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Nucleic Acids Res. 2010 December; 38(22): 7871–7875.
Published online 2010 December 9. doi:  10.1093/nar/gkq1263
PMCID: PMC3001045


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.

ESF-EMBO meeting ‘Applications of antiviral RNA interference (RNAi)’

Sant Feliu de Guixols, Spain, 30 May–4 June 2010

First Prize—Vitantonio Pantaleo (Istituto di Virologia Vegetale, CNR, Italy)

Genome-wide profiling of virus-derived siRNAs and their target sites

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)

Dicer inhibitors as potential antiviral agents

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)

CMV2b interferes RdDM at several aspects

Sadia Hamera et al.


Saxtons River, Vermont, 6–11 June 2010

Best Poster Award Winner: Noah Ribeck (UC Santa Barbara, USA)

Single-molecule measurements reveal details of DnaB’s interactions with both strands at a DNA fork

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.

6th ISCB Student Council Symposium and International Conference on Intelligent Systems for Molecular Biology

Boston, MA, USA, 9 July and 11–13 July 2010

Best Student Presentation Award: Geoff MacIntyre (University of Melbourne, Australia)

is-rSNP: A novel technique for in silico regulatory SNP detection

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)

Dynamics and evolution of genome—nuclear lamina interactions

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)

Human protein–protein interaction prediction

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.

New England Biolabs meeting on DNA restriction and modification

Bremen, Germany, 1–6 August 2010

Outstanding short talk: Mtaladi N. Ndlovu (Université Libre de Bruxelles, Belgium)

Mechanistic link between DNA methylation and histone modifications

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)

Interaction of nucleotide flipping restriction enzymes with their target sites

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)

A novel family of restriction endonucleases as a tool for epigenetic research

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)

Formation of nucleoprotein filaments by the mammalian DNA methyltransferase Dnmt3a

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)

Communication and cleavage by single polypeptide type I restriction–modification enzymes, LlaBIII and LlaGI

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.

figure gkq1263f1
(Left to right): Prof. Henri Grosjean (presenter of outstanding short talk award), Gintautas Tamulaitis, Matladi Ndlovu (outstanding short talk award winner), Devora Cohen-Karni, Renata Jurkowska, Eva Sisakova, Barry Stoddard (NAR; presenter of outstanding ...

IRT conference on Nucleic Acids

Lyon, France, 29 August–3 September 2010

Anna-Skrollan Geiermann (University of Innsbruck, Vienna, Austria)

Semisynthesis of a stable E. coli tRNA-3′-NH-ValValLeuGluMet conjugate containing the genuine tRNA modifications

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)

Synthesis of a chemical probe for affinity-based chemical RNomics & evaluation of its binding characteristics

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.

NACON 8, 8th International Meeting on Recognition Studies in Nucleic Acids

Sheffield, UK, 12–16 September 2010

Daniel Globisch (Ludwig-Maximilians-University Munich, Germany)

The sixth DNA base 5-hydroxymethylcytosine in mammalian brain

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)

High-throughput screening for novel inhibitors of DNA gyrase and topoisomerase VI

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)

Crystal structure of human RNase H2

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)

RNA conformation in catalytically active human telomerase

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.

Radiation Research Society

Maui, Hawaii, USA, 25–29 September 2010

Travel Award Winner: Dr Jennifer Dickey (National Institute of Health, Bethesda, MD, USA)

Transcriptional activity dictates susceptibility to stress-induced bystander DNA damage

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.

6th Annual Meeting of the Oligonucleotide Therapeutics Society

Dana Point, CA, USA, 20–23 October 2010

Marcela V. Karpuj (Hebrew University of Jerusalem, Rehovot, Israel)

A novel method for membrane protein degradation in cell culture mediated by oligodeoxynucleotides

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)

Oligo(deoxyribonucleoside) methylphosphine borane: a novel hybrid molecule for the oligonucleotide chemist’s toolbox

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)

Targeted degradation of toxic RNA in myotonic dystrophy

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)

Detection and suppression of SNP conferring Gleevec-resistance in leukemogenic BCR-ABL chimeric RNA

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)

Aptamers as tools for the identification and detection of pancreatic cancer biomarkers

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.

figure gkq1263f2
Anna-Skrollan Geiermann and Benjamin Strauss.

figure gkq1263f3
Jennifer Dickey and NAR editor Bill Dynan.

Keith Fox, Senior Editor, Nucleic Acids Research

Barry Stoddard, Senior Editor, Nucleic Acids Research

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press