Threading together a map of silkworm DNA modifications

Aspirin leads to beneficial lipids; Variants associated to Paget’s disease of bone; Malaria-induced marrow changes; Stem cells’ biochemistry revealed; Woolly mammoth’s cold adaptation


For papers that will be published online on 02 May 2010

This press release contains:

· Summaries of newsworthy papers:

Neuroscience: See hear

Chemical Biology: Aspirin leads to beneficial lipids

Genetics: Variants associated to Paget’s disease of bone

Biotechnology: Threading together a map of silkworm DNA

Immunology : Malaria-induced marrow changes

Chemical Biology: Stem cells’ biochemistry revealed

And finally…Genetics: Woolly mammoth’s cold adaptation

· 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] Neuroscience: See hear
DOI: 10.1038/nn.2533

The auditory cortex is activated by silent, but sound-associated, visual stimuli reports an imaging study published online this week in Nature Neuroscience. The study shows that not only is the auditory cortex activated by silent visual stimuli that are sound-implying but that this activity also differentiates between sounds related to different categories such as animals, musical instruments and objects.

Antonio Damasio and his colleagues placed participants in an MRI scanner, while showing them silent, short videos which contained an implied sound – for example, a dog barking or a musician playing a violin. When they analyzed the imaging data they found that activity from the auditory cortex recorded while subjects were seeing these videos was sufficient to classify whether the images being seen showed animals, musical instruments, or sound-producing objects.

The auditory cortex is usually thought to be activated only by sounds, and this study adds to evidence supporting the idea that sensory cortex activity is not driven entirely by sensory stimulation such as actually hearing a sound, but instead, also reflects perceptual experiences.

Author contact:
Antonio Damasio (University of Southern California, Los Angeles, CA, USA)
Tel. +1 213 740 3462
E-mail: [email protected]

[2] Chemical Biology: Aspirin leads to beneficial lipids
DOI: 10.1038/nchembio.367

Lipids produced by the aspirin target COX-2 have anti-oxidant and anti-inflammatory properties as presented in a study published online this week in Nature Chemical Biology.

Omega-3 fatty acids are known to have various health benefits including being anti-inflammatory, and playing an important role in brain and retinal development.

By using mass spectrometry, Bruce Freeman and colleagues identified four new lipids that are derived from COX-2 acting on two types of omega-3 fatty acids in the immune system cells called macrophages. The new signalling lipids, termed EFOXs have anti-inflammatory and anti-oxidant effects which can be enhanced by aspirin, through the activation of COX-2.

Author contact:
Bruce Freeman (University of Pittsburgh, PA, USA)
Tel: +1 412 648 9319
Email: [email protected]

[3] Genetics: Variants associated to Paget’s disease of bone
DOI: 10.1038/ng.562

Variants at three genetic loci are associated with Paget’s disease of bone (PDB), according to a new report published online this week in Nature Genetics.

Paget’s disease of bone is characterized by excessive breakdown and formation of bone that leads to enlarged and malformed bones; it can affect any bone in the skeleton. In normal skeletons, bones are dynamically forming and being absorbed in response to stresses put on the skeleton. In PDB, cells that absorb bone are overactive. In turn, cells that form bone vercompensate. Patients with PDB can suffer from bone pain, brittle bones susceptible to fractures, and advanced arthritis.

Stuart Ralston and colleagues studied 1250 patients with CDB and identified three genetic loci associated with risk of PDB.

Author contact:
Stuart Ralston (University of Edinburgh, UK)
Tel: +44 131 651 1037
E-mail: [email protected]

[4] Biotechnology: Threading together a map of silkworm DNA
DOI: 10.1038/nbt.1626

A study published this week in Nature Biotechnology reveals that DNA methylation across the silkworm genome is much less common than in mammals and plants. Understanding methylation—a type of DNA modification that helps determine which genes are switched on and which are switched off—can help in our understanding of the insect lifecycle.

To investigate the level of DNA methylation in the silkworm, Jun Wang and colleagues employed a next-generation sequencing–based approach to create a high-resolution map of methylated and unmethylated cytosines—one of the four DNA bases—in the silkworm genome. Their results suggest that the genome from cells of the silkworm silk gland contains about fifty-fold fewer methylated cytosines than is found in the genomes of human or plant cells.

Silkworm genes containing higher amounts of modified cytosines were confirmed to show higher levels of gene expression, but modifications in other regions of the genome may have different roles in insects compared with mammals and plants.

Author contact:
Jun Wang (BGI-Shenzhen, China)
Tel: +86 138 0120 9025
E-mail: [email protected]

[5] Immunology: Malaria-induced marrow changes
DOI: 10.1038/ni.1869

A unique infection-fighting blood cell precursor that arises during acute malaria infections is identified in a report published online this week in Nature Immunology. These findings can lead to new methods of “tricking” the blood supply system to make more disease fighting immune cells.

New-born blood cells develop in the bone marrow. Alexandre Potocnik and colleagues discovered that mice infected with the parasite Plasmodium chabaudi, a causal agent of malaria, transiently generate a distinct bone marrow cell that can develop into potent disease-fighting innate immune cells.

The infection-induced cells arise in response to a proinflammatory mediator called interferon-gamma, which is released by infections elsewhere in the body. Thus active infection triggers responses in the bone marrow to ramp up production of defensive cells necessary to attack and repel the infection.

Author contact:
Alexandre J. Potocnik (MRC National Institute for Medical Research, London, UK)
Tel: +44 208 816 2193
E-mail: [email protected]

[6] Chemical Biology: Stem cells’ biochemistry revealed
DOI: 10.1038/nchembio.364

A particular class of natural metabolites poise stem cells for differentiation based on a variety of cues. This finding, published this week in Nature Chemical Biology, places new emphasis on the role of metabolites in stem cell behavior and may be important in controlling stem cell function for biotechnological purposes.

Previous stem cell work has focused heavily on understanding what genes are being turned on or off, and correspondingly what proteins are present that may control cellular function. Metabolites—the small molecules created and destroyed in the normal biochemical processes of the cell—have not been similarly investigated.

Gary Siuzdak, Sheng Ding, and colleagues report on a metabolomics analysis of stem cells, in which they look at the concentrations of many known metabolites to determine which compounds are present in stem cells as compared to differentiated cells. They find that stem cells have a high number of oxidized compounds; manipulation of these particular molecules is also shown to affect stem cell differentiation.

Author contact:
Gary Siuzdak (The Scripps Research Institute, La Jolla, CA, USA)
Tel: +1 858 784 9415
E-mail: [email protected]

Sheng Ding (The Scripps Research Institute, La Jolla, CA, USA)
Tel: +1 858 784 7376
E-mail: [email protected]

[7] Genetics: Woolly mammoth’s cold adaptation
DOI: 10.1038/ng.574

Changes in the genes encoding woolly mammoth hemoglobin may have been involved in its adaptation to cold environments of the Arctic, according to a new report published online this week in Nature Genetics.

Ancestors of woolly mammoths and modern-day elephants originated in equatorial Africa, though members of the mammoth lineage migrated to higher latitudes 1.2-2.0 million years ago. This migration coincided with climate changes and a drastic cooling in high-latitude Arctic environments.

Hemoglobin, a protein important in red blood cells, binds and carries oxygen, although its ability to release oxygen to tissues is inhibited at low temperatures. To investigate whether changes within hemoglobin might be linked to the mammoth's adaptation to cold environments, Kevin Campbell, Alan Cooper and colleagues sequenced the genes encoding hemoglobin from a 43,000 year-old woolly mammoth and compared it to modern-day African and Asian elephants. The scientists found changes in mammoth hemoglobin that facilitate release of oxygen at
cold temperatures.

Author contact:
Kevin Campbell (University of Manitoba, Winnipeg, Canada)
Tel: +1 204 474 6397
E-mail: [email protected]


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


[8] Histone H2A deubiquitinase activity of the Polycomb repressive complex PR-DUB
DOI: 10.1038/nature08966

[9] A three-dimensional model of the yeast genome
DOI: 10.1038/nature08973

[10] Modulation of Shigella virulence in response to available oxygen in vivo
DOI: 10.1038/nature08970


[11] Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
DOI: 10.1038/nbt.1621

[12] GREAT improves interpretation of cis-regulatory regions
DOI: 10.1038/nbt.1630

[13] Dynamic single-cell imaging of direct reprogramming reveals an early specifying event
DOI: 10.1038/nbt.1632

[14] Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals conserved multi-exonic lincRNAs
DOI: 10.1038/nbt.1633


[15] MTCH2/MIMP is a major facilitator of tBID recruitment to mitochondria DOI: 10.1038/ncb2057


[16] Small molecules discovered in a pathway screen target the Rho pathway in cytokinesis
DOI: 10.1038/nchembio.363


[17] Efficient stereo- and regioselective hydroxylation of alkanes catalysed by a bulky polyoxometalate
DOI: 10.1038/nchem.648

[18] Ion-triggered spring-like motion of a double helicate accompanied by anisotropic twisting
DOI: 10.1038/nchem.649

[19] Direct detection of CH/pi interactions in proteins
DOI: 10.1038/nchem.650


[20] A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4
DOI: 10.1038/ng.580

[21] De novo mutations of SETBP1 cause Schinzel-Giedion syndrome
DOI: 10.1038/ng.581


[22] The transcription factor PU.1 is required for the development of IL-9-producing T cells and allergic inflammation
DOI: 10.1038/ni.1867

[23] Regulation of thymocyte positive selection and motility by GIT2
DOI: 10.1038/ni.1868

[24] Autonomous role of medullary thymic epithelial cells in central CD4+ cell tolerance
DOI: 10.1038/ni.1874


[25] Organic light-emitting transistors with an efficiency that outperforms the equivalent light-emitting diodes
DOI: 10.1038/nmat2751

[26] Precise control of thermal conductivity at the nanoscale through individual phonon-scattering barriers
DOI: 10.1038/nmat2752


[27] Derepression of an endogenous long terminal repeat activates the CSF1R proto-oncogene in human lymphoma
DOI: 10.1038/nm.2129

[28] Memory CD4+ T cells induce innate responses independently of pathogen
DOI: 10.1038/nm.2142

[29] Epithelial cell cycle arrest in G2/M mediates kidney fibrosis after injury
DOI: 10.1038/nm.2144


[30] Transient cold shock enhances zinc-finger nuclease-mediated gene disruption
DOI: 10.1038/nmeth.1456

[31] GenePRIMP: a Gene Prediction Improvement Pipeline for Prokaryotic genomes
DOI: 10.1038/nmeth.1457


[32] Hybrid superconductor–semiconductor devices made from self-assembled SiGe nanocrystals on silicon
DOI: 10.1038/nnano.2010.84


[33] A genomic atlas of mouse hypothalamic development
DOI: 10.1038/nn.2545

[34] Phototransduction in C. elegans requires a G protein-dependent cGMP pathway and a taste receptor homologue
DOI: 10.1038/nn.2540

[35] Fractionation of an excitatory motor cortex pathway into sub-layer specific corticospinal and corticostriatal microcircuits
DOI: 10.1038/nn.2538

[36] OSVZ-progenitors of human and ferret neocortex retain epithelial features and expand by integrin signaling
DOI: 10.1038/nn.2553


[37] Magnetic recording at 1.5 Pb/m 2 using an integrated plasmonic antenna
DOI: 10.1038/nphoton.2010.90

[38] Microscale planar optical elements based on high-reflectivity,
non-periodic gratings provide a compact and convenient means or focusing and shaping light
DOI: 10.1038/nphoton.2010.116

[39] On-chip beam-steering photonic-crystal lasers
DOI: 10.1038/nphoton.2010.118

[40] Sub-femtojoule all-optical switching using a photonic crystal nanocavity
DOI: 10.1038/nphoton.2010.89

[41] Laser-induced water condensation in air
DOI: 10.1038/nphoton.2010.115


[42] Evidence for a Lifshitz transition in electron-doped iron arsenic superconductors at the onset of superconductivity
DOI: 10.1038/nphys1656

[43] Evidence for the ballistic intrinsic spin Hall effect in HgTe nanostructures
DOI: 10.1038/nphys1655


[44] Toxoplasma gondii calcium-dependent protein kinase 1 is a target for selective kinase inhibitors
DOI: 10.1038/nsmb.1818

[45] Structures of apicomplexan calcium-dependent protein kinases reveal mechanism of activation by calcium
DOI: 10.1038/nsmb.1795


The following paper is for immediate release—the paper was published on Nature’s website at 1700 London time / 1200 US Eastern time and is therefore no longer under embargo. The rest of the above articles on this release remain under embargo until 2 May at 1800 London time / 1300 US Eastern time

[46] A dicer-independent miRNA biogenesis pathway that requires Ago catalysis
DOI: 10.1038/nature09092



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: 7
Melbourne: 3
Newtown: 10
North Adelaide: 21
Perth: 3
Sydney: 3, 21
Victoria: 22, 46

Antwerp: 21
Brussels: 21
Leuven: 21

Rio de Janeiro: 20

Ottawa: 19
Toronto: 45
Vancouver: 20
Winnipeg: 7

Beijing: 20, 34
Chongqing: 4
Hubei: 34
Kunming: 4
Shanghai: 4
Shenzhen: 4
Wuhan: 20
Zhenjiang: 4

Aarhus: 7
Copenhagen: 4, 20

Grenoble: 19, 26, 32
Paris: 10
Talence: 26
Villeurbanne: 41

Berlin: 15, 36, 41
Dresden: 26, 32, 36
Freiburg: 26
Heidelberg: 8
Leipzig: 7
Munich: 24
Stuttgart: 26
Wurzburg: 43

Budapest: 20

Dublin: 20

Rehovot: 15
Tel-Aviv: 13

Bari: 15
Bologna: 25
Palermo: 2
Torino: 3

Kanagawa-ken: 37, 40
Nagoya: 18, 34
Saitama: 17, 33
Tokyo: 17
Yokohama: 7

Amsterdam: 15
Nijmegen: 21

Auckland: 3, 21
Christchurch: 21

Bergen: 20

Coimbra: 21
Porto: 21

Singapore: 20

Salamanca: 3

Uppsala: 10

Geneva: 41
Lausanne: 15

Taoyuan: 20

Birmingham: 10, 21
Durham: 20
Edinburgh: 3, 5
Glasgow: 3
Liverpool: 3
London: 4, 5, 10
Newcastle: 21
Sheffield: 10
York: 7


Berkeley: 11, 23, 42
La Jolla: 6
Los Angeles: 1, 15
Palo Alto: 38
Pasadena: 11
San Francisco: 23
Santa Cruz: 12, 26
San Jose: 37
Stanford: 12

Miami: 20

Chicago: 33, 35
Skokie: 25

Indianapolis: 22

Ames: 42
Iowa City: 20

Pittsburgh: 2, 7, 20

Baltimore: 20, 33
Bethesda: 20
Chevy Chase: 23
College Park: 11

Boston: 7, 14, 16
Cambridge: 13, 14, 16, 23, 34

Ann Arbor: 34

St Louis: 11, 33, 45

New York
Cold Spring Harbor: 46
New York: 8, 20, 46
Stony Brook: 46

Philadelphia: 15

College Station: 43

Logan: 20

Seattle: 9, 44


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)
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)
Sarah Daniels
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)
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: 02 May 2010

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