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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
}

Martin Weigert, Eugene W Myers, Moritz Kreysing
Biobeam - Rigorous wave-optical simulations of light-sheet microscopy
arXiv, Art. No. arXiv:1706.02261 (2017)
   

@article{Weigert6874,
author={Martin Weigert, Eugene W Myers, Moritz Kreysing},
title={Biobeam - Rigorous wave-optical simulations of light-sheet microscopy},
journal={arXiv},
volume={},
pages={null--null},
year=2017
}

Sebastian Boland, Ulrike Schmidt, Vyacheslav Zagoriy, Julio Sampaio, Raphael F Fritsche, Regina Czerwonka, Tilo Lübken, Jakob Reimann, Sider Penkov, Hans-Joachim Knölker, Teymuras V. Kurzchalia
Phosphorylated glycosphingolipids essential for cholesterol mobilization in Caenorhabditis elegans.
Nat Chem Biol, 13(6) 647-654 (2017)
PubMed   

The nematode Caenorhabditis elegans requires exogenous cholesterol to survive and its depletion leads to early developmental arrest. Thus, tight regulation of cholesterol storage and distribution within the organism is indispensable. Here, we present a novel class of C. elegans phosphorylated glycosphingolipids, phosphoethanolamine glucosylceramides (PEGCs), capable of rescuing larval arrest induced by sterol starvation. We describe the total synthesis of a major PEGC species and demonstrate that the PEGC synthetic counterpart suppresses the dauer-constitutive phenotype of Niemann-Pick C1 (NPC1) and DAF-7/TGF-β mutant worms caused by impaired intracellular sterol trafficking. PEGC biosynthesis depends on functional NPC1 and TGF-β, indicating that these proteins control larval development at least partly through PEGC. Furthermore, glucosylceramide deficiency dramatically reduced PEGC amounts. However, the resulting developmental arrest could be rescued by oversaturation of food with cholesterol. Taken together, these data show that PEGC is essential for C. elegans development through its regulation of sterol mobilization.
@article{Boland6838,
author={Sebastian Boland, Ulrike Schmidt, Vyacheslav Zagoriy, Julio Sampaio, Raphael F Fritsche, Regina Czerwonka, Tilo Lübken, Jakob Reimann, Sider Penkov, Hans-Joachim Knölker, Teymuras V. Kurzchalia},
title={Phosphorylated glycosphingolipids essential for cholesterol mobilization in Caenorhabditis elegans.},
journal={Nature chemical biology},
volume={13},
issue ={6},
pages={647--654},
year=2017
}

David G Drubin, Anthony Hyman
Stem cells: the new "model organism".
Mol Biol Cell, 28(11) 1409-1411 (2017)
PubMed   

Human tissue culture cells have long been a staple of molecular and cell biology research. However, although these cells are derived from humans, they have often lost considerable aspects of natural physiological function. Here we argue that combined advances in genome editing, stem cell production, and organoid derivation from stem cells represent a revolution in cell biology. These advances have important ramifications for the study of basic cell biology mechanisms, as well as for the ways in which discoveries in mechanisms are translated into understanding of disease.
@article{Drubin6872,
author={David G Drubin, Anthony Hyman},
title={Stem cells: the new "model organism".},
journal={Molecular biology of the cell},
volume={28},
issue ={11},
pages={1409--1411},
year=2017
}

Arne Jahn, Grishma Rane, Maciej Paszkowski-Rogacz, Sergi Sayols, Alina Bluhm, Chung-Ting Han, Irena Draškovič, J Arturo Londoño-Vallejo, Alan Prem Kumar, Frank Buchholz, Falk Butter, Dennis Kappei
ZBTB48 is both a vertebrate telomere-binding protein and a transcriptional activator.
EMBO Rep, 18(6) 929-946 (2017)
PubMed   

Telomeres constitute the ends of linear chromosomes and together with the shelterin complex form a structure essential for genome maintenance and stability. In addition to the constitutive binding of the shelterin complex, other direct, yet more transient interactions are mediated by the CST complex and HOT1/HMBOX1, while subtelomeric variant repeats are recognized by NR2C/F transcription factors. Recently, the Kruppel-like zinc finger protein ZBTB48/HKR3/TZAP has been described as a novel telomere-associated factor in the vertebrate lineage. Here, we show that ZBTB48 binds directly both to telomeric and to subtelomeric variant repeat sequences. ZBTB48 is found at telomeres of human cancer cells regardless of the mode of telomere maintenance and it acts as a negative regulator of telomere length. In addition to its telomeric function, we demonstrate through a combination of RNAseq, ChIPseq and expression proteomics experiments that ZBTB48 acts as a transcriptional activator on a small set of target genes, including mitochondrial fission process 1 (MTFP1). This discovery places ZBTB48 at the interface of telomere length regulation, transcriptional control and mitochondrial metabolism.
@article{Jahn6868,
author={Arne Jahn, Grishma Rane, Maciej Paszkowski-Rogacz, Sergi Sayols, Alina Bluhm, Chung-Ting Han, Irena Draškovič, J Arturo Londoño-Vallejo, Alan Prem Kumar, Frank Buchholz, Falk Butter, Dennis Kappei},
title={ZBTB48 is both a vertebrate telomere-binding protein and a transcriptional activator.},
journal={EMBO reports},
volume={18},
issue ={6},
pages={929--946},
year=2017
}

Caren Norden
Pseudostratified epithelia - cell biology, diversity and roles in organ formation at a glance.
J Cell Sci, 130(11) 1859-1863 (2017)
  PubMed   

Pseudostratified epithelia (PSE) are widespread and diverse tissue arrangements, and many PSE are organ precursors in a variety of organisms. While cells in PSE, like other epithelial cells, feature apico-basal polarity, they generally are more elongated and their nuclei are more densely packed within the tissue. In addition, nuclei in PSE undergo interkinetic nuclear migration (IKNM, also referred to as INM), whereby all mitotic events occur at the apical surface of the elongated epithelium. Previous reviews have focused on the links between IKNM and the cell cycle, as well as the relationship between IKNM and neurogenesis, which will not be elaborated on here. Instead, in this Cell Science at a Glance article and the accompanying poster, I will discuss the cell biology of PSEs, highlighting how differences in PSE architecture could influence cellular behaviour, especially IKNM. Furthermore, I will summarize what we know about the links between apical mitosis in PSE and tissue integrity and maturation.
@article{Norden6858,
author={Caren Norden},
title={Pseudostratified epithelia - cell biology, diversity and roles in organ formation at a glance.},
journal={Journal of cell science},
volume={130},
issue ={11},
pages={1859--1863},
year=2017
}

Carlos Ocaña-Morgner, Susanne Sales, Manuela Rothe, Andrej Shevchenko, Rolf Jessberger
Tolerogenic versus Immunogenic Lipidomic Profiles of CD11c(+) Immune Cells and Control of Immunogenic Dendritic Cell Ceramide Dynamics.
J Immunol, 198(11) 4360-4372 (2017)
PubMed   

Lipids affect the membrane properties determining essential biological processes. Earlier studies have suggested a role of switch-activated protein 70 (SWAP-70) in lipid raft formation of dendritic cells. We used lipidomics combined with genetic and biochemical assays to analyze the role of SWAP-70 in lipid dynamics. TLR activation using LPS as a ligand represented a pathogenic immunogenic stimulus, physical disruption of cell-cell contacts a tolerogenic stimulus. Physical disruption, but not LPS, caused an increase of phosphatidylcholine ether and cholesteryl esters in CD11c(+) immune cells. An increase of ceramide (Cer) was a hallmark for LPS activation. SWAP-70 was required for regulating the increase and localization of Cers in the cell membrane. SWAP-70 controls Cer accumulation through the regulation of pH-dependent acid-sphingomyelinase activity and of RhoA-dependent transport of endosomal contents to the plasma membrane. Poor accumulation of Cers in Swap70(-/-) cells caused decreased apoptosis. This shows that two different pathways of activation, immunogenic and tolerogenic, induce different changes in the lipid composition of cultured CD11c(+) cells, and highlights the important role of SWAP-70 in Cer dynamics in dendritic cells.
@article{Ocaña-Morgner6845,
author={Carlos Ocaña-Morgner, Susanne Sales, Manuela Rothe, Andrej Shevchenko, Rolf Jessberger},
title={Tolerogenic versus Immunogenic Lipidomic Profiles of CD11c(+) Immune Cells and Control of Immunogenic Dendritic Cell Ceramide Dynamics.},
journal={Journal of immunology (Baltimore, Md. : 1950)},
volume={198},
issue ={11},
pages={4360--4372},
year=2017
}

Jeffrey Woodruff, Beatriz Ferreira Gomes, Per Widlund, J. Mahamid, Alf Honigmann, Anthony Hyman
The Centrosome Is a Selective Condensate that Nucleates Microtubules by Concentrating Tubulin.
Cell, 169(6) 1066-1077 (2017)
PubMed   

Centrosomes are non-membrane-bound compartments that nucleate microtubule arrays. They consist of nanometer-scale centrioles surrounded by a micron-scale, dynamic assembly of protein called the pericentriolar material (PCM). To study how PCM forms a spherical compartment that nucleates microtubules, we reconstituted PCM-dependent microtubule nucleation in vitro using recombinant C. elegans proteins. We found that macromolecular crowding drives assembly of the key PCM scaffold protein SPD-5 into spherical condensates that morphologically and dynamically resemble in vivo PCM. These SPD-5 condensates recruited the microtubule polymerase ZYG-9 (XMAP215 homolog) and the microtubule-stabilizing protein TPXL-1 (TPX2 homolog). Together, these three proteins concentrated tubulin ∼4-fold over background, which was sufficient to reconstitute nucleation of microtubule asters in vitro. Our results suggest that in vivo PCM is a selective phase that organizes microtubule arrays through localized concentration of tubulin by microtubule effector proteins.
@article{Woodruff6871,
author={Jeffrey Woodruff, Beatriz Ferreira Gomes, Per Widlund, J. Mahamid, Alf Honigmann, Anthony Hyman},
title={The Centrosome Is a Selective Condensate that Nucleates Microtubules by Concentrating Tubulin.},
journal={Cell},
volume={169},
issue ={6},
pages={1066--1077},
year=2017
}

Arturo Raya-Sandino, Alejandro Castillo-Kauil, Alaide Domínguez-Calderón, Lourdes Alarcón, David Flores-Benitez, Francisco Cuellar-Perez, Bruno López-Bayghen, Bibiana Chávez-Munguía, José Vázquez-Prado, Lorenza González-Mariscal
Zonula occludens-2 regulates Rho proteins activity and the development of epithelial cytoarchitecture and barrier function.
Biochim Biophys Acta, 1-1 (2017)
  PubMed   

Silencing Zonula occludens 2 (ZO-2), a tight junctions (TJ) scaffold protein, in epithelial cells (MDCK ZO-2 KD) triggers: 1) Decreased cell to substratum attachment, accompanied by reduced expression of claudin-7 and integrin β1, and increased vinculin recruitment to focal adhesions and stress fibers formation; 2) Lowered cell-cell aggregation and appearance of wider intercellular spaces; 3) Increased RhoA/ROCK activity, mediated by GEF-HI recruitment to cell borders by cingulin; 4) Increased Cdc42 activity, mitotic spindle disorientation and the appearance of cysts with multiple lumens; 5) Increased Rac and cofilin activity, multiple lamellipodia formation and random cell migration but increased wound closure; 6) Diminished cingulin phosphorylation and disappearance of planar network of microtubules at the TJ region; and 7) Increased transepithelial electrical resistance at steady state, coupled to an increased expression of ZO-1 and claudin-4 and a decreased expression of claudin-2 and paracingulin. Hence, ZO-2 is a crucial regulator of Rho proteins activity and the development of epithelial cytoarchitecture and barrier function.
@article{Raya-Sandino6863,
author={Arturo Raya-Sandino, Alejandro Castillo-Kauil, Alaide Domínguez-Calderón, Lourdes Alarcón, David Flores-Benitez, Francisco Cuellar-Perez, Bruno López-Bayghen, Bibiana Chávez-Munguía, José Vázquez-Prado, Lorenza González-Mariscal},
title={Zonula occludens-2 regulates Rho proteins activity and the development of epithelial cytoarchitecture and barrier function.},
journal={Biochimica et biophysica acta},
volume={},
pages={1--1},
year=2017
}

Peter Gross, K Vijay Kumar, Stephan W. Grill
How Active Mechanics and Regulatory Biochemistry Combine to Form Patterns in Development.
Ann Rev Biophys, 46 337-356 (2017)
PubMed   

The development of organisms starting from their zygotic state involves a tight integration of the myriad biochemical signaling interactions with the mechanical forces that eventually pattern and shape the resulting embryo. In the past decade, it has become increasingly evident that several important developmental processes involve mechanical forces in an essential manner. In this review, we highlight the multifaceted role of mechanics in pattern formation, from protein and cell sorting to the generation of tissue shape. We then review the ways in which the active cellular cytoskeleton self-organizes to form dynamic patterns. Finally, we focus on mechanochemical feedback, where signaling proteins can establish patterns via coupling to the activity of the cytoskeleton. Throughout the review, we focus on the generic physical principles of the establishment of active mechanochemical patterns and point toward future directions in studying how the principles of mechanics and chemistry combine to drive morphogenetic pattern formation.
@article{Gross6869,
author={Peter Gross, K Vijay Kumar, Stephan W. Grill},
title={How Active Mechanics and Regulatory Biochemistry Combine to Form Patterns in Development.},
journal={Annual review of biophysics},
volume={46},
pages={337--356},
year=2017
}