Plant genetics: A vintage genome sequence

Summaries of newsworthy papers include Developmental biology: New method sets stem cells apart, Human embryonic stem cells do a heart good, Shedding light on animals’ interiors

NATURE AND THE NATURE RESEARCH JOURNALS PRESS RELEASE

For papers that will be published online on 26 August 2007

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

EMBARGO:

This press release contains:

· Summaries of newsworthy papers:

Plant genetics: A vintage genome sequence – Nature

Developmental biology: New method sets stem cells apart – Nature

Human embryonic stem cells do a heart good – Nature Biotechnology

Shedding light on animals’ interiors – Nature Methods

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

· Geographical listing of authors

PDFs of all the papers mentioned on this release can be found in the relevant journal’s section of http://press.nature.com. Press contacts for the Nature journals are listed at the end of this release.

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PLEASE CITE THE SPECIFIC NATURE JOURNAL AND WEBSITE AS THE SOURCE OF THE FOLLOWING ITEMS. IF PUBLISHING ONLINE, PLEASE CARRY A HYPERLINK TO THE APPROPRIATE JOURNAL’S WEBSITE.

****************************************************NATURE************************************************

(http://www.nature.com/nature)

[1] Plant genetics: A vintage genome sequence

DOI: 10.1038/nature06148

A high-quality draft of the grapevine genome sequence is reported online this week in Nature. The analysis of a grapevine line originally derived from Pinot Noir reveals that it contains twice as many enzymes contributing to essential oil and aroma than other sequenced plants, suggesting that it might eventually be possible to trace the diversity of wine flavours down to the genome level.

The French–Italian Public Consortium for Grapevine Genome Characterization sequenced the genome of Vitis vinifera, the fourth sequence produced for a flowering plant and the first for a fruit crop. The authors selected grapevine for their analysis because of its important place in the cultural heritage of humanity, beginning during the Neolithic period. They report that the genes involved in the metabolism of tannins and terpenes – which contribute to a wine’s aromatic features – have been selectively amplified in this genome. They also found an expansion in the family of genes driving the production of resveratrol, the chemical associated with the proposed health benefits of drinking moderate amounts of red wine.

Public access to the grapevine genome sequence should help identify the genes underlying particular agricultural features and domestication traits. This could be of use for not only recognizing which genes are responsible for the characteristic flavours of a wine, but also in speeding up the process of introducing disease-resistant genes, thereby decreasing the need for pesticides.

Author contact:

Patrick Wincker (Genoscope-Centre National de Sequencage and CNRS, Evry, France)
Tel: +33 1 60 87 25 68; E-mail: [email protected]

[2] Developmental biology: New method sets stem cells apart

DOI: 10.1038/nature06090

Researchers have devised a way to distinguish between two similar, yet vitally different, proliferative cell types found in the developing brain. Their findings, published online in this week's Nature, should prove useful in stem cell research.

The developing brain contains many different proliferative cell types including neural stem cells (NSCs), which can give rise to many different types of mature brain cell, and neuroblasts, which are more restricted in their fate. But the signalling differences between these two populations are poorly understood.

Nicholas Gaiano and colleagues now show that differences in the Notch signalling pathway — a highly conserved system known to influence cell fate decisions during embryonic and adult life — may account for the variation between the two cell types. The discovery has yielded a method for separating these two cell types in a dish, a feat that should help researchers to characterise them further.

Author contact:

Nicholas Gaiano (Johns Hopkins School of Medicine, Baltimore, MD, USA)
Tel: +1 443 287 4866; E-mail: [email protected]

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

[3] Structural basis of Dscam isoform specificity

DOI: 10.1038/nature06147

*******************************************NATURE BIOTECHNOLOGY*********************************

(http://www.nature.com/naturebiotechnology)

[4] Human embryonic stem cells do a heart good

DOI: 10.1038/nbt1327

Heart attacks may respond to treatment with cells derived from human embryonic stem (ES) cells, according to a paper published online this week in Nature Biotechnology. Charles Murry and colleagues find that rats subjected to experimental heart attacks show improved cardiac function four weeks after receiving a transplant of heart muscle cells generated in a dish from human ES cells.

Human ES cells are considered a promising source of cells for regenerative medicine because, in theory, they can be taken off the laboratory shelf, coaxed into becoming any kind of specialized cell for repairing damaged organs and given to any patient. But many problems must be solved before this vision is reduced to practice.

Murry and colleagues address two critical problems in heart regeneration. First, they improve the efficiency with which ES cells are converted into heart cells. Second, they improve the survival of such heart cells after transplantation into damaged animal hearts using a ‘survival cocktail’—a mixture of chemicals that blocks various causes of cell death. By combining these techniques, they succeeded in slowing the progression of heart failure in the treated animals.

Author contact:

Charles Murry (University of Washington, Seattle, WA, USA)
Tel: +1 206 616 8685; E-mail: [email protected]

Additional contact for comment on paper:

Loren Field (Indiana University, Indianapolis, IN, USA)
Tel: +1 317 274 5085; E-mail: [email protected]

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

[5] Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors

DOI: 10.1038/nbt1328

[6] A diverse family of thermostable cytochrome P450s created by recombination of stabilizing fragments

DOI: 10.1038/nbt1333

********************************************NATURE METHODS******************************************

(http://www.nature.com/nmeth)

[7] Shedding light on animals’ interiors

DOI: 10.1038/nmeth1083

Bright far-red fluorescent proteins that emit light at longer wavelengths than typical red fluorescent proteins, improving their usefulness for deep imaging in living animals, are reported in a study online in Nature Methods this week.

Fluorescent proteins are invaluable tools for many types of biological investigation. The light from the best performing fluorescent proteins, however, has a difficult time penetrating living tissue due to the relatively short wavelengths emitted. This has limited the usefulness of these proteins for in vivo fluorescence imaging of whole animals. But fluorescent proteins that emit longer wavelength light, in the far-red and infrared regions of the spectrum, have so far been difficult to develop.

Dmitriy Chudakov and colleagues previously cloned a bright red fluorescent protein from a sea anemone. They engineered this protein to increase the wavelength of the emitted light while retaining its brightness. These longer wavelengths of light penetrate tissue more efficiently making detection of fluorescence emanating from deep inside an animal easier than with existing fluorescent proteins. The researchers developed two versions of the protein that are best suited for different applications. These will aid many researchers in different fields of biology who can benefit from the improved in vivo imaging performance the proteins offer.

Author contact:

Dmitriy Chudakov (Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia)
Tel: +7 495 429 8020; E-mail: [email protected]

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

[8] Higher-energy C-trap dissociation for peptide modification analysis

DOI: 10.1038/nmeth1060

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

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

[9] Quantum critical behaviour in the superfluid density of strongly underdoped ultrathin copper oxide films

DOI: 10.1038/nphys707

[10] A single-photon transistor using nanoscale surface plasmons

DOI: 10.1038/nphys708

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

[11] Quantum-spin-liquid states in the two-dimensional kagome antiferromagnets ZnxCu4−x(OD)6Cl2

DOI: 10.1038/nmat1986

[12] Negative birefraction of acoustic waves in a sonic crystal

DOI: 10.1038/nmat1987

[13] Femtosecond modification of electron localization and transfer of angular momentum in nickel

DOI: 10.1038/nmat1985

[14] Order causes secondary Bragg peaks in soft materials

DOI: 10.1038/nmat1995

NATURE NANOTECHNOLOGY (http://www.nature.com/nnano)

[15] Intrinsic peroxidase-like activity of ferromagnetic nanoparticles (N&V)

DOI: 10.1038/nnano.2007.260

Nature MEDICINE (http://www.nature.com/naturemedicine)

[16] Broad HIV-1 neutralization mediated by CD4-binding site antibodies

DOI: 10.1038/nm1624

[17] Platelet CD36 links hyperlipidemia, oxidant stress and a prothrombotic phenotype

DOI: 10.1038/nm1626

[18] High levels of GDF15 in thalassemia suppress expression of the iron regulatory protein hepcidin

DOI: 10.1038/nm1629

[19] A ligand-receptor fusion of growth hormone is a potent agonist with exceptional pharmacokinetics

DOI: 10.1038/nm1610

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

[20] Bayesian inference of epistatic interactions in case-control studies

DOI: 10.1038/ng2110

[21] A gene in the multidrug and toxic compound extrusion (MATE) family confers aluminum tolerance in sorghum

DOI: 10.1038/ng2074

Nature NEUROSCIENCE (http://www.nature.com/natureneuroscience)

[22] OL-protocadherin is essential for growth of striatal axons and thalamocortical projections
DOI: 10.1038/nn1960

Nature IMMUNOLOGY (http://www.nature.com/natureimmunology)

[23] Lymph node chemokines promote sustained T lymphocyte motility without triggering stable integrin adhesiveness in the absence of shear forces

DOI: 10.1038/ni1499

[24] Respiratory protein-generated reactive oxygen species as an antimicrobial strategy

DOI: 10.1038/ni1501

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

[25] Focal adhesion kinase controls actin assembly via a FERM-mediated interaction with the Arp2/3 complex

DOI: 10.1038/ncb1626

[26] Correlated three-dimensional light and electron microscopy reveals transformation of mitochondria during apoptosis

DOI: 10.1038/ncb1630

[27] The lipid droplet is an important organelle for hepatitis C virus production

DOI: 10.1038/ncb1631

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

[28] YY1 functions with INO80 to activate transcription

DOI: 10.1038/nsmb1276

[29] F1-ATPase rotates by an asymmetric, sequential mechanism using all three catalytic subunits

DOI: 10.1038/nsmb1296

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***The following paper will be published on Thursday 23 August at 1500 London time (BST) / 1000 US Eastern time on Nature Chemical Biology’s website, which is when the embargo for this paper will lift. The rest of this press release remains under embargo until Sunday 26 August 1800 London time (BST) / 1300 US Eastern time.***

[30] Light-controlled gene silencing in zebrafish embryos

DOI: 10.1038/nchembio.2007.30

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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.

AUSTRALIA
Sydney: 19

BRAZIL
Minas Gerais: 21

CHINA
Beijing: 15
Nanjing: 12, 15
Shanghai: 12

DENMARK

Copenhagen: 10

FRANCE

Colmar: 1

Evry: 1

Grenoble: 14

Les Ulis: 19

Lyon: 13

Montpellier: 1

St Aubin: 3

GERMANY

Berlin: 11, 13, 19

Bremen: 8

Freiburg: 3

Hamburg: 13, 14

Heidelberg: 5, 27

Martinsried: 8

Munich: 23

Munster: 13

INDIA
Calcutta: 30

ISRAEL

Rehovot: 23

ITALY
Bari: 1
Milan: 1
Padua: 1

Sienna: 1

Udine: 1

Verona: 1

JAPAN

Fukui: 11

Hyogo: 22

Kobe: 22

Kyoto: 22, 27, 29

Osaka: 29

Saitama: 22

Tokyo: 27, 29

Toyoake: 27

Yokohama: 29

KOREA

Seoul: 2

RUSSIA

Moscow: 7

SINGAPORE

Singapore: 24

THAILAND

Nakornpathom: 18

UNITED KINGDOM

Cambridge: 5

Edinburgh: 25

Glasgow: 25

London: 25

Sheffield: 19

UNITED STATES OF AMERICA

Alabama

Birmingham: 16

California

La Jolla: 26

Los Angeles: 18

Menlo Park: 4

Pasadena: 6

San Diego: 12, 26

San Francisco: 23

Stanford: 30

District of Columbia

Washington: 18

Kansas

Manhattan: 21

Maryland

Baltimore: 2

Bethesda: 16, 18

Gaithersburg: 11

Massachusetts

Boston: 3, 28

Cambridge: 6, 10, 20

Missouri

Kansas City: 28

New York

Ithaca: 21

North Carolina

Research Triangle Park: 18

Ohio

Cleveland: 17

Columbus: 9

Pennsylvania

Erie: 21

University Park: 20

Tennessee

Memphis: 26

Texas

College Station: 21

Virginia

Charlottesville: 11

Washington

Seattle: 4

Wisconsin

Milwaukee: 17

PRESS CONTACTS…

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

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Tel: +44 20 7843 4502; E-mail: [email protected]

Ruth Francis (Senior Press Officer, Nature, London)

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

Nature Biotechnology (New York)

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Nature Cell Biology (London)

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Tel: +44 20 7843 4892; E-mail: [email protected]

Nature Chemical Biology (Boston)

Andrea Garvey

Tel: +1 617 475 9241, E-mail: [email protected]

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)

Fabio Pulizzi

Tel: +44 20 7014 4024; E-mail: [email protected]

Nature Medicine (New York)

Juan Carlos Lopez

Tel: +1 212 726 9325; E-mail: [email protected]

Nature Methods (New York)

Allison Doerr

Tel: +1 212 726 9393; E-mail: [email protected]

Nature Nanotechnology (London)

Peter Rodgers
Tel: +44 20 7014 4019; Email: [email protected]

Nature Neuroscience (New York)

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Nature Physics (London)

Alison Wright

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Nature Structural & Molecular Biology (New York)

Michelle Montoya

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Published: 26 Aug 2007

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