Publications in 2015

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Vitaly Citovsky

Bar-Ziv, A., Levy, Y., Citovsky, V., & Gafni, Y. (2015). The Tomato yellow leaf curl virus (TYLCV) V2 protein inhibits enzymatic activity of the host papain-like cysteine protease CYP1. Biochem. Biophys. Res. Comm. 460, 525-529.

Lacroix, B. & Citovsky, V. (2015) Genetically modified organisms, plant transformation by Agrobacterium. In Discoveries in Modern Science: Exploration, Invention, Technology (J. Trefil, ed.), Farmington Hills: Macmillan, pp. 425-431.

Yuan, C., Lazarowitz, S.G., & Citovsky, V. (2015) Identification of a functional plasmodesmal localization signal in a plant viral cell-to-cell movement protein. mBio 7, e02052-15.

Lacroix, B. & Citovsky, V. (2015) Nopaline-type Ti plasmid of Agrobacterium encodes a VirF-like functional F-box protein. Sci. Rep. 5, 16610.

García-Cano, E., Magori, S., Lazarowitz, S.G., & Citovsky, V. (2015) Interaction of Arabidopsis trihelix-domain transcription factors VFP3 and VFP5 with Agrobacterium virulence protein VirF. PLOS ONE 10, e014212.

Yussuf Hannun

Salama, M. F., Carroll, B., Adada, M., Pulkoski-Gross, M., Hannun, Y. A., and Obeid, L. M. (2015) A novel role of sphingosine kinase-1 in the invasion and angiogenesis of VHL mutant clear cell renal cell carcinoma FASEB J 29: 2803-2813. PMCID: PMC4478804

Lu, Z., Li, Y., Jin, J., Zhang, X., Hannun, Y. A., and Huang, Y. (2015) GPR40/FFA1 and Neutral Sphingomyelinase Are Involved in Palmitate-Boosted Inflammatory Response of Microvascular Endothelial Cells to LPS. Atherosclerosis. 240:163-173  PMCID: PMC4397186

Necomb, B. and Hannun, Y. A. (2015) A new twist to the emerging functions of ceramides in cancer: Novel role for platelet acid sphingomyelinase in cancer metastasis. EMBO Molecular Medicine 7: 692- 694.  PMCID: PMC4459812

Ghaleb, A. M., Bialkowska, A. B., Snider, A. J., Gnatenko, D. V., Hannun, Y. A., Yang, V. W., and Schmidt, V. A. (2015) IQ motif-containing GTPase-activating protein 2 (IQGAP2) is a novel regulator of colonic inflammation in mice. PLOS One. 10(6):e0129314.  PMCID: PMC4457730

Airola, M. V., Allen, W. J., Pulkoski-Gross, M. J., Obeid, L. M., Rizzo, R. C., and Hannun, Y. A. (2015). Structural basis for ceramide recognition and hydrolysis by human Neutral Ceramidase. Structure 23: 1482-1491.   NIHMS 705988

 

Wu, B. X, Fan, J., Boyer, N. P., Jenkins, R. W., Koutalos, Y., Hannun, Y. A., and Crosson, C. E. (2015) Lack of acid sphingomyelinase induces age-related retinal degeneration.    PLOS One 10(7):e0133032     PMCID: PMC4500403

Chen, P-W., Fonseca, L. L., Hannun, Y. A., and Voit, E. O. (2015) Dynamics of the Heat Stress Response of Ceramides with Different Fatty-Acyl Chain Lengths in Baker’s Yeast. PLOS Computational Biology (i 11(8):e1004373.   PMCID: PMC4524633

Adada, M. M., Canals, D, Kelkar, A. D., Hernandez-Corbacho, M., Donaldson, J. C., Hannun, Y. A., and Obeid, L. M. (2015) Intracellular Sphingosine Kinase 2-derived S1P mediates EGF-induced ERM phosphorylation and cancer cell invasion. FASEB J 29:4654-4669 PMCID: PMC4608912

Kitatani, K., Toshinori, U., Sriraman, S. K., Tohoshima, M., Ishibashi, M., Shigeta, S., Nagase, S., Sakamoto, M., Hannun, Y. A., Torchilin, V., P., and Yaegashi, N. (2015) Ceramide limits phosphatidylinositol-3-kinase C2β-controlled cell motility in ovarian cancer: potential of ceramide as a metastasis-suppressor lipid. Oncogene (in press).

Chen, P.-W., Fonseca, L. L., Hannun, Y. A., and Voit, E. O. (2015) Dynamics of the Heat Stress Response of Ceramides with Different Fatty-Acyl Chain Lengths in Baker’s Yeast. PLOS Computational Biology 11(8):e1004373.    PMCID: PMC4524633

Kitatani, K., Wada, M., Perry, D., Usui, T., Sun, Y., Obeid, L. M., Yaegashi, N., Grabowski, G. A., and Hannun Y. A. (2015) Activation of p38 mitogen-activated protein kinase in Gaucher’s disease. PLOS One 10(8):e0136633. PMCID: PMC4552301

Shamseddine, A. A., Clarke, C. J., Carroll, B., Airola, M. V., Rella, A., Obeid, L. M., and Hannun, Y. A. (2015) p53-dependent upregulation of neutral sphingomyelinase-2; Role in doxorubicin-induced growth arrest. Cell Death & Disease 6:e1947.    PMCID: PMC4632297

Casasampere, M., Camacho, L., Cingolani, F., Casas, J., Egido-Gabas, M., Abad, J. L., Bedia, C., Xu, R. Wang, K., Canals, D., Hannun, Y. A., Mao, C., and Fabrias, G. (2015) Activity of neutral and alkaline ceramidases on fluorogenic N-acylated coumarine-containing aminodiols.   Lipid Res. (in press)

Hernández-Corbacho, M. J., Canals, D., Adada, M., Liu, M., Senkal, C., Luberto, C., Hannun, Y. A., and Obeid, L. M. (2015) Tumor Necrosis Factor alpha (TNF&[alpha])-induced Ceramide Generation via Ceramide Synthases Regulates Loss of Focal Adhesion Kinase (FAK) and Programmed Cell Death. Biol. Chem. 290: 25356-25373. PMCID: PMC4646185

Newcomb, B. and Hannun, Y. A. (2015). Sphingolipids as Mediators of Breast Cancer Progression, Metastasis, Response and Resistance to Chemotherapy. Chapter in: Bioactive Sphingolipids in Cancer Biology and Therapy. (2015). Y. A. Hannun, C. M. Luberto, C. Mao, and L. M. Obeid. Springer International Publishing, Switzerland.  ISBN 978-3-319-20749-0.   ISBN 978-3-319-20750-6 (eBook).  Pp 81 – 106.

Lu, X., W. J. Zhang, and Hannun, Y. A. (2015). Systems Biology Approaches for Studying. Sphingolipid Signaling. Chapter in: Bioactive Sphingolipids in Cancer Biology and Therapy. (2015).  Y. A. Hannun, C. M. Luberto, C. Mao, and L. M. Obeid. Springer International Publishing, Switzerland.  ISBN 978-3-319-20749-0.   ISBN 978-3-319-20750-6 (eBook).  Pp 297 -310.

Rana, N. A., Singh, A., Del Poeta, M., and Hannun, Y. A. (2015). Qualitative and Quantitative Measurements of Sphingolipids by Mass Spectrometry. Chapter in: Bioactive Sphingolipids in Cancer Biology and Therapy. (2015).  Y. A. Hannun, C. M. Luberto, C. Mao, and L. M. Obeid. Springer International Publishing, Switzerland.  ISBN 978-3-319-20749-0.   ISBN 978-3-319-20750-6 (eBook).  Pp 313-338.

Jones, E. E., Dworksi S., Kamani, M., Canals, D., Wada, M., Liu, X., Hannun, Y. A., Norris, J., Medin, J. A., and Drake, R. R. (2015) Detection and Distribution of Sphingolipids in Tissue by FTICR MALDI-Imaging Mass Spectrometry. Chapter in: Bioactive Sphingolipids in Cancer Biology and Therapy. (2015).  Y. A. Hannun, C. M. Luberto, C. Mao, and L. M. Obeid. Springer International Publishing, Switzerland.  ISBN 978-3-319-20749-0.   ISBN 978-3-319-20750-6 (eBook).  Pp 339- 357.

Zhao, L., Spassieva, S. D., Gable, K., Gupta, S., Shi, L.-Y., Wang, L., Bielawski, J., Hicks, W., Krebs, M. P., Naggert, J. K., Hannun, Y. A., Dunn, T., and Nishina, P. M. (2015) Elevation of 20-carbon long chain bases due to a mutation in serine palmitoyltransferase small subunit b results in neurodegeneration. PNAS 112:12962-12967. PMCID: PMC4620873

Wang, K., Xu, R., Schrandt, J., Gong, Y. Z., Yi, J. K., Lin, C-L., Sun, W., Spyropoulos, D., Rhee, S., Li, M., Zhou, J., Ge, S., Snider, A. J., Hannun, Y. A., Obeid, L. M., and Mao, C. (2015) Alkaline Ceramidase 3 Deficiency Results in Purkinje Cell Degeneration and Cerebellar Ataxia Due to Dyshomeostasis of Sphingolipids in the Brain. PLOS Genetics 11(10):e1005591  PMCID: PMC4608763.

Nancy Hollingsworth

Liu, Y., W. Gaines, T. Callender, V. Busygina, A. Oke, P. Sung, J. Fung and N. M. Hollingsworth (2014) Down-regulation of Rad51 activity during meiosis in yeast prevents competition with Dmc1 for repair of double-strand breaks.  PLoS Genet.  10:e1004005 doi:10.1371/journalpgen.1004005

Suhandynata, R., J. Liang, C. P. Albuquerque, H. Zhou and N. M. Hollingsworth (2014) A method for sporulating budding yeast cells that allows for unbiased identification of kinase substrates using stable isotope labeling by amino acids in cell culture.  G3 4: 2125-2135.

Chen, X., R. T. Suhandynata, R. Sandhu, B. Rockmill, N. Mohibullah, H. Niu, J. Liang, H-C Lo, D. E. Miller, H. Zhou, G. V. Börner, and N. M. Hollingsworth.  (2015) Phosphorylation of the synaptonemal complex protein Zip1 regulates the crossover/noncrossover decision during yeast meiosis.  PLoS Biol 13(12): e1002329. doi: 10.1371/journal.pbio.1002329

Hollingsworth, N. M. (2016) Mek1/Mre4 is a master regulator of meiotic recombination in budding yeast.  Microbial Cell (in press).

Martin Kaczocha

  1. Chakraborty S, Rebecchi MJ, Kaczocha M, and Puopolo M. Dopamine modulation of transient receptor potential vanilloid type 1 (TRPV1) receptor in dorsal root ganglia neurons. (2015) J Physiol. 2015 Nov 13.
  1. Kaczocha M, Glaser ST, Maher T, Clavin B, Hamilton J, O’Rourke J, Rebecchi MJ, Puopolo M, Owada Y, and Thanos PK. Fatty Acid Binding Protein Deletion Suppresses Inflammatory Pain Through Endocannabinoid/N-acylethanolamine-Dependent Mechanisms. (2015) Mol Pain. Aug 28;11(1):52.
  1. Galbavy W, Kaczocha M, Puopolo M, Liu L, and Rebecchi MJ. Neuroimmune and Neuropathic Responses of Spinal Cord and Dorsal Root Ganglia in Middle Age. (2015) PLoS One. Aug 4;10(8):e0134394.
  1. Sirrs S, van Karnebeek C, Peng X, Shyr C, Tarailo-Graovac M, Mandal R, Testa D, Dubin D, Carbonetti G, Glynn SE, Robinson WP, Han B, Wishart D, Ross CJ, Wasserman WW, Hurwitz TA, Sinclair G, and Kaczocha M. Defects in fatty acid amide hydrolase 2 in a male with neurologic and psychiatric symptoms. (2015) Orphanet J Rare Dis. 10:38.
  1. Nicholson J, Azim S, Rebecchi MJ, Galbavy W, Feng T, Reinsel R, Fowler CJ, Benveniste H, and Kaczocha M. Leptin levels are negatively correlated with 2-arachidonoylglycerol in the cerebrospinal fluid of patients with osteoarthritis. (2015) PLoS One. Apr 2;10(4):e0123132.
  1. Elmes MW, Kaczocha M, Berger WT*, Leung K, Ralph BP, Wang L, Sweeney JM, Miyauchi JT, Tsirka SE, Ojima I, Deutsch DG. Fatty Acid Binding Proteins (FABPs) are Intracellular Carriers for ∆9-Tetrahydrocannabinol (THC) and Cannabidiol (CBD). (2015) J Biol Chem. Apr 3;290(14):8711-21.

Hulin Li

1. Bai L, Hu K, Wang T, Jastrab JB, Darwin KH, Li H.  Structural analysis of the dodecameric proteasome activator PafE in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A, in print.

2. Jastrab JB, Wang T, Murphy JP, Bai L, Hu K, Merkx R, Huang J, Chatterjee C, Ovaa H, Gygi SP, Li H, Darwin KH. An adenosine triphosphate-independent proteasome activator contributes to the virulence of Mycobacterium tuberculosis. Proc Natl Acad Sci U S A. 2015, 112, E1763-72.

3. Sun J, Shi Y, Georgescu RE, Yuan Z, Chait BT, Li H, O’Donnell ME. The Architecture of a Eukaryotic Replisome. Nat Struct Mol Biol. 2015; 22(12):976-82.

4. Yuan Z, Bai L, Sun J, Georgescu R, Liu J, O’Donnell ME, Li H. Atomic structure of the eukaryotic replicative CMG helicase by cryo-EM and implication to DNA unwinding, Nat Struct Mol Biol. 2016 Feb 8. doi: 10.1038/nsmb.3170

5. Sun J, Yuan Z, Stillman B, C Speck, Li H. Structure and Function of Replication Initiation Factors. 2016, pp 427-441, Chapter 21 in “The Initiation of DNA Replication in Eukaryotes”, Edited by Daniel Kaplan, published by Springer 2016.

6. Chang F, Riera A, Evrin C, Sun J, Li H, Speck C, Weinreich M. Cdc6 ATPase activity disengages Cdc6 from the pre-replicative complex to promote DNA replication. Elife. 2015 Aug 25;4.

7. Eswaramoorthy S, Sun J, Li H, Singh BR, Swaminathan S. Molecular Assembly of Clostridium botulinum progenitor M complex of type E. Scientific reports. 2015; 5:17795.

8. Yu H, Takeuchi M, LeBarron J, Kantharia J, London E, Bakker H, Haltiwanger RS, Li H, Takeuchi H. Notch-modifying xylosyltransferase structures support an SNi-like retaining mechanism. Nat Chem Biol. 2015 Nov;11(11):847-54.

9. Werneburg G, Henderson NS, Portnoy EB, Sarowar S, Hultgren SJ, Li H, and Thanassi DG. The Pilus Usher Uses Domain Masking to Control Protein-Protein Interactions During Pilus Biogenesis and Functions as an Oligomer In Vivo. Nat Struct Mol Biol., 2015 Jul;22(7):540-6.

10. Tian Y, Wang T, Liu W, Xin H, Li H, Ke Y, Shih W, Gang O. Mesoscale 3D Nanoparticle Clusters with Prescribed Architectures. Nature Nanotechnology 2015 Jul;10(7):637-44.

11. Liu W, Tarawa M, Xin H, Wang T, Emamy H, Li H, Yager KG, Starr FW, Tkachenko AV, Gang O. Diamond family of nanoparticle superlattices. Science, 2016 Feb 5;351(6273):582-6. doi: 10.1126/science.aad2080.

12. Tian Y, Zhang Y, Wang T, Li H, Gang O. Lattice Engineering via Nanoparticle-DNA Frameworks. Nature Materials, 2016 Feb 22. doi: 10.1038/nmat4571.

Erwin London

Lin, Q., and London, E. (2015) Lin “Ordered Raft Domains Induced by Outer Leaflet Sphingomyelin in Cholesterol-Rich Asymmetric Vesicles” Biophys. J., 108, 2212-2022.

London, E. (2015) “Membrane Fusion: A New Role For  Membrane Domains?” Nature Chemical Biology, 11, 383 – 384.

Farnoud, A, Toledo, A.M., Konopka J.B., Del Poeta, M., London, E. (2015) “Raft-Like Membrane Domains in Pathogenic Microorganisms”, Current Topics in Membranes, Volume 75 “Membrane Domains” (A. Kenworthy, Editor), Academic Press/Elsevier, Amsterdam, pages 233-268.

Lin, Q., Wang, T., Li. H, and London, E. (2015) “Decreasing Transmembrane Segment Length Greatly Decreases Perfringolysin O Pore Size”, J. Memb. Biol. 248, 517-527.

Kim, J., and London, E. (2015) “Using sterol substitution to probe the role of membrane domains in membrane functions” Lipids 50, 721-734.

Pathak, P. and London, E. (2015) “Effect of Membrane Lipid Composition Upon the Formation of Ultra-Nanodomains”, Biophys. J., 109, 1630-1638.

Yu, H., Takeuchi, M., LeBarron, J., Kantharia, J., London, E., Bakker, H., Haltiwanger, R.S., Li, H., Takeuchi, H. (2015) “Structures of a Notch-modifying xylosyltransferase support an SNi-like retaining mechanism”, Nature Chemical Biology, 11,847-854.

Kenneth Marcu

Olivotto, E., Otero, M., Marcu, KB and Goldring, MB (2015).  Pathophysiology of  Osteoarthritis: Canonical NF-appaB/IKKeta-dependent and kinase independent effects of IKKlpha in Cartilage Degradation and Chondrocyte Differentiation.   RMD Open 1:e000061.doi:10.1136/rmdopen-

David Matus

D.Q. Matus, L.L. Lohmer, L.C. Kelley, A.J. Schindler, A.Q. Kohrman, M. Barkoulas, W. Zhang, Q. Chi, D.R. Sherwood, Invasive Cell Fate Requires G1 Cell-Cycle Arrest and Histone Deacetylase-Mediated Changes in Gene Expression. 2015. Dev Cell Oct 26.

comment in: Dev Cell, 2015 Oct 26: 143-44

comment in: Scientific American, 2016 Jan 1

Moczek AP, Sears KE, Stollewerk A, Wittkopp PJ, Diggle P, Dworkin I, Ledon-Rettig C, Matus, DQ, Roth S, Abouheif, E, et al. (2015). The significance and scope of evolutionary developmental biology: a vision for the 21st century. Evol Dev 17, 198-219.

Aaron Neiman

Jin, L., Zhang, K., Xu, Y., Sternglanz, R., Neiman, A.M. (2015).  Sequestration of mRNAs Modulates the Timing of Translation during Meiosis in Budding Yeast.  Mol Cell Biol. 35:3448-3458.

Park, J.-S., Halegoua, S., Kishida, S., and Neiman, A. M. (2015).  A conserved function in phosphatidylinositol metabolism for mammalian Vps13 family proteins.  PLoS One, 10:e0124836

 Jin, L. and Neiman, A. M. (2015) Post-transcriptional regulation in budding yeast meiosis Curr Genet. epub 17Nov

Steven Smith

Fu Z, Aucoin D, Davis J, Van Nostrand WE and Smith SO. (2015) Mechanism of Nucleated Conformational Conversion of Aβ Biochemistry 54(27):4197-207.

Opefi CA, Tranter D, Smith SO, and Reeves PJ. (2015) Construction of stable mammalian cell lines for inducible expression of G protein-coupled receptors. Methods Enzymol. 556:283-305.

Kimata N, Reeves PJ, and Smith SO. (2015) Uncovering the triggers for GPCR activation using solid-state NMR spectroscopy. J Magn Reson. 253:111-8.

Kimata N, Pope A, Rashid D, Reeves PJ, Smith SO. (2015) Sequential structural changes in rhodopsin occurring upon photoactivation. Methods Mol Biol. 1271:159-71.

Marinangeli C, Tasiaux B, Opsomer R, Hage S, Sodero AO, Dewachter I, Octave JN, Smith SO, Constantinescu SN, and Kienlen-Campard P (2015) Presenilin transmembrane domain 8 conserved AXXXAXXXG motifs are required for the activity of the γ-secretase complex. J Biol Chem. 290(11):7169-84.

Decock M, El Haylani L, Stanga S, Dewachter I, Octave JN, Smith SO, Constantinescu SN, Kienlen-Campard P. (2015) Analysis by a highly sensitive split luciferase assay of the regions involved in APP dimerization and its impact on processing. FEBS Open Bio 5, 763-773.

Leroy, E., Defour, J.P., Sato, T., Dass, S., Gryshkova, V, Shwe, M.M., Staerk, J., Constantinescu, S.N. and Smith, S.O. (2016) His499 regulates dimerization and prevents oncogenic activation by asparagine mutations of the human thrombopoietin receptor. Biol. Chem., 291, 2974-87.

Rolf Sternglanz

Jin, L., Zhang, K., Xu, Y., Sternglanz, R. and Neiman, A.M.  (2015) Sequestration of mRNAs modulates the timing of translation during meiosis in budding yeast.  Mol. Cell. Biol.  35: 3448-3458.

Lin, C.-J., Smibert, P., Zhao, X., Hu, J.F., Ramroop, J., Kellner, S., Benton, M., Govind, S., Dedon, P., Sternglanz, R. and Lai, E.C. (2015) An extensive allelic series of Drosophila kae1 mutants reveals diverse and tissue-specific requirements for t6A biogenesis. RNA  21, 2103-2118.

Lonnie Wollmuth

Alsaloum, M., R. Kazi, Q. Gan, J. Amin, and P. Wollmuth (2016) A molecular determinant of subtype-specific desensitization in ionotropic glutamate receptors. Journal of Neuroscience. In press.

Gan, Q., Dai, H-X. Zhou, and L. P. Wollmuth (2016) The transmembrane domain mediates tetramerization of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors. Journal of Biological Chemistry. In press.

Gan, Q., C. L. Salussolia, and P. Wollmuth (2015) Assembly of AMPA receptors: mechanisms and regulation. The Journal of Physiology. Invited review. 593:39-48.

Wollmuth, L. P (2015) Is cholesterol good or bad for your brain? – NMDARs have a say. The Journal of Physiology. Invited commentary.

Salussolia, C. L., Q. Gan, and P. Wollmuth (2015) Assaying AMPA receptor oligomerization. In: Ionotropic glutamate receptor technologies, G. Popescu, editor.  Humana Press.  Volume 106:3-14.

Kazi, R., M. Daniel, and P. Wollmuth (2015) Characterizing the thermodynamics of NMDA receptor pore opening. In: Ionotropic glutamate receptor technologies, G. Popescu, editor.  Humana Press.  Volume 106:145-162.

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