E. coli Neighborhood Watch

Latest news from Nature and the Nature journals 19 March 2012

This press release contains:

---Summaries of newsworthy papers:

Nature: Therapeutic treatment of Rett syndrome

Chemistry: Switchable storage

Chemical Biology: E. coli neighborhood watch

Geoscience: Archaean haze

Immunology: Fatty molecules needed for immune cell selection

Finally…Materials: Universal cell-membrane adhesive

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

---Geographical listing of authors

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[1] Nature: Therapeutic treatment of Rett syndrome
DOI: 10.1038/nature10907

Research suggesting a potentially feasible therapeutic approach for Rett syndrome, an autism spectrum disorder, is published in Nature this week. In a mouse model of the neurodevelopmental disorder, bone marrow transplantation from healthy mice is shown to reduce disease symptoms.

Rett syndrome is associated with reduced growth, breathing irregularities and impaired locomotor activity, and is generally caused by mutation of the MECP2 gene. Although this gene is expressed in most tissues, the disease is generally attributed to neuronal dysfunction; however, recent studies have implicated non-neuronal cells called glia in disease development. Jonathan Kipnis and colleagues examine the role of one form of these cells — microglia — in Mecp2-lacking mice, which serve as a model of Rett syndrome. They demonstrate that transplantation of bone marrow from ‘normal’ mice (expressing Mecp2) into the Rett mice results in an invasion of microglia cells expressing normal Mecp2.

The treatment is shown to reduce disease symptoms, such as breathing and locomotor abnormalities, and increases the lifespan of the mice. These results highlight critical roles of microglia in Rett syndrome and open the possibility for a new approach in the treatment of this devastating disorder, the authors conclude.

Author contact:

Jonathan Kipnis (University of Virginia, Charlottesville, VA, USA)
Tel: +1 434 982 3858; E-mail: [email protected]


[2] Chemistry: Switchable storage
DOI: 10.1038/nchem.1295

A catalyst that can reversibly use carbon dioxide and hydrogen to store energy is reported online in Nature Chemistry this week. The catalyst converts these simple compounds into formic acid, a promising hydrogen-storage medium, and also catalyses the reaction to re-release the hydrogen.

Although using hydrogen as a fuel is highly desirable because of its clean nature, it suffers from many drawbacks such as safety risks and transport problems. Storing it as a gas or in solid materials does not fully alleviate the transport concerns, but the current fuel infrastructure — tankers, pipelines, gas pumps — is well suited to a liquid solution. Jonathan Hull, Yuichiro Himeda, Etsuko Fujita and colleagues’ catalyst is energy efficient and green, working under mild conditions and using just water as the solvent.

The parts of the catalyst that surround the central iridium metal atom are able to control whether it produces or consumes hydrogen, because they are sensitive to the pH of the solution.

Author contacts:

Jonathan Hull (Brookhaven National Laboratory, Upton, NY, USA)
Tel: +1 631 344 4357; E-mail: [email protected]

Yuichiro Himeda (National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan)
Tel: +81 2 98619344; E-mail: [email protected]

Etsuko Fujita (Brookhaven National Laboratory, Upton, NY, USA)
Tel: +1 631 344 4356; E-mail: [email protected]


[3] Chemical Biology: E. coli neighborhood watch
DOI: 10.1038/nchembio.915

The bacterial signaling molecule indole is the direct cause of antibiotic resistance by some bacterial cells, reports a paper published online this week in Nature Chemical Biology. These findings improve our understanding of bacterial populations and point toward a potential new direction in the development of more effective antibacterial agents.

Bacterial ‘persisters’ are cells that cannot be eradicated by existing antibiotic treatments even though the cells are genetically identical to cells that are killed by the treatment. Indole has been linked to cellular processes that are important in persisters, but its role was not clear.

James Collins and colleagues show that indole serves as a signal for bacterial cells to enter a protected state. In particular, it decreases the impact of several antibiotics on E. coli, with cells that respond best to the molecule also demonstrating the highest level of protection. The authors also showed that indole activates two cellular pathways – oxidative stress and phage-shock responses – that are involved in persister formation. Importantly, another molecule that could also trigger these pathways causes the same formation of protected cells.

Author contact:

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


[4] Geoscience: Archaean haze
DOI: 10.1038/ngeo1425

The Earth’s atmosphere periodically transitioned between a hydrocarbon haze and haze-free conditions 2.65–2.5 billion years ago, reports a paper published online this week in Nature Geoscience. The haze permanently retreated following the oxygenation of the atmosphere approximately 100 million years later.

Aubrey Zerkle and colleagues analysed the geochemistry of marine sediments deposited between 2.65 and 2.5 billion years ago in what is now South Africa. They found evidence of local production of oxygen by microbes, but carbon and sulphur isotopes indicate that little of that oxygen entered the atmosphere. Instead, the authors suggest that the atmosphere transitioned repeatedly between two states: one with a thick, hydrocarbon haze and the other haze-free. The team attributes the transitions to changes in the rate of methane production by microbes.

Author contact:

Aubrey Zerkle (Newcastle University, UK)
Tel: +44 191 222 6916; E-mail: [email protected]


[5] Immunology: Fatty molecules needed for immune cell selection

A class of fatty molecules that are necessary for developing a unique set of early responding immune cells is identified in a paper published in Nature Immunology this week. These cells, called invariant natural killer T (iNKT) cells are capable of secreting large amounts of cytokines and can influence the responses of other immune cells.

Previous work had shown that iNKT cells recognize a variety of microbial fatty molecules; however, the nature of self-generated fatty molecules that can be recognized by developing iNKT cells in the thymus has proved more controversial.

Gennaro De Libero and colleagues show ether-bonded fat molecules select thymic iNKT cells. The team found that synthetic ether-bonded fatty molecules potently activated mature iNKT cells and promoted thymic iNKT development. They also noted that mice that lack GNPAT – the enzyme that generates these ether-bonded fats – produce considerably fewer iNKT cells and fail to accumulate these cells in peripheral tissues.

Identification of the self-ligands recognized by iNKT cells will lead future efforts to understand rules that govern their development and survival.

Author contact:

Gennaro De Libero (University Hospital Basel, Switzerland)
Tel: +41 61 265 23 27; E-mail: [email protected]


[6] Finally…Materials: Universal cell-membrane adhesive
DOI: 10.1038/nmat3272

Star-shaped macromolecules that bind to mammalian cell membranes and cause the cells to adhere to each other are reported online in Nature Materials this week. This universal cell–cell adhesive could find use as a tissue sealant and a drug-delivery vehicle.

Donald Brooks and colleagues made hyperbranched polyglycerols — macromolecules with repeated alcohol motifs — decorated with multiple chemical groups containing choline phosphate (CP), which has the inverse orientation of the phosphatidyl choline (PC) lipid headgroup that is present in the cell membranes of mammals and many bacteria. The researchers observed that CP-containing macromolecules in solutions of red blood cells caused the cells to form clumps, and that the adhesion between the clumped cells strengthened with increasing density of CP groups in the macromolecules. They also found that binding could be reversed by the addition of PC-decorated macromolecules. The researchers propose that the binding between the CP and PC groups stems from the electrostatic attraction between two nitrogen–phosphorus pairs.

They also show that CP-decorated macromolecules were rapidly taken up by Chinese hamster ovary cells following membrane binding, indicating that the general adhesion and uptake capacity of the CP-containing macromolecules may offer ample opportunities for their application in therapeutics.

Author contacts:

Donald Brooks (University of British Columbia, Vancouver, Canada)
Tel: +1 604 822 7081; E-mail: [email protected]

Jayachandran Kizhakkedathu (University of British Columbia, Vancouver, Canada)
Tel: +1 604 822 7085; E-mail: [email protected]


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

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

[7] Notch-dependent VEGFR3 upregulation allows angiogenesis without VEGF–VEGFR2 signalling
DOI: 10.1038/nature10908

[8] Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment
DOI: 10.1038/nature10905

[9] MAP and kinesin-dependent nuclear positioning is required for skeletal muscle function
DOI: 10.1038/nature10914

[10] Small-molecule inhibitors of the AAA1 ATPase motor cytoplasmic dynein
DOI: 10.1038/nature10936

[11] Trans-synaptic Teneurin signalling in neuromuscular synapse organization and target choice
DOI: 10.1038/nature10923

[12] Teneurins instruct synaptic partner matching in an olfactory map
DOI: 10.1038/nature10926

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

[13] Using virally expressed melanoma cDNA libraries to identify tumor-associated antigens that cure melanoma
DOI: 10.1038/nbt.2157

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

[14] Telomeric DNA damage is irreparable and causes persistent DNA-damage-response activation
DOI: 10.1038/ncb2466

NATURE CHEMICAL BIOLOGY (http://www.nature.com/nchembio)

[15] Programmable enantioselective one-pot synthesis of molecules with eight stereocenters
DOI: 10.1038/nchembio.901

[16] LYP inhibits T cell activation when dissociated from CSK
DOI: 10.1038/nchembio.916

NATURE CHEMISTRY (http://www.nature.com/nchem)

[17] Multidimensional steric parameters in the analysis of asymmetric catalytic reactions
DOI: 10.1038/nchem.1297

[18] Ionization of dimethyluracil dimers leads to facile proton transfer in the absence of hydrogen bonds
DOI: 10.1038/nchem.1298

[19] Protein fold determined by paramagnetic magic-angle spinning solid-state NMR spectroscopy
DOI: 10.1038/nchem.1299

NATURE CLIMATE CHANGE (http://www.nature.com/nclimate)

[20] Do alternative energy sources displace fossil fuels?
DOI: 10.1038/nclimate1451

[21] Assessing confidence in Pliocene sea surface temperatures to evaluate predictive models
DOI: 10.1038/nclimate1455

[22] Vulnerability of cloud forest reserves in Mexico to climate change
DOI: 10.1038/nclimate1453

[23] Europe walks its talk
DOI: 10.1038/nclimate1464

[24] Overestimation of Mediterranean summer temperature projections due to model deficiencies
DOI: 10.1038/nclimate1454

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

[25] Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits
DOI: 10.1038/ng.2213

[26] Mutations in SWI/SNF chromatin remodeling complex gene ARID1B cause Coffin-Siris syndrome
DOI: 10.1038/ng.2217

[27] Mutations affecting components of the SWI/SNF complex cause Coffin-Siris syndrome
DOI: 10.1038/ng.2219

NATURE GEOSCIENCE (http://www.nature.com/ngeo)

[28] Influence of the tropics and southern westerlies on glacial interhemispheric asymmetry
DOI: 10.1038/ngeo1431

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

[29] Liquid–liquid transition without macroscopic phase separation in a water–glycerol mixture
DOI: 10.1038/nmat3271

[30] A silica sol–gel design strategy for nanostructured metallic materials
DOI: 10.1038/nmat3274

[31] Characterization of supercooled liquid Ge2Sb2Te5 and its crystallization by ultrafast-heating calorimetry
DOI: 10.1038/nmat3275

[32] Infrared metamaterial phase holograms
DOI: 10.1038/nmat3278

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

[33] Activation of neuronal P2X7 receptor–pannexin-1 mediates death of enteric neurons during colitis
DOI: 10.1038/nm.2679

[34] Dendritically targeted Bdnf mRNA is essential for energy balance and response to leptin
DOI: 10.1038/nm.2687

[35] CITED2 links hormonal signaling to PGC-1a acetylation in regulation of gluconeogenesis
DOI: 10.1038/nm.2691

[36] A common BIM deletion polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer
DOI: 10.1038/nm.2713

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

[37] Tracking protein aggregation and mislocalization in cells with flow cytometry
DOI: 10.1038/nmeth.1930

[38] Integrated nanopore sensing platform with sub-microsecond temporal resolution
DOI: 10.1038/nmeth.1932

[39] Unsupervised pattern discovery in human chromatin structure through genomic segmentation
DOI: 10.1038/nmeth.1937

[40] Detecting overlapping protein complexes in protein-protein interaction networks
DOI: 10.1038/nmeth.1938

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

[41] Electrical control of a solid-state flying qubit
DOI: 10.1038/nnano.2012.28

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

[42] Plasticity in gray and white: neuroimaging changes in brain structure during learning
DOI: 10.1038/nn.3045

[43] Cortical oscillations and speech processing: emerging computational principles and operations
DOI: 10.1038/nn.3063

[44] UNC-6/Netrin mediates dendritic self-avoidance
DOI: 10.1038/nn.3065

[45] Negative regulation of glial engulfment activity by Draper terminates glial responses to axon injury
DOI: 10.1038/nn.3066

NATURE PHOTONICS (http://www.nature.com/nphoton)

[46] Direct generation of multiple excitons in adjacent silicon nanocrystals revealed by induced absorption
DOI: 10.1038/nphoton.2012.36

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

[47] Probing Planck-scale physics with quantum optics
DOI: 10.1038/nphys2262

[48] Two Ising-like magnetic excitations in a single-layer cuprate superconductor
DOI: 10.1038/nphys2271

[49] Feynman diagrams versus Fermi-gas Feynman emulator
DOI: 10.1038/nphys2273

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

[50] Control of RNP motility and localization by a splicing-dependent structure in oskar mRNA
DOI: 10.1038/nsmb.2257

[51] The molecular architecture of human Dicer
DOI: 10.1038/nsmb.2268

[52] Structure of the activating IL-1 receptor signaling complex
DOI: 10.1038/nsmb.2260



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.

Brisbane: 25
Bundoora: 25
Canberra: 28
Clayton: 37
Dutton Park: 22
Kirrawee: 48
Melbourne: 37
Parkville: 25
St. Lucia: 22
Townsville: 22
Vienna: 5, 47, 48
Ghent: 49
Liege: 16
Calgary: 33
Halifax: 30
Montreal: 14, 16, 42
Toronto: 39
Vancouver: 6
Changchun: 48
Kunming: 5
Pardubice: 31
Aarhus: 8
Copenhagen: 24
Gif-sur-Yvette: 48
Grenoble: 48
Paris: 9, 43, 49
Bonn: 36
Dortmund: 15
Garching: 48
Goettingen: 48
Heidelberg: 50
Munster: 7
Rostock-Wamermuende: 28
Stuttgart: 48
Milan: 14
Milano: 5
Pavia: 14
Turin: 14
Akita: 36
Aumino: 27
Hiroshima: 27
Hyogo: 35
Ibaraki: 2
Ishikari-Tobetsu: 27
Ishikawa: 35
Iwatzuki: 27
Izumi: 27
Kanagawa: 41
Kasugai: 27
Kobe: 35
Koshigaya: 27
Matsumoto: 27
Okinawa: 27
Osaka: 35
Saitama: 27, 41
Sakata: 27
Tochigi: 27, 36
Tokyo: 21, 27, 29, 35, 36, 41
Yamagata: 27
Yokohama: 21, 27
Kuala Lumpur: 36
Mexico: 22
Amsterdam: 46
Bochum: 41
Delft: 46
Hague: 26
Leiden: 26
Rotterdam: 26
Bergen: 28
Oslo: 16
Lisbon: 7
Moscow: 49
Singapore: 5, 36
Basel: 5
Lausanne: 7, 30
Zurich: 5, 49
Pathumthani: 13
Bristol: 21
Cambridge: 25, 31
Durham: 32, 36
Egham: 40
Exeter: 25
Guildford: 13
Leeds: 13, 21
Leicester: 31
London: 13, 47
Newcastle: 4
Norwich: 4
Nottingham: 21
Oxford: 25, 42
Southampton: 31
Berkeley: 18, 49
La Jolla: 16, 51
Los Angeles: 18, 27
San Jose: 44
Stanford: 10, 11, 12, 48, 52
Boulder: 21, 34
Farmington: 19
New Haven: 44
District of Columbia
Washington: 4, 34
Jupiter: 2
Chicago: 10
Bethesda: 19, 42
College Park: 4
Gaithersburg: 16
Amherst: 49
Boston: 3, 25, 38
Cambridge: 25, 49
Worcester: 39, 45
Minneapolis: 48
Rochester: 13
St Louis: 25
New Jersey
Newark: 14
New York
Ithaca: 30, 40
New York: 2, 7, 9, 10, 21, 22, 38, 43
Upton: 2
North Carolina
Chapel Hill: 44
Columbus: 19
Eugene: 20
Portland: 45
Philadelphia: 38
Rhode Island
Narragansett: 8
Providence: 16
Nashville: 43
Salt Lake City: 17
Burlington: 33
Charlottesville: 1
Reston: 21
Seattle: 4, 39
Osceola: 52



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]

Eiji Matsuda (Nature Tokyo)
Tel: +81 3 3267 8751; 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)
Michael Francisco
Tel: +1 212 726 9288; E-mail: [email protected]

Nature Cell Biology (London)
Sowmya Swaminathan
Tel: +44 20 7843 4656; E-mail: [email protected]

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]

Nature Climate Change (London)
Rory Howlett
Tel: +44 20 7014 4009; E-mail: [email protected]

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

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

Nature Immunology (New York)
Laurie Dempsey
Tel: +1 212 726 9372; 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)
Sabbi Lall
Tel: +1 212 726 9326; E-mail: [email protected]


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Published: 18 Mar 2012

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