2010 Rustbelt RNA Meeting






Friday, Oct 22
12:30-12:45pmOpening Remarks - Organizers (Saba Valadkhan, David Rueda, Paula Bubulya, John Means)
Session I: Keynote Lecture I
12:45-01:30pmmiRNAs and mRNPs: where we are today
Timothy W. Nilsen
RNA Center/Biochemistry, Case Western Reserve University
Session II: Non Coding RNAs (Leonard Lipovich)
01:30-01:45pmMechanistic Analysis of The Function of A Large Non-coding RNA
Bing Zhang, Fereshteh Kenari, Saba Valadkhan
Center for RNA Molecular Biology, Case Western Reserve University
01:45-02:00pmA Global Mechanism for Non-coding RNA Dependent Chromatin Formation in Mammals
Ahmad M Khalil, John L. Rinn
RNA Center, Case Western University School of Medicine
02:00-02:15pmDecapping regulates non-coding RNA-dependent histone modification in Saccharomyces cerevisiae
Sarah Geisler, Lisa Lojek, Jeff Coller
Center for RNA Molecular Biology, Case Western Reserve University
02:15-02:30pmBiogenesis of Mirtrons Independent of Splicing and the Microprocessor
Mallory A. Havens, Ashley A. Reich, Michelle L. Hastings
Cell Biology and Anatomy, Chicago Medical School at Rosalind Franklin University, North Chicago, IL, USA
02:30-02:50pmCoffee Break
Session III: Regulation (Rick Padgett)
02:50-03:10pmA meiotic gene regulatory cascade driven by alternative fates for newly synthesized transcripts
Nicole Cremona, Kristine Potter, Jo Ann Wise
Molecular Biology & Microbiology, Case Western Reserve Univ.
03:10-03:25pmDetailed analysis of one step of ribosome biogenesis in Saccharomyces cerevisiae
Aarti Sahasranaman, John Strahler, Philip Andrews, Janine Maddock, John Woolford
Department of Biological Sciences, Carnegie Mellon University
03:25-03:40pmeIF2α phosphorylation dependent regulation of XBP1 mRNA turnover amplifies the UPR signaling during ER stress.
Mithu Majumder, Dawid Krokowski, Charlie Huang, Chuanping Wang, Maria Hatzoglou
Department of Nutrition, Case Western Reserve University.
03:40-03:55pmRibosomal protein L13a-dependent translational silencing resolves inflammation: A study with macrophage-specific KO mouse.
Darshana Poddar, Abhijit Basu, Fatih Gulen, Barsanjit Mazumder
Department of Biology, Geology and Environmental Science, Cleveland State University, Cleveland
03:55-04:15pmProtein contacts among termination and polyadenylation factors that control mRNA 3' end fate.
Thomas Leeper, Gabriele Varani
University of Akron
04:15-04:35pmCoffee Break - PIs Meeting
Session IV: Structure (Barbara Golden)
04:35-04:50pmMechanistic insights into 3'--5' nucleotide addition by tRNAHis guanylyltransferase (Thg1)
Brian A. Smith, Jane E Jackman
The Ohio State University
04:50-05:05pmSingle molecule studies of the c-di-GMP riboswitch
Sharla Wood, Nadia Kulshina, Adrian Ferre-DAmare, David Rueda
Department of Chemistry, Wayne State University
05:05-05:20pmMolecular Mechanics Analysis of Minimum Energy RNA Conformational Dynamics Pathways
Keith P. Van Nostrand, Scott D. Kennedy, Douglas H. Turner, David H. Mathews
Department of Biochemistry and Biophyics, University of Rochester
05:20-05:35pmEfficiency of riboswitch terminator folding during transcription
Michael Widom, Ben Sauerwine
Department of Physics, Carnegie Mellon University
05:35-05:50pmG-quadruplexes in Arabidopsis thaliana: Folding cooperativity and implications for drought stress regulation
Melissa A. Mullen, Kalee J. Olson, Paul Dallaire, Franšois Major, Sarah M. Assmann, Philip C. Bevilacqua
Department of Chemistry, The Pennsylvania State University
Session V: Keynote Lecture II
06:00-07:00pmStructural and sequence-space analysis of natural and artificial catalytic RNAs
Adrian Ferre-DAmare
Howard Hughes Medical Institute, F. Hutchinson Cancer Ctr.
Session VI: Poster Session
08:30-09:45pmOdd Posters
09:45-11:00pmEven Posters
Saturday, Oct 23
07:30-08:30amContinental Breakfast
Session VII: RNA and Pathogens (Pat Limbach)
08:30-08:50amElucidating the RNA-protein complex of Plasmodium telomerase
Kausik Chakrabarti
Dept. of Chemistry, Carnegie Mellon University
08:50-09:05amCharacterization of an RNA-binding pentatricopeptide repeat protein from Trypanosoma brucei.
Pakoyo F Kamba, Jennifer L Ekstrom, David A Dickson, Charles G Hoogstraten
Biochemistry and Molecular Biology / Cell and Molecular Biology Program, Michigan State University
09:05-09:20amIdentification of proteins involved in alternative polyadenylation during infection by herpes simplex virus 1.
Huda Hyjazie, Angela Pearson
INRS-Institut Armand-Frappier
09:20-09:35amMolecular Mimicry of primer tRNALys3 by HIV-1 RNA genome facilitates viral replication
Christopher P. Jones, Jenan Saadatmand, Lawrence Kleiman, Karin Musier-Forsyth
Departments of Chemistry and Biochemistry, Center for Retroviral Research, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210
09:35-09:50amRegulation of PKR by HCV IRES RNA: Importance of Domain II
Rebecca Toroney, Subba Rao Nallagatla, Joshua A. Boyer, Craig E. Cameron, Philip C. Bevilacqua
Department of Chemistry, Penn State University
09:50-10:10amCoffee Break
Session VIII: Modifying RNA (Juan Alfonzo)
10:10-10:25amShining the Light on Dim2
Heather Woolls, Katrin Karbstsein
Chemical Biology Doctoral Program, University of Michigan
10:25-10:40amA Tale of Two Editing Domains: Molecular Basis of Substrate Specificity of Bacterial Prolyl-tRNA Synthetase and YbaK
Sandeep Kumar, Mom Das, Christopher M. Hadad, Karin Musier-Forsyth
Chemistry, Ohio State Biochemistry Program, Center for RNA Biology, Ohio State University
10:40-10:55amInvestigation of debranching enzyme
Molly Evans, Eduardo Paredes, Mark Macbeth, Subha R. Das
Department of Biological Sciences, Carnegie Mellon University
10:55-11:10amAntisense oligonucleotide correction of splicing in a mouse model of Usher syndrome
Francine M. Jodelka, Anthony Hinrich, Kate McCaffrey, Jennifer J. Lentz, Dominik M. Duelli, Michelle L. Hastings
Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA
11:10-11:25amElucidation of the binding determinants for hnRNP A1 on HIV-1 splice site A7
Jeffrey Levengood, Clay Mishler, Brittany Felder, Elissa Falconer, Nitika Dewan, Blanton Tolbert
Department of Chemistry and Biochemistry, Miami University
11:25-11:45amCoffee Break
Session IX: Ribotechniques and Bioinformatics (Phil Bevilacqua)
11:45-12:00pmRNA fingerprinting by the phi29 DNA packaging motor nanopore
Jia Geng, Farzin Haque, Jing Peng, Dan Shu, Peixuan Guo
Nanobiomedical Center, University of Cincinnati
12:00-12:15pmDual-channel single-molecule fluorescent resonance energy transfer to establish distance constraints for RNA nanoparticles
Dan Shu, Hui Zhang, Roman Petrenko, Jarek Meller, Peixuan Guo
Nanobiomedical Center, College of Engineering and Applied Science/College of Medicine, University of Cincinnati
12:15-12:30pmReal-Time Super-Resolution Tracking of Single Deoxyribozyme Based Molecular Robots
Anthony J. Manzo, Alexander Johnson-Buck, Nils G. Walter, Kyle Lund, Jeanette Nangreave, Hao Yan, Nicole Michelotti, Steven K. Taylor, Renjun Pei, Milan N. Stojanovic, Nadine Dabby, Erik Winfree
Department of Chemistry, University of Michigan, Ann Arbor
12:30-12:50pmA 1.9 ┼ crystal structure of the HDV ribozyme precleavage suggest both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage
Jui-Hui Chen, Rieko Yajima, Durga M. Chadalavada, Elaine Chase, Philip C. Bevilacqua, Barbara L. Golden
Department of Biochemistry, Purdue University
12:50-01:10pmTranscription and splicing of large human genes
Richard A. Padgett, Jarnail Singh
Molecular Genetics, Cleveland Clinic
01:10-01:30pmSystems biology of the lncRNAome: computational-experimental integration assigns long non-coding RNA molecules to specific regulatory networks.
Leonard Lipovich, Hui Jia, Jameelah Sheik Mohamed, Paul Robson, Shruti Bagla, Fabien Dachet, Jeffrey A. Loeb
Center for Molecular Medicine and Genetics, Wayne State University
01:30-01:50pmSmall angle x-ray scattering analysis of the basepaired complex of U6 and U2 snRNAs points to an RNA chaperone role for proteins in assembly of the spliceosomal active site
Zheng Li, Shihu Wang, Elena Dormidontova, Farshad Niazi, Caroline Lee, Saba Valadkhan, Alex. M. Jamieson, James L. Manley
Department of Macromolecular Science & Engineering, Case Western Reserve University
01:50-02:00pmClosing Remarks and Awards - 2011 Organizers (Paula Bubulya, John Means)