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Björn Drobot, Juan M Iglesias Artola, Kristian Le Vay, Viktoria Mayr, Mrityunjoy Kar, Moritz Kreysing, Hannes Mutschler, T-Y Dora Tang
Compartmentalized RNA catalysis in membrane-free coacervate protocells
Nat Commun, 1-1 (2018)
Supplementary Website  

@article{Drobot7196,
author={Björn Drobot, Juan M Iglesias Artola, Kristian Le Vay, Viktoria Mayr, Mrityunjoy Kar, Moritz Kreysing, Hannes Mutschler, T-Y Dora Tang},
title={Compartmentalized RNA catalysis in membrane-free coacervate protocells},
journal={Nature communications},
volume={},
pages={1--1},
year=2018
}

Katrin Daniel, Jaroslav Icha, Cindy Horenburg, Doris Müller, Caren Norden, Jorg Mansfeld
Conditional control of fluorescent protein degradation by an auxin-dependent nanobody
Nat Commun, Art. No. doi: 10.1038/s41467-018-05855-5 (2018)
 

@article{Daniel7197,
author={Katrin Daniel, Jaroslav Icha, Cindy Horenburg, Doris Müller, Caren Norden, Jorg Mansfeld},
title={Conditional control of fluorescent protein degradation by an auxin-dependent nanobody },
journal={Nature communications},
volume={},
pages={1--1},
year=2018
}

Marija Matejčić, Guillaume Salbreux, Caren Norden
A non-cell-autonomous actin redistribution enables isotropic retinal growth.
PLoS Biol, 16(8) Art. No. 2006018 (2018)
PubMed Source   

Tissue shape is often established early in development and needs to be scaled isotropically during growth. However, the cellular contributors and ways by which cells interact tissue-wide to enable coordinated isotropic tissue scaling are not yet understood. Here, we follow cell and tissue shape changes in the zebrafish retinal neuroepithelium, which forms a cup with a smooth surface early in development and maintains this architecture as it grows. By combining 3D analysis and theory, we show how a global increase in cell height can maintain tissue shape during growth. Timely cell height increase occurs concurrently with a non-cell-autonomous actin redistribution. Blocking actin redistribution and cell height increase perturbs isotropic scaling and leads to disturbed, folded tissue shape. Taken together, our data show how global changes in cell shape enable isotropic growth of the developing retinal neuroepithelium, a concept that could also apply to other systems.
@article{Matejčić7193,
author={Marija Matejčić, Guillaume Salbreux, Caren Norden},
title={A non-cell-autonomous actin redistribution enables isotropic retinal growth.},
journal={PLoS biology},
volume={16},
issue ={8},
pages={null--null},
year=2018
}

Neil O Carragher, Filippo Piccinini, Anna Tesei, O Joseph Trask Jr, Marc Bickle, Peter Horvath
Concerns, challenges and promises of high-content analysis of 3D cellular models.
Nat Rev Drug Discov, 17(8) Art. No. 606 (2018)
PubMed Source  

@article{Carragher7192,
author={Neil O Carragher, Filippo Piccinini, Anna Tesei, O Joseph Trask Jr, Marc Bickle, Peter Horvath},
title={Concerns, challenges and promises of high-content analysis of 3D cellular models.},
journal={Nature reviews. Drug discovery},
volume={17},
issue ={8},
pages={null--null},
year=2018
}

Peggy Stolt-Bergner, Christian Benda, Tim Bergbrede, Hüseyin Besir, Patrick H N Celie, Cindy Chang, David N. Drechsel, Ariane Fischer, Arie Geerlof, Barbara Giabbai, Joop van den Heuvel, Georg Huber, Wolfgang Knecht, Anita Lehner, Regis P. Lemaitre, Kristina Nordén, Gwynn Pardee, Ines Racke, Kim Remans, Astrid Sander, Judith Scholz, Magda Stadnik, Paola Storici, Daniel Weinbruch, Isabel Zaror, Linda H L Lua, Sabine Suppmann
Baculovirus-driven protein expression in insect cells: A benchmarking study.
J Struct Biol, 203(2) 71-80 (2018)
PubMed Source   

Baculovirus-insect cell expression system has become one of the most widely used eukaryotic expression systems for heterologous protein production in many laboratories. The availability of robust insect cell lines, serum-free media, a range of vectors and commercially-packaged kits have supported the demand for maximizing the exploitation of the baculovirus-insect cell expression system. Naturally, this resulted in varied strategies adopted by different laboratories to optimize protein production. Most laboratories have preference in using either the E. coli transposition-based recombination bacmid technology (e.g. Bac-to-Bac®) or homologous recombination transfection within insect cells (e.g. flashBAC™). Limited data is presented in the literature to benchmark the protocols used for these baculovirus vectors to facilitate the selection of a system for optimal production of target proteins. Taking advantage of the Protein Production and Purification Partnership in Europe (P4EU) scientific network, a benchmarking initiative was designed to compare the diverse protocols established in thirteen individual laboratories. This benchmarking initiative compared the expression of four selected intracellular proteins (mouse Dicer-2, 204 kDa; human ABL1 wildtype, 126 kDa; human FMRP, 68 kDa; viral vNS1-H1, 76 kDa). Here, we present the expression and purification results on these proteins and highlight the significant differences in expression yields obtained using different commercially-packaged baculovirus vectors. The highest expression level for difficult-to-express intracellular protein candidates were observed with the EmBacY baculovirus vector system.
@article{Stolt-Bergner7112,
author={Peggy Stolt-Bergner, Christian Benda, Tim Bergbrede, Hüseyin Besir, Patrick H N Celie, Cindy Chang, David N. Drechsel, Ariane Fischer, Arie Geerlof, Barbara Giabbai, Joop van den Heuvel, Georg Huber, Wolfgang Knecht, Anita Lehner, Regis P. Lemaitre, Kristina Nordén, Gwynn Pardee, Ines Racke, Kim Remans, Astrid Sander, Judith Scholz, Magda Stadnik, Paola Storici, Daniel Weinbruch, Isabel Zaror, Linda H L Lua, Sabine Suppmann},
title={Baculovirus-driven protein expression in insect cells: A benchmarking study.},
journal={Journal of structural biology},
volume={203},
issue ={2},
pages={71--80},
year=2018
}

Oskar Knittelfelder, Sofia Traikov, Olga Vvedenskaya, Andrea Schuhmann, Sandra Segeletz, Anna Shevchenko, Andrej Shevchenko
Shotgun Lipidomics Combined with Laser Capture Microdissection: A Tool To Analyze Histological Zones in Cryosections of Tissues.
Anal Chem, Art. No. doi: 10.1021/acs.analchem.8b02004 (2018)
PubMed Source   

Shotgun analysis provides a quantitative snapshot of the lipidome composition of cells, tissues, or model organisms; however, it does not elucidate the spatial distribution of lipids. Here we demonstrate that shotgun analysis could quantify low-picomole amounts of lipids isolated by laser capture microdissection (LCM) of hundred micrometer-sized histological zones visualized at the cryosections of tissues. We identified metabolically distinct periportal (pp) and pericentral (pc) zones by immunostaining of 20 μm thick cryosections of a healthy mouse liver. LCM was used to ablate, catapult, and collect the tissue material from 10 to 20 individual zones covering a total area of 0.3-0.5 mm2 and containing ca. 500 cells. Top-down shotgun profiling relying upon computational stitching of 61 targeted selective ion monitoring ( t-SIM) spectra quantified more than 200 lipid species from 17 lipid classes including glycero- and glycerophospholipids, sphingolipids, cholesterol esters, and cholesterol. Shotgun LCM revealed the overall commonality of the full lipidome composition of pp and pc zones along with significant ( p < 0.001) difference in the relative abundance of 13 lipid species. Follow-up proteomics analyses of pellets recovered from an aqueous phase saved after the lipid extraction identified 13 known and 7 new protein markers exclusively present in pp or in pc zones and independently validated the specificity of their visualization, isolation, and histological assignment.
@article{Knittelfelder7190,
author={Oskar Knittelfelder, Sofia Traikov, Olga Vvedenskaya, Andrea Schuhmann, Sandra Segeletz, Anna Shevchenko, Andrej Shevchenko},
title={Shotgun Lipidomics Combined with Laser Capture Microdissection: A Tool To Analyze Histological Zones in Cryosections of Tissues.},
journal={Analytical chemistry},
volume={},
pages={1--1},
year=2018
}

Nicolai Wagner, Milena Stephan, Doris Höglinger, André Nadler
A click cage: Organelle-specific uncaging of lipid messengers.
Angew Chem Int Ed Engl, Art. No. doi: 10.1002/anie.201807497 (2018)
PubMed Source   

Lipid messengers exert their function on fast time scales at distinct subcellular locations, yet most experimental approaches for perturbing their levels trigger cell-wide concentration changes. Here, we report a coumarin-based photo-caging group, that can be modified by click chemistry with organelle-targeting moieties and thus enables photo-release of lipid messengers in distinct organelles. We show that caged arachidonic acid and sphingosine derivatives can be selectively delivered to mitochondria, the ER, lysosomes and the plasma membrane. By comparing cellular calcium transients induced by localized uncaging of arachidonic acid and sphingosine, we show that the precise intracellular localization of the released second messenger is instrumental for signaling outcome. Ultimately, we anticipate that this new class of caged compounds will greatly facilitate studying cellular processes on the organelle level.
@article{Wagner7187,
author={Nicolai Wagner, Milena Stephan, Doris Höglinger, André Nadler},
title={A click cage: Organelle-specific uncaging of lipid messengers.},
journal={Angewandte Chemie (International ed. in English)},
volume={},
pages={1--1},
year=2018
}

Jie Wang, Jeong-Mo Choi, Alex S Holehouse, Hyun O. Lee, Xiaojie Zhang, Marcus Jahnel, Shovamayee Maharana, Regis P. Lemaitre, Andrei I. Pozniakovsky, David N. Drechsel, Ina Poser, Rohit V Pappu, Simon Alberti, Anthony Hyman
A Molecular Grammar Governing the Driving Forces for Phase Separation of Prion-like RNA Binding Proteins.
Cell, 174(3) 688-699 (2018)
PubMed Source   

Proteins such as FUS phase separate to form liquid-like condensates that can harden into less dynamic structures. However, how these properties emerge from the collective interactions of many amino acids remains largely unknown. Here, we use extensive mutagenesis to identify a sequence-encoded molecular grammar underlying the driving forces of phase separation of proteins in the FUS family and test aspects of this grammar in cells. Phase separation is primarily governed by multivalent interactions among tyrosine residues from prion-like domains and arginine residues from RNA-binding domains, which are modulated by negatively charged residues. Glycine residues enhance the fluidity, whereas glutamine and serine residues promote hardening. We develop a model to show that the measured saturation concentrations of phase separation are inversely proportional to the product of the numbers of arginine and tyrosine residues. These results suggest it is possible to predict phase-separation properties based on amino acid sequences.
@article{Wang7156,
author={Jie Wang, Jeong-Mo Choi, Alex S Holehouse, Hyun O. Lee, Xiaojie Zhang, Marcus Jahnel, Shovamayee Maharana, Regis P. Lemaitre, Andrei I. Pozniakovsky, David N. Drechsel, Ina Poser, Rohit V Pappu, Simon Alberti, Anthony Hyman},
title={A Molecular Grammar Governing the Driving Forces for Phase Separation of Prion-like RNA Binding Proteins.},
journal={Cell},
volume={174},
issue ={3},
pages={688--699},
year=2018
}

Edouard Mobarak, Matti Javanainen, Waldemar Kulig, Alf Honigmann, Erdinc Sezgin, Noora Aho, Christian Eggeling, Tomasz Rog, Ilpo Vattulainen
How to minimize dye-induced perturbations while studying biomembrane structure and dynamics: PEG linkers as a rational alternative.
Biochim Biophys Acta, Art. No. doi: 10.1016/j.bbamem.2018.07.003 (2018)
PubMed Source   

Organic dye-tagged lipid analogs are essential for many fluorescence-based investigations of complex membrane structures, especially when using advanced microscopy approaches. However, lipid analogs may interfere with membrane structure and dynamics, and it is not obvious that the properties of lipid analogs would match those of non-labeled host lipids. In this work, we bridged atomistic simulations with super-resolution imaging experiments and biomimetic membranes to assess the performance of commonly used sphingomyelin-based lipid analogs. The objective was to compare, on equal footing, the relative strengths and weaknesses of acyl chain labeling, headgroup labeling, and labeling based on poly-ethyl-glycol (PEG) linkers in determining biomembrane properties. We observed that the most appropriate strategy to minimize dye-induced membrane perturbations and to allow consideration of Brownian-like diffusion in liquid-ordered membrane environments is to decouple the dye from a membrane by a PEG linker attached to a lipid headgroup. Yet, while the use of PEG linkers may sound a rational and even an obvious approach to explore membrane dynamics, the results also suggest that the dyes exploiting PEG linkers interfere with molecular interactions and their dynamics. Overall, the results highlight the great care needed when using fluorescent lipid analogs, in particular accurate controls.
@article{Mobarak7185,
author={Edouard Mobarak, Matti Javanainen, Waldemar Kulig, Alf Honigmann, Erdinc Sezgin, Noora Aho, Christian Eggeling, Tomasz Rog, Ilpo Vattulainen},
title={How to minimize dye-induced perturbations while studying biomembrane structure and dynamics: PEG linkers as a rational alternative.},
journal={Biochimica et biophysica acta},
volume={},
pages={1--1},
year=2018
}

Michael Heide, Wieland B. Huttner, Felipe Mora-Bermúdez
Brain organoids as models to study human neocortex development and evolution.
Curr Opin Cell Biol, 55 8-16 (2018)
PubMed Source   

Since their recent development, organoids that emulate human brain tissue have allowed in vitro neural development studies to go beyond the limits of monolayer culture systems, such as neural rosettes. We present here a review of organoid studies that focuses on cortical wall development, starting with a technical comparison between pre-patterning and self-patterning brain organoid protocols. We then follow neocortex development in space and time and list those aspects where organoids have succeeded in emulating in vivo development, as well as those aspects that continue to be pending tasks. Finally, we present a summary of medical and evolutionary insight made possible by organoid technology.
@article{Heide7174,
author={Michael Heide, Wieland B. Huttner, Felipe Mora-Bermúdez},
title={Brain organoids as models to study human neocortex development and evolution.},
journal={Current opinion in cell biology},
volume={55},
pages={8--16},
year=2018
}