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Article Released Wed-5th-November-2008 18:10 GMT
Contact: Ruth Institution: Nature Publishing Group
 The promise of personal genomics

Summaries of newsworthy papers: Cancer genome sequenced, Whose data is it anyway?, Where to find dark matter, Engineered DNA 'scissors' show promise, Bacteria 'chat' with immune system, Sediment cores prompt icy rethink, Structure of key 'bird flu' protein revealed, Ultrafast optical oscilloscopes, Linking lemmings to climate change


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This press release is copyright Nature.

VOL.456 NO.7218 DATED 06 NOVEMBER 2008


This press release contains:

· Summaries of newsworthy papers:

Genetics: The promise of personal genomics *PRESS BRIEFING*

Oncology: Cancer genome sequenced

Commentary: Whose data is it anyway?

Astrophysics: Where to find dark matter

Molecular biology: Engineered DNA ‘scissors’ show promise

Immunology: Bacteria ‘chat’ with immune system

Geoscience: Sediment cores prompt icy rethink

Immunology: Structure of key ‘bird flu’ protein revealed

Electronics: Ultrafast optical oscilloscopes

And finally… Linking lemmings to climate change

· Mention of papers to be published at the same time with the same embargo

· Geographical listing of authors

Editorial contacts: While the best contacts for stories will always be the authors themselves, in some cases the Nature editor who handled the paper will be available for comment if an author is unobtainable. Editors are contactable via Ruth Francis on +44 20 7843 4562. Feel free to get in touch with Nature's press contacts in London, Washington and Tokyo (as listed at the end of this release) with any general editorial inquiry.

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[1] & [2] Genetics: The promise of personal genomics (pp 53-59; 60-65; N&V) *PRESS BRIEFING*

The power of next-generation genome sequencing technology is demonstrated in two collaborations published in Nature this week. The papers shed light on the nature of human genomic variation with ethnicity, and more broadly the studies have major implications regarding the feasibility of making ‘personal genomics’ a reality.

One paper, from a team led by David Bentley, describes the sequencing and initial characterization of the genome of an African individual from the Yoruba ethnic group of West Africa. The work demonstrates the utility of the Illumina (formerly Solexa) massively parallel sequencing approach, which is already being widely used in fields ranging from medical resequencing through to assessment of copy number variation.

The other paper reports the genome of an Asian individual, sequenced using the same technology. Jun Wang and colleagues illustrate the potential of personal genomics in disease diagnosis, and by comparing this genome with the other individual genomes already available, those of J. D. Watson and J. C. Venter, they are able to shed light on the genetic variation in individuals of different ethnicity.

CONTACT
David Bentley (Illumina Cambridge, Little Chesterford, UK) Author paper [1]
Tel: +44 1799 532300; E-mail: DBentley@illumina.com

Jun Wang (Beijing Genomics Institute at Shenzhen, China) Author paper [2]
Tel: +86 755 2527 3796; E-mail: wangj@genomics.org.cn

Zhuo Li (Beijing Genomics Institute-Shenzhen, China) Co-author paper [2]
Tel: +86 0755 2527 3796; E-mail: lizhuo@genomics.org.cn

Samuel Levy (J. Craig Venter Institute, Rockville, MD, USA) N&V co-author
Tel: +1 301 795 7389; E-mail: slevy@jcvi.org

Robert Strausberg (J. Craig Venter Institute, Rockville, MD, USA) N&V co-author
Tel: +1 240 268 2708; E-mail: rls@venterinstitute.org

A press briefing related to paper [2] will take place on embargo lift on Friday 7 November at 0900 China Time / 0300 London Time (GMT) in Shenzhen Dameisha Sheraton Hotel, Shenzhen, China

Jun Wang, the first author will talk about the research in the paper, followed by other attendees from Chinese Academy of Sciences and Shenzhen municipal government.

For further information please contact:
Jia Ye (Beijing Genomics Institute-Shenzhen, China) Public relations contact
Tel: +86 755 2527 3870; E-mail: yejia@genomics.org.cn

A press briefing related to papers [1], [2] & [3] will be held at the Philadelphia Convention Center on 11 November at 1800 US Eastern Time, in room 307B.

Jun Wang of the Beijing Genomics Institute, Rick Wilson of Washington University and Scott Kahn will discuss their findings. There will be opportunity for one-on-one interviews and a live webcast will be available from www.illumina.com.

For further information please contact:
Maurissa Bornstein (Illumina, San Diego, USA) Public relations contact
Tel: +1 908 208 9254; E-mail: mbornstein@illumina.com



[3] Oncology: Cancer genome sequenced (pp 66-72)

An individual cancer genome has been sequenced for the first time, identifying mutated genes that probably have a role in the development of acute myeloid leukaemia. The high-throughput sequencing technique, described in this week’s Nature, could be applied to other cancers and aid the design of targeted therapeutics.

Acute myeloid leukaemia is a white blood cell cancer that affects around 13,000 adults yearly in the United States alone, killing about one-third. Elaine Mardis and colleagues sequenced cancerous and normal tissue from a patient with acute myeloid leukaemia, and then compared the two sequences. Ten mutated genes were identified. Of these, two were previously reported to be associated with acute myeloid leukaemia whereas the others probably represent new genes that are involved in the development of the disease.

CONTACT

Elaine Mardis (Washington University School of Medicine, St. Louis, MO, USA)
Tel: +1 314 286 1805; E-mail: emardis@wustl.edu


Commentary: Whose data is it anyway? (pp 32-33; 34-35)

As more medical data are collected, and personal genetic testing grows in popularity, the need to regulate how this information is used is becoming increasingly important. In this issue of Nature's special focus on personal genomes, Patrick Taylor argues, in a Commentary, that regulations requiring patient consent for research purposes are based on the mistaken reasoning that autonomy and ownership of personal data inherently protects people's privacy. Such regulations, including one currently pending in the US Congress, could hamper productive research. "Ethics that care only about ownership and consented transfers are, by exclusion, indifferent to distributional justice and optimizing social outcomes," Taylor says.

In a second Commentary, Barbara Prainsack and her coauthors argue that calls to regulate direct-to-consumer genetic and genomic testing, without clear evidence of harm, risk irreversible effects. Instances of harm, in terms of genetic discrimination or psychological distress, that everyone has feared, have failed to materialize. And the industry is moving too fast to make informed regulations at present: "The business is still very much ‘in the making’, embedded in dense relations between data, services, economic models and research endeavours."

From 18:00 gmt Wednesday 5 November, a discussion forum on these issues will be available here: http://network.nature.com/groups/naturenewsandopinion/forum/topics/3292

CONTACT
Patrick Taylor (Harvard Medical School and Children’s Hospital Boston, MA, USA)
Tel: +1 617 355 4935; E-mail: patrick.taylor@childrens.harvard.edu

Barbara Prainsack (King’s College London, Strand, UK)
Tel: +44 20 7848 1585; E-mail: barbara.prainsack@kcl.ac.uk


[4] Astrophysics: Where to find dark matter (pp 73-76; N&V)

If you’re looking for telltale signs of dark matter, the main halo of the Milky Way may be your best bet, a computer simulation study in this week’s Nature suggests.

Dark matter is the dominant form of matter in the Universe, but its nature is unknown. Destruction of dark matter in the Milky Way’s halo should produce detectable levels of gamma-rays and some have argued that this annihilation signal will be dominated by emission from small clumps of dark matter in dwarf satellite galaxies of the Milky Way. Volker Springel and colleagues disagree, and instead suggest that the dominant and most easily detectable signal will be produced by diffuse dark matter in the main halo of the Milky Way.

CONTACT
Volker Springel (Max Planck Institute for Astrophysics, Garching, Germany) Author paper [4]
Tel: +49 89 3000 2238; E-mail: volker@mpa-garching.mpg.de

Carlos Frenk (University of Durham, UK) Co-author paper [4]
Tel: +44 191 334 3641; E-mail: c.s.frenk@durham.ac.uk

Stephane Colombi (Institut d’Astrophysique de Paris, France) N&V author
Tel: +33 1 44 32 81 20; E-mail: colombi@iap.fr


[5] Molecular biology: Engineered DNA ‘scissors’ show promise (pp 107-111)

A molecular ‘pair of scissors’ that snips out specific chunks of DNA has yielded promising results both in vitro and in cells. It is hoped that the engineered protein, reported in this week’s Nature, will lead to treatments for xeroderma pigmentosum and other diseases caused by mutations in single genes.

Patients with xeroderma pigmentosum have a faulty DNA repair pathway and are hypersensitive to ultraviolet light; for this reason, afflicted individuals are particularly prone to skin cancer. Guillermo Montoya and his colleagues have engineered two enzymes that can cleave DNA from the human xeroderma pigmentosum group C gene in vitro and in cellular experiments. The engineered proteins are based on a wild-type homing endonuclease — called I-CreI — which recognizes and cleaves specific DNA sites, and they seem to work by a similar mechanism.

CONTACT
Guillermo Montoya (Spanish National Cancer Center, Madrid, Spain)
Tel: +34 912246986; E-mail: gmontoya@cnio.es


[6] Immunology: Bacteria ‘chat’ with immune system (AOP)
DOI: 10.1038/nature07450

***This paper will be published electronically on Nature's website on 05 November at 1800 London time / 1300 US Eastern time (which is also when the embargo lifts) as part of our AOP (ahead of print) programme. Although we have included it on this release to avoid multiple mailings it will not appear in print on 06 November, but at a later date. ***

Bacteria living in the large intestine communicate with the intestinal immune system via the NOD1 receptor to induce the formation of lymphoid tissue, a Nature paper reveals. The study shows how constructive ‘dialogue’ between bacteria and host contribute to intestinal homeostasis, which is vital for digestion and protection from intestinal pathogens.

The gut bacteria induce the formation of isolated lymphoid follicles — clusters of antibody-producing white blood cells — within the intestine, and in turn these follicles exert control over the makeup of the bacteria community, Gérard Eberl and colleagues report. Disruption of this delicate balance could lead to conditions such as inflammatory bowel disease.

CONTACT
Gérard Eberl (Institut Pasteur, Paris, France)
Tel : +33 1 44 38 94 46; E-mail : geberl@pasteur.fr


[7] Geoscience: Sediment cores prompt icy rethink (pp 85-88; N&V)

Changes in global ice volume do not necessarily precede changes in oceanic circulation, a Nature study suggests. The findings, which contradict the predominant theory linking glacial cycles with ocean mixing, show we have much to learn about Earth orbit–climate interactions and have implications for modelling past and future climate.

Lorraine Lisiecki and colleagues reanalysed sediment cores from the Atlantic floor to approximate global ice volume and ocean circulation over the past 425,000 years. Changes in oceanic circulation do not have to follow changes in ice volume, they report, and the situation is depth dependent.

Variations in the Earth’s orbit, most importantly the tilt and direction of the axis of rotation relative to the Sun, are related to glacial cycles, and consequently to global ice volume and the strength of ocean mixing. Established wisdom holds that orbital changes also induce modifications in climate and ocean circulation, but the new data suggest this is not always the case.

CONTACT
Lorraine Lisiecki (University of California, Santa Barbara, CA, USA)
Tel: +1 617 699 1166; E-mail: lisiecki@alumni.brown.edu

Michel Crucifix (Universite Catholique de Louvain, Louvain-la-Neuve, Belgium) N&V author
Tel : + 32 10 47 33 00; E-mail: michel.crucifix@uclouvain.be


[8] Immunology: Structure of key ‘bird flu’ protein revealed (AOP)
DOI: 10.1038/nature07444

***This paper will be published electronically on Nature's website on 05 November at 1800 London time / 1300 US Eastern time (which is also when the embargo lifts) as part of our AOP (ahead of print) programme. Although we have included it on this release to avoid multiple mailings it will not appear in print on 06 November, but at a later date. ***

The structure of the NS1 protein, a critical virulence factor of the influenza virus, is revealed in this week’s Nature, offering insights into how the pathogen evades the host immune response.

The NS1 protein antagonizes the host antiviral response by multiple mechanisms, including the binding and ‘locking away’ of double-stranded RNA (dsRNA). Zachary Bornholdt and B. V. Venkataram Prasad describe the structure of the full-length NS1 protein from an H5N1 avian influenza virus strain associated with 60% of human deaths in a 2004 Vietnamese ‘bird flu’ outbreak. They show how the two domains of the protein interact to form tubules, which they suggest sequester dsRNA, allowing the virus to avoid detection by the host immune system.

CONTACT
Zachary Bornholdt (Baylor College of Medicine, Houston, TX, USA)
Tel: +1 713 798 5686; E-mail: zachb@scripps.edu

B. V. Venkataram Prasad (Baylor College of Medicine, Houston, TX, USA)
Tel: +1 713 798 5686; E-mail: vprasad@bcm.tmc.edu


[9] Electronics: Ultrafast optical oscilloscopes (pp 81-84)

An ultrafast oscilloscope that measures complex waveforms using optics rather than electronics is reported in Nature this week. The device offers promise in creating an instrument that could be used in many branches of science where simple measurements of optical waveforms are required.

The latest state-of-the-art oscilloscopes can achieve single-shot waveform measurements with a resolution of about 30 picoseconds. But ever greater telecommunication data rates and an expanding interest in ultrafast chemical and physical phenomena mean that there is now a demand for devices that measure optical waveforms with subpicosecond resolution.

Alexander Gaeta and colleagues demonstrate an all-optical method for real-time measurements of temporal optical waveforms with a resolution that is a hundredfold higher than that of electronic techniques. The heart of the device is a silicon photonic chip, which is fabricated with the same materials and techniques as standard microprocessors but which manipulates photons instead of electrons.

CONTACT
Alexander Gaeta (Cornell University, Ithaca, NY, USA)
Tel: +1 607 255 9983; E-mail: a.gaeta@cornell.edu


[10] And finally… Linking lemmings to climate change (pp 93-97; N&V)

Climate change is threatening lemming populations in southern Norway, according to a study published online this week in Nature. Their dwindling numbers could explain the dramatic decline in animals higher in the food chain, including arctic foxes and snowy owls, in the area.

Lemming populations used to undergo massive explosions every few years but these peaks in numbers have not been observed since the 1990s. Nils Stenseth and colleagues compared the effects of winter weather fluctuations on snow conditions with a 38-year record of rodent population dynamics, to see if climate holds the answer.

Small rodents such as lemmings rely on the insulated zone underneath the snow layer to provide warmth, access to food plants and protection from predators — all of which are essential to the survival of their young. The team present evidence that unseasonable increases in temperature and humidity are altering snow conditions and threatening their habitat. Overall, they show that warming is linked to a reduction in the lemming population and that the knock-on effects have been felt throughout the ecosystem.

CONTACT
Nils Stenseth (University of Oslo, Norway)
Tel: +47 22 85 4584; E-mail: n.c.stenseth@bio.uio.no

Tim Coulson (Imperial College London, Ascot, UK) N&V author
Tel: +44 20 7594 2237; E-mail: t.coulson@imperial.ac.uk

ALSO IN THIS ISSUE…

[11] Emergence of preformed Cooper pairs from the doped Mott insulating state in Bi2Sr2CaCu2O81d (pp 77-80)

[12] The Earth’s missing lead may not be in the core (pp 89-92)

ADVANCE ONLINE PUBLICATION

***This paper will be published electronically on Nature's website on 05 November at 1800 London time / 1300 US Eastern time (which is also when the embargo lifts) as part of our AOP (ahead of print) programme. Although we have included it on this release to avoid multiple mailings it will not appear in print on 06 November, but at a later date. ***

[13] X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation
DOI: 10.1038/nature07462

[14] Structure of a potentially open state of a proton-activated pentameric ligand-gated ion channel
DOI: 10.1038/nature07461

[15] G protein Gai functions immediately downstream of Smoothened in Hedgehog signaling
DOI: 10.1038/nature07459

[16] WNT11 acts as a directional cue to organize the elongation of early muscle fibres
DOI: 10.1038/nature07564

GEOGRAPHICAL LISTING OF AUTHORS…

The following list of places refers to the whereabouts of authors on the papers numbered in this release. For example, London: 4 - this means that on paper number four, there will be at least one author affiliated to an institute or company in London. 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.

BELGIUM
Ghent: 1

CANADA:
Edmonton: 2
Victoria: 4

CHINA
Beijing: 2
Shenzen: 2

DENMARK
Aarhus: 2
Odense: 2

FRANCE
Marseille: 16
Paris: 5, 6, 10, 13

GERMANY
Bonn: 12
Garching: 4
Mainz: 12
Munster: 12

NETHERLANDS
Groningen: 4

NORWAY
Bergen: 10
Oslo: 10
Tromso: 10

RUSSIA
Novosibirsk: 12

SPAIN
Barcelona: 5
Derio: 5
Madrid: 5, 6

SWITZERLAND
Coinsins: 1
Zurich: 14

UNITED KINGDOM
Cambridge: 1, 2
Durham: 4
Hinxton: 1
Kidlington: 1
Little Chesterton: 1
Norwich: 1

UNITED STATES OF AMERICA

California
Berkeley: 2
Hayward: 1
San Diego: 1
Santa Barbara: 7

Maryland
Bethesda: 1

Massachusetts
Amherst: 4
Boston: 7, 16
Woods Hole: 7

Missouri
St Louis: 3

New Hampshire
Hanover: 15
Lebanon: 15

New York
Ithaca: 9
Upton: 11

Texas
Houston: 8

Washington
Seattle: 3

PRESS CONTACTS…

From North America and Canada
Katherine Anderson, Nature New York
Tel: +1 212 726 9231; E-mail: k.anderson@natureny.com

Katie McGoldrick, Nature Washington
Tel: +1 202 737 2355; E-mail: k.mcgoldrick@naturedc.com

From Japan, Korea, China, Singapore and Taiwan
Mika Nakano, Nature Tokyo
Tel: +81 3 3267 8751; E-mail: m.nakano@natureasia.com

From the UK/Europe/other countries not listed above
Jen Middleton, Nature London
Tel: +44 20 7843 4502; E-mail j.middleton@nature.com

About Nature Publishing Group (NPG):

Nature Publishing Group is a division of Macmillan Publishers Ltd, dedicated to serving the academic and professional scientific and medical communities. NPG’s flagship title, Nature, was first published in 1869. Other publications include Nature research journals, Nature Reviews, Nature Clinical Practice and a range of prestigious academic journals including society-owned publications. NPG also provides news content through Nature News. Scientific career information and free job postings are offered on Naturejobs.

NPG is a global company with principal offices in London and New York and offices in Basingstoke, Boston, Buenos Aires, Delhi, Hong Kong, Madrid, Melbourne, Munich, Paris, San Francisco, Tokyo and Washington DC. For more information, please go to www.nature.com.

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