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This press release is copyright Nature
VOL.470 NO.7332 DATED 03 FEBRUARY 2011
This press release contains:
Summaries of newsworthy papers:
Stem cells: Spots of bother
Biology: Prostate cancer progression
Climate science: Solving the methane question
Comment: Policies needed to protect deep-sea denizens from mining
Physics: Biological imaging with an X-ray laser
Genetics: Plants ‘predict’ infection?
And finally… Once upon a thymus
[UPDATE] Astronomy: An exoplanet sextet
Mention of papers to be published at the same time with the same embargo
Geographical listing of authors
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[1] Stem cells: Spots of bother (AOP)
DOI: 10.1038/nature09798
***This paper will be published electronically on Nature's website on 02 February at 1800 London time / 1300 US Eastern Time 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 03 February, but at a later date. ***
Human induced pluripotent stem cells (iPSCs) can be derived from somatic cells but certain ‘hotspots’ in the genome are aberrantly reprogrammed and these errors in reprogramming are transmitted to differentiated cells. The research, published online in Nature, shows that iPSCs are distinct from embryonic stem (ES) cells and indicates that more research on iPSCs is needed before they can be used in therapy.
Joseph Ecker and colleagues report high-resolution, whole-genome DNA methylation profiling of several human ES cell, iPSC and somatic progenitor lines. It has been shown previously in mice that iPSCs have a ‘memory’ of the somatic cell from which they derive and Ecker and his team report that this may also be the case in human iPSCs. They found hotspots in the genome, near cetromeres and telomeres, which are not adequately reprogrammed or where reprogramming doesn’t take place completely.
The findings add to our understanding of the epigenomic programming process and could potentially provide diagnostic markers for incomplete iPSC reprogramming.
CONTACT
Joseph Ecker (The Salk Institute for Biological Studies, La Jolla, CA, USA)
Tel: +1 858 453 4100 x1752; E-mail: [email protected]
[2] Biology: Prostate cancer progression (AOP)
DOI: 10.1038/nature09677
***This paper will be published electronically on Nature's website on 02 February at 1800 London time / 1300 US Eastern Time 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 03 February, but at a later date. ***
A pathway that limits prostate cancer progression and spread in a mouse model is identified in a paper published online this week in Nature. The work also proposes a four-gene signature associated with poor outcome in human prostate cancers and could be useful for the development of a better test for disease prognosis.
Effective clinical management of prostate cancer is challenged by lack of understanding of the genomic and pathologic levels and genetic elements governing disease progression. Ronald DePinho and colleagues find in a mouse model of prostate cancer that the TGF-beta signalling pathway limits tumour progression and metastasis. Using markers of this pathway along with other biological factors, they develop a genetic signature that is associated with poorer clinical outcomes in human cancers. Their work could lead to the development of better prognostic test for those cases of prostate cancer in which it is currently difficult to select the right treatment regime while avoiding over-treatment.
CONTACT
Ronald DePinho (Dana-Farber Cancer Institute, Boston, MA, USA)
Tel: +1 617 632 6085; E-mail: [email protected]
[3] Climate science: Solving the methane question (pp 82-85; N&V)
Increased levels of methane in the atmosphere before the industrial revolution can be attributed to natural causes rather than human influence, according to research published in Nature.
The question of how long humans have influenced global climate by greenhouse gas emissions is fundamental to our understanding of the climate system and attribution of global warming. Atmospheric methane is a greenhouse gas known to be influenced by both natural and anthropogenic sources, but pinpointing the source of an anomalous rise in methane levels before the industrial revolution has so far proven difficult. Possible explanations for the rise in methane levels include very early agricultural activity, but there is still a vigorous debate as to whether natural sources, such as an increase in natural wetland emissions, might be responsible.
Joy Singarayer and colleagues used climate and wetland models to calculate atmospheric methane trends over the past 130,000 years. They demonstrate that there is no need to invoke human sources, as the known pre-industrial increase mainly resulted from changes in natural sources in the Southern Hemisphere tropics. In turn, these changes seem to have been driven by variations in Earth’s orbit. They suggest that there is therefore no need to invoke additional human sources.
CONTACT
Joy Singarayer (University of Bristol, UK)
Tel: +44 117 9289068; E-mail: [email protected]
Eric Wolff (British Antarctic Survey, Cambridge, UK) N&V author
Tel: +44 1223 221491; E-mail: [email protected]
Comment: Policies needed to protect deep-sea denizens from mining (pp 31-33)
Offshore mining companies with their sights on minerals in the sea floor are gearing up to start drilling, says Cindy Lee Van Dover in a Comment article in Nature this week. But, she warns, conservation policies needed to protect rare sea life and habitats have not kept pace with commercial activities.
Two companies have already begun exploratory drilling expeditions (off the coasts of Papua New Guinea and the Solomon Islands). In January, one of these companies — Nautilus Minerals of Toronto, Canada — was granted the first 20-year mining lease by the government of Papua New Guinea. Its target: the metal-rich deposits that surround hydrothermal vents. Discovered in the late 1970s, these deep-sea vents are underwater hot springs, supporting unique life forms and providing much needed nutrients to the deep ocean. Van Dover, who works with Nautilus Minerals as a scientific adviser, says she would prefer these vents to remain pristine, untouched by mining. But she recognizes that commercial pressures, including rising prices for commodities such as copper, make deep-sea mining almost inevitable.
Worryingly, the International Seabed Authority has responsibility both for granting mining leases in international waters and for establishing environmental regulations to protect this marine environment. At a minimum, says Van Dover, the agency will need proper independent oversight. And rather than leave it to chance, or to the goodwill of a few companies, Van Dover proposes new guidelines for mining in both territorial and international waters. Until these are in place, she says, commercial mining would be premature.
CONTACT
Cindy Lee Van Dover (Duke University, NC, USA)
Tel: +1 252 504 7655; E-mail: [email protected]
[4] & [5] Physics: Biological imaging with an X-ray laser (pp 73-81)
A new approach to structural imaging of biological systems is demonstrated by two experiments published in Nature this week. Intense, ultra-short X-ray pulses from a free-electron laser have been used to collect high-resolution diffraction data from protein nanocrystals, and from non-crystalline virus particles.
X-ray diffraction has been an invaluable tool for structure determination across the sciences, but its success has depended on the availability of crystalline samples of sufficient size. With conventional X-ray sources, increasing the dose to compensate for a small crystal can lead to extensive structural damage before a diffraction pattern can be recorded. This problem has been particularly acute for some biological materials, which can be difficult or impossible to crystallize.
A decade ago, it was suggested (Nature 406, 752–757; 2000) that femtosecond pulses from a free-electron laser could provide sufficiently short but intense X-ray doses to collect useful structural information before significant radiation damage could occur. This “diffraction before destruction” concept has now been tested in experiments at the Linac Coherent Light Source, in California.
The new studies both feature novel sample injection systems, which avoid the need for cryogenic cooling or other special preparations. Henry Chapman and colleagues used a water jet to deliver a stream of protein nanocrystals to the pulsed X-ray beam, and combined tens of thousands of single-crystal diffraction snapshots into one high-resolution data set. Janos Hajdu and colleagues exposed a stream of aerosolized mimivirus particles to the X-ray beam, and showed that sufficient data can be collected to image these non-crystalline objects before they are damaged. Further improvements in resolution — and measurements on even smaller nanocrystals — should be possible in the near future, using shorter, brighter and shorter-wavelength X-ray pulses.
CONTACT
Henry Chapman (DESY, Hamburg, Germany) Author paper [4]
Tel: +49 40 8998 4155; E-mail: [email protected]
Janos Hajdu (Uppsala University, Sweden) Author paper [5]
Tel: +46 70 4250194; E-mail: [email protected]
[6] Genetics: Plants ‘predict’ infection? (pp 110-114; N&V)
Certain plants may be able to ‘anticipate’ infection and time their immune response accordingly, a Nature paper suggests.
Xinnian Dong and colleagues studied plant defence against a fungal pathogen which causes downy mildew disease in Arabidopsis, and identified a novel set of defence genes that are influenced by the circadian regulator, CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1). It’s thought that CCA1 helps plants time their immune response, enabling them to prepare for infection at dawn when the fungus normally disperses its spores.
The animal immune response is also thought to be influenced by the circadian clock, so understanding the molecular link between the circadian clock and immunity has broad implications in biology.
CONTACT
Xinnian Dong (Duke University, Durham, NC, USA)
Tel: +1 919 613 8176; E-mail: [email protected]
C. Robertson McClung (Dartmouth College, Hanover, NH, USA) N&V author
Tel: +1 603 646 3940; E-mail: [email protected]
[7] And finally… Once upon a thymus (pp 90-94)
The identification of a thymus-like organ in lampreys is reported in Nature this week. The finding provides a starting point for comparative studies between jawless fish and jawed vertebrates.
The nature of the immune system of lampreys and other jawless vertebrates has been debated since the nineteenth century. Histological surveys of lampreys failed to reveal an organ equivalent to the thymus, which, in mammals, has a role in the development of T lymphocytes.
Thomas Boehm and colleagues identify and characterize thymus-like structures (named ‘thymoids’ by the authors) at the tips of gill filaments of lamprey larvae. The dispersed nature and relatively inconspicuous morphology of the thymoid could explain why it went unnoticed for so long and why it could only be revealed by an extensive gene expression analysis, prompted by the recent discovery that lampreys possess T- and B-like lymphocytes.
The finding provides evidence that similarities in the underlying adaptive immune systems of both jawless and jawed vertebrates extend to the primary lymphoid organs. The authors also suggest that the common ancestor of the two sister groups may have possessed not just T- and B-like lymphocytes but also anatomically distinct tissues for their spatially separated development.
CONTACT
Thomas Boehm (Max-Planck-Institute of Immunobiology, Freiburg, Germany)
Tel: +49 761 5108 328; E-mail: [email protected]
[UPDATE] Astronomy: An exoplanet sextet
The discovery of a remarkable extrasolar system consisting of a Sun-like star called Kepler-11 with six transiting planets is reported in Nature this week. The paper describes observations made by the Kepler spacecraft that could provide useful insights into the formation of the system and of planetary systems in general.
Few stars have more than one known transiting planet, which makes Kepler-11 and its planetary system very unusual. Observations of multiple transiting planets yield many types of information. Jack Lissauer and colleagues report that the star’s five inner planets have relatively short orbits of 10 to 47 days and a very compact configuration, whereas a sixth transiting planet has a longer orbit. The inner five planets are among the smallest planets to have both their masses and sizes measured; these suggest that the planets contain substantial envelopes of light gases.
The Kepler spacecraft is scheduled to continue collecting data on the system for the rest of its mission and with longer-term data, it will be possible to make more accurate measurements of the planets and their interactions.
Two News Features in this week’s Nature take stock of astronomers’ hunt for planets beyond our Solar System. NASA’s Kepler planet-finding mission has identified several hundred candidate exoplanets, and writer Eugenie Samuel Reich asks how close it really is to finding another Earth. But while the exoplanet search has been successful, multi-billion dollar missions to follow Kepler have been cancelled and postponed. Lee Billings finds that the planet-hunting community is getting creative in devising ways to discover exoplanets ‘on the cheap’.
CONTACT
Jack Lissauer (NASA-Ames Research Center, Moffett Field, CA, USA)
Tel: +1 650 604 2293; E-mail: [email protected]
Please note this author will be travelling on Tuesday 01 and Wednesday 02 February
Jonathan Fortney (University of California, Santa Cruz, CA, USA)
Tel: +1 831 502 7285; E-mail: [email protected]
Daniel Fabrycky (University of California, Santa Cruz, CA, USA)
Tel: +1 831 459 3539; E-mail: [email protected]
Eric Ford (University of Florida, Gainesville, FL, USA)
Tel: +1 352 392 2052 x209; On Tuesday 01 February: +1 352 225 3648
E-mail: [email protected]
Contact for background information on the News Features:
Mitch Waldrop (News Features Editor, Nature)
E-mail: [email protected]
ALSO IN THIS ISSUE…
[8] Mapping copy number variation by population-scale genome sequencing (pp 59-65)
[9] Alternative stable states explain unpredictable biological control of Salvinia molesta in Kakadu (pp 86-89; N&V)
[10] MMSET regulates histone H4K20 methylation and 53BP1 accumulation at DNA damage sites (pp 124-128)
ADVANCE ONLINE PUBLICATION
***This paper will be published electronically on Nature's website on 02 February at 1800 London time / 1300 US Eastern Time 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 03 February, but at a later date. ***
[11] Three-dimensional atomic imaging of crystalline nanoparticles
DOI: 10.1038/nature09741
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.
AUSTRALIA
Indooroopilly: 9
Jabiru: 9
BELGIUM
Antwerp: 11
Wilrijk: 11
CANADA
Burnaby: 8
CHINA
Shenzhen: 8
DENMARK
Copenhagen: 8
FRANCE
Marseille: 5
GERMANY
Berlin: 4, 5
Freiburg: 7
Garching: 4, 5
Hamburg: 4, 5
Heidelberg: 4, 5, 8
Jülich: 4, 5
Munich: 4, 5
Siegen: 5
JAPAN
Kagawa: 6
NETHERLANDS
Amsterdam: 11
Leiden: 8
SWEDEN
Gothenburg: 4
Uppsala: 4, 5
SWITZERLAND
Dübendorf: 11
Lausanne: 6
Zurich: 11
UNITED KINGDOM
Bristol: 3
Exeter: 3
Hinxton: 8
Oxford: 8
Saffron Walden: 8
Sheffield: 3
Worcester: 6
UNITED STATES OF AMERICA
Arizona
Scottsdale: 10
Tempe: 4, 5
California
Berkeley: 4, 5
La Jolla: 1, 6, 8
Livermore: 4, 5
Menlo Park: 4, 5
Stanford: 2, 8
Connecticut
New Haven: 8
Georgia
Atlanta: 7
Augusta: 7
Louisiana
Baton Rouge: 8
Maryland
Beltsville: 6
Massachusetts
Boston: 2, 8
Beverly: 8
Cambridge: 2, 8
Minnesota
Rochester: 10
Missouri
St Louis: 8, 10
New York
Bronx: 8
New York: 8
North Carolina
Durham: 6
Washington
Seattle: 8
Wisconsin
Madison: 1, 2, 9
PRESS CONTACTS…
From North America and Canada
Neda Afsarmanesh, Nature New York
Tel: +1 212 726 9231; E-mail: [email protected]
From Japan, Korea, China, Singapore and Taiwan
Mika Nakano, Nature Tokyo
Tel: +81 3 3267 8751; E-mail: [email protected]
From the UK
Rebecca Walton, Nature, London
Tel: +44 20 7843 4502; E-mail: [email protected]
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