics for life-science.},
journal={Journal of biotechnology},
volume={261},
pages={131--136},
year=2017
}

T-Y Dora Tang, Dario Cecchi, Giorgio Fracasso, Davide Accardi, Angelique Coutable-Pennarun, Sheref S Mansy, Adam W Perriman, J L Ross Anderson, Stephen Mann
Gene-Mediated Chemical Communication in Synthetic Protocell Communities.
ACS Synth Biol, Art. No. doi: 10.1021/acssynbio.7b00306 (2017)
PubMed Source   

A gene-directed chemical communication pathway between synthetic protocell signaling transmitters (lipid vesicles) and receivers (proteinosomes) was designed, built and tested using a bottom-up modular approach comprising small molecule transcriptional control, cell-free gene expression, porin-directed efflux, substrate signaling, and enzyme cascade-mediated processing.
@article{Tang6971,
author={T-Y Dora Tang, Dario Cecchi, Giorgio Fracasso, Davide Accardi, Angelique Coutable-Pennarun, Sheref S Mansy, Adam W Perriman, J L Ross Anderson, Stephen Mann},
title={Gene-Mediated Chemical Communication in Synthetic Protocell Communities.},
journal={ACS synthetic biology},
volume={},
pages={null--null},
year=2017
}

Yusuke Toyoda, Cedric J Cattin, Martin P Stewart, Ina Poser, Mirko Theis, Teymuras V. Kurzchalia, Frank Buchholz, Anthony Hyman, Daniel J. Müller
Genome-scale single-cell mechanical phenotyping reveals disease-related genes involved in mitotic rounding.
Nat Commun, 8(1) 1266-1266 (2017)
PubMed Source   

To divide, most animal cells drastically change shape and round up against extracellular confinement. Mitotic cells facilitate this process by generating intracellular pressure, which the contractile actomyosin cortex directs into shape. Here, we introduce a genome-scale microcantilever- and RNAi-based approach to phenotype the contribution of > 1000 genes to the rounding of single mitotic cells against confinement. Our screen analyzes the rounding force, pressure and volume of mitotic cells and localizes selected proteins. We identify 49 genes relevant for mitotic rounding, a large portion of which have not previously been linked to mitosis or cell mechanics. Among these, depleting the endoplasmic reticulum-localized protein FAM134A impairs mitotic progression by affecting metaphase plate alignment and pressure generation by delocalizing cortical myosin II. Furthermore, silencing the DJ-1 gene uncovers a link between mitochondria-associated Parkinson's disease and mitotic pressure. We conclude that mechanical phenotyping is a powerful approach to study the mechanisms governing cell shape.
@article{Toyoda6976,
author={Yusuke Toyoda, Cedric J Cattin, Martin P Stewart, Ina Poser, Mirko Theis, Teymuras V. Kurzchalia, Frank Buchholz, Anthony Hyman, Daniel J. Müller},
title={Genome-scale single-cell mechanical phenotyping reveals disease-related genes involved in mitotic rounding.},
journal={Nature communications},
volume={8},
issue ={1},
pages={1266--1266},
year=2017
}

Barbara Ludwig, Stefan Ludwig, Anja Steffen, Yvonne Knauf, Baruch Zimerman, Sophie Heinke, Susann Lehmann, Undine Schubert, Janine Schmid, Martina Bleyer, Uwe Schönmann, Clark K Colton, Enzio Bonifacio, Michele Solimena, A. Reichel, Andrew V Schally, Avi Rotem, Uriel Barkai, Helena Grinberg-Rashi, Franz-Josef Kaup, Yuval Avni, Peter Jones, Stefan Bornstein
Favorable outcome of experimental islet xenotransplantation without immunosuppression in a nonhuman primate model of diabetes.
Proc Natl Acad Sci U.S.A., 114(44) 11745-11750 (2017)
PubMed Source   

Transplantation of pancreatic islets for treating type 1 diabetes is restricted to patients with critical metabolic lability resulting from the need for immunosuppression and the shortage of donor organs. To overcome these barriers, we developed a strategy to macroencapsulate islets from different sources that allow their survival and function without immunosuppression. Here we report successful and safe transplantation of porcine islets with a bioartificial pancreas device in diabetic primates without any immune suppression. This strategy should lead to pioneering clinical trials with xenotransplantation for treatment of diabetes and, thereby, represents a previously unidentified approach to efficient cell replacement for a broad spectrum of endocrine disorders and other organ dysfunctions.
@article{Ludwig6977,
author={Barbara Ludwig, Stefan Ludwig, Anja Steffen, Yvonne Knauf, Baruch Zimerman, Sophie Heinke, Susann Lehmann, Undine Schubert, Janine Schmid, Martina Bleyer, Uwe Schönmann, Clark K Colton, Enzio Bonifacio, Michele Solimena, A. Reichel, Andrew V Schally, Avi Rotem, Uriel Barkai, Helena Grinberg-Rashi, Franz-Josef Kaup, Yuval Avni, Peter Jones, Stefan Bornstein},
title={Favorable outcome of experimental islet xenotransplantation without immunosuppression in a nonhuman primate model of diabetes.},
journal={Proceedings of the National Academy of Sciences of the United States of America},
volume={114},
issue ={44},
pages={11745--11750},
year=2017
}

Vladimir Ulman, Martin Maška, Klas E. G. Magnusson, Olaf Ronneberger, Carsten Haubold, Nathalie Harder, Pavel Matula, Pavel Matula, David Svoboda, Miroslav Radojevic, Ihor Smal, Karl Rohr, Joakim Jaldén, Helen M. Blau, Oleh Dzyubachyk, Boudewijn Lelieveldt, Pengdong Xiao, Yuexiang Li, Siu-Yeung Cho, Alexandre C Dufour, Jean-Christophe Olivo-Marin, Constantino C Reyes-Aldasoro, Jose A Solis-Lemus, Robert Bensch, Thomas Brox, Johannes Stegmaier, Ralf Mikut, Steffen Wolf, Fred A Hamprecht, Tiago Esteves, Pedro Quelhas, Ömer Demirel, Lars Malmström, Florian Jug, Pavel Tomancak, Erik Meijering, Arrate Muñoz-Barrutia, Michal Kozubek, Carlos Ortiz-de-Solorzano
An objective comparison of cell-tracking algorithms.
Nat Methods, Art. No. doi: 10.1038/nmeth.4473 (2017)
  PubMed Source   

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.
@article{Ulman6956,
author={Vladimir Ulman, Martin Maška, Klas E. G. Magnusson, Olaf Ronneberger, Carsten Haubold, Nathalie Harder, Pavel Matula, Pavel Matula, David Svoboda, Miroslav Radojevic, Ihor Smal, Karl Rohr, Joakim Jaldén, Helen M. Blau, Oleh Dzyubachyk, Boudewijn Lelieveldt, Pengdong Xiao, Yuexiang Li, Siu-Yeung Cho, Alexandre C Dufour, Jean-Christophe Olivo-Marin, Constantino C Reyes-Aldasoro, Jose A Solis-Lemus, Robert Bensch, Thomas Brox, Johannes Stegmaier, Ralf Mikut, Steffen Wolf, Fred A Hamprecht, Tiago Esteves, Pedro Quelhas, Ömer Demirel, Lars Malmström, Florian Jug, Pavel Tomancak, Erik Meijering, Arrate Muñoz-Barrutia, Michal Kozubek, Carlos Ortiz-de-Solorzano},
title={An objective comparison of cell-tracking algorithms.},
journal={Nature methods},
volume={},
pages={1--1},
year=2017
}

Simon Alberti
Phase separation in biology.
Curr Biol, 27(20) 1097-1102 (2017)
PubMed Source   

Cells have to organize their complex biochemistry to regulate their metabolism and respond to changes in the environment. Traditionally, intracellular organization has been associated with compartments that are surrounded by lipid membranes. However, in recent years, phase transitions have emerged as a novel form of cellular organization. Phase transition is a physical process whereby a substance changes from one physical state to another. Examples are provided by the freezing of water into ice (liquid to solid) or the heating of water to generate water vapor (liquid to gas).
@article{Alberti6957,
author={Simon Alberti},
title={Phase separation in biology.},
journal={Current biology : CB},
volume={27},
issue ={20},
pages={1097--1102},
year=2017
}

Natalja Strelnikova, Nora Sauter, Manuel Guizar-Sicairos, Michael Göllner, Ana Diaz, Petrina Delivani, Mariola R. Chacón, Iva M Tolić, Vasily Zaburdaev, Thomas Pfohl
Live cell X-ray imaging of autophagic vacuoles formation and chromatin dynamics in fission yeast.
Sci Rep, 7(1) 13775-13775 (2017)
PubMed Source   

Seeing physiological processes at the nanoscale in living organisms without labeling is an ultimate goal in life sciences. Using X-ray ptychography, we explored in situ the dynamics of unstained, living fission yeast Schizosaccharomyces pombe cells in natural, aqueous environment at the nanoscale. In contrast to previous X-ray imaging studies on biological matter, in this work the eukaryotic cells were alive even after several ptychographic X-ray scans, which allowed us to visualize the chromatin motion as well as the autophagic cell death induced by the ionizing radiation. The accumulated radiation of the sequential scans allowed for the determination of a characteristic dose of autophagic vacuole formation and the lethal dose for fission yeast. The presented results demonstrate a practical method that opens another way of looking at living biological specimens and processes in a time-resolved label-free setting.
@article{Strelnikova6974,
author={Natalja Strelnikova, Nora Sauter, Manuel Guizar-Sicairos, Michael Göllner, Ana Diaz, Petrina Delivani, Mariola R. Chacón, Iva M Tolić, Vasily Zaburdaev, Thomas Pfohl},
title={Live cell X-ray imaging of autophagic vacuoles formation and chromatin dynamics in fission yeast.},
journal={Scientific reports},
volume={7},
issue ={1},
pages={13775--13775},
year=2017
}