Genomes and Genes
Jeremy C Simpson
Affiliation: European Molecular Biology Laboratory
- Biogenesis of tubular ER-to-Golgi transport intermediatesJeremy C Simpson
Cell Biology and Biophysics Programme, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
Mol Biol Cell 17:723-37. 2006....
- The subcellular localization of the mammalian proteome comes a fraction closerJeremy C Simpson
Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Genome Biol 7:222. 2006..Here we discuss this new work in the context of other strategies for large-scale subcellular localization...
- A role for kinesin-2 in COPI-dependent recycling between the ER and the Golgi complexTobias Stauber
Cell Biology and Biophysics Programme, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Curr Biol 16:2245-51. 2006..Our data strongly support a role for kinesin-2 in the KDEL-R-/COPI-dependent retrograde transport pathway from the Golgi complex to the ER...
- Maturation of the mammalian secretomeJeremy C Simpson
Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
Genome Biol 8:211. 2007....
- An RNAi screening platform to identify secretion machinery in mammalian cellsJeremy C Simpson
Cell Biology and Biophysics Unit, European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
J Biotechnol 129:352-65. 2007..Correlating these findings with other screens and bioinformatic information makes these candidates highly likely to be novel membrane traffic machinery components...
- Imaging platforms for measurement of membrane traffickingRainer Pepperkok
Cell Biology and Cell Biophysics Program, European Molecular Biology Laboratory, Heidelberg, Germany
Methods Enzymol 404:8-18. 2005..We further describe the use of software macros and plugins in Image J that allow the quantification of the kinetics of membrane transport intermediates in fluorescence microscopy time-lapse sequences...
- High-content screening microscopy identifies novel proteins with a putative role in secretory membrane trafficVytaute Starkuviene
Cell Biology and Biophysics Programme, European Molecular Biology Laboratory EMBL, 69117 Heidelberg, Germany
Genome Res 14:1948-56. 2004..It will also serve as an example for similar microscope-based screens addressing different biological questions...
- Gamma-BAR, a novel AP-1-interacting protein involved in post-Golgi traffickingVeronika E Neubrand
Cell Biology and Cell Biophysics Programme, European Molecular Biology Laboratory EMBL, Heidelberg, Germany
EMBO J 24:1122-33. 2005..This suggests that the direct interaction of 2c18 and gamma1-adaptin is crucial for membrane association and thus the function of the AP-1 complex in living cells. We propose to name this protein gamma-BAR...
- High-content microscopy identifies new neurite outgrowth regulatorsVibor Laketa
Cell Biology and Biophysics Unit, European Molecular Biology Laboratory Heidelberg, 69117 Heidelberg, Germany
Mol Biol Cell 18:242-52. 2007..Altogether, we demonstrate the potential of the systematic microscope-based screening approaches described here to tackle the complex biological process of neurite outgrowth regulation...
- A microscope-based screening platform for large-scale functional protein analysis in intact cellsUrban Liebel
Cell Biology and Cell Biophysics Programme, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
FEBS Lett 554:394-8. 2003..Two automated functional assays addressing protein secretion and the integrity of the Golgi complex were developed and tested. This shows the potential of the system in large-scale, cell-based functional proteomic projects...
- siRNA cell arrays for high-content screening microscopyHolger Erfle
European Molecular Biology Laboratory, Heidelberg, Germany
Biotechniques 37:454-8, 460, 462. 2004..We demonstrate such an siRNA cell array in a microscope-based functional assay in living cells to determine the effect of various siRNA oligonucleotides against endogenous targets on cellular secretion...
- Spatiotemporal dynamics of the COPI vesicle machineryMarkus Elsner
Cell Biology and Cell Biophysics Programme, EMBL, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
EMBO Rep 4:1000-4. 2003..The addition of aluminium fluoride locks coatomer onto Golgi membranes and also decreases the binding kinetics of both ARF1 and ARFGAP1, suggesting that these proteins function in concert to mediate sorting and vesicle formation...
- A novel laser nanosurgery approach supports de novo Golgi biogenesis in mammalian cellsCarolina Tängemo
Cell Biology and Biophysics Unit, European Molecular Biology Laboratory EMBL, Meyerhofstr 1, 69117 Heidelberg, Germany
J Cell Sci 124:978-87. 2011..Altogether, our data provide evidence that de novo Golgi biogenesis can occur in mammalian cells...
- A role for the small GTPase Rab21 in the early endocytic pathwayJeremy C Simpson
Cell Biology and Biophysics Programme, European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
J Cell Sci 117:6297-311. 2004..Collectively, our data provide the first characterisation of Rab21 function in early endosome dynamics...
- Localizing the proteomeJeremy C Simpson
Cell Biology and Cell Biophysics Program, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Genome Biol 4:240. 2003..Comparison with less comprehensive studies of mammalian cells provides insights into the localization of the mammalian proteome...
- Malectin: a novel carbohydrate-binding protein of the endoplasmic reticulum and a candidate player in the early steps of protein N-glycosylationThomas Schallus
European Molecular Biology Laboratory, 69117 Heidelberg, Germany
Mol Biol Cell 19:3404-14. 2008..The localization, structure, and binding specificity of this protein, which we have named malectin, open the way to studies of its role in the genesis, processing and secretion of N-glycosylated proteins...
- Impact of live cell imaging on coated vesicle researchEls Wessels
Cell Biology and Biophysics Unit, European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Semin Cell Dev Biol 18:412-23. 2007..Here, we present an overview of live cell-imaging experiments that have been used in the study of coated-vesicle transport, and provide specific examples of their impact on our understanding of coat function...
- ojoplano-mediated basal constriction is essential for optic cup morphogenesisJuan Ramon Martinez-Morales
Developmental Unit, EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Development 136:2165-75. 2009..We propose a model of retinal morphogenesis whereby opo-mediated formation of focal contacts is required to transmit the mechanical tensions that drive the macroscopic folding of the vertebrate optic cup...
- Early endocytic Rabs: functional prediction to functional characterizationJeremy C Simpson
Cell Biology and Biophysics Programme, European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, D69117, Heidelberg, Germany
Biochem Soc Symp . 2005..In this review, we compare experiments that describe similarities and differences in endosome morphology and function that is mediated by their expression in cells...
- Functional profiling: from microarrays via cell-based assays to novel tumor relevant modulators of the cell cycleDorit Arlt
Division of Molecular Genome Analysis, German Cancer Research Center, Heidelberg, Germany
Cancer Res 65:7733-42. 2005..We have established a novel functional profiling strategy that links genomics to cell biology and showed its potential for discerning cancer relevant modulators of the cell cycle in the candidate lists from microarray studies...
- Navigating the secretory pathway: conference on exocytosis membrane structure and dynamicsEmmanuel G Reynaud
Cell Biology and Biophysics Programme, European Microbiology Laboratory, Heidelberg, Germany
EMBO Rep 3:828-33. 2002
- Interferon-induced, antiviral human MxA protein localizes to a distinct subcompartment of the smooth endoplasmic reticulumSilke Stertz
Abteilung Virologie, Institut fur Medizinische Mikrobiologie und Hygiene, Universitat Freiburg, D 79008 Freiburg, Germany
J Interferon Cytokine Res 26:650-60. 2006..The present results demonstrate that MxA is an IFN-induced antiviral effector protein that resembles the constitutively expressed large GTPase family members in its capacity to localize to and reorganize intracellular membranes...
- Rab18 and Rab43 have key roles in ER-Golgi traffickingSelma Y Dejgaard
Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada H3A2B2
J Cell Sci 121:2768-81. 2008..Rab18-S22N also potentiated brefeldin-A-induced ER-Golgi fusion. This study is the first comprehensive application of large-scale proteomics to the cell biology of small GTPases of the secretory pathway...
- Automated recognition system to classify subcellular protein localizations in images of different cell lines acquired by different imaging systemsYuh Show Tsai
Department of Biomedical Engineering, Chung Yuan Christian University, Jhongli, Taiwan, Republic of China
Microsc Res Tech 71:305-14. 2008..In summary, we have established a single system that can recognize subcellular protein localizations from two different sources for location-proteomic studies. studies...
- Cytoglobin is a respiratory protein in connective tissue and neurons, which is up-regulated by hypoxiaMarc Schmidt
Institute of Zoology, Johannes Gutenberg University, D 55099 Mainz, Germany
J Biol Chem 279:8063-9. 2004..Surprisingly, cytoglobin is localized in both the cytoplasm and nucleus of neurons, indicating a possible additional role of this protein in neuronal tissues...
- RNA bacteriophage capsid-mediated drug delivery and epitope presentationWilliam L Brown
Ashbury Centre for Structural Molecular Biology, University of Leeds, UK
Intervirology 45:371-80. 2002..To use our knowledge of the three-dimensional structure and self-assembly mechanism of RNA bacteriophage capsids to develop novel virus-like particles (VLPs) for drug delivery and epitope presentation...
- Intracellular traffic and fate of protein transduction domains HIV-1 TAT peptide and octaarginine. Implications for their utilization as drug delivery vectorsSaly Al-Taei
Welsh School of Pharmacy, Cardiff University, Cardiff, CF10 3XF, Wales, United Kingdom
Bioconjug Chem 17:90-100. 2006..Disruption of Golgi and endoplasmic reticulum dynamics was without effect on peptide localization, suggesting that endosomes and lysosomes rather than these organelles are the major acceptor compartments for these molecules...
- The systematic functional characterisation of Xq28 genes prioritises candidate disease genesAnja Kolb-Kokocinski
Division of Molecular Genome Analysis, German Cancer Research Centre DKFZ, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
BMC Genomics 7:29. 2006..To expedite disease gene identification, we have initiated the functional characterisation of all known Xq28 genes...
- Confocal microscopy analysis of native, full length and B-domain deleted coagulation factor VIII trafficking in mammalian cellsSven Becker
Institute for Transfusion Medicine and Immunohematology, Red Cross Blood Donor Service Baden Wuerttemberg Hesse, Sandhofstr 1, D 60528 Frankfurt, Germany
Thromb Haemost 92:23-35. 2004..Our data provide new details about the secretory route of FVIII, which may ultimately help to identify factors currently limiting the efficient and physiological expression of FVIII in gene therapy and manufacture...
- Cellular uptake of arginine-rich peptides: roles for macropinocytosis and actin rearrangementIkuhiko Nakase
Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Mol Ther 10:1011-22. 2004..The above observations suggest that penetratin and R8 peptides have distinct internalization mechanisms...
- LETM1, a gene deleted in Wolf-Hirschhorn syndrome, encodes an evolutionarily conserved mitochondrial proteinStephanie Schlickum
Institute of Human Genetics, Friedrich Alexander University Erlangen Nuremberg, Schwabachanlage 10, D 91054 Erlangen, Germany
Genomics 83:254-61. 2004..The present study presents information about a possible function for LETM1 and suggests that at least some (neuromuscular) features of WHS may be caused by mitochondrial dysfunction...
- Association of CD2AP with dynamic actin on vesicles in podocytesThilo Welsch
Department of Anatomy and Cell Biology, University of Heidelberg, D 69120 Heidelberg, Germany
Am J Physiol Renal Physiol 289:F1134-43. 2005....
- Boosting multiclass learning with repeating codes and weak detectors for protein subcellular localizationChung Chih Lin
Faculty of Life Sciences and Institute of Genomes, National Yang Ming University, Taipei, Taiwan
Bioinformatics 23:3374-81. 2007..One trend is the advances in multiclass learning with error-correcting output codes (ECOC). Another trend is the use of a large number of weak detectors with boosting for detecting objects in images of real-world scenes...