This week's new publications of the IMPRS faculty

Siveke, I., Leibold, C., Kaiser, K., Grothe, B., and Wiegrebe, L. (2010).
Level dependent latency shifts quantified through binaural processing.
J. Neurophysiol., [Epub ahead of print].

Cuntz, H., Forstner, F., Borst, A., and Hausser, M. (2010).
One rule to grow them all: a general theory of neuronal branching and its practical application.
PLoS Comput Biol 6, pii: e1000877.

Bennecke, M., Kriegl, L., Bajbouj, M., Retzlaff, K., Robine, S., Jung, A., Arkan, M.C., Kirchner, T., and Greten, F.R. (2010).
Ink4a/Arf and Oncogene-Induced Senescence Prevent Tumor Progression during Alternative Colorectal Tumorigenesis.
Cancer Cell 18, 135-146.

This week's new publications of the IMPRS faculty

Patla, I., Volberg, T., Elad, N., Hiershfeld-Warneken, V., Grashoff, C., Fassler, R., Spatz, J.P., Geiger, B., and Medalia, O. (2010).
Dissecting the molecular architecture of integrin adhesion sites by cryo-electron tomography.
Nat. Cell Biol., [Epub ahead of print].

Haass, C., and Mandelkow, E. (2010).
Fyn-Tau-Amyloid: A Toxic Triad.
Cell 142, 356-358.

Fett, M.E., Pilsl, A., Paquet, D., van Bebber, F., Haass, C., Tatzelt, J., Schmid, B., and Winklhofer, K.F. (2010).
Parkin Is Protective against Proteotoxic Stress in a Transgenic Zebrafish Model.
PLoS One 5, e11783.

Gnad, F., Forner, F., Zielinska, D.F., Birney, E., Gunawardena, J., and Mann, M. (2010).
Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes and mitochondria.
Mol. Cell Proteomics., [Epub ahead of print].

Hubener, M., and Bonhoeffer, T. (2010).
Searching for Engrams.
Neuron 67, 363-371.

Szwagierczak, A., Bultmann, S., Schmidt, C.S., Spada, F., and Leonhardt, H. (2010).
Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA.
Nucleic Acids Res., [Epub ahead of print].

Schwenkert, S., Soll, J., and Bolter, B. (2010).
Protein import into chloroplasts - how chaperones feature into the game.
Biochim. Biophys. Acta., [Epub ahead of print].

Balsera, M., Soll, J., and Buchanan, B.B. (2010).
Redox extends its regulatory reach to chloroplast protein import.
Trends Plant Sci., [Epub ahead of print].

Weber, A., Kehl, V., Mittermeyer, T., Herberich, E., Rothling, N., Schmid, R.M., and Prinz, C. (2010).
Prognostic Factors for Survival in Patients With Unresectable Pancreatic Cancer.
Pancreas., [Epub ahead of print].Saugel, B., Gaa, J., Phillip, V., Schmid, R.M., and Huber, W. (2010).
Splenic artery embolization in a woman with bleeding gastric varices and splenic vein thrombosis: a case report.
J. Med. Case Reports 4, 247.

August 6th, 2010

This week's new publications of the IMPRS faculty

Kuhn, P.H., Wang, H., Dislich, B., Colombo, A., Zeitschel, U., Ellwart, J.W., Kremmer, E., Rossner, S., and Lichtenthaler, S.F. (2010).
ADAM10 is the physiologically relevant, constitutive alpha-secretase of the amyloid precursor protein in primary neurons.
EMBO J., Jul 30. [Epub ahead of print].

Grothe, B., Pecka, M., and McAlpine, D. (2010).
Mechanisms of sound localization in mammals.
Physiol Rev 90, 983-1012.

Chuang, C.K., Rockel, B., Seyit, G., Walian, P.J., Schonegge, A.M., Peters, J., Zwart, P.H., Baumeister, W., and Jap, B.K. (2010).
Hybrid molecular structure of the giant protease tripeptidyl peptidase II.
Nat. Struct. Mol. Biol. 17, 990-996.

Sun, N., Pan, C., Mann, M., Nickell, S., Baumeister, W., and Nagy, I. (2010).
Quantitative proteome and transcriptome analysis of the archaeon Thermoplasma acidophilum cultured under aerobic and anaerobic conditions.
J. Proteome Res., Jul 29. [Epub ahead of print].

July 30th, 2010

Publication of IMPRS student Rashmi Gupta

Gupta, R., Lakshmipathy, S.K., Chang, H.C., Etchells, S.A., and Hartl, F.U.

Trigger factor lacking the PPIase domain can enhance the folding of eukaryotic multi-domain proteins in E. coli.
Recombinant expression of eukaryotic proteins in bacteria often results in misfolding and aggregation. The ribosome-binding Trigger factor (TF) is the first molecular chaperone that interacts with nascent polypeptide chains in bacteria. Here we show that mutant TF lacking the PPIase domain (TFNC) is more efficient than wild-type TF in enhancing the folding yield of multi-domain proteins such as firefly luciferase. We find that TFNC has a shorter residence time on nascent chains, thus facilitating co-translational folding. By delaying folding relative to translation, the PPIase domain may increase the propensity of misfolding for certain eukaryotic proteins that rely on a mechanism of co-translational, domain-wise folding.

FEBS Lett., (2010) Jul 23. [Epub ahead of print].
Pubmed

July 30th, 2010

This week's new publications of the IMPRS faculty

Hassfurth, B., Grothe, B., and Koch, U. (2010).
The Mammalian Interaural Time Difference Detection Circuit Is Differentially Controlled by GABAB Receptors during Development.
J. Neurosci. 30, 9715-9727.

Grimaud, C., and Becker, P.B. (2010).
Form and function of dosage-compensated chromosomes - a chicken-and-egg relationship.
Bioessays 32, 709-717.

Spavieri, D.L., Eichner, H., and Borst, A. (2010).
Coding efficiency of fly motion processing is set by firing rate, not firing precision.
PLoS Comput Biol 6, e1000860.

Gupta, R., Lakshmipathy, S.K., Chang, H.C., Etchells, S.A., and Hartl, F.U. (2010).
Trigger factor lacking the PPIase domain can enhance the folding of eukaryotic multi-domain proteins in E. coli.
FEBS Lett., Jul 23. [Epub ahead of print].

This week's new publications of the IMPRS faculty

Pasini, E.M., Kirkegaard, M., Mortensen, P., Mann, M., and Thomas, A.W. (2010).
Deep-coverage rhesus red blood cell proteome: a first comparison with the human and mouse red blood cell.
Blood Transfus. 8, s126-s139.

Geiger, T., Cox, J., and Mann, M. (2010).
Proteomics on an Orbitrap benchtop mass spectrometer using all ion fragmentation.
Mol. Cell Proteomics, Jul 7. [Epub ahead of print].

Meyer, N.H., Tripsianes, K., Vincendeau, M., Madl, T., Kateb, F., Brack-Werner, R., and Sattler, M. (2010).
Structural basis for homodimerization of the Src-associated during mitosis, 68 kDa protein (Sam68) Qua1 domain.
J. Biol. Chem., Jul 6. [Epub ahead of print].

Schermelleh, L., Heintzmann, R., and Leonhardt, H. (2010).
A guide to super-resolution fluorescence microscopy.
J. Cell Biol., Jul 19. [Epub ahead of print].

Michalakis, S., Muhlfriedel, R., Tanimoto, N., Krishnamoorthy, V., Koch, S., Fischer, M.D., Becirovic, E., Bai, L., Huber, G., Beck, S.C., Fahl, E., Buning, H., Paquet-Durand, F., Zong, X., Gollisch, T., Biel, M., and Seeliger, M.W. (2010).
Restoration of Cone Vision in the CNGA3(-/-) Mouse Model of Congenital Complete Lack of Cone Photoreceptor Function.
Mol. Ther., Jul 13. [Epub ahead of print].

Nagerl, U.V., and Bonhoeffer, T. (2010).
Imaging living synapses at the nanoscale by STED microscopy.
J. Neurosci. 30, 9341-9346.

Hoesl, M.G., Larregola, M., Cui, H., and Budisa, N. (2010).
Azatryptophans as tools to study polarity requirements for folding of green fluorescent protein.
J. Pept. Sci., Jul 13. [Epub ahead of print].

Aso, Y., Siwanowicz, I., Bracker, L., Ito, K., Kitamoto, T., and Tanimoto, H. (2010).
Specific Dopaminergic Neurons for the Formation of Labile Aversive Memory.
Curr. Biol., Jul 14. [Epub ahead of print].

Weir, J.R., Bonneau, F., Hentschel, J., and Conti, E. (2010).
Structural analysis reveals the characteristic features of Mtr4, a DExH helicase involved in nuclear RNA processing and surveillance.
Proc. Natl. Acad. Sci. U S A 107, 12139-12144.

Schneider, G., Kramer, O.H., Fritsche, P., Schuler, S., Schmid, R.M., and Saur, D. (2010).
Targeting histone deacetylases in pancreatic ductal adenocarcinoma.
Journal of Cellular and Molecular Medicine 14, 1255-1263.

July 16th, 2010

Publication of IMPRS student Pawel Mazur

Mazur, P.K., Einwachter, H., Lee, M., Sipos, B., Nakhai, H., Rad, R., Zimber-Strobl, U., Strobl, L.J., Radtke, F., Kloppel, G., Schmid, R.M., and Siveke, J.T.

Notch2 is required for progression of pancreatic intraepithelial neoplasia and development of pancreatic ductal adenocarcinoma.
Pancreatic cancer is one of the most fatal malignancies lacking effective therapies. Notch signaling is a key regulator of cell fate specification and pancreatic cancer development; however, the role of individual Notch receptors and downstream signaling is largely unknown. Here, we show that Notch2 is predominantly expressed in ductal cells and pancreatic intraepithelial neoplasia (PanIN) lesions. Using genetically engineered mice, we demonstrate the effect of conditional Notch receptor ablation in Kras(G12D) -driven pancreatic carcinogenesis. Deficiency of Notch2 but not Notch1 stops PanIN progression, prolongs survival, and leads to a phenotypical switch toward anaplastic pancreatic cancer with epithelial-mesenchymal transition. By expression profiling, we identified increased Myc signaling regulated by Notch2 during tumor development, placing Notch2 as a central regulator of PanIN progression and malignant transformation. Our study supports the concept of distinctive roles of individual Notch receptors in cancer development.

Proc. Natl. Acad. Sci. U S A, (2010) Jul 12. [Epub ahead of print].
Pubmed

This week's new publications of the IMPRS faculty

Kieseier, B.C., and Hohlfeld, R. (2010).
Regulatory T cells in myositis - Good Samaritans at the site of inflammation?
J. Neuroimmunol., Jul 8. [Epub ahead of print].

Mira, H., Andreu, Z., Suh, H., Lie, D.C., Jessberger, S., Consiglio, A., San Emeterio, J., Hortiguela, R., Marques-Torrejon, M.A., Nakashima, K., Colak, D., Gotz, M., Farinas, I., and Gage, F.H. (2010).
Signaling through BMPR-IA Regulates Quiescence and Long-Term Activity of Neural Stem Cells in the Adult Hippocampus.
Cell Stem Cell 7, 78-89.

Reiff, D.F., Plett, J., Mank, M., Griesbeck, O., and Borst, A. (2010).
Visualizing retinotopic half-wave rectified input to the motion detection circuitry of Drosophila.
Nat. Neurosci., Jul 11. [Epub ahead of print].

Mazur, P.K., Einwachter, H., Lee, M., Sipos, B., Nakhai, H., Rad, R., Zimber-Strobl, U., Strobl, L.J., Radtke, F., Kloppel, G., Schmid, R.M., and Siveke, J.T. (2010).
Notch2 is required for progression of pancreatic intraepithelial neoplasia and development of pancreatic ductal adenocarcinoma.
Proc. Natl. Acad. Sci. U S A, Jul 12. [Epub ahead of print].

Dormann, D., Rodde, R., Edbauer, D., Bentmann, E., Fischer, I., Hruscha, A., Than, M.E., Mackenzie, I.R., Capell, A., Schmid, B., Neumann, M., and Haass, C. (2010).
ALS-associated fused in sarcoma (FUS) mutations disrupt Transportin-mediated nuclear import.
EMBO J., Jul 6. [Epub ahead of print].

Blanchard, S.C., Cooperman, B.S., and Wilson, D.N. (2010).
Probing translation with small-molecule inhibitors.
Chem Biol 17, 633-645.

Polier, S., Hartl, F.U., and Bracher, A. (2010).
Interaction of the Hsp110 Molecular Chaperones from S. Cerevisiae with Substrate Protein.
J. Mol. Biol., Jul 9. [Epub ahead of print].

Prestel, M., Feller, C., Straub, T., Mitlohner, H., and Becker, P.B. (2010).
The Activation Potential of MOF Is Constrained for Dosage Compensation.
Mol. Cell 38, 815-826.

July 9th, 2010

Publication of IMPRS students Manal Chatila and Jyoti Sinha

Chakraborty, K., Chatila, M., Sinha, J., Shi, Q., Poschner, B.C., Sikor, M., Jiang, G., Lamb, D.C., Hartl, F.U., and Hayer-Hartl, M. (2010).

Chaperonin-Catalyzed Rescue of Kinetically Trapped States in Protein Folding.
GroEL and GroES form a chaperonin nano-cage for single protein molecules to fold in isolation. The folding properties that render a protein chaperonin dependent are not yet understood. Here, we address this question using a double mutant of the maltose-binding protein DM-MBP as a substrate. Upon spontaneous refolding, DM-MBP populates a kinetically trapped intermediate that is collapsed but structurally disordered. Introducing two long-range disulfide bonds into DM-MBP reduces the entropic folding barrier of this intermediate and strongly accelerates native state formation. Strikingly, steric confinement of the protein in the chaperonin cage mimics the kinetic effect of constraining disulfides on folding, in a manner mediated by negative charge clusters in the cage wall. These findings suggest that chaperonin dependence correlates with the tendency of proteins to populate entropically stabilized folding intermediates. The capacity to rescue proteins from such folding traps may explain the uniquely essential role of chaperonin cages within the cellular chaperone network.

Cell 142, 112-122.
Pubmed

This week's new publications of the IMPRS faculty

Chakraborty, K., Chatila, M., Sinha, J., Shi, Q., Poschner, B.C., Sikor, M., Jiang, G., Lamb, D.C., Hartl, F.U., and Hayer-Hartl, M. (2010).
Chaperonin-Catalyzed Rescue of Kinetically Trapped States in Protein Folding.
Cell 142, 112-122.

Lakshmipathy, S.K., Gupta, R., Pinkert, S., Etchells, S.A., and Hartl, F.U. (2010).
Versatility of trigger factor interactions with ribosome-nascent chain complexes.
J. Biol. Chem., Jul 1. [Epub ahead of print].

Saugel, B., Umgelter, A., Martin, F., Phillip, V., Schmid, R.M., and Huber, W. (2010).
Systemic Capillary Leak Syndrome associated with hypovolemic shock and compartment syndrome. Use of transpulmonary thermodilution technique for volume management.
Scand J Trauma Resusc Emerg Med 18, 38.

Bertz, M., Chen, J., Feige, M.J., Franzmann, T.M., Buchner, J., and Rief, M. (2010).
Structural and Mechanical Hierarchies in the alpha-Crystallin Domain Dimer of the Hyperthermophilic Small Heat Shock Protein Hsp16.5.
J. Mol. Biol., Jun 2. [Epub ahead of print].

Lammens, A., and Hopfner, K.P. (2010).
Structural Basis for Adenylate Kinase Activity in ABC ATPases.
J. Mol. Biol., Jun 19. [Epub ahead of print].

Mitterreiter, S., Page, R.M., Kamp, F., Hopson, J., Winkler, E., Ha, H.R., Hamid, R., Herms, J., Mayer, T.U., Nelson, D.J., Steiner, H., Stahl, T., Zeitschel, U., Rossner, S., Haass, C., and Lichtenthaler, S.F. (2010).
Bepridil and amiodarone simultaneously target the Alzheimer's disease beta- and gamma-secretase via distinct mechanisms.
J. Neurosci. 30, 8974-8983.

Karakose, E., Schiller, H.B., and Fassler, R. (2010).
The kindlins at a glance.
J. Cell Sci. 123, 2353-2356.

Chioda, M., and Becker, P.B. (2010).
Soft skills turned into hard facts: nucleosome remodelling at developmental switches.
Heredity 105, 71-79.

Ditzen, C., Varadarajulu, J., Czibere, L., Gonik, M., Targosz, B.S., Hambsch, B., Bettecken, T., Kessler, M.S., Frank, E., Bunck, M., Teplytska, L., Erhardt, A., Holsboer, F., Muller-Myhsok, B., Landgraf, R., and Turck, C.W. (2010).
Proteomic-based genotyping in a mouse model of trait anxiety exposes disease-relevant pathways.
Mol. Psychiatry 15, 702-711.

July 2nd, 2010

This week's new publications of the IMPRS faculty

Fukumori, A., Fluhrer, R., Steiner, H., and Haass, C. (2010).
Three-amino acid spacing of presenilin endoproteolysis suggests a general stepwise cleavage of gamma-secretase-mediated intramembrane proteolysis.
J. Neurosci 30, 7853-7862.

Enes, J., Langwieser, N., Ruschel, J., Carballosa-Gonzalez, M.M., Klug, A., Traut, M.H., Ylera, B., Tahirovic, S., Hofmann, F., Stein, V., Moosmang, S., Hentall, I.D., and Bradke, F. (2010).
Electrical Activity Suppresses Axon Growth through Ca(v)1.2 Channels in Adult Primary Sensory Neurons.
Curr Biol., Jun 23. [Epub ahead of print].

Lepthien, S., Merkel, L., and Budisa, N. (2010).
In Vivo Double and Triple Labeling of Proteins Using Synthetic Amino Acids.
Angew Chem Int Ed Engl., Jun 23. [Epub ahead of print].

Merkel, L., Schauer, M., Antranikian, G., and Budisa, N. (2010).
Parallel Incorporation of Different Fluorinated Amino Acids: On the Way to "Teflon" Proteins.
Chembiochem., Jun 22. [Epub ahead of print].

Parnas, O., Zipin-Roitman, A., Pfander, B., Liefshitz, B., Mazor, Y., Ben-Aroya, S., Jentsch, S., and Kupiec, M. (2010).
Elg1, an alternative subunit of the RFC clamp loader, preferentially interacts with SUMOylated PCNA.
EMBO J., Jun 22. [Epub ahead of print].

June 25th, 2010

This week's new publications of the IMPRS faculty

Schafer, A., Zick, M., Kief, J., Steger, M., Heide, H., Duvezin-Caubet, S., Neupert, W., and Reichert, A.S. (2010).
Intramembrane proteolysis of Mgm1 by the mitochondrial rhomboid protease is highly promiscuous regarding the sequence of the cleaved hydrophobic segment.
J. Mol. Biol., Jun 14. [Epub ahead of print].

Blum, R., Heinrich, C., Sanchez, R., Lepier, A., Gundelfinger, E.D., Berninger, B., and Gotz, M. (2010).
Neuronal Network Formation from Reprogrammed Early Postnatal Rat Cortical Glial Cells.
Cereb. Cortex., Jun 18. [Epub ahead of print].

Singhal, N., Graumann, J., Wu, G., Arauzo-Bravo, M.J., Han, D.W., Greber, B., Gentile, L., Mann, M., and Scholer, H.R. (2010).
Chromatin-Remodeling Components of the BAF Complex Facilitate Reprogramming.
Cell 141, 943-955.

Chen, X., Kovalchuk, Y., Adelsberger, H., Henning, H.A., Sausbier, M., Wietzorrek, G., Ruth, P., Yarom, Y., and Konnerth, A. (2010).
Disruption of the olivo-cerebellar circuit by Purkinje neuron-specific ablation of BK channels.
Proc. Natl. Acad. Sci. U S A, Jun 21. [Epub ahead of print].

Weir, J.R., Bonneau, F., Hentschel, J., and Conti, E. (2010).
Structural analysis reveals the characteristic features of Mtr4, a DExH helicase involved in nuclear RNA processing and surveillance.
Proc. Natl. Acad. Sci. U S A, Jun 21. [Epub ahead of print].

Joffe, B., Leonhardt, H., and Solovei, I. (2010).
Differentiation and large scale spatial organization of the genome.
Curr. Opin. Genet. Dev., Jun 17. [Epub ahead of print].

Baumgart, A., Seidl, S., Vlachou, P., Michel, L., Mitova, N., Schatz, N., Specht, K., Koch, I., Schuster, T., Grundler, R., Kremer, M., Fend, F., Siveke, J.T., Peschel, C., Duyster, J., and Dechow, T. (2010).
ADAM17 Regulates Epidermal Growth Factor Receptor Expression through the Activation of Notch1 in Non-Small Cell Lung Cancer.
Cancer Res., Jun 15. [Epub ahead of print].

June 18th, 2010

This week's new publications of the IMPRS faculty

Dettmer, U., Kuhn, P.H., Abou-Ajram, C., Lichtenthaler, S.F., Krueger, M., Kremmer, E., Haass, C., and Haffner, C. (2010).
The transmembrane protein 147 (TMEM147) is a novel component of the nicalin-nomo protein complex.
J. Biol. Chem., Jun 10. [Epub ahead of print].

Starosta, A.L., Karpenko, V.V., Shishkina, A.V., Mikolajka, A., Sumbatyan, N.V., Schluenzen, F., Korshunova, G.A., Bogdanov, A.A., and Wilson, D.N. (2010).
Interplay between the ribosomal tunnel, nascent chain, and macrolides influences drug inhibition.
Chem. Biol. 17, 504-514.

Meggendorfer, M., Weierich, C., Wolff, H., Brack-Werner, R., and Cremer, T. (2010).
Functional nuclear topography of transcriptionally inducible extra-chromosomal transgene clusters.
Chromosome Res., Jun 8. [Epub ahead of print].

Eke, I., Koch, U., Hehlgans, S., Sandfort, V., Stanchi, F., Zips, D., Baumann, M., Shevchenko, A., Pilarsky, C., Haase, M., Baretton, G.B., Calleja, V., Larijani, B., Fassler, R., and Cordes, N. (2010).
PINCH1 regulates Akt1 activation and enhances radioresistance by inhibiting PP1alpha.
J. Clin. Invest., Jun 7. [Epub ahead of print].

Marozin, S., De Toni, E.N., Rizzani, A., Altomonte, J., Junger, A., Schneider, G., Thasler, W.E., Kato, N., Schmid, R.M., and Ebert, O. (2010).
Cell cycle progression or translation control is not essential for vesicular stomatitis virus oncolysis of hepatocellular carcinoma.
PLoS One 5, e10988.

Becker, V., van den Broek, F.J., Buchner, A.M., Dekker, E., Wallace, M.B., von Delius, S., Schneider, A., Schmid, R.M., and Meining, A. (2010).
Optimal fluorescein dose for intravenous application in miniprobe-based confocal laser scanning microscopy in pigs.
J. Biophotonics, Jun 8. [Epub ahead of print].

Vereecke, L., Sze, M., Guire, C.M., Rogiers, B., Chu, Y., Schmidt-Supprian, M., Pasparakis, M., Beyaert, R., and van Loo, G. (2010).
Enterocyte-specific A20 deficiency sensitizes to tumor necrosis factor-induced toxicity and experimental colitis.
J. Exp. Med., Jun 7. [Epub ahead of print].

Weintz, G., Olsen, J.V., Fruhauf, K., Niedzielska, M., Amit, I., Jantsch, J., Mages, J., Frech, C., Dolken, L., Mann, M., and Lang, R. (2010).
The phosphoproteome of toll-like receptor-activated macrophages.
Mol. Syst. Biol. 6, 371.

Eichinger, C.S., and Jentsch, S. (2010).
Synaptonemal complex formation and meiotic checkpoint signaling are linked to the lateral element protein Red1.
Proc. Natl. Acad. Sci. U S A, Jun 3. [Epub ahead of print].

Aron, L., Klein, P., Pham, T.T., Kramer, E.R., Wurst, W., and Klein, R. (2010).
Pro-survival role for Parkinson's associated gene DJ-1 revealed in trophically impaired dopaminergic neurons.
PLoS Biol 8, e1000349.

June 4th, 2010

This week's new publications of the IMPRS faculty

Zielinska, D.F., Gnad, F., Wisniewski, J.R., and Mann, M. (2010).
Precision mapping of an in vivo N-glycoproteome reveals rigid topological and sequence constraints.
Cell 141, 897-907.

Soufi, B., Kumar, C., Gnad, F., Mann, M., Mijakovic, I., and Macek, B. (2010).
Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) applied to quantitative proteomics of Bacillus subtilis.
J. Proteome Res., May 28. [Epub ahead of print].

Heinrich, C., Blum, R., Gascon, S., Masserdotti, G., Tripathi, P., Sanchez, R., Tiedt, S., Schroeder, T., Gotz, M., and Berninger, B. (2010).
Directing astroglia from the cerebral cortex into subtype specific functional neurons.
PLoS Biol 8, e1000373.

Beck, K., Vannini, A., Cramer, P., and Lipps, G. (2010).
The archaeo-eukaryotic primase of plasmid pRN1 requires a helix bundle domain for faithful primer synthesis.
Nucleic Acids Res., May 28. [Epub ahead of print].

Saugel, B., Umgelter, A., Schuster, T., Phillip, V., Schmid, R.M., and Huber, W. (2010).
Transpulmonary thermodilution using femoral indicator injection: a prospective trial in patients with a femoral and a jugular central venous catheter.
Crit. Care 14, R95.

Kriehuber, T., Rattei, T., Weinmaier, T., Bepperling, A., Haslbeck, M., and Buchner, J. (2010).
Independent evolution of the core domain and its flanking sequences in small heat shock proteins.
FASEB J., May 25. [Epub ahead of print].

May 28th, 2010

This week's new publications of the IMPRS faculty

Tahirovic, S., Hellal, F., Neukirchen, D., Hindges, R., Garvalov, B.K., Flynn, K.C., Stradal, T.E., Chrostek-Grashoff, A., Brakebusch, C., and Bradke, F. (2010).
Rac1 regulates neuronal polarization through the WAVE complex.
J. Neurosci. 30, 6930-6943.

Friedrich, M.W., Aramuni, G., Mank, M., Mackinnon, J.A., and Griesbeck, O. (2010).
Imaging CREB activation in living cells.
J. Biol. Chem., May 18. [Epub ahead of print].

Saugel, B., Phillip, V., Moessmer, G., Schmid, R.M., and Huber, W. (2010).
Argatroban therapy for heparin-induced thrombocytopenia in ICU patients with multiple organ dysfunction syndrome: a retrospective study.
Crit. Care 14, R90.

Gaul, U. (2010).
Decoding transcription and microRNA-mediated translation control in Drosophila development.
Biol. Chem., May 19. [Epub ahead of print].

Rother, S., Burkert, C., Brunger, K.M., Mayer, A., Kieser, A., and Strasser, K. (2010).
Nucleocytoplasmic shuttling of the La motif-containing protein Sro9 might link its nuclear and cytoplasmic functions.
RNA., May 21. [Epub ahead of print].

Hofer, S.B., Mrsic-Flogel, T.D., Horvath, D., Grothe, B., and Lesica, N.A. (2010).
Optimization of population decoding with distance metrics.
Neural Netw., May 5. [Epub ahead of print].

Cramer, P. (2010).
Towards molecular systems biology of gene transcription and regulation.
Biol. Chem., May 19. [Epub ahead of print].

Malnar, M., Kosicek, M., Mitterreiter, S., Omerbasic, D., Lichtenthaler, S.F., Goate, A., and Hecimovic, S. (2010).
Niemann Pick type C cells show cholesterol dependent decrease of APP expression at the cell surface its increased processing through the beta-secretase pathway.
Biochim. Biophys. Acta, May 18. [Epub ahead of print].

May 21st, 2010

Publications of IMPRS student Nina Hubner

Hubner, N.C., Bird, A.W., Cox, J., Splettstoesser, B., Bandilla, P., Poser, I., Hyman, A., and Mann, M.

Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions.
Protein interactions are involved in all cellular processes. Their efficient and reliable characterization is therefore essential for understanding biological mechanisms. In this study, we show that combining bacterial artificial chromosome (BAC) TransgeneOmics with quantitative interaction proteomics, which we call quantitative BAC-green fluorescent protein interactomics (QUBIC), allows specific and highly sensitive detection of interactions using rapid, generic, and quantitative procedures with minimal material. We applied this approach to identify known and novel components of well-studied complexes such as the anaphase-promoting complex. Furthermore, we demonstrate second generation interaction proteomics by incorporating directed mutational transgene modification and drug perturbation into QUBIC. These methods identified domain/isoform-specific interactors of pericentrin- and phosphorylation-specific interactors of TACC3, which are necessary for its recruitment to mitotic spindles. The scalability, simplicity, cost effectiveness, and sensitivity of this method provide a basis for its general use in small-scale experiments and in mapping the human protein interactome.

J. Cell. Biol. (2010) 189, 739-754.
Pubmed

May 21st, 2010

This week's new publications of the IMPRS faculty

Forster, F., Lasker, K., Nickell, S., Sali, A., and Baumeister, W. (2010).
Towards an integrated structural model of the 26S proteasome.
Mol. Cell. Proteomics, May 13. [Epub ahead of print].

Martins-de-Souza, D., Maccarrone, G., Wobrock, T., Zerr, I., Gormanns, P., Reckow, S., Falkai, P., Schmitt, A., and Turck, C.W. (2010).
Proteome analysis of the thalamus and cerebrospinal fluid reveals glycolysis dysfunction and potential biomarkers candidates for schizophrenia.
J. Psychiatr. Res.,May 12. [Epub ahead of print].

Gajera, C.R., Emich, H., Lioubinski, O., Christ, A., Beckervordersandforth-Bonk, R., Yoshikawa, K., Bachmann, S., Christensen, E.I., Gotz, M., Kempermann, G., Peterson, A.S., Willnow, T.E., and Hammes, A. (2010).
LRP2 in ependymal cells regulates BMP signaling in the adult neurogenic niche.
J. Cell. Sci., May 11. [Epub ahead of print].

Hubner, N.C., Bird, A.W., Cox, J., Splettstoesser, B., Bandilla, P., Poser, I., Hyman, A., and Mann, M. (2010).
Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions.
J. Cell. Biol. 189, 739-754.

Ostasiewicz, P., Zielinska, D., Mann, M., and Wisniewski, J.R. (2010).
The Phosphoproteome is Quantitatively Preserved in Formalin-Fixed Paraffin-Embedded Tissue and Analyzable by High-resolution Mass Spectrometry.
J. Proteome Res., May 16. [Epub ahead of print].

Choudhary, C., and Mann, M. (2010).
Decoding signalling networks by mass spectrometry-based proteomics.
Nat. Rev. Mol. Cell Biol., May 12. [Epub ahead of print].

Madl, T., Felli, I.C., Bertini, I., and Sattler, M. (2010).
Structural Analysis of Protein Interfaces from (13)C Direct-Detected Paramagnetic Relaxation Enhancements.
J. Am. Chem. Soc., May 12. [Epub ahead of print].

Buchwald, G., Ebert, J., Basquin, C., Sauliere, J., Jayachandran, U., Bono, F., Le Hir, H., and Conti, E. (2010).
Insights into the recruitment of the NMD machinery from the crystal structure of a core EJC-UPF3b complex.
Proc. Natl. Acad. Sci. USA, May 17. [Epub ahead of print].

May 14th, 2010

This week's new publications of the IMPRS faculty

Mohan, H., Krumbholz, M., Sharma, R., Eisele, S., Junker, A., Sixt, M., Newcombe, J., Wekerle, H., Hohlfeld, R., Lassmann, H., and Meinl, E. (2010).
Extracellular Matrix in Multiple Sclerosis Lesions: Fibrillar Collagens, Biglycan and Decorin are Upregulated and Associated with Infiltrating Immune Cells.
Brain Pathol., Mar 25. [Epub ahead of print].

Derfuss, T., Linington, C., Hohlfeld, R., and Meinl, E. (2010).
Axo-glial antigens as targets in multiple sclerosis: implications for axonal and grey matter injury.
J. Mol. Med., May 6. [Epub ahead of print].

Martins-De-Souza, D., Wobrock, T., Zerr, I., Schmitt, A., Gawinecka, J., Schneider-Axmann, T., Falkai, P., and Turck, C.W. (2010).
Different apolipoprotein E, apolipoprotein A1 and prostaglandin-H2 D-isomerase levels in cerebrospinal fluid of schizophrenia patients and healthy controls.
World J. Biol. Psychiatry., May 7. [Epub ahead of print].

Bashaw, G.J., and Klein, R. (2010).
Signaling from axon guidance receptors.
Cold Spring Harb. Perspect. Biol. 2, a001941.

Paixao, S., and Klein, R. (2010).
Neuron-astrocyte communication and synaptic plasticity.
Curr. Opin. Neurobiol., May 12. [Epub ahead of print].

Lugert, S., Basak, O., Knuckles, P., Haussler, U., Fabel, K., Gotz, M., Haas, C.A., Kempermann, G., Taylor, V., and Giachino, C. (2010).
Quiescent and active hippocampal neural stem cells with distinct morphologies respond selectively to physiological and pathological stimuli and aging.
Cell Stem Cell 6, 445-456.

Johansson, P.A., Cappello, S., and Gotz, M. (2010).
Stem cells niches during development-lessons from the cerebral cortex.
Curr. Opin. Neurobiol., May 4. [Epub ahead of print].

von Delius, S., Wilhelm, D., Feussner, H., Sager, J., Becker, V., Schuster, T., Schneider, A., Schmid, R.M., and Meining, A. (2010).
Natural orifice transluminal endoscopic surgery: cardiopulmonary safety of transesophageal mediastinoscopy.
Endoscopy 42, 405-412.

This week's new publications of the IMPRS faculty

Jia, H., Rochefort, N.L., Chen, X., and Konnerth, A. (2010).
Dendritic organization of sensory input to cortical neurons in vivo.
Nature 464, 1307-1312.

Budisa, N., Wenger, W., and Wiltschi, B. (2010).
Residue-specific global fluorination of Candida antarctica lipase B in Pichia pastoris.
Mol. Biosyst., Apr 29. [Epub ahead of print].

Wekerle, H., and Hohlfeld, R. (2010).
Zero tolerance (to acetylcholine receptor) and ways to overcome it.
Ann. Neurol. 67, 422-424.

Busch, S., and Tanimoto, H. (2010).
Cellular configuration of single octopamine neurons in Drosophila.
J. Comp. Neurol. 518, 2355-2364.

Ullrich, S., Muench, A., Neumann, S., Kremmer, E., Tatzelt, J., and Lichtenthaler, S.F. (2010).
The novel membrane protein TMEM59 modulates complex glycosylation, cell surface expression and secretion of the amyloid precursor protein.
J. Biol. Chem., Apr 28. [Epub ahead of print].

Feige, M.J., Simpson, E.R., Herold, E.M., Bepperling, A., Heger, K., and Buchner, J. (2010).
Dissecting the alternatively folded state of the antibody Fab fragment.
J. Mol. Biol., Apr 28. [Epub ahead of print].

Feige, M.J., Hendershot, L.M., and Buchner, J. (2010).
How antibodies fold.
Trends Biochem. Sci. 35, 189-198.

Mourao, A., Varrot, A., Mackereth, C.D., Cusack, S., and Sattler, M. (2010).
Structure and RNA recognition by the snRNA and snoRNA transport factor PHAX.
RNA, Apr 29. [Epub ahead of print].

Fottner, C., Mettler, E., Goetz, M., Schirrmacher, E., Anlauf, M., Strand, D., Schirrmacher, R., Kloppel, G., Delaney, P., Schreckenberger, M., Galle, P.R., Neurath, M.F., Kiesslich, R., and Weber, M.M. (2010).
In vivo molecular imaging of somatostatin receptors in pancreatic islet cells and neuroendocrine tumors by miniaturized confocal laser-scanning fluorescence microscopy.
Endocrinology 151, 2179-2188.

April 30th, 2010

This week's new publications of the IMPRS faculty

Rudolph, B., Gebendorfer, K.M., Buchner, J., and Winter, J. (2010).
Evolution of Escherichia coli for growth at high temperatures.
J. Biol. Chem., Apr 20. [Epub ahead of print].

Ludwig, L., Buchler, P., Kleeff, J., Gaa, J., Stangl, M., Prinz, C., Langer, R., Friess, H., Schmid, R.M., and Algul, H. (2010).
Multidisciplinary Treatment of Aggressive and Rapidly Progressing Biliary Papillomatosis.
Dig. Dis. Sci., Apr 22. [Epub ahead of print].

Tartaglia, G.G., Dobson, C.M., Hartl, F.U., and Vendruscolo, M. (2010).
Physico-Chemical Determinants of Chaperone Requirements.
J. Mol. Biol., Apr 20. [Epub ahead of print].

Strittmatter, P., Soll, J., and Bolter, B. (2010).
The chloroplast protein import machinery: a review.
Methods Mol. Biol. 619, 307-321.

Pech, M., Spreter, T., Beckmann, R., and Beatrix, B. (2010).
Dual binding mode of the nascent polypeptide-associated complex (NAC) reveals a novel universal adapter site on the ribosome.
J. Biol. Chem., Apr 21. [Epub ahead of print].

Wi 347 Niewski, J.R., Nagaraj, N., Zougman, A., Gnad, F., and Mann, M. (2010).
Brain Phosphoproteome Obtained by a FASP-Based Method Reveals Plasma Membrane Protein Topology.
J. Proteome. Res., Apr 26. [Epub ahead of print].

Nourshargh, S., Hordijk, P.L., and Sixt, M. (2010).
Breaching multiple barriers: leukocyte motility through venular walls and the interstitium.
Nat. Rev. Mol. Cell Biol. 11, 366-378.

Walther, T.C., Olsen, J.V., and Mann, M. (2010).
YEAST EXPRESSION PROTEOMICS BY HIGH-RESOLUTION MASS SPECTROMETRY.
In Methods in Enzymology, Vol 470: Guide to Yeast Genetics: (San Diego, Elsevier Academic Press Inc), pp. 259-280.

April 23rd, 2010

This week's new publications of the IMPRS faculty

Karras, G.I., and Jentsch, S. (2010).
The RAD6 DNA damage tolerance pathway operates uncoupled from the replication fork and is functional beyond S phase.
Cell 141, 255-267.

Hartung, S., Niederberger, T., Hartung, M., Tresch, A., and Hopfner, K.P. (2010).
Quantitative analysis of processive RNA degradation by the archaeal RNA exosome.
Nucleic Acids Res.,Apr 14. [Epub ahead of print].

Jawerka, M., Colak, D., Dimou, L., Spiller, C., Lagger, S., Montgomery, R.L., Olson, E.N., Wurst, W., Gottlicher, M., and Gotz, M. (2010).
The specific role of histone deacetylase 2 in adult neurogenesis.
Neuron Glia Biol, 1-15.

Moroder, L., and Budisa, N. (2010).
Synthetic Biology of Protein Folding.
Chemphyschem. 11, 1181-1187.

Schuler, S., Fritsche, P., Diersch, S., Arlt, A., Schmid, R.M., Saur, D., and Schneider, G. (2010).
HDAC2 attenuates TRAIL-induced apoptosis of pancreatic cancer cells.
Mol. Cancer 9, 80.

Echeverria, P.C., Figueras, M.J., Vogler, M., Kriehuber, T., de Miguel, N., Deng, B., Dalmasso, M.C., Matthews, D.E., Matrajt, M., Haslbeck, M., Buchner, J., and Angel, S.O. (2010).
The Hsp90 co-chaperone p23 of Toxoplasma gondii: Identification, functional analysis and dynamic interactome determination.
Mol. Biochem. Parasitol., Apr 16. [Epub ahead of print].

April 16th, 2010

Publications of IMPRS student Koyeli Mapa

Mapa, K., Sikor, M., Kudryavtsev, V., Waegemann, K., Kalinin, S., Seidel, C.A., Neupert, W., Lamb, D.C., and Mokranjac, D.
The conformational dynamics of the mitochondrial hsp70 chaperone.
Heat shock proteins 70 (Hsp70) represent a ubiquitous and conserved family of molecular chaperones involved in a plethora of cellular processes. The dynamics of their ATP hydrolysis-driven and cochaperone-regulated conformational cycle are poorly understood. We used fluorescence spectroscopy to analyze, in real time and at single-molecule resolution, the effects of nucleotides and cochaperones on the conformation of Ssc1, a mitochondrial member of the family. We report that the conformation of its ADP state is unexpectedly heterogeneous, in contrast to a uniform ATP state. Substrates are actively involved in determining the conformation of Ssc1. The J protein Mdj1 does not interact transiently with the chaperone, as generally believed, but rather is released slowly upon ATP hydrolysis. Analysis of the major bacterial Hsp70 revealed important differences between highly homologous members of the family, possibly explaining tuning of Hsp70 chaperones to meet specific functions in different organisms and cellular compartments. 2010 Elsevier Inc. All rights reserved.
Mol. Cell (2010), 38, 89-100.
Pubmed

April 16th, 2010

This week's new publications of the IMPRS faculty

Mapa, K., Sikor, M., Kudryavtsev, V., Waegemann, K., Kalinin, S., Seidel, C.A., Neupert, W., Lamb, D.C., and Mokranjac, D. (2010).
The conformational dynamics of the mitochondrial hsp70 chaperone.
Mol. Cell 38, 89-100.

Dames, P., Puff, R., Weise, M., Parhofer, K.G., Goke, B., Gotz, M., Graw, J., Favor, J., and Lechner, A. (2010).
Relative roles of the different Pax6 domains for pancreatic alpha cell development. BMC Dev. Biol.10, 39.

Wekerle, H., and Hohlfeld, R. (2010).
Molecular oracles for multiple sclerosis therapy.
Nat. Med. 16, 376-377.

van Bebber, F., Paquet, D., Hruscha, A., Schmid, B., and Haass, C. (2010).
Methylene blue fails to inhibit Tau and polyglutamine protein dependent toxicity in Zebrafish.
Neurobiol. Dis., Apr 7. [Epub ahead of print].

Boeke, J., Regnard, C., Cai, W., Johansen, J., Johansen, K.M., Becker, P.B., and Imhof, A. (2010).
Phosphorylation of SU(VAR)3-9 by the chromosomal kinase JIL-1.
PLoS One 5, e10042.

Schmidthals, K., Helma, J., Zolghadr, K., Rothbauer, U., and Leonhardt, H. (2010).
Novel antibody derivatives for proteome and high-content analysis.
Anal. Bioanal. Chem., Apr 7. [Epub ahead of print].

Aron, L., Klein, P., Pham, T.T., Kramer, E.R., Wurst, W., and Klein, R. (2010).
Pro-survival role for Parkinson's associated gene DJ-1 revealed in trophically impaired dopaminergic neurons.
PLoS Biol. 8, e1000349.

Von Delius, S., Sager, J., Feussner, H., Wilhelm, D., Thies, P., Huber, W., Schuster, T., Schneider, A., Schmid, R.M., and Meining, A. (2010).
Carbon dioxide versus room air for natural orifice transluminal endoscopic surgery (NOTES) and comparison with standard laparoscopic pneumoperitoneum.
Gastrointest Endosc., Apr 7. [Epub ahead of print].

Martins-de-Souza, D., Schmitt, A., Roder, R., Lebar, M., Schneider-Axmann, T., Falkai, P., and Turck, C.W. (2010).
Sex-specific proteome differences in the anterior cingulate cortex of schizophrenia.
J. Psychiatr. Res., Apr 6. [Epub ahead of print].

Pantelic, R.S., Meyer, J.C., Kaiser, U., Baumeister, W., and Plitzko, J.M. (2010).
Graphene oxide: a substrate for optimizing preparations of frozen-hydrated samples.
J. Struct. Biol 170, 152-156.

Schebesch, G., Lingner, A., Firzlaff, U., Wiegrebe, L., and Grothe, B. (2010).
Perception and neural representation of size-variant human vowels in the Mongolian gerbil (Meriones unguiculatus).
Hear. Res. 261, 1-8.

Holthoff, K., Zecevic, D., and Konnerth, A. (2010).
Effects of substitution of Cx43 by Cx32 on myocardial energy metabolism, tolerance to ischaemia and preconditioning protection.
Journal of Physiology-London 588, 1085-1096.

April 9th, 2010

This week's new publications of the IMPRS faculty

Rinke, I., Artmann, J., and Stein, V. (2010).
ClC-2 voltage-gated channels constitute part of the background conductance and assist chloride extrusion.
J. Neurosci. 30, 4776-4786.

Nemeth, A., Conesa, A., Santoyo-Lopez, J., Medina, I., Montaner, D., Peterfia, B., Solovei, I., Cremer, T., Dopazo, J., and Langst, G. (2010).
Initial genomics of the human nucleolus.
PLoS Genet 6, e1000889.

Usher, L.C., Johnstone, A., Erturk, A., Hu, Y., Strikis, D., Wanner, I.B., Moorman, S., Lee, J.W., Min, J., Ha, H.H., Duan, Y., Hoffman, S., Goldberg, J.L., Bradke, F., Chang, Y.T., Lemmon, V.P., and Bixby, J.L. (2010).
A chemical screen identifies novel compounds that overcome glial-mediated inhibition of neuronal regeneration.
J. Neurosci. 30, 4693-4706.

Gartmann, M., Blau, M., Armache, J.P., Mielke, T., Topf, M., and Beckmann, R. (2010).
Mechanism of eIF6-mediated inhibition of ribosomal subunit joining.
J. Biol. Chem., Mar 31. [Epub ahead of print].

Geiger, T., Cox, J., Ostasiewicz, P., Wisniewski, J.R., and Mann, M. (2010).
Super-SILAC mix for quantitative proteomics of human tumor tissue.
Nat. Methods, Apr 4. [Epub ahead of print].

April 2nd, 2010

This week's new publications of the IMPRS faculty

Hambsch, B., Chen, B.G., Brenndorfer, J., Meier, M., Avrabos, C., Maccarrone, G., Liu, R.H., Eder, M., Turck, C.W., and Landgraf, R. (2010).
Methylglyoxal-mediated anxiolysis involves increased protein modification and elevated expression of glyoxalase 1 in the brain.
J. Neurochem., Mar 20. [Epub ahead of print].

Buchner, J. (2010).
Bacterial Hsp90 - desperately seeking clients.
Mol. Microbiol., Mar 25. [Epub ahead of print].

Resemann, A., Wunderlich, D., Rothbauer, U., Warscheid, B., Leonhardt, H., Fuchser, J., Kuhlmann, K., and Suckau, D. (2010).
Top-Down de Novo Protein Sequencing of a 13.6 kDa Camelid Single Heavy Chain Antibody by Matrix-Assisted Laser Desorption Ionization-Time-of-Flight/Time-of-Flight Mass Spectrometry.
Anal. Chem., Mar 23. [Epub ahead of print].

Page, R.M., Gutsmiedl, A., Fukumori, A., Winkler, E., Haass, C., and Steiner, H. (2010).
APP mutants respond to {gamma}-secretase modulators.
J. Biol. Chem., Mar 26. [Epub ahead of print].

Lammich, S., Buell, D., Zilow, S., Ludwig, A.K., Nuscher, B., Lichtenthaler, S.F., Prinzen, C., Fahrenholz, F., and Haass, C. (2010).
Expression of the anti-amyloidogenic secretase ADAM10 is suppressed by its 5'-untranslated region.
J. Biol. Chem., Mar 26. [Epub ahead of print].

Reddy-Alla, S., Schmitt, B., Birkenfeld, J., Eulenburg, V., Dutertre, S., Bohringer, C., Gotz, M., Betz, H., and Papadopoulos, T. (2010).
PH-Domain-driven targeting of collybistin but not Cdc42 activation is required for synaptic gephyrin clustering.
Eur. J. Neurosci., Mar 19. [Epub ahead of print].

March 26th, 2010

Publications of IMPRS student Michaela Filou

Filiou, M.D., Bisle, B., Reckow, S., Teplytska, L., Maccarrone, G., and Turck, C.W.
Profiling of mouse synaptosome proteome and phosphoproteome by IEF.
Synapses play important roles in neurotransmission and neuroplasticity. For an in-depth analysis of the synaptic proteome and phosphoproteome, synaptosomal proteins from whole mouse brain were analyzed by IEF and MS resulting in the largest synaptosome proteome described to date, with 2980 unique proteins identified with two or more peptides. At the same time, 118 synaptosomal phosphoproteins were identified, eight of which are reported for the first time as phosphorylated. Expression of selected proteins in synaptosomes was investigated by Western blot. We demonstrate that IEF is a powerful method to interrogate complex samples such as brain tissue both at the proteome and the phosphoproteome level without the need of additional enrichment for phosphoproteins. The detailed synaptoproteome data set reported here will help to elucidate the molecular complexity of the synapse and contribute to our understanding of synaptic systems biology in health and disease.
Electrophoresis (2010), Mar 22. [Epub ahead of print].
Pubmed

March 26th, 2010

This week's new publications of the IMPRS faculty

Illner, D., Zinner, R., Handtke, V., Rouquette, J., Strickfaden, H., Lanctot, C., Conrad, M., Seiler, A., Imhof, A., Cremer, T., and Cremer, M. (2010).
Remodeling of nuclear architecture by the thiodioxoxpiperazine metabolite chaetocin.
Exp. Cell Res., Mar 16. [Epub ahead of print].

Filiou, M.D., Bisle, B., Reckow, S., Teplytska, L., Maccarrone, G., and Turck, C.W. (2010).
Profiling of mouse synaptosome proteome and phosphoproteome by IEF.
Electrophoresis, Mar 22. [Epub ahead of print].

Schnaitmann, C., Vogt, K., Triphan, T., and Tanimoto, H. (2010).
Appetitive and aversive visual learning in freely moving Drosophila.
Front Behav Neurosci 4, 10.

Umgelter, A., Reindl, W., Geisler, F., Saugel, B., Huber, W., Berger, H., and Schmid, R.M. (2010).
Effects of TIPS on global end-diastolic volume and cardiac output and renal resistive index in ICU patients with advanced alcoholic cirrhosis.
Ann Hepatol 9, 40-45.

Grivennikov, S.I., Greten, F.R., and Karin, M. (2010).
Immunity, Inflammation, and Cancer.
Cell 140, 883-899.

Walther, T.C. (2010).
Keeping sphingolipid levels nORMal.
Proc. Natl. Acad. Sci.USA, Mar 16. [Epub ahead of print].

March 19th, 2010

This week's new publications of the IMPRS faculty

Schnorrer, F., Schonbauer, C., Langer, C.C., Dietzl, G., Novatchkova, M., Schernhuber, K., Fellner, M., Azaryan, A., Radolf, M., Stark, A., Keleman, K., and Dickson, B.J. (2010).
Systematic genetic analysis of muscle morphogenesis and function in Drosophila.
Nature 464, 287-291.

Jahrling, N., Becker, K., Schonbauer, C., Schnorrer, F., and Dodt, H.U. (2010).
Three-dimensional reconstruction and segmentation of intact Drosophila by ultramicroscopy.
Front Syst. Neurosci 4, 1.

Hirtreiter, A., Damsma, G.E., Cheung, A.C., Klose, D., Grohmann, D., Vojnic, E., Martin, A.C., Cramer, P., and Werner, F. (2010).
Spt4/5 stimulates transcription elongation through the RNA polymerase clamp coiled-coil motif.
Nucleic Acids Res., Mar 2. [Epub ahead of print].

Klein, R. (2010).
Topography in Hippocampal Mossy Fiber Plasticity.
Neuron 65, 580-582.

Kudryashev, M., Lepper, S., Baumeister, W., Cyrklaff, M., and Frischknecht, F. (2010).
Geometric constrains for detecting short actin filaments by cryogenic electron tomography.
PMC Biophys. 3, 6.

Aguilar, P.S., Heiman, M.G., Walther, T.C., Engel, A., Schwudke, D., Gushwa, N., Kurzchalia, T., and Walter, P. (2010).
Structure of sterol aliphatic chains affects yeast cell shape and cell fusion during mating.
Proc. Natl. Acad. Sci. USA 107, 4170-4175.

Sharma, M.R., Donhofer, A., Barat, C., Marquez, V., Datta, P.P., Fucini, P., Wilson, D.N., and Agrawal, R.K. (2010).
PSRP1 is not a ribosomal protein, but a ribosome-binding factor that is recycled by the ribosome-recycling factor (RRF) and elongation factor G (EF-G).
J. Biol. Chem. 285, 4006-4014.

Blamowska, M., Sichting, M., Mapa, K., Mokranjac, D., Neupert, W., and Hell, K. (2010).
ATPase domain and interdomain linker play a key role in aggregation of mitochondrial Hsp70 chaperone Ssc1.
J. Biol. Chem. 285, 4423-4431.

Press release March 10th, 2010

Fruit Flies – A Model for Bodybuilders

The human body operates by a precisely regulated interplay of different cell types such as blood, nerve and muscle cells. Together with colleagues from the Research Institute of Molecular Pathology (IMP) in Vienna, Austria, scientists of the Max Planck Institute (MPI) of Biochemistry in Martinsried near Munich, Germany, have now succeeded in identifying all genes of the fruit fly Drosophila that play a role in the development and function of muscles. more...

Original Publication:
F. Schnorrer, C. Schönbauer, C. C. H. Langer, G. Dietzl, M. Novatchkova, K. Schernhuber, M. Fellner, A. Azaryan, M. Radolf, A. Stark, K. Keleman and B. J. Dickson: Systematic genetic analysis of muscle morphogenesis and function in Drosophila. Nature, March 11, 2010

March 5th, 2010

This week's new publications of the IMPRS faculty

Riedl, J., Flynn, K.C., Raducanu, A., Gartner, F., Beck, G., Bosl, M., Bradke, F., Massberg, S., Aszodi, A., Sixt, M., and Wedlich-Soldner, R. (2010).
Lifeact mice for studying F-actin dynamics.
Nat. Methods 7, 168-169.

Bekku, Y., Vargova, L., Goto, Y., Vorisek, I., Dmytrenko, L., Narasaki, M., Ohtsuka, A., Fassler, R., Ninomiya, Y., Sykova, E., and Oohashi, T. (2010).
Bral1: Its Role in Diffusion Barrier Formation and Conduction Velocity in the CNS.
J. Neurosci 30, 3113-3123.

Hofer, S.B., and Bonhoeffer, T. (2010).
Dendritic Spines: The Stuff That Memories Are Made Of?
Curr. Biol. 20, R157-R159.

Rigort, A., Bauerlein, F.J., Leis, A., Gruska, M., Hoffmann, C., Laugks, T., Bohm, U., Eibauer, M., Gnaegi, H., Baumeister, W., and Plitzko, J.M. (2010).
Micromachining tools and correlative approaches for cellular cryo-electron tomography.
J. Struct. Biol., Feb 21. [Epub ahead of print].

Mann, K., Poustka, A.J., and Mann, M. (2010).
Phosphoproteomes of Strongylocentrotus purpuratus shell and tooth matrix: identification of a major acidic sea urchin tooth phosphoprotein, phosphodontin.
Proteome Sci. 8, 6.

February 26th, 2010

This week's new publications of the IMPRS faculty

Chen, J., Feige, M.J., Franzmann, T.M., Bepperling, A., and Buchner, J. (2010).
Regions outside the alpha-crystallin domain of the small heat shock protein Hsp26 are required for its dimerization.
J. Mol. Biol., Feb 17. [Epub ahead of print].

Retzlaff, M., Hagn, F., Mitschke, L., Hessling, M., Gugel, F., Kessler, H., Richter, K., and Buchner, J. (2010).
Asymmetric Activation of the Hsp90 Dimer by Its Cochaperone Aha1.
Mol. Cell 37, 344-354.

Cook, A.G., and Conti, E. (2010).
Nuclear export complexes in the frame.
Curr. Opin. Struct. Biol., Feb 18. [Epub ahead of print].

Paquet, D., Schmid, B., and Haass, C. (2010).
Transgenic Zebrafish as a Novel Animal Model to Study Tauopathies and Other Neurodegenerative Disorders in vivo.
Neurodegener. Dis. 7, 99-102.

Luber, C.A., Cox, J., Lauterbach, H., Fancke, B., Selbach, M., Tschopp, J., Akira, S., Wiegand, M., Hochrein, H., O'Keeffe, M., and Mann, M. (2010).
Quantitative Proteomics Reveals Subset-Specific Viral Recognition in Dendritic Cells. Immunity, Feb 17. [Epub ahead of print].

Bienko, M., Green, C.M., Sabbioneda, S., Crosetto, N., Matic, I., Hibbert, R.G., Begovic, T., Niimi, A., Mann, M., Lehmann, A.R., and Dikic, I. (2010).
Regulation of Translesion Synthesis DNA Polymerase eta by Monoubiquitination.
Mol. Cell 37, 396-407.

Pasini, E.M., Lutz, H.U., Mann, M., and Thomas, A.W. (2010).
Red blood cell (RBC) membrane proteomics--Part II: Comparative proteomics and RBC patho-physiology.
J. Proteomics 73, 421-435.

February 12th, 2010

Publication of IMPRS student Falk Butter

Butter, F., Kappei, D., Buchholz, F., Vermeulen, M., and Mann, M.
A domesticated transposon mediates the effects of a single-nucleotide polymorphism responsible for enhanced muscle growth.

Single-nucleotide polymorphisms (SNPs) in the regulatory regions of the genome can have a profound impact on phenotype. The G3072A polymorphism in intron 3 of insulin-like growth factor 2 (IGF2) is implicated in higher muscle content and reduced fat in European pigs and is bound by a putative repressor. Here, we identify this repressor-which we call muscle growth regulator (MGR)-by using a DNA protein interaction screen based on quantitative mass spectrometry. MGR has a bipartite nuclear localization signal, two BED-type zinc fingers and is highly conserved between placental mammals. Surprisingly, the gene is located in an intron and belongs to the hobo-Ac-Tam3 transposase superfamily, suggesting regulatory use of a formerly parasitic element. In transactivation assays, MGR differentially represses the expression of the two SNP variants. Knockdown of MGR in C2C12 myoblast cells upregulates Igf2 expression and mild overexpression retards growth. Thus, MGR is the repressor responsible for enhanced muscle growth in the IGF2 G3072A polymorphism in commercially bred pigs.
EMBO Rep. (2010), Feb 5. [Epub ahead of print].
Pubmed 

February 12th, 2010

This week's new publications of the IMPRS faculty

Bhushan, S., Gartmann, M., Halic, M., Armache, J.P., Jarasch, A., Mielke, T., Berninghausen, O., Wilson, D.N., and Beckmann, R. (2010).
alpha-Helical nascent polypeptide chains visualized within distinct regions of the ribosomal exit tunnel.
Nat. Struct. Mol. Biol., Feb 7. [Epub ahead of print].

Griese, J.J., Witte, G., and Hopfner, K.P. (2010).
Structure and DNA binding activity of the mouse condensin hinge domain highlight common and diverse features of SMC proteins.
Nucleic Acids Res., Feb 5. [Epub ahead of print].

Langer, C.C., Ejsmont, R.K., Schonbauer, C., Schnorrer, F., and Tomancak, P. (2010).
In vivo RNAi rescue in Drosophila melanogaster with genomic transgenes from Drosophila pseudoobscura.
PLoS One 5, e8928.

Butter, F., Kappei, D., Buchholz, F., Vermeulen, M., and Mann, M. (2010).
A domesticated transposon mediates the effects of a single-nucleotide polymorphism responsible for enhanced muscle growth.
EMBO Rep., Feb 5. [Epub ahead of print].

Bono, F., Cook, A.G., Grunwald, M., Ebert, J., and Conti, E. (2010).
Nuclear Import Mechanism of the EJC Component Mago-Y14 Revealed by Structural Studies of Importin 13.
Mol. Cell 37, 211-222.

Wendler, P., and Saibil, H.R. (2010).
Cryo electron microscopy structures of Hsp100 proteins: crowbars in or out?
Biochem. Cell Biol. 88, 89-96.

Koschubs, T., Lorenzen, K., Baumli, S., Sandstrom, S., Heck, A.J., and Cramer, P. (2010).
Preparation and topology of the Mediator middle module.
Nucleic Acids Res., Jan 31. [Epub ahead of print].

Fauth, T., Muller-Planitz, F., Konig, C., Straub, T., and Becker, P.B. (2010).
The DNA binding CXC domain of MSL2 is required for faithful targeting the Dosage Compensation Complex to the X chromosome.
Nucleic Acids Res., Feb 5. [Epub ahead of print].

February 5th, 2010

This week's new publications of the IMPRS faculty


Hirschberg, A., Deng, S., Korostylev, A., Paldy, E., Costa, M.R., Worzfeld, T., Vodrazka, P., Wizenmann, A., Gotz, M., Offermanns, S., and Kuner, R. (2010).
Gene deletion mutants reveal a role for semaphorin receptors of the plexin-B family in mechanisms underlying corticogenesis.
Mol. Cell. Biol. 30, 764-780.

Uhrin, P., Zaujec, J., Breuss, J.M., Olcaydu, D., Chrenek, P., Stockinger, H., Fuertbauer, E., Moser, M., Haiko, P., Fassler, R., Alitalo, K., Binder, B.R., and Kerjaschki, D. (2010).
Novel function for blood platelets and podoplanin in developmental separation of blood and lymphatic circulation.
Blood. Jan 28. [Epub ahead of print].

Ben Dror, L., Barnea, E., Beer, I., Mann, M., and Admon, A. (2010).
The HLA-B*2705 peptidome.
Arthritis Rheum. 62, 420-429.

Mokranjac, D., and Neupert, W. (2010).
The many faces of the mitochondrial TIM23 complex.
Biochim. Biophys. Acta. Jan 27. [Epub ahead of print].

Martins-De-Souza, D., Dias-Neto, E., Schmitt, A., Falkai, P., Gormanns, P., Maccarrone, G., Turck, C.W., and Gattaz, W.F. (2010).
Proteome analysis of schizophrenia brain tissue.
World J. Biol. Psychiatry. Jan 29. [Epub ahead of print].

January 29th, 2010

Publications of IMPRS students Erika Kovács-Bogdán and Bettina Schnell

Kovács-Bogdán, E., Soll, J., and Bolter, B. .
Protein import into chloroplasts: The Tic complex and its regulation.

Chloroplasts like mitochondria derived from an endosymbiontic event. Due to the massive gene transfer to the nucleus during endosymbiosis, only a limited number of chloroplastic proteins are still encoded for in the plastid genome. Most of the nuclear-encoded plastidic proteins are post-translationally translocated back to the chloroplast via the general import pathway through distinct outer and inner envelope membrane protein complexes, the Toc and Tic translocons (Translocon at the outer/inner envelope membrane of chloroplasts). Eight Tic subunits have been described so far, including two potential channel proteins (Tic110 and Tic20), the "motor complex" (Tic40 associated with the stromal chaperone Hsp93) and the "redox regulon" (Tic62, Tic55, and Tic32) involved in regulation of protein import via the metabolic redox status of the chloroplast. Regulation can additionally occur via thioredoxins (Tic110 and Tic55) or via the calcium/calmodulin network (Tic110 and Tic32). In this review we present the current knowledge about the Tic complex focusing on its regulation and addressing some still open questions.
Biochim. Biophys. Acta., (2010) Jan 22. [Epub ahead of print].
Pubmed 

Schnell, B., Joesch, M., Foerstner, F., Raghu, S.V., Otsuna, H., Ito, K., Borst, A., and Reiff, D.F.
Processing of Horizontal Optic Flow in Three Visual Interneurons of the Drosophila Brain.

Motion vision is essential for navigating through the environment. Due to its genetic amenability, the fruit fly Drosophila has served for long as a model organism for studying optomotor behavior as elicited by large-field horizontal motion. However, the neurons underlying the control of this behavior have not been studied in Drosophila so far. Here we report the first whole-cell recordings from three cells of the horizontal system (HSN, HSE and HSS) in the lobula plate of Drosophila. All three HS-cells are tuned to large-field horizontal motion in a direction-selective way: They become excited by front-to-back motion and inhibited by back-to-front motion in the ipsilateral field of view. The response properties of HS-cells like contrast and velocity dependence are in accordance with the correlation-type model of motion detection. Neurobiotin injection suggests extensive coupling among ipsilateral HS-cells and additional coupling to tangential cells that have their dendrites in the contralateral hemisphere of the brain. This connectivity scheme accounts for the complex layout of their receptive fields and explains their sensitivity to ipsilateral as well as to contralateral motion. Thus, the main response properties of Drosophila HS-cells are strikingly similar to the responses of their counterparts in the blow fly Calliphora although we found substantial differences with respect to their dendritic structure and connectivity. This long awaited functional characterization of HS-cells in Drosophila provides the basis for the future dissection of optomotor behavior and the underlying neural circuitry by combining genetics, physiology and behavior
J. Neurophysiol., (2010), Jan 20. [Epub ahead of print].
Pubmed 

January 29th, 2010

This week's new publications of the IMPRS faculty

Chen, Z.A., Jawhari, A., Fischer, L., Buchen, C., Tahir, S., Kamenski, T., Rasmussen, M., Lariviere, L., Bukowski-Wills, J.C., Nilges, M., Cramer, P., and Rappsilber, J. (2010).
Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry.
EMBO J., Jan 21. [Epub ahead of print].

Costa, M.R., Gotz, M., and Berninger, B. (2010).
What determines neurogenic competence in glia?
Brain Res. Rev., Jan 20. [Epub ahead of print].

Sirko, S., von Holst, A., Weber, A., Wizenmann, A., Theocharidis, U., Gotz, M., and Faissner, A. (2010).
Chondroitin Sulfates are Required for FGF-2-dependent Proliferation and Maintenance in Neural Stem Cells and for EGF-dependent Migration of Their Progeny.
Stem Cells., Jan 19. [Epub ahead of print].

Kappos, L., Radue, E.W., O'Connor, P., Polman, C., Hohlfeld, R., Calabresi, P., Selmaj, K., Agoropoulou, C., Leyk, M., Zhang-Auberson, L., and Burtin, P. (2010).
A Placebo-Controlled Trial of Oral Fingolimod in Relapsing Multiple Sclerosis.
N. Engl. J. Med., Jan 20. [Epub ahead of print].

Kovacs-Bogdan, E., Soll, J., and Bolter, B. (2010).
Protein import into chloroplasts: The Tic complex and its regulation.
Biochim. Biophys. Acta., Jan 22. [Epub ahead of print].

Maccarrone, G., Turck, C.W., and Martins-de-Souza, D. (2010).
Shotgun Mass Spectrometry Workflow Combining IEF and LC-MALDI-TOF/TOF.
Protein J., Jan 22. [Epub ahead of print].

January 22nd, 2010

This week's new publications of the IMPRS faculty

Liu, C., Young, A.L., Starling-Windhof, A., Bracher, A., Saschenbrecker, S., Rao, B.V., Rao, K.V., Berninghausen, O., Mielke, T., Hartl, F.U., Beckmann, R., and Hayer-Hartl, M. (2010).
Coupled chaperone action in folding and assembly of hexadecameric Rubisco.
Nature 463, 197-202.

Olsen, J.V., Vermeulen, M., Santamaria, A., Kumar, C., Miller, M.L., Jensen, L.J., Gnad, F., Cox, J., Jensen, T.S., Nigg, E.A., Brunak, S., and Mann, M. (2010).
Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.
Sci Signal 3, ra3.

Jinwal, U.K., Koren, J., 3rd, Borysov, S.I., Schmid, A.B., Abisambra, J.F., Blair, L.J., Johnson, A.G., Jones, J.R., Shults, C.L., O'Leary, J.C., 3rd, Jin, Y., Buchner, J., Cox, M.B., and Dickey, C.A. (2010).
The Hsp90 cochaperone, FKBP51, increases Tau stability and polymerizes microtubules.
J Neurosci 30, 591-599.

January 15th, 2010

This week's new publications of the IMPRS faculty

Stiess, M., Maghelli, N., Kapitein, L.C., Gomis-Ruth, S., Wilsch-Brauninger, M., Hoogenraad, C.C., Tolic Norrelykke, I.M., and Bradke, F. (2010).
Axon Extension Occurs Independently of Centrosomal Microtubule Nucleation.
Science, Jan 7. [Epub ahead of print].

Tahirovic, S., and Bradke, F. (2009).
Neuronal polarity.
Cold Spring Harbor Perspect Biol 1, a001644.

Fernandez-Busnadiego, R., Zuber, B., Maurer, U.E., Cyrklaff, M., Baumeister, W., and Lucic, V. (2010).
Quantitative analysis of the native presynaptic cytomatrix by cryoelectron tomography.
J Cell Biol 188, 145-156.

Merkel, L., Hoesl, M.G., Albrecht, M., Schmidt, A., and Budisa, N. (2010).
Blue Fluorescent Amino Acids As In Vivo Building Blocks for Proteins.
Chembiochem, Jan 7. [Epub ahead of print].

Winklhofer, K.F., and Haass, C. (2010).
Mitochondrial dysfunction in Parkinson's disease.
Biochimica Et Biophysica Acta-Molecular Basis of Disease 1802, 29-44.

January 8th, 2010

Publications of IMPRS students Anna Stengel and Cuipin Pan

Stengel, A., Benz, J.P., Soll, J., and Bolter, B.
Redox-regulation of protein import into chloroplasts and mitochondria: Similarities and differences.

Redox signals play important roles in many developmental and metabolic processes, in particular in chloroplasts and mitochondria. Furthermore, redox reactions are crucial for protein folding via the formation of inter- or intramolecular disulfide bridges. Recently, redox signals were described to be additionally involved in regulation of protein import: in mitochondria, a disulfide relay system mediates retention of cystein-rich proteins in the intermembrane space by oxidizing them. Two essential proteins, the redox-activated receptor Mia40 and the sulfhydryl oxidase Erv1 participate in this pathway. In chloroplasts, it becomes apparent that protein import is affected by redox signals on both the outer and inner envelope: at the level of the Toc complex (translocon at the outer envelope of chloroplasts), the formation/reduction of disulfide bridges between the Toc components has a strong influence on import yield. Moreover, the stromal metabolic redox state seems to be sensed by the Tic complex (translocon at the inner envelope of chloroplasts) that is able to adjust translocation efficiency of a subgroup of redox-related preproteins accordingly. This review summarizes the current knowledge of these redox-regulatory pathways and focuses on similarities and differences between chloroplasts and mitochondria.
Plant Signal Behav. (2010) 5, [Epub ahead of print].
Pubmed 

Pan, C., Olsen, J.V., Daub, H., and Mann, M.
Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics.

Aberrant signaling causes many diseases, and manipulating signaling pathways with kinase inhibitors has emerged as a promising area of drug research. Most kinase inhibitors target the conserved ATP-binding pocket; therefore specificity is a major concern. Proteomics has previously been used to identify the direct targets of kinase inhibitors upon affinity purification from cellular extracts. Here we introduce a complementary approach to evaluate the effects of kinase inhibitors on the entire cell signaling network. We used triple labeling SILAC (stable isotope labeling by amino acids in cell culture) to compare cellular phosphorylation levels for control, epidermal growth factor stimulus, and growth factor combined with kinase inhibitors. Of thousands of phosphopeptides, less than 10% had a response pattern indicative of targets of U0126 and SB202190, two widely used MAPK inhibitors. Interestingly, 83% of the growth factor-induced phosphorylation events were affected by either or both inhibitors, showing quantitatively that early signaling processes are predominantly transmitted through the MAPK cascades. In contrast to MAPK inhibitors, dasatinib, a clinical drug directed against BCR-ABL, which is the cause of chronic myelogenous leukemia, affected nearly 1,000 phosphopeptides. In addition to the proximal effects on ABL and its immediate targets, dasatinib broadly affected the downstream MAPK pathways. Pathway mapping of regulated sites implicated a variety of cellular functions, such as chromosome remodeling, RNA splicing, and cytoskeletal organization, some of which have been described in the literature before. Our assay is streamlined and generic and could become a useful tool in kinase drug development.
Mol. Cell Proteomics (2009) 8, 2796-2808.
Pubmed 

January 8th, 2010

This week's new publications of the IMPRS faculty

Perez-Revuelta, B.I., Fukumori, A., Lammich, S., Yamasaki, A., Haass, C., and Steiner, H. (2009).
Requirement for small side chain residues within the GxGD-motif of presenilin for gamma-secretase substrate cleavage.
J. Neurochem., Dec 15. [Epub ahead of print].

Yanagida, K., Okochi, M., Tagami, S., Nakayama, T., Kodama, T.S., Nishitomi, K., Jiang, J., Mori, K., Tatsumi, S., Arai, T., Ikeuchi, T., Kasuga, K., Tokuda, T., Kondo, M., Ikeda, M., Deguchi, K., Kazui, H., Tanaka, T., Morihara, T., Hashimoto, R., Kudo, T., Steiner, H., Haass, C., Tsuchiya, K., Akiyama, H., Kuwano, R., and Takeda, M. (2009).
The 28-amino acid form of an APLP1-derived Abeta-like peptide is a surrogate marker for Abeta42 production in the central nervous system.
EMBO Mol. Med. 1, 223-235.

Rottach, A., Frauer, C., Pichler, G., Bonapace, I.M., Spada, F., and Leonhardt, H. (2009).
The multi-domain protein Np95 connects DNA methylation and histone modification.
Nucleic Acids Res., Dec 21. [Epub ahead of print].

Kirchhofer, A., Helma, J., Schmidthals, K., Frauer, C., Cui, S., Karcher, A., Pellis, M., Muyldermans, S., Casas-Delucchi, C.S., Cardoso, M.C., Leonhardt, H., Hopfner, K.P., and Rothbauer, U. (2009).
Modulation of protein properties in living cells using nanobodies.
Nat. Struct. Mol. Biol. 17, 133-138.

Schebesch, G., Lingner, A., Firzlaff, U., Wiegrebe, L., and Grothe, B. (2009).
Perception and neural representation of size-variant human vowels in the Mongolian gerbil (Meriones unguiculatus).
Hear Res., Dec 18. [Epub ahead of print].

Feige, M.J., Hendershot, L.M., and Buchner, J. (2009).
How antibodies fold.
Trends Biochem. Sci., Dec 18. [Epub ahead of print].

Ashida, H., Kim, M., Schmidt-Supprian, M., Ma, A., Ogawa, M., and Sasakawa, C. (2010).
A bacterial E3 ubiquitin ligase IpaH9.8 targets NEMO/IKKgamma to dampen the host NF-kappaB-mediated inflammatory response.
Nat. Cell Biol. 12, 66-73; sup pp 61-69.

Nguyen, Q.T., Schroeder, L.F., Mank, M., Muller, A., Taylor, P., Griesbeck, O., and Kleinfeld, D. (2010).
An in vivo biosensor for neurotransmitter release and in situ receptor activity.
Nat. Neurosci. 13, 127-132.

Stengel, A., Benz, J.P., Soll, J., and Bolter, B. (2010).
Redox-regulation of protein import into chloroplasts and mitochondria: Similarities and differences.
Plant Signal Behav 5., [Epub ahead of print].

Hohlfeld, R. (2010).
'Gimme five': future challenges in multiple sclerosis. ECTRIMS Lecture 2009.
Mult. Scler. 16, 3-14.

Dornmair, K., Meinl, E., and Hohlfeld, R. (2009).
Novel approaches for identifying target antigens of autoreactive human B and T cells.
Seminars in Immunopathology 31, 467-477.

Blamowska, M., Sichting, M., Mapa, K., Mokranjac, D., Neupert, W., and Hell, K. (2009).
ATPase domain and interdomain linker play a key role in aggregation of mitochondrial Hsp70 chaperone Ssc1.
J. Biol. Chem., Dec 10. [Epub ahead of print].

Dahlhoff, M., Algul, H., Siveke, J.T., Lesina, M., Wanke, R., Wartmann, T., Halangk, W., Schmid, R.M., Wolf, E., and Schneider, M.R. (2009).
Betacellulin protects from pancreatitis by activating SAPK.
Gastroenterology, Dec 25. [Epub ahead of print].

Pantelic, R.S., Meyer, J.C., Kaiser, U., Baumeister, W., and Plitzko, J.M. (2009).
Graphene oxide: A substrate for optimizing preparations of frozen-hydrated samples.
J. Struct. Biol., Dec 22. [Epub ahead of print].

Wickstrom, S.A., Lange, A., Montanez, E., and Fassler, R. (2009).
The ILK/PINCH/parvin complex: the kinase is dead, long live the pseudokinase!
EMBO J., Dec 24. [Epub ahead of print].

Olsen, J.V., Schwartz, J.C., Griep-Raming, J., Nielsen, M.L., Damoc, E., Denisov, E., Lange, O., Remes, P., Taylor, D., Splendore, M., Wouters, E.R., Senko, M., Makarov, A., Mann, M., and Horning, S. (2009).
A dual pressure linear ion trap orbitrap instrument with very high sequencing speed.
Mol. Cell Proteomics 8, 2759-2769.

Pan, C., Olsen, J.V., Daub, H., and Mann, M. (2009).
Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics.
Mol. Cell Proteomics 8, 2796-2808.

December 18th, 2009

This week's new publications of the IMPRS faculty

Pflicke, H., and Sixt, M. (2009).
Preformed portals facilitate dendritic cell entry into afferent lymphatic vessels.
J. Exp. Med., Dec 7. [Epub ahead of print].

Martins-de-Souza, D., Harris, L.W., Guest, P.C., Turck, C.W., and Bahn, S. (2009).
The role of proteomics in depression research.
Eur. Arch. Psychiatry Clin. Neurosci., Dec 9. [Epub ahead of print].

Jastorff, A.M., Haegler, K., Maccarrone, G., Holsboer, F., Weber, F., Ziemssen, T., and Turck, C.W. (2009).
Regulation of proteins mediating neurodegeneration in experimental autoimmune encephalomyelitis and multiple sclerosis.
Proteomics Clinical Applications 3, 1273-1287.

December 11th, 2009

Publications of IMPRS student Anna Stengel

Stengel, A., Benz, J.P., Buchanan, B.B., Soll, J., and Bolter, B.

Molecular Plant (2009) 2, 1181-1197.

Preprotein Import into Chloroplasts via the Toc and Tic Complexes Is Regulated by Redox Signals in Pisum sativum.

The import of nuclear-encoded preproteins is necessary to maintain chloroplast function. The recognition and transfer of most precursor proteins across the chloroplast envelopes are facilitated by two membrane-inserted protein complexes, the translocons of the chloroplast outer and inner envelope (Toc and Tic complexes, respectively). Several signals have been invoked to regulate the import of preproteins. In our study, we were interested in redox-based import regulation mediated by two signals: regulation based on thiols and on the metabolic NADP+/NADPH ratio. We sought to identify the proteins participating in the regulation of these transport pathways and to characterize the preprotein subgroups whose import is redox-dependent. Our results provide evidence that the formation and reduction of disulfide bridges in the Toc receptors and Toc translocation channel have a strong influence on import yield of all tested preproteins that depend on the Toc complex for translocation. Furthermore, the metabolic NADP+/NADPH ratio influences not only the composition of the Tic complex, but also the import efficiency of most, but not all, preproteins tested. Thus, several Tic subcomplexes appear to participate in the translocation of different preprotein subgroups, and the redox-active components of these complexes likely play a role in regulating transport.

Pubmed 

December 11th, 2009

This week's new publications of the IMPRS faculty

Hohlfeld, R., and Kappos, L. (2009).
Progress in understanding inflammatory and autoimmune diseases of the central nervous system.
Semin. Immunopathol., Dec 3. [Epub ahead of print].

Junker, A., Krumbholz, M., Eisele, S., Mohan, H., Augstein, F., Bittner, R., Lassmann, H., Wekerle, H., Hohlfeld, R., and Meinl, E. (2009).
Micro-ribonucleic acid profiling of multiple sclerosis lesions identifies modulators of the regulatory protein CD47.
Brain, Dec 1. [Epub ahead of print].

Fassler, M., Zocher, M., Klare, S., de la Fuente, A.G., Scheuermann, J., Capell, A., Haass, C., Valkova, C., Veerappan, A., Schneider, D., and Kaether, C. (2009).
Masking of Transmembrane-Based Retention Signals Controls ER Export of gamma-Secretase.
Traffic, Nov 5. [Epub ahead of print].

Sharma, M.R., Donhofer, A., Barat, C., Marquez, V., Datta, P.P., Fucini, P., Wilson, D.N., and Agrawal, R.K. (2009).
PSRP1 is not a ribosomal protein, but a ribosome binding factor that is recycled by RRF and EF-G.
J. Biol. Chem., Dec 4. [Epub ahead of print].

Mann, M. (2009).
Comparative analysis to guide quality improvements in proteomics.
Nat. Methods 6, 717-719.

Haas, B., Mayer, P., Jennissen, K., Scholz, D., Diaz, M.B., Bloch, W., Herzig, S., Fassler, R., and Pfeifer, A. (2009).
Protein kinase G controls brown fat cell differentiation and mitochondrial biogenesis.
Sci. Signal 2, ra78.

Stengel, A., Benz, J.P., Buchanan, B.B., Soll, J., and Bolter, B. (2009).
Preprotein Import into Chloroplasts via the Toc and Tic Complexes Is Regulated by Redox Signals in Pisum sativum.
Molecular Plant 2, 1181-1197.

Benz, M., Bals, T., Gugel, I.L., Piotrowski, M., Kuhn, A., Schunemann, D., Soll, J., and Ankele, E. (2009). Alb4 of Arabidopsis Promotes Assembly and Stabilization of a Non Chlorophyll-Binding Photosynthetic Complex, the CF1CF0-ATP Synthase.
Molecular Plant 2, 1410-1424.

December 4th, 2009

This week's new publications of the IMPRS faculty

Palaniappan, N., Dhote, V., Ayers, S., Starosta, A.L., Wilson, D.N., and Reynolds, K.A. (2009).
Biosynthesis of the aminocyclitol subunit of hygromycin A in Streptomyces hygroscopicus NRRL 2388.
Chem Biol 16, 1180-1189.

Wertz, A., Gaub, B., Plett, J., Haag, J., and Borst, A. (2009).
Robust coding of ego-motion in descending neurons of the fly.
J Neurosci 29, 14993-15000.

Saugel, B., Gaa, J., Phillip, V., Schmid, R.M., and Huber, W. (2009).
Life-threatening Erosion Bleeding of the Carotid Artery after Esophagectomy: Emergency Placement of a Covered Carotid Artery Stent.
J Vasc Interv Radiol. Nov 24. [Epub ahead of print].

Krahmer, N., Guo, Y., Farese, R.V., Jr., and Walther, T.C. (2009).
SnapShot: Lipid Droplets.
Cell 139, 1024-1024 e1021.

Farese, R.V., Jr., and Walther, T.C. (2009).
Lipid droplets finally get a little R-E-S-P-E-C-T.
Cell 139, 855-860.

December 1st, 2009

Registration for <interact> 2010 student symposium is activated

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November 27th, 2009

This week's new publications of the IMPRS faculty

Becker, T., Bhushan, S., Jarasch, A., Armache, J.P., Funes, S., Jossinet, F., Gumbart, J., Mielke, T., Berninghausen, O., Schulten, K., Westhof, E., Gilmore, R., Mandon, E., and Beckmann, R. (2009).
Structure of Monomeric Yeast and Mammalian Sec61 Complexes Interacting with the Translating Ribosome.
Science. Oct 29. [Epub ahead of print].

Seidelt, B., Innis, C.A., Wilson, D.N., Gartmann, M., Armache, J.P., Villa, E., Trabuco, L.G., Becker, T., Mielke, T., Schulten, K., Steitz, T.A., and Beckmann, R. (2009).
Structural Insight into Nascent Polypeptide Chain-Mediated Translational Stalling.
Science. Oct 29. [Epub ahead of print].

Wilson, D.N. (2009).
The A-Z of bacterial translation inhibitors.
Crit Rev Biochem Mol Biol 44, 393-433.

Schneider, G., Kramer, O.H., Fritsche, P., Schuler, S., Schmid, R.M., and Saur, D. (2009).
Targeting histone deacetylases in pancreatic ductal adenocarcinoma.
J Cell Mol Med. Nov 19. [Epub ahead of print].

Jentsch, S., and Siepe, D. (2009).
Pin1, a novel switch in the ubiquitin pathway.
Cell Cycle 8. Dec 31. [Epub ahead of print].

November 23rd, 2009

IMPRS faculty member Tim Gollisch honored with Bernard Katz Lecture award

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November 22nd, 2009

Munich scientists attract funding for new SFB "Assembly and Function of Neuronal Circuits in Sensory Processing"

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November 20th, 2009

This week's new publications of the IMPRS faculty

Renkawitz, J., Schumann, K., Weber, M., Lammermann, T., Pflicke, H., Piel, M., Polleux, J., Spatz, J.P., and Sixt, M. (2009). Adaptive force transmission in amoeboid cell migration. Nat Cell Biol., Nov 15. [Epub ahead of print].

Schymeinsky, J., Gerstl, R., Mannigel, I., Niedung, K., Frommhold, D., Panthel, K., Heesemann, J., Sixt, M., Quast, T., Kolanus, W., Mocsai, A., Wienands, J., Sperandio, M., and Walzog, B. (2009). A fundamental role of mAbp1 in neutrophils: impact on beta(2) integrin-mediated phagocytosis and adhesion in vivo. Blood 114, 4209-4220.

Sydow, J.F., and Cramer, P. (2009). RNA polymerase fidelity and transcriptional proofreading. Curr Opin Struct Biol., Nov 12. [Epub ahead of print].

Cramer, P., and Arnold, E. (2009). Proteins: how RNA polymerases work. Curr Opin Struct Biol., Nov 10. [Epub ahead of print].

Andrecka, J., Treutlein, B., Arcusa, M.A., Muschielok, A., Lewis, R., Cheung, A.C., Cramer, P., and Michaelis, J. (2009). Nano positioning system reveals the course of upstream and nontemplate DNA within the RNA polymerase II elongation complex. Nucleic Acids Res 37, 5803-5809.

Frank, E., Kessler, M.S., Filiou, M.D., Zhang, Y., Maccarrone, G., Reckow, S., Bunck, M., Heumann, H., Turck, C.W., Landgraf, R., and Hambsch, B. (2009). Stable isotope metabolic labeling with a novel N-enriched bacteria diet for improved proteomic analyses of mouse models for psychopathologies. PLoS One 4, e7821.

Nigg, E.A., and Raff, J.W. (2009). Centrioles, centrosomes, and cilia in health and disease. Cell 139, 663-678.

November 19th, 2009

Publication of IMPRS student Jörg Renkawitz

Renkawitz, J., Schumann, K., Weber, M., Lammermann, T., Pflicke, H., Piel, M., Polleux, J., Spatz, J.P., and Sixt, M.

Nat. Cell Biol. 2009 Nov 15. [Epub ahead of print]

Adaptive force transmission in amoeboid cell migration.

The leading front of a cell can either protrude as an actin-free membrane bleb that is inflated by actomyosin-driven contractile forces, or as an actin-rich pseudopodium, a site where polymerizing actin filaments push out the membrane. Pushing filaments can only cause the membrane to protrude if the expanding actin network experiences a retrograde counter-force, which is usually provided by transmembrane receptors of the integrin family. Here we show that chemotactic dendritic cells mechanically adapt to the adhesive properties of their substrate by switching between integrin-mediated and integrin-independent locomotion. We found that on engaging the integrin-actin clutch, actin polymerization was entirely turned into protrusion, whereas on disengagement actin underwent slippage and retrograde flow. Remarkably, accelerated retrograde flow was balanced by an increased actin polymerization rate; therefore, cell shape and protrusion velocity remained constant on alternating substrates. Due to this adaptive response in polymerization dynamics, tracks of adhesive substrate did not dictate the path of the cells. Instead, directional guidance was exclusively provided by a soluble gradient of chemoattractant, which endowed these 'amoeboid' cells with extraordinary flexibility, enabling them to traverse almost every type of tissue.

Press relase 

Pubmed 

November 13th, 2009

This week's new publications of the IMPRS faculty

Wisniewski, J.R., and Mann, M. (2009). Spin filter-based sample preparation for shotgun proteomics Reply. Nature Methods 6, 785-786.

Bonneau, F., Basquin, J., Ebert, J., Lorentzen, E., and Conti, E. (2009). The yeast exosome functions as a macromolecular cage to channel RNA substrates for degradation. Cell 139, 547-559.

Frohlich, F., and Walther, T.C. (2009). Comparing cellular proteomes by mass spectrometry. Genome Biol 10, 240.

Wickstrom, S.A., Masoumi, K.C., Khochbin, S., Fassler, R., and Massoumi, R. (2009). CYLD negatively regulates cell-cycle progression by inactivating HDAC6 and increasing the levels of acetylated tubulin. EMBO J. Nov 5. [Epub ahead of print].

Meffin, H., and Grothe, B. (2009). Selective filtering to spurious localization cues in the mammalian auditory brainstem. J. Acoust. Soc. Am. 126, 2437-2454.

Bollrath, J., and Greten, F.R. (2009). IKK/NF-kappaB and STAT3 pathways: central signalling hubs in inflammation-mediated tumour promotion and metastasis. EMBO Rep. Nov 6. [Epub ahead of print].

Krammer, C., Schatzl, H.M., and Vorberg, I. (2009). Prion-like propagation of cytosolic protein aggregates-insights from cell culture models. Prion 3.Oct 4. [Epub ahead of print].

Mortensen, P., Gouw, J.W., Olsen, J.V., Ong, S.E., Rigbolt, K.T., Bunkenborg, J., Cox, J., Foster, L., Heck, A.J., Blagoev, B., Andersen, J.S., and Mann, M. (2009). MSQuant, an open source platform for mass spectrometry-based quantitative proteomics. J. Proteome Res. Nov 4. [Epub ahead of print].

Hubner, N.C., Wang, L.H., Kaulich, M., Descombes, P., Poser, I., and Nigg, E.A. (2009). Re-examination of siRNA specificity questions role of PICH and Tao1 in the spindle checkpoint and identifies Mad2 as a sensitive target for small RNAs. Chromosoma Nov 11. [Epub ahead of print].

November 12th, 2009

Publication of IMPRS student Alessandro Filosa 

Filosa, A., Paixao, S., Honsek, S.D., Carmona, M.A., Becker, L., Feddersen, B., Gaitanos, L., Rudhard, Y., Schoepfer, R., Klopstock, T., Kullander, K., Rose, C.R., Pasquale, E.B., and Klein, R.

Nat. Neurosci. 2009 Oct;12(10) 1285-1292

Neuron-glia communication via EphA4/ephrin-A3 modulates LTP through glial glutamate transport.

Astrocytes are critical participants in synapse development and function, but their role in synaptic plasticity is unclear. Eph receptors and their ephrin ligands have been suggested to regulate neuron-glia interactions, and EphA4-mediated ephrin reverse signaling is required for synaptic plasticity in the hippocampus. Here we show that long-term potentiation (LTP) at the CA3-CA1 synapse is modulated by EphA4 in the postsynaptic CA1 cell and by ephrin-A3, a ligand of EphA4 that is found in astrocytes. Lack of EphA4 increased the abundance of glial glutamate transporters, and ephrin-A3 modulated transporter currents in astrocytes. Pharmacological inhibition of glial glutamate transporters rescued the LTP defects in EphA4 (Epha4) and ephrin-A3 (Efna3) mutant mice. Transgenic overexpression of ephrin-A3 in astrocytes reduces glutamate transporter levels and produces focal dendritic swellings possibly caused by glutamate excitotoxicity. These results suggest that EphA4/ephrin-A3 signaling is a critical mechanism for astrocytes to regulate synaptic function and plasticity.

Pubmed

November 10th, 2009

Five new full faculty members appointed to IMPRS-LS

The commission for IMPRS faculty recruitment has appointed five new full faculty members to the International Max Planck Research School for Molecular and Cellular Life Sciences. All new  faculty members actively recruit PhD students in this round of application. For details regarding the groups please follow the respective links.

Michael Sattler, Technical University Munich and Helmholtz Zentrum München,
"Structural Basis of Protein-RNA Interactions"

Manajit K. Hayer-Hartl, Max Planck Institute of Biochemistry,
"Chaperone-assisted Folding and Assembly "

Reinhard Hohlfeld, Max Planck Institute of Neurobiology and Ludwig Maximilian University,
"Autoimmune mechanisms and pathogenesis of neuroimmunological diseases"

Jörg Tatzelt, Ludwig Maximilian University,
"Aberrant Protein Folding and Neurodegeneration"

Oliver Griesbeck, Max Planck Institute of Neurobiology,
"Visualizing the Physiology of Live Neurons"

November 6th, 2009

This week's new publications of the IMPRS faculty

Griessmeier, K., Cuny, H., Rotzer, K., Griesbeck, O., Harz, H., Biel, M., and Wahl-Schott, C. (2009). Calmodulin is a functional regulator of Cav1.4 L-type Ca2+ channels. J. Biol. Chem. 284, 29809-29816.

Ducros, M., Moreaux, L., Bradley, J., Tiret, P., Griesbeck, O., and Charpak, S. (2009). Spectral unmixing: analysis of performance in the olfactory bulb in vivo. PLoS One 4, e4418.

Robel, S., Mori, T., Zoubaa, S., Schlegel, J., Sirko, S., Faissner, A., Goebbels, S., Dimou, L., and Gotz, M. (2009). Conditional deletion of beta1-integrin in astroglia causes partial reactive gliosis. Glia 57, 1630-1647.

Brill, M.S., Ninkovic, J., Winpenny, E., Hodge, R.D., Ozen, I., Yang, R., Lepier, A., Gascon, S., Erdelyi, F., Szabo, G., Parras, C., Guillemot, F., Frotscher, M., Berninger, B., Hevner, R.F., Raineteau, O., and Gotz, M. (2009). Adult generation of glutamatergic olfactory bulb interneurons. Nat. Neurosci., Nov 1. [Epub ahead of print]

Starosta, A.L., Qin, H., Mikolajka, A., Leung, G.Y., Schwinghammer, K., Nicolaou, K.C., Chen, D.Y., Cooperman, B.S., and Wilson, D.N. (2009). Identification of distinct thiopeptide-antibiotic precursor lead compounds using translation machinery assays. Chem Biol 16, 1087-1096.

Kudryashev, M., Lepper, S., Stanway, R., Bohn, S., Baumeister, W., Cyrklaff, M., and Frischknecht, F. (2009). Positioning of large organelles by a membrane associated cytoskeleton in Plasmodium sporozoites. Cell Microbiol., Oct 27. [Epub ahead of print]

Strelau, J., Strzelczyk, A., Rusu, P., Bendner, G., Wiese, S., Diella, F., Altick, A.L., von Bartheld, C.S., Klein, R., Sendtner, M., and Unsicker, K. (2009). Progressive postnatal motoneuron loss in mice lacking GDF-15. J. Neurosci. 29, 13640-13648.

Grimaud, C., and Becker, P.B. (2009). The dosage compensation complex shapes the conformation of the X chromosome in Drosophila. Genes Dev. 23, 2490-2495.

October 30th, 2009

Six new Junior faculty members associated to IMPRS-LS

The commission for IMPRS faculty appointments has selected six new junior faculty members to be associated to the International Max Planck Research School for Molecular and Cellular Life Sciences. All newly associated junior faculty members actively recruit PhD students in this round of application. For details regarding the groups please follow the respective links.

Eva Wolf, Max Planck Institute of Biochemistry,
"Structural and biochemical characterisation of circadian clock proteins"

Friedrich Förster, Max Planck Institute of Biochemistry,
"Modeling of Protein complexes"

Esben Lorentzen, Max Planck Institute of Biochemistry,
"Intraflagellar transport"

Michael Sixt, Max Planck Institute of Biochemistry,
"Molecular Mechanisms of Cell Migration"

Petra Wendler, Ludwig Maximilians Universität,
"Protein remodeling and AAA+ assemblies"

Gaia Tavosanis, Max Planck Institute of Neurobiology,
"Dendrite Differentiation"

October 29th, 2009

This week's new publications of the IMPRS faculty

Choudhary, C., Olsen, J.V., Brandts, C., Cox, J., Reddy, P.N., Bohmer, F.D., Gerke, V., Schmidt-Arras, D.E., Berdel, W.E., Muller-Tidow, C., Mann, M., and Serve, H. (2009). Mislocalized activation of oncogenic RTKs switches downstream signaling outcomes. Mol. Cell 36, 326-339.

Wi 347 Niewski, J.R., Zougman, A., and Mann, M. (2009). Combination of FASP and StageTip-based Fractionation Allows In-Depth Analysis of the Hippocampal Membrane Proteome. J. Proteome Res. Oct 22. [Epub ahead of print]

Waanders, L.F., Chwalek, K., Monetti, M., Kumar, C., Lammert, E., and Mann, M. (2009). Quantitative proteomic analysis of single pancreatic islets. Proc. Natl. Acad. Sci. U S A Oct 21. [Epub ahead of print]

Pecka, M., Siveke, I., Grothe, B., and Lesica, N.A. (2009). Enhancement of ITD coding within the initial stages of the auditory pathway. J. Neurophysiol. Oct 21. [Epub ahead of print]

October 23th, 2009

This week's new publications of the IMPRS faculty

Tsutsumi, S., Mollapour, M., Graf, C., Lee, C.T., Scroggins, B.T., Xu, W., Haslerova, L., Hessling, M., Konstantinova, A.A., Trepel, J.B., Panaretou, B., Buchner, J., Mayer, M.P., Prodromou, C., and Neckers, L. (2009). Hsp90 charged-linker truncation reverses the functional consequences of weakened hydrophobic contacts in the N domain. Nat. Struct. Mol. Biol. Oct 18. [Epub ahead of print]

Wertz, A., Haag, J., and Borst, A. (2009). Local and global motion preferences in descending neurons of the fly. J. Comp. Physiol. A Neuroethol. Sens. Neural Behav. Physiol. Oct 15. [Epub ahead of print]

Lange, A., Wickstrom, S.A., Jakobson, M., Zent, R., Sainio, K., and Fassler, R. (2009). Integrin-linked kinase is an adaptor with essential functions during mouse development. Nature 461, 1002-1006.

Bartholomaus, I., Kawakami, N., Odoardi, F., Schlager, C., Miljkovic, D., Ellwart, J.W., Klinkert, W.E., Flugel-Koch, C., Issekutz, T.B., Wekerle, H., and Flugel, A. (2009). Effector T cell interactions with meningeal vascular structures in nascent autoimmune CNS lesions. Nature. Oct 14. [Epub ahead of print]

Hirtreiter, A.M., Calloni, G., Forner, F., Scheibe, B., Puype, M., Vandekerckhove, J., Mann, M., Hartl, F.U., and Hayer-Hartl, M. (2009). Differential substrate specificity of group I and group II chaperonins in the archaeon Methanosarcina mazei. Mol. Microbiol. Oct 15. [Epub ahead of print]

Rouquette, J., Genoud, C., Vazquez-Nin, G.H., Kraus, B., Cremer, T., and Fakan, S. (2009). Revealing the high-resolution three-dimensional network of chromatin and interchromatin space: A novel electron-microscopic approach to reconstructing nuclear architecture. Chromosome Research 17, 801-810.

October 16th, 2009

This week's new publications of the IMPRS faculty

Soufi, B., Kelstrup, C.D., Stoehr, G., Frohlich, F., Walther, T.C., and Olsen, J.V. (2009). Global analysis of the yeast osmotic stress response by quantitative proteomics. Mol. Biosyst. 5, 1337-1346.

Forner, F., Kumar, C., Luber, C.A., Fromme, T., Klingenspor, M., and Mann, M. (2009). Proteome differences between brown and white fat mitochondria reveal specialized metabolic functions. Cell Metab. 10, 324-335.

Gilch, S., Bach, C., Lutzny, G., Vorberg, I., and Schatzl, H.M. (2009). Inhibition of cholesterol recycling impairs cellular PrP(Sc) propagation. Cell Mol. Life Sci. Oct 13. [Epub ahead of print]

Kostrewa, D., Zeller, M.E., Armache, K.J., Seizl, M., Leike, K., Thomm, M., and Cramer, P. (2009). RNA polymerase II-TFIIB structure and mechanism of transcription initiation. Nature. Oct 9. [Epub ahead of print]

Altomonte, J., Marozin, S., Schmid, R.M., and Ebert, O. (2009). Engineered Newcastle Disease Virus as an Improved Oncolytic Agent Against Hepatocellular Carcinoma. Mol Ther. Oct 6. [Epub ahead of print]

Retzlaff, M., Stahl, M., Eberl, H.C., Lagleder, S., Beck, J., Kessler, H., and Buchner, J. (2009). Hsp90 is regulated by a switch point in the C-terminal domain. EMBO Rep. 10, 1147-1153.

October 12th, 2009

Announcement

Open Interdisciplinary Symposium at the Max Planck Institute of Biochemistry

October 16th, 2009: 10:00 - 19:00

“New Frontiers in Science”

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October 9th, 2009

This week's new publications of the IMPRS faculty

Meilinger, D., Fellinger, K., Bultmann, S., Rothbauer, U., Bonapace, I.M., Klinkert, W.E., Spada, F., and Leonhardt, H. (2009). Np95 interacts with de novo DNA methyltransferases, Dnmt3a and Dnmt3b, and mediates epigenetic silencing of the viral CMV promoter in embryonic stem cells. EMBO Rep. Oct 2. [Epub ahead of print]

Hopfner, K.P. (2009). DNA double-strand breaks come into focus. Cell 139, 25-27.

Montanez, E., Wickstrom, S.A., Altstatter, J., Chu, H., and Fassler, R. (2009). alpha-parvin controls vascular mural cell recruitment to vessel wall by regulating RhoA/ROCK signalling. EMBO J. Oct 1. [Epub ahead of print]

Kogata, N., Tribe, R.M., Fassler, R., Way, M., and Adams, R.H. (2009). Integrin-linked kinase controls vascular wall formation by negatively regulating Rho/ROCK-mediated vascular smooth muscle cell contraction. Genes Dev 23, 2278-2283.

Hoogenraad, C.C., and Bradke, F. (2009). Control of neuronal polarity and plasticity - a renaissance for microtubules? Trends Cell Biol. Oct 2. [Epub ahead of print]

Hassfurth, B., Magnusson, A.K., Grothe, B., and Koch, U. (2009). Sensory deprivation regulates the development of the hyperpolarization-activated current in auditory brainstem neurons. Eur J Neurosci 30, 1227-1238.

Gnad, F., de Godoy, L.M., Cox, J., Neuhauser, N., Ren, S., Olsen, J.V., and Mann, M. (2009). High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast. Proteomics. Sep 30. [Epub ahead of print]

Sohmen, D., Harms, J.M., Schlunzen, F., and Wilson, D.N. (2009). SnapShot: Antibiotic Inhibition of Protein Synthesis I. Cell 138, 1248-A1248.

Sohmen, D., Harms, J.M., Schlunzen, F., and Wilson, D.N. (2009). Enhanced SnapShot: Antibiotic inhibition of protein synthesis II. Cell 139, 212-212 e211

October 5th, 2009

Announcement

Open Symposium at the Max Planck Institute of Biochemistry

October 9th, 2009: 08:30 - 18:30

“20 years of electrospray mass spectrometry for large molecules”

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October 1st, 2009

Professor Franz-Ulrich Hartl receives Otto Warburg Medal

Proteins are the cell’s molecular building material and machineries, and they are involved in nearly every bioprocess of the cell. For his research on protein folding Franz-Ulrich Hartl, a director at the Max Planck Institute of Biochemistry, has now been awarded with the Otto Warburg Medal. The institute is located in Martinsried in the outskirts of Munich in Germany. The prize was presented to him in Aachen during the international meeting entitled “Signal Transduction and Disease”. Based on his research, an important field in biology and medicine was founded. Among other things, Professor Hartl was able to prove that special protein complexes (Chaperones) are responsible for the correct folding of proteins. Only when the proteins are folded correctly, can they fulfil their biological tasks. Problems in protein folding can lead to severe neurodegenerative disorders like Alzheimer’s disease or Parkinson. Defective protein folding also plays a role in the process of aging.

The Otto Warburg Medal is regarded as the highest award for biochemists and molecular biologists in Germany. It has been awarded by the German Society for Biochemistry and Molecular Biology (Gesellschaft für Biochemie und Molekularbiologie, GBM) since 1963.

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September 25th, 2009

This week's new publications of the IMPRS faculty

Rautenberg, P.L., Grothe, B., and Felmy, F. (2009). Quantification of the three-dimensional morphology of coincidence detector neurons in the medial superior olive of gerbils during late postnatal development. J Comp Neurol 517, 385-396.

Dhote, V., Starosta, A.L., Wilson, D.N., and Reynolds, K.A. (2009). The final step of step of hygromycin A biosynthesis, oxidation of C5''- dihydrohygromycin A, is linked to a putative proton gradient-dependent efflux. Antimicrob Agents Chemother, [Epub ahead of print].

Heiseke, A., Aguib, Y., and Schatzl, H.M. (2009). Autophagy, Prion Infection and their Mutual Interactions. Curr Issues Mol Biol 12, 87-98.

Meves, A., Stremmel, C., Gottschalk, K., and Fassler, R. (2009). The Kindlin protein family: new members to the club of focal adhesion proteins. Trends Cell Biol., [Epub ahead of print].

Damsma, G.E., and Cramer, P. (2009). Molecular basis of transcriptional mutagenesis at 8-oxoguanine. J Biol Chem., [Epub ahead of print].

Hou, B.H., Takanaga, H., Griesbeck, O., and Frommer, W.B. (2009). Osmotic induction of calcium accumulation in human embryonic kidney cells detected with a high sensitivity FRET calcium sensor. Cell Calcium 46, 130-135.

Weber, A., Prinz, C., Gerngross, C., Ludwig, L., Huber, W., Neu, B., Ebert, M.P., Meining, A., Weidenbach, H., Schmid, R.M., and Schulte-Frohlinde, E. (2009). Long-term outcome of endoscopic and/or percutaneous transhepatic therapy in patients with biliary stricture after orthotopic liver transplantation. J Gastroenterol., [Epub ahead of print].

Rognoni, E., Widmaier, M., Haczek, C., Mantwill, K., Holzmuller, R., Gansbacher, B., Kolk, A., Schuster, T., Schmid, R.M., Saur, D., Kaszubiak, A., Lage, H., and Holm, P.S. (2009). Adenovirus-based virotherapy enabled by cellular YB-1 expression in vitro and in vivo. Cancer Gene Ther 16, 753-763.

September 18th, 2009

This week's new publications of the IMPRS faculty

Rottach, A., Leonhardt, H., and Spada, F. (2009). DNA methylation-mediated epigenetic control. J Cell Biochem 108, 43-51.

Pinto, L., Drechsel, D., Schmid, M.-T., Ninkovic, J., Irmler, M., Brill, M.S., Restani, L., Gianfranceschi, L., Cerri, C., Weber, S.N., Tarabykin, V., Baer, K., Guillemot, F., Beckers, J., Zecevic, N., Dehay, C., Caleo, M., Schorle, H., and Gotz, M. (2009). AP2[gamma] regulates basal progenitor fate in a region- and layer-specific manner in the developing cortex. Nat Neurosci advance online publication.

Klein, U.R., and Nigg, E.A. (2009). SUMO-dependent regulation of centrin-2. J Cell Sci 122, 3312-3321.

Schifferer, M., and Griesbeck, O. (2009). Application of aptamers and autofluorescent proteins for RNA visualization. Integr Biol 1, 499-505.

Zhang, X., Mernaugh, G., Yang, D.H., Gewin, L., Srichai, M.B., Harris, R.C., Iturregui, J.M., Nelson, R.D., Kohan, D.E., Abrahamson, D., Fassler, R., Yurchenco, P., Pozzi, A., and Zent, R. (2009). {beta}1 integrin is necessary for ureteric bud branching morphogenesis and maintenance of collecting duct structural integrity. Development 136, 3357-3366.

September 7th, 2009

Star-shaped cells in the brain aid with learning

Every movement and every thought requires the passing of specific information between networks of nerve cells. To improve a skill or to learn something new entails more efficient or a greater number of cell contacts. Scientists at the Max Planck Institute of Neurobiology in Martinsried could now show, together with an international team of researchers, that certain cells in the brain, the astrocytes, actively influence this information exchange. Until now, astrocytes were thought to have their main role in the development and nutrition of the brain's nerve cells. The new findings improve our comprehension of how the brain learns and remembers. They could also aid in the basic research of diseases such as epilepsy and the amyotrophic lateral sclerosis (ALS). (Nature Neuroscience, September 7th, 2009)

September 1st, 2009

Activity-dependent plasticity of developing climbing fiber–Purkinje cell synapses

Elimination of redundant synapses and strengthening of the surviving ones are crucial steps in the development of the nervous system. Both processes can be readily followed at the climbing fiber to Purkinje cell synapse in the cerebellum. Shortly after birth, around five equally strong climbing fiber synapses are established. Subsequently, one of these five synaptic connections starts to grow in size and synaptic strength, while the others degenerate and eventually disappear. Both the elimination of the redundant climbing fiber synapses and the strengthening of the surviving one depend on a combination of a genetically coded blueprint and synaptic activity. Recently, it has been shown that synaptic activity affects the synaptic strength of developing climbing fibers. Remarkably, the same pattern of paired activity of the presynaptic climbing fiber and the postsynaptic Purkinje cell resulted in strengthening of already “large” climbing fibers and weakening of already “weak” climbing fibers. In this review, we will integrate the current knowledge of synaptic plasticity of climbing fibers with that of other processes affecting climbing fiber development.

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August 18th, 2009

Proteome-wide prediction of acetylation substrates

Acetylation is a well-studied posttranslational modification that has been associated with a broad spectrum of biological processes, notably gene regulation. Many studies have contributed to our knowledge of the enzymology underlying acetylation, including efforts to understand the molecular mechanism of substrate recognition by several acetyltransferases, but traditional experiments to determine intrinsic features of substrate site specificity have proven challenging. Here,wecombine experimental methods with clustering analysis of protein sequences to predict protein acetylation based on the sequence characteristics of acetylated lysines within histones with our unique prediction tool PredMod. We define a local amino acid sequence composition that represents potential acetylation sites by implementing a clustering analysis of histone and nonhistone sequences. We show that this sequence composition has predictive power on 2 independent experimental datasets of acetylation marks. Finally, we detect acetylation for selected putative substrates using mass spectrometry, and report several nonhistone acetylated substrates in budding yeast. Our approach, combined with more traditional experimental methods, may be useful for identifying acetylated substrates proteome-wide.

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August 17th, 2009

From cell division to ageing

Max Planck scientists locate main cell switches

Protein function and gene expression are often regulated by reversible modifications of already existing proteins. Scientists from the Max Planck Institute of Biochemistry and the University of Copenhagen have now been able to prove that the reversible attachment of acetyl groups influences virtually all functions of human cells and therefore has a much greater importance than previously assumed. Whether it is cell division, signal transduction or ageing - all these processes are affected by acetyl groups acting as molecular switches. Therefore, these switches may prove to be a crucial factor in the development of new therapies against diseases like cancer, Alzheimer’s or Parkinson’s. (Science, August 14th 2009)

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