2016

Ayciriex S, Gerber H, Osuna GM, Chami M, Stahlberg H, Shevchenko A, Fraering PC. The lipidome associated with the γ-secretase complex is required for its integrity and activity. Biochem J. 2016 Feb 1;473(3):321-34.

Baranov MV, Revelo NH, Dingjan I, Maraspini R, Ter Beest M, Honigmann A, van den Bogaart G. SWAP70 Organizes the Actin Cytoskeleton and Is Essential for Phagocytosis. Cell Rep. 2016 Nov 1;17(6):1518-1531.

Ben Halima S, Mishra S, Raja KMP, Willem M, Baici A, Simons K, Brüstle O, Koch P, Haass C, Caflisch A, Rajendran L. Specific Inhibition of β-Secretase Processing of the Alzheimer Disease Amyloid Precursor Protein. Cell Rep. 2016 Mar 8;14(9):2127-2141.

Bilgin M, Born P, Fezza F, Heimes M, Mastrangelo N, Wagner N, Schultz C, Maccarrone M, Eaton S, Nadler A, Wilm M, Shevchenko A. Lipid Discovery by Combinatorial Screening and Untargeted LC-MS/MS. Sci Rep. 2016 Jun 17;6:27920.

Chaudhuri J, Bose N, Gong J, Hall D, Rifkind A, Bhaumik D, Peiris TH, Chamoli M, Le CH, Liu J, Lithgow GJ, Ramanathan A, Xu XZS, Kapahi P. A Caenorhabditis elegans Model Elucidates a Conserved Role for TRPA1-Nrf Signaling in Reactive α-Dicarbonyl Detoxification. Curr Biol. 2016 Nov 21;26(22):3014-3025.

Chiang YN, Tan KJ, Chung H, Lavrynenko O, Shevchenko A, Yew JY. Steroid Hormone Signaling Is Essential for Pheromone Production and Oenocyte Survival. PLoS Genet. 2016 Jun 22;12(6):e1006126.

Çiçek IÖ, Karaca S, Brankatschk M, Eaton S, Urlaub H, Shcherbata HR. Hedgehog Signaling Strength Is Orchestrated by the mir-310 Cluster of MicroRNAs in Response to Diet. Genetics. 2016 Mar;202(3):1167-83.

Cockcroft S and Raghu P. Topological organisation of the phosphatidylinositol 4,5-bisphosphate-phospholipase C resynthesis cycle: PITPs bridge the ER–PM gap. Biochem J. 2016 Dec 1;473(23):4289-4310.

Cockcroft S, Garner K, Yadav S, Gomez-Espinoza E, Raghu P. RdgBα reciprocally transfers PA and PI at ER-PM contact sites to maintain PI(4,5)P2 homoeostasis during phospholipase C signalling in Drosophila photoreceptors. Biochem Soc Trans. 2016 Feb;44(1):286-92.

Dey G, Thattai M, Baum B. On the Archaeal Origins of Eukaryotes and the Challenges of Inferring Phenotype from Genotype. Trends Cell Biol. 2016 Jul;26(7):476-485

Eggeling C, Honigmann A. Closing the gap: The approach of optical and computational microscopy to uncover biomembrane organization. Biochim Biophys Acta. 2016 Oct;1858(10):2558-2568.

Erkut C, Gade VR, Laxman S, Kurzchalia TV. The glyoxylate shunt is essential for desiccation tolerance in C. elegans and budding yeast. Elife. 2016 Apr 19;5. pii: e13614.

Honigmann A, Pralle A. Compartmentalization of the Cell Membrane. J Mol Biol. 2016 Dec 4;428(24 Pt A):4739-4748.

Hövelmann F, Kedziora KM, Nadler A, Müller R, Jalink K, Schultz C. Optotaxis: Caged Lysophosphatidic Acid Enables Optical Control of a Chemotactic Gradient. Cell Chem Biol. 2016 May 19;23(5):629-634.

Kalaidzidis I, Miaczynska M, Brewińska-Olchowik M, Hupalowska A, Ferguson C, Parton RG, Kalaidzidis Y, Zerial M. APPL endosomes are not obligatory endocytic intermediates but act as stable cargo-sorting compartments. J Cell Biol. 2015 Oct 12;211(1):123-44.

Katewa SD, Akagi K, Bose N, Rakshit K, Camarella T, Zheng X, Hall D, Davis S, Nelson CS, Brem RB, Ramanathan A, Sehgal A, Giebultowicz JM, Kapahi P. Peripheral Circadian Clocks Mediate Dietary Restriction-Dependent Changes in Lifespan and Fat Metabolism in Drosophila. Cell Metab. 2016 Jan 12;23(1):143-54.

Kjellqvist S, Klose C, Surma MA, Hindy G, Mollet IG, Johansson A, Chavaux P, Gottfries J, Simons K, Melander O, Fernandez C. Identification of Shared and Unique Serum Lipid Profiles in Diabetes Mellitus and Myocardial Infarction. J Am Heart Assoc. 2016 Nov 29;5(12).

Kolay, S., Basu, U and Raghu, P. Control of diverse sub-cellular processes by a single multi-functional lipid phosphatidylinositol 4,5 bisphosphate [PI(4,5)P2]. Biochemical Journal. (2016) Jun 15;473(12):1681-92.

Kopprasch S, Dheban S, Schuhmann K, Xu A, Schulte KM, Simeonovic CJ, Schwarz PE, Bornstein SR, Shevchenko A, Graessler J. Detection of Independent Associations of Plasma Lipidomic Parameters with Insulin Sensitivity Indices Using Data Mining Methodology. PLoS One. 2016 Oct 13;11(10):e0164173.

Mani S, Thattai M. Stacking the odds for Golgi cisternal maturation. Elife. 2016 Aug 19;5. pii: e16231

Mark KA, Dumas KJ, Bhaumik D, Schilling B, Davis S, Oron TR, Sorensen DJ, Lucanic M, Brem RB, Melov S, Ramanathan A, Gibson BW, Lithgow GJ. Vitamin D Promotes Protein Homeostasis and Longevity via the Stress Response Pathway Genes skn-1, ire-1, and xbp-1. Cell Rep. 2016 Oct 25;17(5):1227-1237.

Milovanovic D, Platen M, Junius M, Diederichsen U, Schaap IA, Honigmann A, Jahn R, van den Bogaart G. Calcium Promotes the Formation of Syntaxin 1 Mesoscale Domains through Phosphatidylinositol 4,5-Bisphosphate. J Biol Chem. 2016 Apr 8;291(15):7868-76.

Morales-Navarrete H, Segovia-Miranda F, Klukowski P, Meyer K, Nonaka H, Marsico G, Chernykh M, Kalaidzidis A, Zerial M, Kalaidzidis Y. A versatile pipeline for the multi-scale digital reconstruction and quantitative analysis of 3D tissue architecture. Elife. 2015 Dec 27;4.

Murray DH, Jahnel M, Lauer J, Avellaneda MJ, Brouilly N, Cezanne A, Morales-Navarrete H, Perini ED, Ferguson C, Lupas AN, Kalaidzidis Y, Parton RG, Grill SW, Zerial M. An endosomal tether undergoes an entropic collapse to bring vesicles together. Nature. 2016 Sep 1;537(7618):107-111.

Nemetschke L, Knust E. Drosophila Crumbs prevents ectopic Notch activation in developing wings by inhibiting ligand-independent endocytosis. Development. 2016 Dec 1;143(23):4543-4553.

S Sonnet D, N O’Leary M, A Gutierrez M, M Nguyen S, Mateen S, Hsu Y, P Mitchell K, J Lopez A, Vockley J, K Kennedy B, Ramanathan A. Metformin inhibits Branched Chain Amino Acid (BCAA) derived ketoacidosis and promotes metabolic homeostasis in MSUD. Sci Rep. 2016 Jul 4;6:28775.

Sales S, Graessler J, Ciucci S, Al-Atrib R, Vihervaara T, Schuhmann K, Kauhanen D, Sysi-Aho M, Bornstein SR, Bickle M, Cannistraci CV, Ekroos K, Shevchenko A. Gender, Contraceptives and Individual Metabolic Predisposition Shape a Healthy Plasma Lipidome. Sci Rep. 2016 Jun 14;6:27710.

Sezgin E, Can FB, Schneider F, Clausen MP, Galiani S, Stanly TA, Waithe D, Colaco A, Honigmann A, Wüstner D, Platt F, Eggeling C. A comparative study on fluorescent cholesterol analogs as versatile cellular reporters. J Lipid Res. 2016 Feb;57(2):299-309.

Simons K, Coskun Ü. Membrane Lipid Galore. J Mol Biol. 2016 Dec 4;428(24 PtA):4737-4738.

Simons K. Cell membranes: A subjective perspective. Biochim Biophys Acta. 2016 Oct;1858(10):2569-2572.

Simons K. My Early Days with Ari Helenius: Detergents and Viruses. Traffic. 2016 Apr;17(4):305-7.

Steshenko O, Andrade DM, Honigmann A, Mueller V, Schneider F, Sezgin E, Hell SW, Simons M, Eggeling C. Reorganization of Lipid Diffusion by Myelin Basic Protein as Revealed by STED Nanoscopy. Biophys J. 2016 Jun 7;110(11):2441-2450.

Thakur R, Panda A, Coessens E, Raj N, Yadav S, Balakrishnan S, Zhang Q, Georgiev P, Basak B, Pasricha R, Wakelam MJ, Ktistakis NT, Raghu P. Phospholipase D activity couples plasma membrane endocytosis with retromer dependent recycling. Elife. 2016 Nov 16;5. pii: e18515.

Villaseñor R, Kalaidzidis Y, Zerial M. Signal processing by the endosomal system. Curr Opin Cell Biol. 2016 Apr;39:53-60.

Wiley CD, Velarde MC, Lecot P, Liu S, Sarnoski EA, Freund A, Shirakawa K, Lim HW, Davis SS, Ramanathan A, Gerencser AA, Verdin E, Campisi J. Mitochondrial Dysfunction Induces Senescence with a Distinct Secretory Phenotype. Cell Metab. 2016 Feb 9;23(2):303-14.

Yadav S, Cockcroft S and Raghu P. The Drosophila photoreceptor as a model system for studying signalling at membrane contact sites. Biochem Soc Trans. (2016) Apr 15;44(2):447-51.

Yin H, Bogorad RL, Barnes C, Walsh S, Zhuang I, Nonaka H, Ruda V, Kuchimanchi S, Nechev L, Akinc A, Xue W, Zerial M, Langer R, Anderson DG, Koteliansky V. RNAi-nanoparticulate manipulation of gene expression as a new functional genomics tool in the liver. J Hepatol. 2016 Apr;64(4):899-907.

Yushchenko DA, Nadler A, Schultz C. Manipulating cell signaling with subcellular spatial resolution. Cell Cycle. 2016;15(8):1023-4.

Zurzolo C, Simons K. Glycosylphosphatidylinositol-anchored proteins: Membrane organization and transport. Biochim Biophys Acta. 2016 Apr;1858(4):632-9.

2015

Bilgin M, Bindila L, Graessler J, Shevchenko A. Quantitative profiling of endocannabinoids in lipoproteins by LC-MS/MS. Anal Bioanal Chem. 2015 Jul;407(17):5125-31.

Böttger J, Arnold K, Thiel C, Rennert C, Aleithe S, Hofmann U, Vlaic S, Sales S, Shevchenko A, Matz-Soja M. RNAi in murine hepatocytes: the agony of choice–a study of the influence of lipid-based transfection reagents on hepatocyte metabolism. Arch Toxicol. 2015 Sep;89(9):1579-88.

Chakrabarti P, Kolay S, Yadav S, Kumari K, Nair A, Trivedi D, Raghu P. A dPIP5K dependent pool of phosphatidylinositol 4,5 bisphosphate (PIP2) is required for G-protein coupled signal transduction in Drosophila photoreceptors. PLoS Genet. 2015 Jan 29;11(1):e1004948.

Chi T, Kim MS, Lang S, Bose N, Kahn A, Flechner L, Blaschko SD, Zee T, Muteliefu G, Bond N, Kolipinski M, Fakra SC, Mandel N, Miller J, Ramanathan A, Killilea DW, Brückner K, Kapahi P, Stoller ML. A Drosophila model identifies a critical role for zinc in mineralization for kidney stone disease. PLoS One. 2015 May 13;10(5):e0124150.

Gilleron J, Paramasivam P, Zeigerer A, Querbes W, Marsico G, Andree C, Seifert S, Amaya P, Stöter M, Koteliansky V, Waldmann H, Fitzgerald K, Kalaidzidis Y, Akinc A, Maier MA, Manoharan M, Bickle M, Zerial M. Identification of siRNA delivery enhancers by a chemical library screen. Nucleic Acids Res. 2015 Sep 18;43(16):7984-8001.

Habeck M, Haviv H, Katz A, Kapri-Pardes E, Ayciriex S, Shevchenko A, Ogawa H, Toyoshima C, Karlish SJ. Stimulation, inhibition, or stabilization of Na,K-ATPase caused by specific lipid interactions at distinct sites. J Biol Chem. 2015 Feb 20;290(8):4829-42.

Hebbar S, Sahoo I, Matysik A, Argudo Garcia I, Osborne KA, Papan C, Torta F, Narayanaswamy P, Fun XH, Wenk MR, Shevchenko A, Schwudke D, Kraut R. Ceramides And Stress Signalling Intersect With Autophagic Defects In Neurodegenerative Drosophila blue cheese (bchs) Mutants. Sci Rep. 2015 Dec 7;5:15926.

Hell SW, Sahl SJ, Bates M, Zhuang X, Heintzmann R, Booth MJ, Bewersdorf J, Shtengel G, Hess H, Tinnefeld P, Honigmann A, Jakobs S, Testa I, Cognet L, Lounis B, Ewers H, Davis SJ, Eggeling C, Klenerman D, Willig KI, Vicidomini G, Castello M, Diaspro A, Cordes T. The 2015 super-resolution microscopy roadmap. J Phys D: Appl Phys. 2015, 48(44) Art. No. 443001.

Kaszuba K, Grzybek M, Orłowski A, Danne R, Róg T, Simons K, Coskun Ü, Vattulainen I. N-Glycosylation as determinant of epidermal growth factor receptor conformation in membranes. Proc Natl Acad Sci U S A. 2015 Apr 7;112(14):4334-9.

Khaliullina H, Bilgin M, Sampaio JL, Shevchenko A, Eaton S. Endocannabinoids are conserved inhibitors of the Hedgehog pathway. Proc Natl Acad Sci U S A. 2015 Mar 17;112(11):3415-20.

Lavrynenko O, Rodenfels J, Carvalho M, Dye NA, Lafont R, Eaton S, Shevchenko A. The ecdysteroidome of Drosophila: influence of diet and development. Development. 2015 Nov 1;142(21):3758-68.

Nadler A, Yushchenko DA, Müller R, Stein F, Feng S, Mulle C, Carta M, Schultz C. Exclusive photorelease of signalling lipids at the plasma membrane. Nat Commun. 2015 Dec 21;6:10056.

Olmi S, Martens EA, Thutupalli S, Torcini A. Intermittent chaotic chimeras for coupled rotators. Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Sep;92(3):030901.

Purkanti R, Thattai M. Ancient dynamin segments capture early stages of host-mitochondrial integration. Proc Natl Acad Sci U S A. 2015 Mar 3;112(9):2800-5

Sáenz JP, Grosser D, Bradley AS, Lagny TJ, Lavrynenko O, Broda M, Simons K. Hopanoids as functional analogues of cholesterol in bacterial membranes. Proc Natl Acad Sci U S A. 2015 Sep 22;112(38):11971-6.

Sevcsik E, Brameshuber M, Fölser M, Weghuber J, Honigmann A, Schütz GJ. GPI-anchored proteins do not reside in ordered domains in the live cell plasma membrane. Nat Commun. 2015 Apr 21;6:6969.

Sezgin E, Gutmann T, Buhl T, Dirkx R, Grzybek M, Coskun Ü, Solimena M, Simons K, Levental I, Schwille P. Adaptive lipid packing and bioactivity in membrane domains. PLoS One. 2015 Apr 23;10(4):e0123930.

Surma MA, Herzog R, Vasilj A, Klose C, Christinat N, Morin-Rivron D, Simons K, Masoodi M, Sampaio JL. An automated shotgun lipidomics platform for high throughput, comprehensive, and quantitative analysis of blood plasma intact lipids. Eur J Lipid Sci Technol. 2015 Oct;117(10):1540-1549.

Thutupalli S, Sun M, Bunyak F, Palaniappan K, Shaevitz JW. Directional reversals enable Myxococcus xanthus cells to produce collective one-dimensional streams during fruiting-body formation. J R Soc Interface. 2015 Aug 6;12(109):20150049.

Vicidomini G, Ta H, Honigmann A, Mueller V, Clausen MP, Waithe D, Galiani S, Sezgin E, Diaspro A, Hell SW, Eggeling C. STED-FLCS: An Advanced Tool to Reveal Spatiotemporal Heterogeneity of Molecular Membrane Dynamics. Nano Lett. 2015 Sep 9;15(9):5912-8.

Villaseñor R, Nonaka H, Del Conte-Zerial P, Kalaidzidis Y, Zerial M. Regulation of EGFR signal transduction by analogue-to-digital conversion in endosomes. Elife. 2015 Feb 4;4.

Yadav S, Garner K, Georgiev P, Li M, Gomez-Espinosa E, Panda A, Mathre S, Okkenhaug H, Cockcroft S, Raghu P. RDGBα, a PtdIns-PtdOH transfer protein, regulates G-protein-coupled PtdIns(4,5)P2 signalling during Drosophila phototransduction. J Cell Sci. 2015 Sep 1;128(17):3330-44.

Zeigerer A, Bogorad RL, Sharma K, Gilleron J, Seifert S, Sales S, Berndt N, Bulik S, Marsico G, D’Souza RCJ, Lakshmanaperumal N, Meganathan K, Natarajan K, Sachinidis A, Dahl A, Holzhütter HG, Shevchenko A, Mann M, Koteliansky V, Zerial M. Regulation of liver metabolism by the endosomal GTPase Rab5. Cell Rep. 2015 May 12;11(6):884-892.

Zeigerer A, Bogorad RL, Sharma K, Gilleron J, Seifert S, Sales S, Berndt N, Bulik S, Marsico G, D’Souza RCJ, Lakshmanaperumal N, Meganathan K, Natarajan K, Sachinidis A, Dahl A, Holzhütter HG, Shevchenko A, Mann M, Koteliansky V, Zerial M. Regulation of liver metabolism by the endosomal GTPase Rab5. Cell Rep. 2015 May 12;11(6):884-892.