Gene elements that control cell evolution

Summaries of newsworthy papers include A better engineered beer, Lead atmosphere and Dead layers provide lifeline for Moore’s Law


For papers that will be published online on 19 April 2009

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

This press release contains:

· Summaries of newsworthy papers:

Biotechnology: A better engineered beer

Geoscience: Lead atmosphere

Genetics: Gene elements that control cell evolution

And finally … Materials: Dead layers provide lifeline for Moore’s Law

· 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 Press contacts for the Nature journals are listed at the end of this release.

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[1] Biotechnology: A better engineered beer
DOI: 10.1038/nbt.1536

Synthetic biology could complement genetic engineering by providing tools to synthesize complex gene networks from simpler parts. A new approach, published this week in Nature Biotechnology, promises to make it easier to construct synthetic gene networks for biomedical, research, and industrial applications, such as brewing beer and producing biofuels.

James Collins and colleagues show how computer modeling and a library of well-characterized cell parts can be used to predict the behavior of a gene network before it is built. This eliminates much of the inefficient guess-work and trial-and-error tweaking that plagues traditional genetic engineering efforts today. The researchers use their approach to engineer yeast cells that clump together after a specified amount of time, a critical parameter to various applications, such as when brewing beer.

Author contact:
James Collins (Boston University, MA, USA)
Tel: +1 617 353 0390; E-mail: [email protected]

[2] Geoscience: Lead atmosphere
DOI: 10.1038/ngeo499

Lead-containing aerosols are highly efficient propagators of atmospheric ice formation, according to a study published online in Nature Geoscience. The findings provide insight into the influence of the large quantities of lead present in the atmosphere before the switch to unleaded fuel last century.

Daniel Cziczo and colleagues examined the ability of lead to generate ice crystals in artificial clouds. They found that lead particles generated nearly half of the ice formed. Furthermore, analysis of residues from atmospheric ice revealed that a third of ice-forming particles contained lead, suggesting that lead triggers ice formation in natural conditions. They estimate that if lead was present in all ice-forming particles, ice production would increase, and more sunlight would be reflected back to space.

The authors suggest that post-industrial emissions of particulate lead may have offset a proportion of the warming attributed to greenhouse gases.

Author contact:
Daniel Cziczo (Pacific Northwest National Laboratories, Richland, WA, USA)
Tel: +1 509 375 2725; E-mail: [email protected]

[3], [4] & [5] Genetics: Gene elements that control cell evolution
DOI: 10.1038/ng.375
DOI: 10.1038/ng.312
DOI: 10.1038/ng.368

Three large studies unravel the network underlying the genetic elements that control how cells transform and evolve from precursors to mature cells, as reported online in this week’s Nature Genetics.

The complete development of functional organs relies on compatibility between immature cells that are still growing and mature cells that have acquired a specific function. Understanding the switch between growth and specified functions has been elusive, until now.

Three independent groups led by Yoshihide Hayashizaki, John Mattick, and Piero Carninci, part of the FANTOM4 project, have utilized in-depth sequencing technologies to evaluate genome-wide changes in gene expression that occur during cell development. One finding from the Carninci group is the genome-wide expression of repetitive mobile elements. These authors identified over 250,000 previously unknown gene expression start sites as well as the functional consequences of the repetitive elements on the global expression of neighboring genes. Another interesting finding from the Mattick group is the identification of a novel class of evolutionarily conserved short RNAs that are located at the start sites of active genes. Together, with the pioneering work from the Hayashizaki group, these studies collectively provide a comprehensive look at the dynamic regulatory framework that supports the switch from immature growing cells to mature functioning cells.

Author contacts:
Yoshihide Hayashizaki (RIKEN Yokohama Institute, Yokohama, Japan) Paper [3]
Tel: +81 45 508 9222; E-mail: [email protected]

John Mattick (University of Queensland, St. Lucia, Australia) Paper [4]
Tel: +61 73346 2079; E-mail: [email protected]

Piero Carninci (RIKEN Yokohama Institute, Yokohama, Japan) Paper [5]
Tel: +81 45 503 9222; E-mail: [email protected]

[6] Materials: Dead layers provide lifeline for Moore’s Law
DOI: 10.1038/nmat2429

A solution to one of the major problems plaguing the microelectronics industry — the difficulty in shrinking capacitors, the largest device components in microelectronic circuits — is reported online this week in Nature Materials. These devices could lead to significantly reduced microelectronic memory chips with record storage densities.

Capacitors are used for computer memory chips. However, their size reduction has been limited by a ‘dead layer’ at the surface that reduces the overall performance. Nicola Spaldin and colleagues studied the origin of the dead layer and discovered that for certain material combinations the dead layer effect is reversed. For these ‘negative’ dead layers, predicted, for example, for platinum metal contacts in combination with barium titanate capacitors, the overall capacitance is increased, not reduced. As a result, microelectronic memory chips can be made much smaller, suggesting a significant extension of Moore’s law that predicts the performance improvements of computer chips.

Author contacts:
Nicola Spaldin (University of California, Santa Barbara, CA, USA)
Tel: +1 805 893 7920; E-mail: [email protected]

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

Nature (

[7] GlcNAcylation of a histone methyltransferase in retinoic-acid-induced granulopoiesis
DOI: 10.1038/nature07954


[8] KRAB-type zinc-finger protein Apak specifically regulates p53-dependent apoptosis
DOI: 10.1038/ncb1864

[9] Bone morphogenetic protein heterodimers assemble heteromeric type I receptor complexes to pattern the dorsoventral axis
DOI: 10.1038/ncb1870

[10] Arginine methylation of Piwi proteins catalysed by dPRMT5 is required for Ago3 and Aub stability
DOI: 10.1038/ncb1872

[11] WIP1 phosphatase is a negative regulator of NF‑kB signalling
DOI: 10.1038/ncb1873


[12] Using small molecules to facilitate exchange of bicarbonate and chloride anions across liposomal membranes
DOI: 10.1038/nchem.178

[13] G-quadruplex self-assembly regulated by Coulombic interactions
DOI: 10.1038/nchem.177

[14] Chiral imprinting of palladium with cinchona alkaloids
DOI: 10.1038/nchem.180


[15] RNA Polymerase V transcription guides ARGONAUTE4 to chromatin
DOI: 10.1038/ng.365

[16] A systematic, large-scale resequencing screen of the X chromosome coding exons in mental retardation
DOI: 10.1038/ng.367


[17] From chessboard tweed to chessboard nanowire structure during pseudospinodal decomposition
DOI: 10.1038/nmat2431

[18] Spraying asymmetry into functional membranes Layer-by-Layer
DOI: 10.1038/nmat2430


[19] The parametric response map is an imaging biomarker for early cancer treatment outcome
DOI: 10.1038/nm.1919

[20] Histone H2AX is integral to hypoxia-driven neovascularization
DOI: 10.1038/nm.1947


[21] Universal sample preparation method for proteome analysis
DOI: 10.1038/nmeth.1322


[22] The crossover from two dimensions to one dimension in granular electronic materials
DOI: 10.1038/nnano.2009.81

[23] Direct measurement of electrical conductance through a self-assembled molecular layer
DOI: 10.1038/nnano.2009.82


[24] Reinforcement learning can account for associative and perceptual learning on a visual-decision task
DOI: 10.1038/nn.2304

[25] Synaptic mGluR activation drives plasticity of calcium-permeable AMPA receptors
DOI: 10.1038/nn.2309

[26] Tubulin tyrosination navigates the kinesin-1 motor domain to axons
DOI: 10.1038/nn.2314

[27] Myosin-dependent targeting of transmembrane proteins to neuronal dendrites
DOI: 10.1038/nn.2318


[28] Controlling the near-field oscillations of loaded plasmonic nanoantennas
DOI: 10.1038/nphoton.2009.46

[29] Electrical detection of confined gap plasmons in metal–insulator–metal waveguides
DOI: 10.1038/nphoton.2009.47

Nature PHYSICS (

[30] Single-shot carrier–envelope phase measurement of few-cycle laser pulses
DOI: 10.1038/nphys1250

[31] A unified explanation of the Kadowaki–Woods ratio in strongly correlated metals
DOI: 10.1038/nphys1249


[32] Gemin5-snRNA interaction reveals an RNA binding function for WD repeat domains
DOI: 10.1038/nsmb.1584

[33] A plant 5S ribosomal RNA mimic regulates alternative splicing of transcription factor IIIA pre-mRNAs
DOI: 10.1038/nsmb.1588

[34] miR-24–mediated downregulation of H2AX suppresses DNA repair in terminally differentiated blood cells
DOI: 10.1038/nsmb.1589

[35] Single-molecule force spectroscopy reveals a highly compliant helical folding for the 30-nm chromatin fiber
DOI: 10.1038/nsmb.1590

[36] Developmental programming of CpG island methylation profiles in the human genome
DOI: 10.1038/nsmb.1594

[37] The nucleotide binding dynamics of human MSH2–MSH3 are lesion dependent
DOI: 10.1038/nsmb.1596


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.

Adelaide: 3, 16
Brisbane: 3, 5, 31
Nathan: 3, 4, 5
St Lucia: 3, 4
Warateh: 16
Woolloongabba: 4

Leuven: 16, 29

Quebec: 3

Beijing: 8
Hangshou: 23
Shanghai: 8

Aarhus: 23
Copenhagen: 3
Lyngby: 23

Turku: 23

Grenoble: 23
Paris: 16
Tours: 16

Berlin: 16
Darmstadt: 2
Frankfurt: 2
Garching: 30
Heidelberg: 33
Jena: 30
Karlsruhe: 2
Leipzig: 2
Mainz: 2
Martinsried: 21
Munich: 28
Regensburg: 3
Tubingen: 33

Haifa: 36
Jerusalem: 14, 36
Rehovot: 14, 34
Tel Aviv: 36

Naples: 3, 4, 5
Rome: 4, 5

Chiba: 3
Gunma: 3
Kanagawa: 3, 4, 5
Osaka: 3
Saitama: 3, 7
Shizouka: 3, 26
Tokyo: 3, 7, 26
Tottori: 3
Yokohama: 3

Amsterdam: 14
Eindhoven: 13
Leiden: 35
Nijmegen: 16, 35
Utrecht: 13

Bergen: 3
Trondheim: 23

Immunos: 11
Proteos: 11
Singapore: 3

Bellville: 3
Cape Town: 6

Bizkaia: 16
Burgos: 12
Madrid: 11, 12
San Sebastian: 28
Valencia: 16

Linkoping: 3
Lund: 23
Norrkoping: 3
Stockholm: 3

Basel: 3
Zurich: 2

Bristol: 3
Cambridge: 3, 16, 28, 34
Edinburgh: 3
Glasgow: 16
Hinxton: 3, 16
Liverpool: 23
London: 16, 25
Nottingham: 23
Roslin: 3, 4, 5
Southampton: 12
Surrey: 16


Berkeley: 37
La Jolla: 3
Los Angeles: 27
Pasadena: 22
Santa Barbara: 6
Santa Clara: 36

Boulder: 2

New Haven: 33

District of Columbia
Washington: 3

Jupiter: 3

Bethesda: 20

Boston: 1, 3, 34
Cambridge: 18, 36

Ann Arbor: 19

Rochester: 37

St Louis: 15

New Jersey
Piscataway: 6, 17

New York
New York: 7
Yorktown Heights: 10

Philadelphia: 9, 10, 20, 24, 32

South Carolina
Greenwood: 16

College Station: 30

Ashburn: 27

Richland: 2


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

Rachel Twinn (Nature London)
Tel: +44 20 7843 4658; E-mail: [email protected]

Neda Afsarmanesh (Nature New York)
Tel: +1 212 726 9231; E-mail: [email protected]

Ruth Francis (Head of Press, Nature, London)
Tel: +44 20 7843 4562; E-mail: [email protected]

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

Nature Biotechnology (New York)
Peter Hare
Tel: +1 212 726 9284; E-mail: [email protected]

Nature Cell Biology (London)
Bernd Pulverer
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 Chemistry (London)
Stuart Cantrill
Tel: +44 20 7014 4018; E-mail: [email protected]

Nature Genetics (New York)
Lily Khidr
Tel: +1 212 726 9324; E-mail: [email protected]

Nature Geoscience (London)
Heike Langenberg
Tel: +44 20 7843 4042; E-mail: [email protected]

Nature Materials (London)
Vincent Dusastre
Tel: +44 20 7843 4531; E-mail: [email protected]

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

Nature Methods (New York)
Hugh Ash
Tel: +1 212 726 9627; E-mail: [email protected]

Nature Nanotechnology (London)
Peter Rodgers
Tel: +44 20 7014 4019; Email: [email protected]

Nature Neuroscience (New York)
Kalyani Narasimhan
Tel: +1 212 726 9319; E-mail: [email protected]

Nature Photonics (Tokyo)
Oliver Graydon
Tel: +81 3 3267 8776; E-mail: [email protected]

Nature Physics (London)
Alison Wright
Tel: +44 20 7843 4555; E-mail: [email protected]

Nature Structural & Molecular Biology (New York)
Michelle Montoya
Tel: +1 212 726 9326; E-mail: [email protected]

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Published: 19 Apr 2009

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