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For the fifth year running, NAR and Oxford Journals have awarded prizes to students in recognition of their outstanding achievements. This year, prizes were awarded at eight different meetings. A detail list of the awards is presented below. Our warm congratulations go to the prize winners.
Sant Feliu de Guixols, Spain, 30 May–4 June 2010
First Prize—Vitantonio Pantaleo (Istituto di Virologia Vegetale, CNR, Italy)
Laura Miozzi, Jozsef Burgyan and Vitantonio Pantaleo
In plants, RNA silencing is a surveillance mechanism against invading viruses. In this work, the authors have used a high-throughput sequencing approach in order to identify both viral siRNAs and their targets along the viral genomes of two viruses in their own natural host. A consistent fraction of vsiRNAs did not account for cleavage sites, suggesting that relatively few vsiRNAs are involved in the antiviral response.
Anna Kurzynska-Kokorniak (Institute of Bioorganic Chemistry, Poznan, Poland)
Anna Kurzynska-Kokorniak, Zofia Maja Pietrusiewicz and Marek Figlerowicz
MicroRNAs (miRNAs) have been shown to be important factors shaping host–virus interactions. Anna’s results suggest that one can affect viral replication cycle by using RNA aptamers specifically regulating the activity of human Dicer, the key enzyme involved in miRNA biogenesis.
Sadia Hamera (Institute of Microbiology, Beijing, China)
Sadia Hamera et al.
Saxtons River, Vermont, 6–11 June 2010
Best Poster Award Winner: Noah Ribeck (UC Santa Barbara, USA)
Noah Ribeck, Daniel L. Kaplan, Irina Bruck and Omar A. Saleh
Single-molecule manipulation experiments with magnetic tweezers reveal a DNA geometry-dependent interaction between DnaB helicase and the double-stranded DNA fork, and evidence that single-stranded DNA is bound by DnaB in a compacted geometry.
Boston, MA, USA, 9 July and 11–13 July 2010
Best Student Presentation Award: Geoff MacIntyre (University of Melbourne, Australia)
Geoff Macintyre, James Bailey, Izhak Haviv and Adam Kowalczyk
Geoff used transcription factor (TF) binding matrices to successfully determine, in silico, if a SNP has the potential to affect TF binding.
Best Poster Award Winner: Wouter Meuleman (Netherlands Cancer Institute, Amsterdam, The Netherlands)
Wouter Meuleman, Daan Peric Hupkes, Marcel Reinders, Lodewyk Wessels and Bas van Steensel
Our genome—nuclear lamina interaction maps show that although the genome is highly reorganized during cell differentiation, a substantial portion of the genome is organized identically in all assayed cell types and that this organization is highly conserved between mouse and human.
Best Poster Award Runner Up: Mark McDowall (European Bioinformatics Institute, Cambridge, UK)
Mark D. McDowall, Michelle S. Scott and Geoffrey J. Barton
Mark’s poster described the prediction of human protein–protein interactions by integrating experimental and annotative evidence within a semi-naïve Bayesian framework.
Bremen, Germany, 1–6 August 2010
Outstanding short talk: Mtaladi N. Ndlovu (Université Libre de Bruxelles, Belgium)
Matladi N. Ndlovu, François Fuks et al.
Epigenetic mechanisms including DNA methylation and histone modifications are increasingly regarded as the cornerstones of gene function ensuring the correct deployment of developmental programs and the maintenance of cell fates; the authors studied the cooperation of these key mechanisms in cancer cells.
Outstanding poster: Gintautas Tamulaitis (Institute of Biotechnology, Vilnius, Lithuania)
Gintautas Tamulaitis, Mindaugas Zaremba, Bernard A. Connolly and Virginijus Siksnys
The cleavage and binding of nucleotide flipping restriction enzymes could be elegantly tuned up by using X-linked DNA substrates or exogenous nucleobases.
Outstanding poster: Devora Cohen-Karni (New England Biolabs, Ipswich, MA, USA)
Devora Cohen-Karni, Derrick Xu, Alexy Formenkov, Shuang-yong Xu, Megumu Yamada- Mabuchi, Sriharsa Pradhan, Richard J. Roberts and Yu Zheng
MspJI family is a unique modification-dependent restriction endonuclease family which cleaves at fixed distance away from the modification site generating a 32-mer fragment around it, which can be directly isolated and sequenced, thus enabling a novel tool for DNA modification investigation and epigenetic research.
Outstanding poster: Dr Renata Jurkowska (Jacobs University, Bremen, Germany)
Renata Z. Jurkowska, Arumugam Rajavelu, Nils Anspach, Sergei Ragozine, Claus Urbanke, Wolfgang Nellen and Albert Jeltsch
The authors show that Dnmt3a, a mammalian C5 DNA methyltransferase, polymerizes on the DNA and that this polymerization contributes to the localization of the enzyme to pericentromeric heterochromatin in the cell, indicating that filament formation by Dnmt3a on DNA might support its function.
Outstanding poster: Dr Eva Sisakova (University of Bristol, UK)
Eva Sisakova, Rachel Smith and Mark Szczelkun
The objective of this study is to understand how the helicase-based Type I restriction–modification enzymes cooperate over long DNA distances to activate their endonuclease activity by measuring the complete series of events that lead from DNA translocation to DNA cleavage.
Lyon, France, 29 August–3 September 2010
Anna-Skrollan Geiermann (University of Innsbruck, Vienna, Austria)
Dagmar Graber, Anna-Skrollan Geiermann, Jessica Steger, Holger Moroder and Ronald Micura
The authors developed an innovative approach for the efficient synthesis of 3′-peptidyl tRNAs containing all genuine nucleoside modifications and an artificial 3′-amido linkage by using a combination of chemical and enzymatic tools.
Benjamin Strauss (Heidelberg University, Germany)
Benjamin Strauss, Ayan Samanta and Andres Jäschke
The authors’ work shows the development of a photoaffinity probe that is specifically recognized by the Lysine riboswitch, as demonstrated by in-line probing studies.
Sheffield, UK, 12–16 September 2010
Daniel Globisch (Ludwig-Maximilians-University Munich, Germany)
Daniel Globisch, Martin Münzel, Tobias Brückl, Markus Müller and Thomas Carell
Daniel presented varying values of 5-hydroxymethylcytosine together with constant 5-methylcytosine values in different mouse brain regions using HPLC–ESI–MS analysis indicating an important epigenetic role.
James A. Taylor (John Innes Centre, Norwich, UK)
James A. Taylor, Robert A. Field and Anthony Maxwell
A novel high-throughput screen was utilized to identify new inhibitors of Escherichia coli DNA gyrase and Methanosarcina mazei topoisomerase VI, which were subsequently characterized in vitro and in vivo.
Malgorzata Figiel (IInternational Institute of Molecular and Cell Biology, Warsaw, Poland)
Małgorzata Figiel, Hyongi Chon, Susana Cerritelli, Magdalena Cybulska, Robert J. Crouch and Marcin Nowotny
Solving the crystal structure of human RNase H2 enabled the authors to structurally map all 29 Aicardi-Goutières Syndrome-related point mutations identified in this enzyme as well as to build a model of substrate binding by human RNase H2 using a bacterial RNaseH2–substrate complex structure.
Justin A. Yeoman (University of Cambridge, Cambridge, UK)
Justin A. Yeoman, Angel Orte, Beth Ashbridge, David Klenerman and Shankar Balasubramanian
The authors have used single-molecule fluorescence microscopy to study the folded state of human telomerase RNA (hTR), and show that hTR adopts a new conformation on binding to human telomerase reverse transcriptase (hTERT) and reconstitution of an active ribonucleoprotein complex.
Maui, Hawaii, USA, 25–29 September 2010
Travel Award Winner: Dr Jennifer Dickey (National Institute of Health, Bethesda, MD, USA)
Jennifer S. Dickey, Brandon J. Baird, Christophe E. Redon, Valeriya Avdoshina, Guillermo Palchik, Alexei Kondratyev, William M. Bonner and Olga A. Sedelnikova
The authors found for the first time that non-replicating primary cells with high transcription rates (specifically cerebellar granular cells) are vulnerable to bystander signalling that induces DNA double-strand breaks in susceptible cell populations, offering critical insights into which tissues may be vulnerable to bystander effects in vivo.
Dana Point, CA, USA, 20–23 October 2010
Marcela V. Karpuj (Hebrew University of Jerusalem, Rehovot, Israel)
Sagit Gelibter Niv, Angelika Rambold, Jorg Tatzel, Max Nunzinante, Hermann Shatzel and Marcela Viviana Karpuj
The authors describe a novel approach for attenuating levels of membrane proteins in mammalian cultured cells. The amounts of native as well as transfected prion protein (PrP) are transiently lowered in various cell lines following phosphorothioate oligodeoxynucleotides (PS-DNA) exposure. The N-terminus domain of PrP is essential for this degradation that is independent of the PS-DNA sequence. Proteins not responsive to PS-DNA could be degraded upon PS-DNA exposure, following introduction of the N-terminus of the PrP into their sequence. These observations may serve as the basis for a general method for transient targeted modulation of the levels of desired recombinant surface proteins in cell cultures, and for the development of Prion disease future therapeutic strategies.
Heera Krishna (University of Colorado-Boulder, USA)
Heera Krishna and Marvin H. Caruthers
The major hurdle associated with utilizing oligo deoxyribonucleotides for therapeutic purposes has been their poor delivery into cells coupled with high nuclease susceptibility. Heera proposed that the relatively unexplored methylphosphine borane linkage (Me-P-BH3), derived from precursors of known antisense activity, might prove to be more effective than its well-known individual counterparts. She developed efficient solid-phase synthesis strategies for synthesizing chimeric oligonucleotides bearing novel methylphosphine–borane linkages. Preliminary biological studies on the uptake and cellular distribution of these compounds have been evaluated. Preliminary results imply that the potential utility of these molecules as efficient tools in antisense research and RNAi needs to be explored.
Johanna E. Lee (Baylor College of Medicine, Houston, TX, USA)
Johanna E. Lee and Thomas A. Cooper
The authors have shown that antisense oligonucleotide treatment induces degradation of toxic CUG-repeat RNA in cells and mice, which may lead to a potential therapeutic approach for myotonic dystrophy patients.
Kkothanahreum Park (Konkuk University, Seoul, Republic of Korea)
Kkothanahreum Park, Bo-Ra Choi and Dong-Eun Kim
In this study, the authors have designed Peptide Nucleic Acid (PNA)-directed clamping PCR method to quantitatively detect the amount of cellular RNAs harboring the ABL gene of T315I point mutation conferring the drug-resistance. PNA-directed clamping PCR method allows them to discriminate and quantify the amount of mixed alleles which differ by only one base pair. They also designed RNA-cleaving DNAzymes that specifically target and cleave both the BCR–ABL junction and the site of point mutation (T315I) in BCR–ABL mRNA. The designed DNAzymes are effective in cleaving the target RNA specifically, distinguishing the T315I point mutation from the wild type RNA. When the DNAzymes are transfected into pro-B lymphoid cell line with Gleevec resistance (BCR–ABL/BaF3T315I), both expression of BCR-ABL protein and proliferation of Gleevec-resistant leukemic cells are inhibited.
Partha Ray (Duke University Medical Center, Durham, NC, USA)
Partha Ray, Bruce A. Sullenger and Rebekah R. White
With the goal to find potential biomarkers for pancreatic cancer the authors employed SELEX (Systematic Evolution of Ligands by Exponential Enrichment) technique and isolated a 2′-fluoro pyrimidine modified RNA aptamers that binds to pancreatic patient sera with high affinity compared to control sera collected from healthy donors.
Keith Fox, Senior Editor, Nucleic Acids Research
Barry Stoddard, Senior Editor, Nucleic Acids Research