APTX helps mend broken DNA

NATURE AND THE NATURE RESEARCH JOURNALS PRESS RELEASE. Summaries of newsworthy papers include RNA interference screens questioned, Bacterial genome provides clues for better bioplastics, Attention can impair visual perception, Regulating the immune response

NATURE AND THE NATURE RESEARCH JOURNALS PRESS RELEASE

For papers that will be published online on 10 September 2006

This press release is copyrighted to the Nature journals mentioned below.

This press release contains:

* Summaries of newsworthy papers:

Cell biology: APTX helps mend broken DNA - Nature
Genetics: RNA interference screens questioned - Nature
Understanding why H5N1 is so lethal - Nature Medicine
Bacterial genome provides clues for better bioplastics - Nature Biotechnology
Attention can impair visual perception - Nature Neuroscience
Regulating the immune response - Nature Immunology

* Mention of papers to be published at the same time with the same embargo
* Geographical listing of authors

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[1] Cell biology: APTX helps mend broken DNA

DOI: 10.1038/nature05164

Mutations in the gene aprataxin (APTX) are responsible for the rare neurological disorder ataxia oculomotor apraxia-1 (AOA1). Stephen West and his colleagues show in a paper published online by Nature this week that this protein is involved in DNA repair, and suggest that AOA1 may be caused by the gradual accumulation of unrepaired breaks in the DNA of neuronal cells.

Aprataxin associates with other DNA repair proteins, but it was not known whether it has a direct role in the process of DNA repair. The researchers used purified extracts containing normal and mutant aprataxin protein to show that the protein helps join together double-strand breaks in DNA induced by reactive oxygen molecules, or free radicals. Specifically, it removes chemical groups called adenylates from one of the DNA ends to allow them to be stitched back together.

Author contact:

Stephen West (Cancer Research UK, London, UK)
Tel: +44 1707 625 868; E-mail: [email protected]r.org.uk

[2] Genetics: RNA interference screens questioned
DOI: 10.1038/nature05179

Many genes identified as targets of RNA interference (RNAi) in the fruitfly Drosophila could be false, suggests a paper published online by Nature this week.

During RNAi, short fragments of RNA bind to complementary sequences in the messenger RNA produced by a target gene, effectively silencing expression of that gene. Some studies have suggested that these small RNAs can each have hundreds of target genes in a genome.

Philip Beachy and his colleagues say that many proposed targets of RNAi screens could be artefacts. The team searched for new members of the well-studied Wingless signalling pathway by inserting multiple interfering RNAs into Drosophila cells. They found that the RNAs displayed significant off-target effects: the majority of targets are false positives resulting from interactions between three-letter repeats present in these target genes and the interfering RNAs, and from indirect effects on known Wingless pathway components. The authors suggest several measures to produce more reliable lists of genes targeted by RNAi.

Author contact:

Philip A Beachy (Stanford University, CA, USA)
Tel: +1 650 723-4521; E-mail: [email protected]

Other papers from Nature to be published online at the same time and with the same embargo:

[3] Molecular architecture and assembly of the DDB1-CUL4A ubiquitin ligase machinery

DOI: 10.1038/nature05175

*********************************NATURE BIOTECHNOLOGY********************
(http://www.nature.com/naturebiotechnolgy)

[5] Bacterial genome provides clues for better bioplastics
DOI: 10.1038/nbt1244

The genome of a bacterium that makes biodegradable plastics is reported in the October issue of Nature Biotechnology. Ralstonia eutropha H16 is one of many bacteria that store energy as plastic-like molecules - polyhydroxyalkanoates or PHAs - in much the same way that animals accumulate fat reserves. Unlike most other bacteria, it also needs only hydrogen and carbon dioxide to support its survival.

Over 350 billion pounds of plastic are manufactured from fossil fuel annually, primarily from oil. PHAs produced from renewable resources are an environmentally friendly alternative to petroleum-based plastics. They can be modified to satisfy requirements needed for a range of applications: from strong plastics needed for molded products through softer, elastic latex-like compositions with film-forming properties, to resin coatings.

The genome of R. eutropha H16 adds to current knowledge of PHA accumulation in this bacterium by revealing more than fifty new genes that likely participate in the bacteria’s bioplastic manufacturing machinery. Until now, the requisite properties of bioplastics could be modified by changing the feedstock provided to bacteria. These new genes introduce the possibility that bacteria, or even plants, might be genetically modified to extend the versatility of bioplastics used in everyday life.

Author contact:
Bärbel Friedrich (Humboldt-Universität zu Berlin, Germany)
Tel: +49 30 2093 8107; E-mail: [email protected]

Other papers from Nature Biotechnology to be published online at the same time and with the same embargo:

[6] A probability-based approach for high-throughput protein phosphorylation analysis and site localization

DOI: 10.1038/nbt1240

*************************NATURE NEUROSCIENCE **************************
(<http://www.nature.com/natureneuroscience>)

[7] Attention can impair visual perception

DOI: 10.1038/nn1761

We normally think of paying attention to an object as a way to perceive it better, but sustained attention actually worsens the perception of some visual stimuli, reports a study in the October issue of Nature Neuroscience.

Visual stimuli with more contrast between their lighter and darker areas are easier to see. Previous work has suggested that attention makes a visual stimulus easier to see by effectively increasing its contrast. However, contrast sensitivity decreases after prolonged periods of looking at high-contrast stimuli. Ling and Carrasco showed people black and white stripes, and had them report whether these stripes leaned to the left or the right; this task is harder to do when the contrast between the stripes is lower. The researchers found that when people paid attention to a particular set of stripes, they could initially do the task even with low-contrast stripes. However, after a prolonged period of attention, people needed higher-contrast stimuli to succeed at the same task. These results indicate that prolonged periods of attention to specific stimuli may eventually impair rather than improve perception.

Author contact:

Samuel Ling (New York University, NY, USA)
Tel: +1 212 998 3894; E-mail: [email protected]

Other papers from Nature Neuroscience to be published online at the same time and with the same embargo:

[8] The meninges control the tangential migration of hem-derived Cajal-Retzius cells via CXCL12/CXCR4 signaling
DOI: 10.1038/nn1764

[9] Soluble adenylyl cyclase is required for netrin-1 signaling in nerve growth cones
DOI: 10.1038/nn1767

[10] Nonlinear, binocular interactions underlying flow field selectivity of a motion-sensitive neuron
DOI: 10.1038/nn1769

[11] Brain state and contrast sensitivity in the awake visual thalamus
DOI: 10.1038/nn1760

[12] Emotional enhancement of memory via amygdala-driven facilitation of rhinal interactions
DOI: 10.1038/nn1771

****************************NATURE IMMUNOLOGY **********************
(<http://www.nature.com/natureimmunology>)

[13] Regulating the immune response

DOI: 10.1038/ni1382

A protein called SARM - SAM and ARM-containing protein - helps to regulate the immune response against invading pathogens, according to a report in the October issue of Nature Immunology.

SARM is a member of the so-called ‘TIR’ - Toll-interleukin 1 receptor - adaptor protein family. All other members of this family help to transmit signals triggered by pathogens to promote an immune response. Andrew Bowie and colleagues now show that in contrast to the other four members of the TIR family, SARM unexpectedly blocks rather than promotes signals triggered by pathogens. The identification of SARM as a regulator, rather than a promoter, of the immune response may prove useful therapeutically.

Author contact:
Andrew Bowie (Trinity College, Dublin, Ireland)
Tel: +353 1 6082435; E-mail: [email protected]

Other papers from Nature Immunology to be published online at the same time and with the same embargo:

[14] Surface-bound chemokines capture and prime T cells for synapse formation
DOI: 10.1038/ni1384

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Items from other Nature journals to be published online at the same time and with the same embargo:

NATURE CHEMICAL BIOLOGY (http://www.nature.com/nchembio <http://www.nature.com/natureneuroscience>)

[15] Structural and mechanistic insights into polyketide macrolactonization from polyketide-based affinity labels
DOI: 10.1038/nchembio822

[16] Structural basis for macrolactonization by the pikromin thioesterase
DOI: 10.1038/nchembio824

Nature PHYSICS (http://www.nature.com/naturephysics <http://www.nature.com/naturematerials>)

[17] Full quantum distribution of contrast in interference experiments between interacting one-dimensional Bose liquids

DOI: 10.1038/nphys410

[18] Observation of the Nernst signal generated by fluctuating Cooper pairs
DOI: 10.1038/nphys413

NATURE MATERIALS (<http://www.nature.com/naturematerials>)

[19] All-solid-state Z-scheme in CdS-Au-TiO2 three-component nanojunction system

DOI: 10.1038/nmat1734

NATURE GENETICS (<http://www.nature.com/naturegenetics>)

[20] Nucleosome positions predicted through comparative genomics
DOI: 10.1038/ng1878

[21] iASPP preferentially binds p53 proline-rich region and modulates apoptotic function of codon 72-polymorphic p53
DOI: 10.1038/ng1879

[22] Wnk4 controls blood pressure and potassium homeostasis via regulation of mass and activity of the distal convoluted tubule

DOI: 10.1038/ng1877

[23] Hereditary parkinsonism with dementia is caused by mutations in ATP13A2, encoding a lysosomal type 5 P-type ATPase

DOI: 10.1038/ng1884

NATURE CELL BIOLOGY (<http://www.nature.com/naturecellbiology>)

[24] FOXO4 transcriptional activity is regulated by monoubiquitination and USP7/HAUSP
DOI: 10.1038/ncb1469

[25] Modification of p53 with O-linked N-acetylglucosamine regulates p53 activity and stability
DOI: 10.1038/ncb1470

[26] A K+-selective cGMP-gated ion channel controls chemosensation of sperm
DOI: 10.1038/ncb1473

[27] Meiotic regulation of the CDK activator RINGO/Speedy by ubiquitin-proteasome-mediated processing and degradation
DOI: 10.1038/ncb1472

[28] Anti-oncogenic role of the endoplasmic reticulum differentially activated by mutations in the MAPK pathway
DOI: 10.1038/ncb1471

Nature STRUCTURAL & MOLECULAR BIOLOGY (<http://www.nature.com/natstructmolbiol>)

[29] CDK Pho85 targets CDK inhibitor Sic1 to relieve yeast G1 checkpoint arrest after DNA damage
DOI: 10.1038/nsmb1139

[30] Structure and TBP binding of the Mediator head subcomplex Med8-Med18-Med20
DOI: 10.1038/nsmb1143

[31] Structural insights into the Notch-modifying glycosyltransferase Fringe
DOI: 10.1038/nsmb1144

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GEOGRAPHICAL LISTING OF AUTHORS

The following list of places refers to the whereabouts of authors on the papers numbered in this release. The listing may be for an author's main affiliation, or for a place where they are working temporarily. Please see the PDF of the paper for full details.

AUSTRIA
Vienna: 27

CHILE
Santiago: 23
Valdivia: 23

CHINA
Hong Kong: 4

DENMARK
Copenhagen: 31

EGYPT:
Cairo: 1

FRANCE
Montpellier: 27
Paris: 24

GERMANY
Berlin: 5, 26
Bonn: 23
Cologne: 23
Gottingen: 5
Heidelberg: 27, 31
Julich: 26
Marburg: 23
Martinsried: 10, 27, 31
Munich: 30
Munster: 5

IRELAND
Dublin: 13

ITALY
Cuneo: 21
Trieste: 21

JAPAN
Osaka: 19

JORDAN
Amman: 23

KOREA
Seoul: 25

POLAND
Wroclaw: 29

SPAIN
Sant Joan d’Alacant: 8

SWITZERLAND
Zurich: 27

THE NETHERLANDS
Utrecht: 24

UNITED KINGDOM
Brighton: 1
Cambridge: 23
Hertfordshire: 1
Leeds: 23
London: 21
Wakefield: 23

UNITED STATES OF AMERICA
California
La Jolla: 27
San Francisco: 14, 28
Stanford: 2
Connecticut
New Haven: 22
Storrs: 11
Illinois
Chicago: 29
Maryland
Baltimore: 2, 21
Massachusetts
Beverley: 6
Boston: 6, 10
Woods Hole: 26
Worcester: 22
Michigan
Ann Arbor: 15, 16, 28
Minnesota
Minneapolis: 15, 16
New Hampshire
Lebanon: 6
New Jersey
Newark: 12
New York
New York: 7, 9, 11
Ohio
Columbus: 20
Oregon
Portland: 22
Pennsylvania
University Park: 20
Tennessee
Memphis: 1
Texas
Dallas: 2
Washington
Seattle: 3

VIETNAM
Ho Chi Minh City: 4

PRESS CONTACTS…

For media inquiries relating to embargo policy for all the Nature Research Journals:

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Tel: +44 20 7843 4658; E-mail: [email protected]

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For media inquiries relating to editorial content/policy for the Nature Research Journals, please contact the journals individually:

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Nature Chemical Biology (Boston)
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Nature Genetics (New York)
Orli Bahcall
Tel: +1 212 726 9311; E-mail: [email protected]

Nature Immunology (New York)
Laurie Dempsey
Tel: +1 212 726 9372; E-mail: [email protected]

Nature Materials (London)
Maria Bellantone
Tel: +44 20 7843 4556; E-mail: [email protected]

Nature Medicine (New York)
Juan Carlos Lopez
Tel: +1 212 726 9325; E-mail: [email protected]

Nature Neuroscience (New York)
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Tel: +1 530 795 3256; E-mail: [email protected]

Nature Physics (London)

Alison Wright

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Published: 10 Sep 2006

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