Nature Research News, 23 October 2011: from nerve stimulation to climate change and much more.

--- Summaries of newsworthy papers:
Materials: Nerve stimulation in situ
Genetics: Natural variation in regulating grain size and yield in rice
Climate Change: Feasibility of achieving climate targets
Cell Biology: An RNA barrier to reprogramming of somatic cells
Climate Change: A new perspective on climate change projections
Genetics: Identification of new loci influencing susceptibility to leprosy
Climate Change: Sinking expectations
Geoscience: Coastal acidification exacerbated by nutrients
Immunology: Maintaining the quiet
And finally…Nanotechnology: A mechanical memory

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

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[1] Materials: Nerve stimulation in situ

DOI: 10.1038/nmat3146

An electrochemical method that stimulates nerves locally and blocks the propagation of electrical signals along nerve fibres, thus minimizing undesirable side effects, is reported online this week in Nature Materials. The proof-of-concept demonstration, shown in frogs, may one day pave the way to low-power, flexible neuroprosthetic devices that can be wrapped around nerves.

Patients affected by paralysis from stroke, spinal cord injury or other neurological disorders can undergo functional electrical stimulation to activate affected motor nerves and perform physical therapy. However, conventional stimulation of motor nerves often causes pain, as the electric currents used can also affect neighbouring sensory nerves. Jongyoon Han and colleagues modulated the excitability of a frog's sciatic nerve in vitro by using microfabricated electrodes with membranes that are selective to calcium, potassium and sodium ions — the ions involved in nerve impulses. Electrical modulation of the ions’ local concentration allowed the researchers to control nerve activation at the site of stimulation, and to suppress signal propagation on demand. In addition, the method reduces the electrical threshold to induce nerve twitching by up to 40%. Although the approach could eventually be applied to implantable neuroprosthetic devices, the authors point out that further work to validate the method in vivo and to extend it to mammalian nerves is needed.

Author contacts:
Jongyoon Han (Massachusetts Institute of Technology, Cambridge, MA, USA)
Tel: +1 617 253 2290; E-mail: [email protected]

Samuel J. Lin (Harvard Medical School, Boston, MA, USA)
Tel: +1 617 632 7369; E-mail: [email protected]

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[2] Genetics: Natural variation in regulating grain size and yield in rice

DOI: 10.1038/ng.977

A naturally occurring gene variant from rice grown across a broad geographic region contributes to the size of the rice grains, according to research published online in this week in Nature Genetics. These findings may be directly useful for yield improvement in rice and potentially in other cereal crops that carry similar variation in the corresponding gene.

Increasing crop yield without intensifying input is one of the main goals of plant breeding research. Grain size is an important property of the cereals that we have domesticated and artificially selected.

Qifa Zhang and colleagues report the mapping and isolation of the variable gene called GS5, which regulates grain size and yield in rice. Increased GS5 expression is associated with larger grains, reflected in the traits of grain width, rate of filling and weight.

Author contact:
Qifa Zhang (Huazhong Agricultural University, Wuhan, China)
Tel: +86 27 87282429; E-mail: [email protected]

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[3] Climate Change: Feasibility of achieving climate targets

DOI: 10.1038/nclimate1258

The internationally agreed goal of limiting global temperature rise to 2 °C is still achievable, but may be slipping out of reach, according to research published online in Nature Climate Change this week.

At the United Nations climate conference in Copenhagen in 2009, countries recognized that global average temperature rise should be limited to 2 °C above pre-industrial levels. To achieve this goal, decision-makers need to know how much global emissions need to be cut to keep temperatures below the 2 °C threshold, and whether it is technically and economically feasible to make such cuts.

In the most comprehensive assessment of these factors so far, which extends and confirms earlier work by the United Nations Environment Programme, Joeri Rogelj and colleagues re-analyse ‘feasible’ emission scenarios from the literature to see whether they limit warming to ‘safe’ levels. They find that to have a ‘likely’ (greater than 66%) chance of keeping temperature rise below 2 °C, global emissions will probably need to peak before 2020, fall to about 44 gigatonnes of carbon dioxide equivalent in 2020, then keep falling — a pathway that will be very challenging to achieve.

Author contacts:
Joeri Rogelj (ETH Zurich, Switzerland)
Tel: +41 44 63 27 709; E-mail: [email protected]

Neil Edwards (Open University, Milton Keynes, UK) N&V Author
Tel: +44 1908 659358; E-mail: [email protected]

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[4] Cell Biology: An RNA barrier to reprogramming of somatic cells

DOI: 10.1038/ncb2366

A small RNA called miR-34 impedes the activation of pluripotency-associated genes, reports a paper published online in Nature Cell Biology this week. The work goes on to suggest that inhibiting the action of this RNA may increase the efficiency of reprogramming.

During the development of a fertilized egg into an organism, pluripotent stem cells differentiate into various cell types, including lung cells, blood cells and cells of the nervous system. Differentiated cells can be changed back to the pluripotent state in the laboratory by inducing the expression of a specific set of pluripotency-associated genes in a process called reprogramming. p53, a protein that suppresses tumour formation, has previously been shown to repress the ability to revert differentiated cells into the pluripotent state. Lin He and colleagues found that p53 induces the expression of miR-34. They then showed that deletion of the genetic sequence that encodes miR-34 increased reprogramming efficiency without compromising the pluripotency or proliferation status of the reprogrammed cells.

These findings could have implications for the ability to make stem cells in the laboratory for use in research.

Author contact:
Lin He (University of California, Berkeley, CA, USA)
Tel: +1 510 642 9338; E-mail: [email protected]

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[5] Climate Change: A new perspective on climate change projections

DOI: 10.1038/nclimate1261

A new, policy-relevant method of displaying climate change projections is presented in a Perspective published online in Nature Climate Change this week.

Climate change projections are usually presented as 'snapshots' of change at a particular time in the future. Instead, Manoj Joshi and colleagues reanalyse existing projections and present them in ways that show when particular temperature thresholds will be crossed, shifting the emphasis from ‘what might happen’ to ‘when it might happen’.

This new approach can convey important, policy-relevant information about the timing of change that isn’t available from traditional maps of future change. In particular, it emphasizes that lowering greenhouse-gas emissions would delay the crossing of temperature thresholds and buy valuable time for planning adaptation measures. For example, if emissions remain high, global average warming will probably exceed 2 °C above pre-industrial levels by 2060, but reducing emissions could delay the time this threshold is crossed by up to several decades.

Author contact:
Manoj Joshi (University of Reading, UK)
Tel: +44 118 378 7991; E-mail: [email protected]

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[6] Genetics: Identification of new loci influencing susceptibility to leprosy

DOI: 10.1038/ng.973

Two gene variants provide clues into why some individuals are more susceptible to contracting leprosy than others, according to research published online this week in Nature Genetics.

Furen Zhang and colleagues report a genome-wide association study for susceptibility to leprosy. They identify two new risk variants near IL23R and RAB32 genes. The involvement of the IL23R gene variant suggests that cells’ defense against leprosy bacteria involves a normal cellular process known as autophagy, in which a human cell progressively recycles its own components. In this respect, the mechanism of susceptibility of two very different diseases, leprosy and the inflammatory bowel disease Crohn’s disease, may share a biological basis.

Author contacts:
Furen Zhang (Shandong Provincial Institute of Dermatology and Venereology, Jinan, China)
Tel: +86 0531 87298801; E-mail [email protected]

Jianjun Liu (Genome Institute of Singapore, Singapore)
Tel: +65 64788088; E-mail: [email protected]

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[7] Climate Change: Sinking expectations

DOI: 10.1038/nclimate1264

Fire prevention measures and large-scale bioenergy harvest in US West Coast forests could lead to 2–14% higher emissions over the next 20 years compared with current management practices. These findings, published online this week in Nature Climate Change, could have implications for the role of forest bioenergy in carbon mitigation policy in the US.

To investigate whether bioenergy harvest and forest thinning can meet the twin goals of reducing fire risk and carbon emissions, Tara Hudiburg and co-workers analysed inventory data for 80 forest types from US West Coast forests. They found that for the majority of ecoregions, the current carbon sink is sufficiently strong that it cannot be matched by substitution of fossil fuels by forest bioenergy.
The situation may change, however, if the carbon sink in these regions weakens below the current level owing to insect infestations, fire emissions or reduced primary production, say the authors. These findings emphasize the need to consider current forest carbon balance, local forest conditions and ecosystem sustainability in establishing effective mitigation policy.

Author contact:
Tara Hudiburg (Oregon State University, Corvallis, OR, USA)
Tel: +1 360 204 1019; E-mail: [email protected]

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[8] Geoscience: Coastal acidification exacerbated by nutrients

DOI: 10.1038/ngeo1297

High nutrient levels could make coastal waters more susceptible to ocean acidification, suggests a study published online this week in Nature Geoscience. Alongside atmospheric inputs of carbon dioxide, human inputs of nutrients to the coastal ocean can lead to an increase in the acidity of these waters.
Wei-Jun Cai and colleagues use data collected in the northern Gulf of Mexico and the East China Sea to examine the influence of nutrient inputs on the acidity of coastal waters. As expected, high levels of nutrients led to phytoplankton blooms and an increase in seawater acidity, owing to a rise in microbial activity. But model simulations suggest that the rise in acidity exceeded that expected from simply adding the separate effects of phytoplankton blooms and atmospheric inputs of carbon dioxide.
The researchers suggest that the additional increase in acidity results from a reduction in the ability of these waters to buffer changes in pH.

Author contact:
Wei-Jun Cai (University of Georgia, Athens, GA, USA)
Tel: +1 706 542 1285; E-mail: [email protected]

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[9] Immunology: Maintaining the quiet

DOI:10.1038/ni.2135

Loss of a key regulatory molecule, A20, in immune sentinel cells is sufficient to trigger colitis and colitis-associated arthritic disease according to a report published this week in Nature Immunology.

A20 suppresses inflammation by turning off multiple signaling pathways that activate the transcription factor NF-kappaB, which is needed to turn on the genes encoding inflammatory mediators. Mice lacking A20 die prenatally, pointing to its important role. Ma and colleagues generated mice that lack A20 only in dendritic cells, which activate adaptive immune cells upon infection or immunization. Uninfected A20 mice have increased numbers of activated T cells and spontaneously develop overt autoinflammatory disease, but were largely devoid of autoantibodies and antibody-triggered immunopathologies.

The disease spectrum observed in the A20-deficient mice is reminiscent of that seen in human patients with colitis and other antibody-independent arthritic diseases. Genomic analyses on a cohort of Crohn’s patients likewise identified disease-linked point mutations in the human A20 gene. These data suggest altered expression of A20 can predispose individuals to autoinflammatory diseases.

Author contact:
Averil I. Ma (University of California, San Francisco, CA, USA)
Tel: +1 415 502 9405; E-mail: [email protected]

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[10] And finally…Nanotechnology: A mechanical memory

DOI: 10.1038/nnano.2011.180

A tiny beam of silicon can be used as a mechanical memory device that is able to retain information without being connected to a power supply, reports a paper published online this week in Nature Nanotechnology. The device in this study could have applications in optical communication systems and signal processing.
The silicon beam is part of an optomechanical circuit that allows energy to be exchanged between laser light in an optical cavity and the mechanical energy of the beam. Both ends of the beam are attached to a silicon chip, and it is designed to have a slight buckle, which means that it is either in an up or down state. However, the beam can also be made to vibrate by shining a laser into the optical cavity. Hong Tang and colleagues have now shown that optomechanical amplification can be used to excite the beam into a state with high-amplitude oscillations, and that optomechanical cooling can then be used to quench these vibrations so that the beam returns to a specific state when the laser is turned off. It is this control over the final state of the beam that allows information to be written to the device. The information can be read by another laser.
Many early computers had mechanical memories, but magnetic and electronic memories dominate data storage today. The amount of energy needed to store one bit of data with the new mechanical approach is more than a million times higher than that needed to store one bit in a modern memory device, but it should in future be possible to reduce the energy requirements of the nanomechanical memories by using higher-quality cavities.

Author contact:
Hong Tang (Yale University, New Haven, CT, USA)
Tel: +1 203 432 4256; E-mail: [email protected]

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NATURE

[11] Killer cell immunoglobulin-like receptor 3DL1-mediated recognition of human leukocyte antigen B
DOI: 10.1038/nature10517

[12] Rad51 paralogues Rad55–Rad57 balance the antirecombinase Srs2 in Rad51 filament formation
DOI: 10.1038/nature10522

[13] Homeostatic response to hypoxia is regulated by the N-end rule pathway in plants
DOI: 10.1038/nature10534

[14] Oxygen sensing in plants is mediated by an N-end rule pathway for protein destabilization
DOI: 10.1038/nature10536

[15] Membrane protein sequestering by ionic protein–lipid interactions
DOI: 10.1038/nature10545

[16] Image-based genome-wide siRNA screen identifies selective autophagy factors
DOI: 10.1038/nature10546

[17] The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements
DOI: 10.1038/nature10547

[18] Aspartate 112 is the selectivity filter of the human voltage-gated proton channel
DOI: 10.1038/nature10557

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NATURE BIOTECHNOLOGY

[19] SIRPA is a specific cell-surface marker for isolating cardiomyocytes derived from human pluripotent stem cells
DOI: 10.1038/nbt.2005

[20] Efficient targeted resequencing of human germline and cancer genomes by oligonucleotide-selective sequencing
DOI: 10.1038/nbt.1996

[21] A zymogen-like factor Xa variant corrects the coagulation defect in hemophilia
DOI: 10.1038/nbt.1995

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NATURE CELL BIOLOGY

[22] E-box-independent regulation of transcription and differentiation by MYC
DOI: 10.1038/ncb2355

[23] Cdc14 phosphatase promotes segregation of telomeres through repression of RNA polymerase II transcription
DOI: 10.1038/ncb2365

[24] The ubiquitin-selective segregase VCP/p97 orchestrates the response to DNA double-strand breaks
DOI: 10.1038/ncb2367

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NATURE CHEMICAL BIOLOGY

[25] Efficient discovery of anti-inflammatory small molecule combinations using evolutionary computing
DOI: 10.1038/nchembio.689

[26] GPCRs regulate the assembly of a multienzyme complex for purine biosynthesis
DOI: 10.1038/nchembio.690

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NATURE CHEMISTRY

[27] Cytocompatible click-based hydrogels with dynamically tunable properties through orthogonal photoconjugation and photocleavage reactions
DOI: 10.1038/nchem.1174

[28] Stability of quantum dots in live cells
DOI: 10.1038/nchem.1177

[29] Remodelling of the natural product fumagillol employing a reaction discovery approach
DOI: 10.1038/nchem.1178

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NATURE CLIMATE CHANGE

Africa’s ‘tree lady’
DOI: 10.1038/nclimate1275

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NATURE GENETICS

[30] A genome-wide association study identifies common variants near LBX1 associated with adolescent idiopathic scoliosis
DOI: 10.1038/ng.974

[31] Evidence for compensatory upregulation of expressed X-linked genes in mammals, C. elegans, and Drosophila
DOI: 10.1038/ng.948

[32] Loss of function variant in DNASE1L3 causes a familial form of systemic lupus erythematosus
DOI: 10.1038/ng.975

[33] A rare penetrant mutation in CFH confers high risk of age-related macular degeneration
DOI: 10.1038/ng.976

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NATURE GEOSCIENCE

[34] A deep mantle origin for the primitive signature of ocean island basalt
DOI: 10.1038/ngeo1295

[35] Signatures of the Antarctic ozone hole in Southern Hemisphere surface climate change
DOI: 10.1038/ngeo1296

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NATURE MATERIALS
[36] Catalytically highly active top gold atom on palladium nanocluster
DOI: 10.1038/nmat3143

[37] Hierarchical folding of elastic membranes under biaxial compressive stress
DOI: 10.1038/nmat3144

[38] Colloidal nanoplatelets with two-dimensional electronic structure
DOI: 10.1038/nmat3145

[39] Tuning upconversion through energy migration in core–shell nanoparticles
DOI: 10.1038/nmat3149

[40] Atomic structure of nanoclusters in oxide-dispersion-strengthened steels
DOI: 10.1038/nmat3150

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NATURE MEDICINE

[41] Patient-derived tumor grafts authentically reflect tumor pathology, growth, metastasis, and disease outcomes
DOI: 10.1038/nm.2454

[42] Suppression of bone formation by osteoclastic expression of semaphorin 4D
DOI: 10.1038/nm.2489

[43] Tissue factor-PAR2 signaling promotes diet-induced obesity and adipose inflammation
DOI: 10.1038/nm.2461

[44] Polymeric IgA1 controls erythroblast proliferation and accelerates erythropoiesis recovery in anemia
DOI: 10.1038/nm.2462

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NATURE METHODS

[45] A homozygous mutant embryonic stem cell bank applicable for phenotype-driven genetic screening
DOI: 10.1038/nmeth.1739

[46] NKX2-5GFP/w hESCs for isolation of human cardiac progenitors and cardiomyocytes
DOI: 10.1038/nmeth.1740

[47] A scalable pipeline for highly effective genetic modification of a malaria parasite
DOI: 10.1038/nmeth.1742

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NATURE NANOTECHNOLOGY

[48] Electron microscopy of specimens in liquid
DOI: 10.1038/nnano.2011.161

[49] Accumulation of sub-100 nm polymeric micelles in poorly permeable tumours depends on size
DOI: 10.1038/nnano.2011.166

[50] Skin-like pressure and strain sensors based on transparent elastic films of carbon nanotubes
DOI: 10.1038/nnano.2011.184

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NATURE NEUROSCIENCE

[51] Pain sensitivity and vasopressin analgesia are mediated by a gene-sex-environment interaction
DOI: 10.1038/nn.2941

[52] Attention induces conservative subjective biases in visual perception
DOI: 10.1038/nn.2948

[53] Ribbon synapses compute temporal contrast and encode luminance in retinal rod bipolar cells
DOI: 10.1038/nn.2945

[54] PI3Kg is required for NMDAR-dependent long-term depression and behavioral flexibility
DOI: 10.1038/nn.2937

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NATURE PHOTONICS

[55] Molecular imaging true-colour spectroscopic optical coherence tomography
DOI: 10.1038/nphoton.2011.257

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NATURE PHYSICS

[56] Evidence for a fractionally quantized Hall state with anisotropic longitudinal transport
DOI: 10.1038/nphys2118

[57] Attoclock reveals natural coordinates of the laser-induced tunnelling current flow in atoms
DOI: 10.1038/nphys2125

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NATURE STRUCTURAL & MOLECULAR BIOLOGY

[58] ErbB1 dimerization is promoted by domain co-confinement and stabilized by ligand-binding
DOI: 10.1038/nsmb.2135

[59] Messenger RNA interactions in the decoding center control the rate of translocation
DOI: 10.1038/nsmb.2140

[60] Tubulin tyrosine ligase structure reveals adaptation of an ancient fold to bind and modify tubulin
DOI: 10.1038/nsmb.2148

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[61] IL-17RE is the functional receptor for IL-17C and mediates mucosal immunity to infection with intestinal pathogens
DOI: 10.1038/ni.2155

[62] IL-17C regulates the innate immune function of epithelial cells in an autocrine manner
DOI: 10.1038/ni.2156

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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
Clayton: 11, 19, 46
Melbourne: 3, 35, 46
Parkville: 11, 46
Perth: 42
Sydney: 35

AUSTRIA
Laxenburg: 3

BELGIUM
Louvain-la-Neuve: 3

CANADA:
Montreal: 51
Toronto: 16, 19, 35, 54
Winnipeg: 4

CHINA
Beijing: 3, 45
Fujian: 39
Hefei: 6
Hong Kong: 40
Jinan: 6
Shanghai: 40, 61
Weshan: 6
Wuhan: 2
Xiamen: 8

DENMARK
Aarhus: 57
Copenhagen: 24

EGYPT
Cairo: 1

FRANCE
Fortenay aux Roses: 12
Gif-sur-Yvette: 7
Limoges: 44
Montpellier: 37
Paris: 13, 34, 38, 44

GERMANY
Goettingen: 15
Heidelberg: 17
Leipzig: 7
Munich: 23
Potsdam: 3
Potsdam-Golm: 14

ITALY
Monterotondo Scalo: 17
Pisa: 14

JAPAN
Fukuoka: 30
Hyogo: 49
Ibaraki: 3
Kobe: 30
Mibu: 30
Nagoya: 30
Osaka: 36, 45
Saitama: 36, 45
Sakura: 30
Sapporo: 30
Sendai: 40
Tokyo: 30, 36, 42, 49
Yamaguchi: 36
Yokohama: 30

NETHERLANDS
Bilthoven: 3
Nijmegen: 52
Utrecht: 3, 14, 46, 58
Wageningen: 14

NEW ZEALAND
Wellington: 5

OMAN
Muscat: 32

SAUDI ARABIA
Riyadh: 32
Thuwal: 39, 47

SINGAPORE
Singapore: 6, 39

SOUTH KOREA
Daejeon: 37
Daegu: 54
Seoul: 54

SPAIN
Barcelona: 22
Salamanca: 23

SWEDEN
Lund: 44

SWITZERLAND
Basel: 12
Zurich: 3, 24, 34, 57

TAIWAN
Keelung: 8

UNITED KINGDOM
Bristol: 54
Cambridge: 17, 45, 47
Cardiff: 11
Exeter: 5
Harpenden: 13
London: 23
Loughborough: 13
Manchester: 25
Oxford: 5
Reading: 3, 5

UNITED STATES OF AMERICA
California
Berkeley: 4
Davis: 12
Foster City: 4
Irvine: 56
La Jolla: 43, 59
Palo Alto: 20
Pasadena: 56
Riverside: 13
San Diego: 43
San Francisco: 9, 62
Stanford: 20, 26, 50
Colorado
Boulder: 27, 35
Fort Collins: 35
Connecticut
New Haven: 10, 31
District of Columbia
Washington: 38
Florida
Gainesville: 51
Gulf Breeze: 8
Georgia
Athens: 8
Atlanta: 18
Illinois
Chicago: 18
Maryland
Baltimore: 26, 33, 51, 52
Bethesda: 11, 16, 31, 51, 53, 60
Frederick: 11, 45
Massachusetts
Amherst: 28
Boston: 1, 16, 29, 33
Cambridge: 1, 4, 16, 21, 33
New Bedford: 8
Waltham: 60
Minnesota
Rochester: 10
Twin Cities: 1
Mississippi
Stennis Space Center: 8
Missouri
St Louis: 31
New Jersey
Princeton: 37, 56
New Mexico
Albuquerque: 58
New York
Cold Spring Harbor: 4
Corning: 26
New York: 9, 31, 42, 52
Woodbury: 4
Yorktown Heights: 48
North Carolina
Chapel Hill: 31
Durham: 33, 55
Ohio
Columbus: 45
Oregon
Corvallis: 7
Pennsylvania
Haverford: 51
Philadelphia: 21
Pittsburgh: 51
University Park: 26
Tennessee
Nashville: 48
Texas
Dallas: 16
Houston: 1
Utah
Salt Lake City: 41
Virginia
Blacksburg: 25
Washington
Seattle: 31, 61

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

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Tel: +1 212 726 9231; E-mail: [email protected]

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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:

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Nature Chemical Biology (Boston)
Elissa Bolt
Tel: +1 617 475 9241, E-mail: [email protected]

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

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Olive Heffernan
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Nature Materials (London)
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Nature Medicine (New York)
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Tel: +1 212 726 9325; E-mail: [email protected]

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

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

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Tel: +44 20 7843 4555; E-mail: [email protected]

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

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