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Book of Abstracts: Albany 2009

category image Albany 2009
Conversation 16
June 16-20 2009
© Adenine Press (2008)
Showing 1 to 100 of 218 items.  Page: 1 3

Eukaryotic mRNA Decapping Occurs on Polyribosomes

Wenqian Hu, Thomas Sweet, Kristian Baker, Jeff Coller

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Functional Interactions Between the Ribosome and the Nascent Peptide

Nora Vazquez-Laslop, Blanca Martinez-Garriga, Haripriya Ramu, Dorota Klepacki, Alexander Mankin

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Homology Modeling and Molecular Dynamics Simulations of RNA Polymerases

Ivan Barvik, Kamil Malac

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Identification of the Evolving RNA Nano-machine for Protein Biosynthesis Within the Contemporary Ribosome

Ada Yonath

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Investigations of Translational GTPases using Isothermal Titration Calorimetry Reveal G-nulceotide Dependent Structural Rearrangements

Vladimir A. Mitkevich, Alexander A. Makarov, Artem Kononenko, Tanel Tenson, Mans Ehrenberg, Vasili Hauryliuk

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Kinetics of mRNA and tRNA Selection by the Ribosome

Marina V. Rodnina

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Kinetics of the rRNA-Catalyzed Peptidyl-Transfer to Native aa-tRNAs

Magnus Johansson, Kaweng Ieong, Elli Bouakaz, Martin Lovmar, Peter Strazewski, Michael Pavlov, Måns Ehrenberg

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Structural Diversity and Functional Versatility Among Phenylalanyl-tRNA Synthetases in Primary Kingdoms

Mark Safro, Nina Moor, Igal Finarov, Liron Klipcan

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Structural Dynamics of Elbow Segment of E. coli Ribosomal A-site Finger. Comparison of Simulations with Cryo-EM Data and with Equivalent Segments in Other Species.

Kamila Reblova, Filip Razga, Wen Li, Haixiao Gao, Joachim Frank, Jiri Sponer,

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The Mechanism of aa-tRNA Entry into the Ribosome

Wen Li, Elizabeth Villa, Joachim Frank

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The P-site tRNA Reaches the P/E Position Through Intermediate Positions

Jie Fu, Drew Kennedy, James B. Munro, Jianlin Lei, Scott C. Blanchard, Joachim Frank

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The Ribosomal Stalk Plays a Key-role in the Translation Initiation in Bacteria

Chenhui Huang, Chandra Sekhar Mandava, Suparna Sanyal,

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A PX DNA Triangle Oligomerized Using a Novel Three-Domain Motif

Wenyan Liu, Xing Wang, Tong Wang, Ruojie Sha, Nadrian C. Seeman

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Braided DNA

Tanashaya Ciengshin, Ruojie Sha, Nadrian C. Seeman

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Dynamic Patterning Programmed by DNA Tiles Captured on a DNA Origami Substrate

Hongzhou Gu, Jie Chao, Shou-Jun Xiao, Nadrian C. Seeman

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Exploring the Rigidity of DNA Nanotubes

Tong Wang, Sergio Martinez, Deborah Kuchnir Fygenson, Nadrian C. Seeman

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Self-assembly of DNA into Nanoscale Three-Dimensional Shapes

William M. Shih, Shawn M. Douglas, Hendrik Dietz, Tim Liedl, Bjorn Hogberg, Franziska Graf

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The Rational Design and Structural Analysis of a Self-Assembled Three-Dimensional DNA Crystal

Jianping Zheng, Jens J. Birktoft, Yi Chen, Ruojie Sha, Tong Wang, Pamela E. Constantinou, Chengde Mao, Stephan L. Ginell, Nadrian C. Seeman

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Wires, Reporters and Information Capsules: Cellular journalism with DNA

Yamuna Krishnan

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Dendritic DNA Molecules: Towards Controllable Nanomaterials

Karina M. M. Carneiro, Faisal A. Aldaye, Hanadi F. Sleiman

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Modular Construction of DNA Nanotubes of Tunable Geometry, Alternating Size and Single- or Double-stranded Character

Pik Kwan Lo, Faisal A. Aldaye, Hanadi F. Sleiman

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Supramolecular DNA Nanotechnology

Hanadi Sleiman, Faisal Aldaye, Peggy Lo, Hua Yang, Chris McLaughlin, Karina Carneiro

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A Stochastic Single-Molecule Event Triggers Phenotype Switching of a Bacterial Cell

X. Sunney Xie

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Conformational Equilibria of Intrinsically Disordered Proteins Probed by Single Molecule Methodologies

Bruno Samori

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DNA Interaction Properties of Nucleic Acid Chaperone Proteins From Retrotransposons

Kathy Chaurasiya, Fei Wang, Gael Cristofari, Jean-Luc Darlix, Sandra L. Martin, Mark C. Williams

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Interrogating Single Nucleic Acid and Protein Molecules with a Nanopore

Liviu Movileanu

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Kinetics of DNA Force-Induced Melting

Micah J. McCauley, Leila Shokri, Ioulia Rouzina, Mark C.Williams

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Nucleic Acid Interaction Kinetics Modulate the Chaperone Activity of Retroviral Nucleocapsid Proteins

Fei Wang, Kristen M. Stewart-Maynard, Margareta Cruceanu, Dominic F. Qualley, Mithun Mitra, Robert J. Gorelick, Ioulia Rouzina, Karin Musier-Forsyth, Mark C. Williams

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Quantifying Multiple DNA Binding Modes of Actinomycin D Using Optical Tweezers

Thayaparan Paramanathan, Ioana D Vladescu, Micah J. McCauley, Ioulia Rouzina, Mark C.Williams

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Single molecule analysis of motors moving on RNA

Taekjip Ha

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Analysis of the Role of Intrinsic Disorder in Multiple Specificity

Christopher J. Oldfield, Vladimir N. Uversky, A. Keith Dunker

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Comparative Genomics of Alternative Splicing

Mikhail Gelfand

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Human Induced Pluripotent Stem Cells Derived with Episomal Vectors

James Thomson

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Hypothesis: Signaling Diversification Is Enabled by Alternative Splicing, Posttranslational Modification, and Multiple Partner Binding at Loci Within Intrinsically Disordered Protein Regions

A. Keith Dunker

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RNA-Protein Interactions Reveal Alternative Splicing Networks in Human Embryonic Stem Cells

Gene W. Yeo, Nicole G. Coufal, Tiffany Liang, Grace Peng, Xiang-dong Fu, Fred H. Gage

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Contribution of miRNA-mediated Gene Regulation to the Evolution of Animal Eye

Atsushi Ogura

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Effects of Human Genetic Variation on the Structure of mRNA UTRs

Matthew Halvorsen, Abhinab Ray, Katrina Simmons, Joshua Martin, Alain Laederach

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Light Activated RNA Interference Using Photo-cleavable siRNA

Samit Shah, Piyush Jain, Dipu Karunakaran, Ashish Kala, Subhashree Rangarajan, Simon H. Friedman

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Modulation of Gene Expression by Synthetic Nucleic Acids

David Corey, Masayuki Matsui, Jiaxin Hu, Bethany Janowski, Scott Younger, Jacob Schwartz

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Regulatory RNAs in Bacteria: Biological Roles and Mechanisms

E. Gerhart H. Wagner

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Structure-based Genetic Surveillance Mechanisms

Andrew Fire

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What is the Function of Dicer's Helicase Domain?

Noah C. Welker, Tuhin S. Maity, P. Joe Aruscavage, Brenda L. Bass

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Analysis of reprogramming of cellular fate induced by a large non-coding RNA

Fereshteh Jahaniani, Farshad Niazi, Bing Zhang, Saba Valadkhan

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Force and Form in RNA Folding

Dan Herschlag

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Group II Intron Structure and Function: The Accidental Architects of Biological Diversity

Anna Marie Pyle

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Investigation of Natural and Selected Nucleic Acid Enzymes that Depend on Coenzymes

Subha Das, Eduardo Paredes,

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Reversible Backbone Linkages and Intercalators as Key Components of the Proto-RNA World

Aaron E. Engelhart , Eric D. Horowitz, David Lynn, Nicholas V. Hud

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Splicing Mechanisms: Lessons from Single-Molecule Spectroscopy

David Rueda, Zhuojun Guo, Krishanthi Karunatilaka

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Structural and Functional Studies of the Drosophila Melanogaster Small Nuclear RNA Activating Protein Complex (DmSNAPc)

William E. Stumph, Ko-Hsuan Hung, Hsien-Tsung Lai, Nermeen H. Barakat, Mitchell Titus, Shu-Chi Chiang

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Structural Insight into RNA Catalysis Revealed by Molecular Dynamics Simulations and QM/MM Calculation

Pavel Banas, Nils G. Walter, Jiri Sponer, Michal Otyepka

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Structural Insights into Ribonucleoprotein Enzymes

Bo Liang, Jing ZhouElliot Kahen, Rebecca M. Terns, Michael P. Terns, Hong Li

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The role of Noncoding RNAs in splicing and neurogenesis

Saba Valadkhan

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A Modular Strategy for Tailoring Ribonucleopeptide-based Fluorescent Sensors

Takashi Morii

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All-Atom RNA Tertiary Structure Prediction

Matthew G. Seetin, David H. Mathews

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Carbocyclic Sugars Constrained to North and South Conformations Stabilize and Control RNA Conformations

Taejin Kim, Victor E. Marquez, Bruce A. Shapiro

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Classification and Energetics of the Base-Phosphate Interactions in RNA

Craig L. Zirbel, Judit E. Sponer, Jiri Sponer, Jesse Stombaugh, Neocles B. Leontis

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Computational Design Strategies for RNA Nanostructures

Bruce A. Shapiro

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Conformation Change of the Loop Adenine of Avian Leukosis Virus RNA Upon Antibiotic Binding Revealed by 2-Aminopurine Fluorescence

E.E. Minyat, I.Z. Shukshina

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Exploration of Structural Building Block Properties for RNA Nanostructures

Wojciech Kasprzak, Eckart Bindewald, Tae-Jin Kim, Bruce A. Shapiro

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From RNA Bioinformatics to RNA Ontology

Neocles B. Leontis

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Modeling of Structure and Dynamics of Eukaryotic Ribosomal Termination Complex of eRF1-mRNA-tRNA

Y.N. Vorobjev

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Molecular Dynamics Simulations and Quantum Chemistry as Useful Complements to RNA Structural Bioinformatics

Jiri Sponer

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Molecular Mechanics Analysis of Minimal Energy RNA Conformational Change Pathways

Keith Van Nostrand, Scott D. Kennedy, David H. Mathews

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Peculiarities of Interaction of Porphyrins with tRNA

Y. Dalyan, I. Vardanyan, A. Chavushyan

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RNA Binding Aspects of Isoquinoline Alkaloids: Affinity, Specificity, and Energetics

Md. Maidul Islam, Gopinatha Suresh Kumar

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RNA Sequence Design by Reconstruction from Shape and Guiding Observables

Assaf Avihoo, Nir Dromi, Danny Barash

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RNA Simulation - Part I: SwS: Solvation Web Service for Nucleic Acids, a New Tool Dedicated to the Analysis of Nucleic Acids Solvation

Yaser Hashem, Pascal Auffinger

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RNA Simulations - Part 2: Molecular Dynamics Simulations of RNA Fragments at Hydrogen Resolution

Yaser Hashem, Pascal Auffinger

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RNA Simulations - Part 3: Mapping Solvent Binding Sites of the Aminoglycoside Bacterial rRNA A-site Target

Yaser Hashem, Pascal Auffinger

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RNA Three-Way Junctions Can Act as Flexible RNA Structural Elements in Large RNA Molecules: A Molecular Simulation Analysis

Ivana Besseova, Kamila Reblova, Neocles B. Leontis, and Jiri Sponer

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RNAstructure: Software for RNA Secondary Structure Prediction and Analysis

Jessica Reuter, David H. Mathews

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Sequence-dependent Deformability of RNA Helical Regions. What We Have Learned So Far

Mauricio Esguerra, Wilma K. Olson

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Structural characterization of cationic lipid-tRNA complexes

H. A. Tajmir-Riahi, D. Charbonneau, R. Marty, C. N. N?soukpoé-Kossi, L. Kreplak

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Thermal Behavior of Retrovirus RNA Dimers and Its Stabilization by Paromomycin Using Fluorescence Melting

Dmitry N. Kaluzhny, Artemy D. Beniaminov, Elvira E. Minyat

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Bidirectional expression of trinucleotide repeats: Studies of the DM1 and FMR1 loci suggest that trinucleotide repeats are associated with an RNA-mediated heterochromatin modification and insulator function

Paula Ladd, Diane Cho, Stephen Tapscott, Galina Filippova

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CAG repeat hairpins as potential triggers of RNA-mediated pathogenesis and therapeutic targets in polyglutamine diseases

Agnieszka Mykowska, Mateusz deMezer, Agnieszka Fiszer, Marta Olejniczak, Krzysztof Sobczak, Piotr Kozlowski, Maciej Figiel, Pawel Switonski, Wlodzimierz J. Krzyzosiak

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DNA Structure-induced Genetic Instability

Guliang Wang, Karen M. Vasquez

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Genome-wide screen to identify genes involved in inverted repeat and GAA/TTC-mediated fragility

Yu Zhang, Vidhya Narayanan, Kirill S. Lobachev

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Interaction of Triplex Forming Oligonucleotides (TFOs) and Various Anti-cancer Drugs with a Promoter Regions of c-met and c-myc

Moganty R. Rajeswari, Garima Singhal, and Akanchha

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Role of Oxidative DNA Damage and Repair in Triplet Repeat Expansion

Amalia Avila-Figueroa, Daniel Jarem, Nicole Wilson, Sarah Delaney

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Small molecules that enhance GAA/TTC fragility

Lobachev K.S., Kim H-M., Narayanan V, Persil O., Hud N.V.

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Triplex-Forming Oligonucleotides (TFO-s) as Probes for Promoter Region of Cancer Relevant Human mdr1 Gene

Anna Gabrielian

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Yeast system to study expansions of DNA repeats

Alexander A. Shishkin, Irina Voineagu, Robert Matera, Nicole Cherng, Brook T. Chernet, Maria M. Krasilnikova, Vidhya Narayanan, Kirill S. Lobachev, Sergei M. Mirkin

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Analysis of Hydrogen Bonds Involving Backbone Atoms in Ribosomal RNA

Nikolai B. Ulyanov, Thomas L. James

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Evidence for Proximal to Distal Appendage Amputation Site Effects from Global Gene Expression Correlations Found in Newt Microarrays

Chia-Ho Cheng, Kenneth A. Marx, John Sharko, Georges G. Grinstein, Shannon Odelberg, Hans-Georg Simon

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Evolution of the Central Nervous System: Comparative Gene Expressionics Approach

Takashi Gojobori

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Evolution of the Translational GTPase Superfamily

Gemma Atkinson, Sandra Baldauf

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Metabolome Analysis and Systems Biology

Masaru Tomita

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On the Evolutionary Origin of Mammalian Specific Features of the Neocortex

Ikuo Suzuki, Tatsumi Hirata, Takashi Gojobori

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The ?protein-scape? of eukaryotic chromatin

L. Aravind

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Unique Correlation Patterns of Sequence Repeats and Splice Junctions in Eukaryotic Protein Sequences

E. Aharonovsky, E.N. Trifonov

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Conformational Change of a Group II Chaperonin in Different States Revealed by Single-particle Cryo-EM

Junjie Zhang, Matthew L. Baker, Gunnar Schröder, Nick R. Douglas, Joanita Jakana, Caroline J. Fu, Michael Levitt, Steven J. Ludtke, Judith Frydman, Wah Chiu

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Electron Cryo-microscopy of Molecular Nanomachines and Cells

Wah Chiu

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Molecular Anatomy Of The Human Pathogen Leptospira interrogans

Martin Beck

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The Molecular Architecture of Integrin-Mediated Focal Adhesion by Cryo-Electron Tomography

Ohad Medalia

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Probing Protein Folding on the Ribosome by Solution State NMR Spectroscopy

Shang-Te Danny Hsu, Lisa D. Cabrita, Paola Fucini, Christopher M Dobson, John Christodoulou

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RNA sequencing: A deeper look into persisters, drug tolerant bacteria

Huiyi Chen , Paul J. Choi, Eric J. Rubin , X.Sunney Xie

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Structural Aspects of Oligonucleotide-mediated Artificial Ribonucleases

Steven M. Miles, Mengisteab B. Gebrezgiabher, Dmitrii V. Pyshnyi, Nadezhda L. Mironova, Marina A. Zenkova, Valentin V. Vlassov, Elena V. Bichenkova

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Using Photoactivation Light Microscopy (PALM) to construct comprehensive, nanometer precision atlases of signaling complexes

Jan Liphardt

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Visualizing lowly-populated regions of the free energy landscape of macromolecular complexes by paramagnetic relaxation enhancement

G. Marius Clore

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Showing 1 to 100 of 218 items.  Page: 1 3